Starting phenix.real_space_refine on Thu Sep 18 00:54:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ijv_60644/09_2025/9ijv_60644.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ijv_60644/09_2025/9ijv_60644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ijv_60644/09_2025/9ijv_60644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ijv_60644/09_2025/9ijv_60644.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ijv_60644/09_2025/9ijv_60644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ijv_60644/09_2025/9ijv_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-2.0-5805/lib/python3.9/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, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.45, per 1000 atoms: 0.27 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: 1.53 Conformation dependent library (CDL) restraints added in 579.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.46 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: 2.19 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2125 1.31 - 1.45: 3784 1.45 - 1.58: 6991 1.58 - 1.71: 0 1.71 - 1.84: 104 Bond restraints: 13004 Sorted by residual: bond pdb=" CA SER C 315 " pdb=" CB SER C 315 " ideal model delta sigma weight residual 1.538 1.464 0.074 1.22e-02 6.72e+03 3.72e+01 bond pdb=" C ASN D 200 " pdb=" O ASN D 200 " ideal model delta sigma weight residual 1.236 1.185 0.050 8.80e-03 1.29e+04 3.25e+01 bond pdb=" C VAL D 349 " pdb=" O VAL D 349 " ideal model delta sigma weight residual 1.235 1.181 0.054 1.02e-02 9.61e+03 2.80e+01 bond pdb=" CA SER C 298 " pdb=" CB SER C 298 " ideal model delta sigma weight residual 1.537 1.469 0.068 1.41e-02 5.03e+03 2.30e+01 bond pdb=" C THR C 236 " pdb=" O THR C 236 " ideal model delta sigma weight residual 1.236 1.180 0.056 1.22e-02 6.72e+03 2.09e+01 ... (remaining 12999 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 16909 2.96 - 5.92: 616 5.92 - 8.89: 84 8.89 - 11.85: 25 11.85 - 14.81: 10 Bond angle restraints: 17644 Sorted by residual: angle pdb=" N PRO B 386 " pdb=" CA PRO B 386 " pdb=" C PRO B 386 " ideal model delta sigma weight residual 111.41 96.60 14.81 1.50e+00 4.44e-01 9.75e+01 angle pdb=" N SER C 298 " pdb=" CA SER C 298 " pdb=" C SER C 298 " ideal model delta sigma weight residual 114.12 101.35 12.77 1.39e+00 5.18e-01 8.44e+01 angle pdb=" N PRO A 386 " pdb=" CA PRO A 386 " pdb=" C PRO A 386 " ideal model delta sigma weight residual 111.22 98.44 12.78 1.40e+00 5.10e-01 8.34e+01 angle pdb=" N THR A 95 " pdb=" CA THR A 95 " pdb=" C THR A 95 " ideal model delta sigma weight residual 113.97 103.00 10.97 1.28e+00 6.10e-01 7.34e+01 angle pdb=" N PRO C 386 " pdb=" CA PRO C 386 " pdb=" C PRO C 386 " ideal model delta sigma weight residual 111.19 98.47 12.72 1.57e+00 4.06e-01 6.57e+01 ... (remaining 17639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.12: 7855 24.12 - 48.23: 507 48.23 - 72.35: 80 72.35 - 96.46: 39 96.46 - 120.58: 35 Dihedral angle restraints: 8516 sinusoidal: 4132 harmonic: 4384 Sorted by residual: dihedral pdb=" CB CYS B 183 " pdb=" SG CYS B 183 " pdb=" SG CYS B 230 " pdb=" CB CYS B 230 " ideal model delta sinusoidal sigma weight residual -86.00 -170.97 84.97 1 1.00e+01 1.00e-02 8.76e+01 dihedral pdb=" CB CYS C 183 " pdb=" SG CYS C 183 " pdb=" SG CYS C 230 " pdb=" CB CYS C 230 " ideal model delta sinusoidal sigma weight residual -86.00 -170.48 84.48 1 1.00e+01 1.00e-02 8.68e+01 dihedral pdb=" CB CYS D 183 " pdb=" SG CYS D 183 " pdb=" SG CYS D 230 " pdb=" CB CYS D 230 " ideal model delta sinusoidal sigma weight residual -86.00 -165.96 79.96 1 1.00e+01 1.00e-02 7.93e+01 ... (remaining 8513 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.164: 1984 0.164 - 0.327: 84 0.327 - 0.491: 20 0.491 - 0.654: 9 0.654 - 0.818: 3 Chirality restraints: 2100 Sorted by residual: chirality pdb=" C1 MAN T 6 " pdb=" O6 BMA T 3 " pdb=" C2 MAN T 6 " pdb=" O5 MAN T 6 " both_signs ideal model delta sigma weight residual False 2.40 1.58 0.82 2.00e-02 2.50e+03 1.67e+03 chirality pdb=" C1 MAN P 5 " pdb=" O2 MAN P 4 " pdb=" C2 MAN P 5 " pdb=" O5 MAN P 5 " both_signs ideal model delta sigma weight residual False 2.40 1.66 0.74 2.00e-02 2.50e+03 1.39e+03 chirality pdb=" C1 MAN H 5 " pdb=" O2 MAN H 4 " pdb=" C2 MAN H 5 " pdb=" O5 MAN H 5 " both_signs ideal model delta sigma weight residual False 2.40 1.76 0.64 2.00e-02 2.50e+03 1.03e+03 ... (remaining 2097 not shown) Planarity restraints: 2220 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG R 1 " 0.305 2.00e-02 2.50e+03 2.68e-01 8.98e+02 pdb=" C7 NAG R 1 " -0.066 2.00e-02 2.50e+03 pdb=" C8 NAG R 1 " 0.081 2.00e-02 2.50e+03 pdb=" N2 NAG R 1 " -0.480 2.00e-02 2.50e+03 pdb=" O7 NAG R 1 " 0.159 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " 0.312 2.00e-02 2.50e+03 2.64e-01 8.69e+02 pdb=" C7 NAG N 2 " -0.082 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " 0.188 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " -0.455 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " -0.282 2.00e-02 2.50e+03 2.39e-01 7.17e+02 pdb=" C7 NAG J 1 " 0.074 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " -0.177 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " 0.412 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " -0.027 2.00e-02 2.50e+03 ... (remaining 2217 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 117 2.55 - 3.14: 9698 3.14 - 3.72: 21322 3.72 - 4.31: 33164 4.31 - 4.90: 52504 Nonbonded interactions: 116805 Sorted by model distance: nonbonded pdb=" O ASP A 293 " pdb="CA CA A 503 " model vdw 1.958 2.510 nonbonded pdb=" O ASP D 293 " pdb="CA CA D 503 " model vdw 1.981 2.510 nonbonded pdb=" O HIS A 347 " pdb="CA CA A 503 " model vdw 2.046 2.510 nonbonded pdb=" O GLY D 345 " pdb="CA CA D 503 " model vdw 2.065 2.510 nonbonded pdb=" OG SER C 334 " pdb=" OE2 GLU C 343 " model vdw 2.118 3.040 ... (remaining 116800 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 83 through 430 or (resid 431 and (name N or name CA or nam \ e C or name O or name CB )) or resid 432 through 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: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.930 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 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:6.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.076 13100 Z= 0.484 Angle : 1.399 27.116 17896 Z= 0.748 Chirality : 0.092 0.818 2100 Planarity : 0.022 0.432 2196 Dihedral : 17.908 120.581 5616 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.31 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 aren 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 covalent geometry : bond 0.00765 (13004) covalent geometry : angle 1.26274 (17644) SS BOND : bond 0.00698 ( 36) SS BOND : angle 1.38737 ( 72) hydrogen bonds : bond 0.20493 ( 367) hydrogen bonds : angle 9.20697 ( 1026) link_ALPHA1-2 : bond 0.00292 ( 4) link_ALPHA1-2 : angle 4.19647 ( 12) link_ALPHA1-3 : bond 0.02292 ( 8) link_ALPHA1-3 : angle 9.18896 ( 24) link_ALPHA1-6 : bond 0.04966 ( 4) link_ALPHA1-6 : angle 8.09308 ( 12) link_BETA1-4 : bond 0.01587 ( 20) link_BETA1-4 : angle 4.89523 ( 60) link_NAG-ASN : bond 0.01804 ( 24) link_NAG-ASN : angle 5.64964 ( 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 : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7406 (m-30) cc_final: 0.7120 (m-30) REVERT: A 381 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7591 (mm-30) REVERT: A 415 LYS cc_start: 0.7899 (tttp) cc_final: 0.7377 (mtmt) REVERT: B 399 ASP cc_start: 0.7994 (t70) cc_final: 0.7722 (t70) REVERT: B 416 SER cc_start: 0.8026 (p) cc_final: 0.7551 (m) REVERT: B 465 ASN cc_start: 0.8257 (t0) cc_final: 0.8025 (m110) REVERT: C 150 ARG cc_start: 0.7241 (ttt180) cc_final: 0.6868 (mtm180) REVERT: C 313 VAL cc_start: 0.8605 (t) cc_final: 0.8365 (m) REVERT: C 415 LYS cc_start: 0.8392 (tttt) cc_final: 0.8105 (ttmp) REVERT: D 308 LYS cc_start: 0.8054 (mtmt) cc_final: 0.7708 (mtpt) REVERT: D 368 GLU cc_start: 0.8046 (mp0) cc_final: 0.7829 (mp0) REVERT: D 431 LYS cc_start: 0.7212 (tppt) cc_final: 0.6790 (tptp) REVERT: D 465 ASN cc_start: 0.8021 (m-40) cc_final: 0.7764 (p0) outliers start: 4 outliers final: 2 residues processed: 227 average time/residue: 0.6920 time to fit residues: 169.6220 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 : 0.510 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3557 r_free = 0.3557 target = 0.132241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.107772 restraints weight = 12963.561| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.66 r_work: 0.3138 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13100 Z= 0.177 Angle : 0.858 20.967 17896 Z= 0.396 Chirality : 0.052 0.357 2100 Planarity : 0.004 0.041 2196 Dihedral : 12.917 110.525 2900 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.79 % Favored : 97.14 % Rotamer: Outliers : 1.86 % Allowed : 15.96 % Favored : 82.18 % 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 aren not related in a simple way. whole: -0.29 (0.21), residues: 1540 helix: -0.06 (0.87), residues: 28 sheet: 0.36 (0.21), residues: 604 loop : -0.55 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 150 TYR 0.014 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 C 144 Details of bonding type rmsd covalent geometry : bond 0.00369 (13004) covalent geometry : angle 0.74181 (17644) SS BOND : bond 0.00459 ( 36) SS BOND : angle 1.24672 ( 72) hydrogen bonds : bond 0.05130 ( 367) hydrogen bonds : angle 7.44122 ( 1026) link_ALPHA1-2 : bond 0.01236 ( 4) link_ALPHA1-2 : angle 2.23877 ( 12) link_ALPHA1-3 : bond 0.00730 ( 8) link_ALPHA1-3 : angle 5.50704 ( 24) link_ALPHA1-6 : bond 0.00993 ( 4) link_ALPHA1-6 : angle 2.01184 ( 12) link_BETA1-4 : bond 0.01084 ( 20) link_BETA1-4 : angle 3.85752 ( 60) link_NAG-ASN : bond 0.00660 ( 24) link_NAG-ASN : angle 4.76346 ( 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 : 0.528 Fit side-chains revert: symmetry clash REVERT: A 343 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7492 (mt-10) REVERT: A 381 GLU cc_start: 0.7869 (mt-10) cc_final: 0.7360 (mp0) REVERT: A 415 LYS cc_start: 0.8344 (tttp) cc_final: 0.7574 (mtmt) REVERT: B 416 SER cc_start: 0.7687 (p) cc_final: 0.7412 (m) REVERT: B 465 ASN cc_start: 0.8288 (t0) cc_final: 0.8010 (m110) REVERT: C 127 ASP cc_start: 0.7722 (m-30) cc_final: 0.7409 (m-30) REVERT: C 150 ARG cc_start: 0.7291 (ttt180) cc_final: 0.6766 (mtm180) REVERT: C 210 ARG cc_start: 0.8734 (ptp90) cc_final: 0.8469 (ptp-110) REVERT: C 261 LYS cc_start: 0.8218 (ttmm) cc_final: 0.7830 (tptp) REVERT: C 399 ASP cc_start: 0.8023 (t70) cc_final: 0.7640 (m-30) REVERT: C 415 LYS cc_start: 0.8492 (tttt) cc_final: 0.8128 (tttp) REVERT: D 465 ASN cc_start: 0.8249 (m-40) cc_final: 0.7733 (p0) outliers start: 25 outliers final: 10 residues processed: 170 average time/residue: 0.6525 time to fit residues: 120.1696 Evaluate side-chains 132 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 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 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 C residue 369 THR 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: 3.9990 chunk 90 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 HIS B 147 ASN C 465 ASN D 147 ASN D 347 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.134196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.110288 restraints weight = 13153.859| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.56 r_work: 0.3197 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13100 Z= 0.182 Angle : 0.783 12.249 17896 Z= 0.368 Chirality : 0.051 0.376 2100 Planarity : 0.004 0.041 2196 Dihedral : 11.770 101.103 2896 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.69 % Rotamer: Outliers : 2.52 % Allowed : 16.56 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.21), residues: 1540 helix: -0.59 (0.92), residues: 24 sheet: 0.27 (0.22), residues: 580 loop : -0.54 (0.19), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 150 TYR 0.015 0.002 TYR D 121 PHE 0.014 0.002 PHE B 354 TRP 0.015 0.002 TRP C 178 HIS 0.004 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00385 (13004) covalent geometry : angle 0.69882 (17644) SS BOND : bond 0.00365 ( 36) SS BOND : angle 0.98133 ( 72) hydrogen bonds : bond 0.04648 ( 367) hydrogen bonds : angle 7.16722 ( 1026) link_ALPHA1-2 : bond 0.01469 ( 4) link_ALPHA1-2 : angle 2.04727 ( 12) link_ALPHA1-3 : bond 0.00449 ( 8) link_ALPHA1-3 : angle 5.05953 ( 24) link_ALPHA1-6 : bond 0.00613 ( 4) link_ALPHA1-6 : angle 1.77036 ( 12) link_BETA1-4 : bond 0.01121 ( 20) link_BETA1-4 : angle 3.55750 ( 60) link_NAG-ASN : bond 0.00483 ( 24) link_NAG-ASN : angle 3.37449 ( 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 165 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 131 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9025 (OUTLIER) cc_final: 0.8798 (mt0) REVERT: A 251 ASP cc_start: 0.7969 (m-30) cc_final: 0.7699 (m-30) REVERT: A 304 ASP cc_start: 0.8036 (m-30) cc_final: 0.7835 (m-30) REVERT: A 381 GLU cc_start: 0.7965 (mt-10) cc_final: 0.7495 (mp0) REVERT: A 415 LYS cc_start: 0.8374 (tttp) cc_final: 0.7675 (mtmt) REVERT: C 150 ARG cc_start: 0.7274 (ttt180) cc_final: 0.6839 (mtm180) REVERT: C 210 ARG cc_start: 0.8745 (ptp90) cc_final: 0.8495 (ptp-110) REVERT: C 261 LYS cc_start: 0.8349 (ttmm) cc_final: 0.8144 (tptp) REVERT: C 399 ASP cc_start: 0.8139 (t70) cc_final: 0.7854 (m-30) REVERT: C 415 LYS cc_start: 0.8618 (tttt) cc_final: 0.8316 (ttpp) REVERT: D 387 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8142 (mmtm) REVERT: D 465 ASN cc_start: 0.8385 (m-40) cc_final: 0.7842 (p0) outliers start: 34 outliers final: 13 residues processed: 152 average time/residue: 0.6503 time to fit residues: 107.5602 Evaluate side-chains 129 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 114 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 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 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 267 THR 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: 2.9990 chunk 16 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 HIS B 91 GLN B 147 ASN B 465 ASN D 347 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.126714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.101219 restraints weight = 13021.413| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.69 r_work: 0.3042 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 13100 Z= 0.278 Angle : 0.864 14.860 17896 Z= 0.413 Chirality : 0.054 0.376 2100 Planarity : 0.005 0.043 2196 Dihedral : 12.132 104.716 2896 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.38 % Favored : 96.56 % Rotamer: Outliers : 2.67 % Allowed : 16.41 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.20), residues: 1540 helix: -0.69 (0.89), residues: 24 sheet: 0.09 (0.21), residues: 584 loop : -0.71 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 156 TYR 0.016 0.003 TYR B 121 PHE 0.016 0.003 PHE C 97 TRP 0.019 0.002 TRP C 178 HIS 0.004 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00607 (13004) covalent geometry : angle 0.77427 (17644) SS BOND : bond 0.00501 ( 36) SS BOND : angle 1.35541 ( 72) hydrogen bonds : bond 0.05130 ( 367) hydrogen bonds : angle 7.31708 ( 1026) link_ALPHA1-2 : bond 0.01511 ( 4) link_ALPHA1-2 : angle 2.19443 ( 12) link_ALPHA1-3 : bond 0.00456 ( 8) link_ALPHA1-3 : angle 5.07077 ( 24) link_ALPHA1-6 : bond 0.00411 ( 4) link_ALPHA1-6 : angle 2.12413 ( 12) link_BETA1-4 : bond 0.01024 ( 20) link_BETA1-4 : angle 3.63483 ( 60) link_NAG-ASN : bond 0.00560 ( 24) link_NAG-ASN : angle 3.93811 ( 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 165 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 129 time to evaluate : 0.394 Fit side-chains revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8923 (mt0) REVERT: A 251 ASP cc_start: 0.8160 (m-30) cc_final: 0.7810 (m-30) REVERT: A 304 ASP cc_start: 0.8107 (m-30) cc_final: 0.7893 (m-30) REVERT: A 381 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7368 (mp0) REVERT: A 415 LYS cc_start: 0.8583 (tttp) cc_final: 0.7578 (mtmt) REVERT: B 128 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8309 (pttm) REVERT: B 416 SER cc_start: 0.7634 (p) cc_final: 0.7397 (m) REVERT: C 150 ARG cc_start: 0.7357 (ttt180) cc_final: 0.6744 (mtm180) REVERT: C 261 LYS cc_start: 0.8514 (ttmm) cc_final: 0.8189 (tptp) REVERT: C 399 ASP cc_start: 0.8220 (t70) cc_final: 0.7958 (m-30) REVERT: C 415 LYS cc_start: 0.8677 (tttt) cc_final: 0.8305 (tttp) REVERT: C 432 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6673 (mp0) REVERT: D 309 ASP cc_start: 0.7662 (OUTLIER) cc_final: 0.7429 (m-30) REVERT: D 387 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8126 (mtmm) REVERT: D 435 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7720 (mp0) REVERT: D 465 ASN cc_start: 0.8429 (m-40) cc_final: 0.7821 (p0) outliers start: 36 outliers final: 17 residues processed: 150 average time/residue: 0.5834 time to fit residues: 95.5653 Evaluate side-chains 138 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 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 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 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 Chi-restraints excluded: chain D residue 387 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 78 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 0.0670 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 336 HIS B 147 ASN B 264 HIS B 391 GLN 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 = 0.3578 r_free = 0.3578 target = 0.133087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.108518 restraints weight = 12956.217| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.61 r_work: 0.3163 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13100 Z= 0.154 Angle : 0.745 11.135 17896 Z= 0.352 Chirality : 0.050 0.345 2100 Planarity : 0.003 0.045 2196 Dihedral : 11.419 100.536 2896 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.99 % Favored : 96.95 % Rotamer: Outliers : 1.93 % Allowed : 17.74 % Favored : 80.33 % 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 aren not related in a simple way. whole: -0.53 (0.20), residues: 1540 helix: -0.37 (0.97), residues: 24 sheet: 0.15 (0.21), residues: 584 loop : -0.66 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 150 TYR 0.013 0.002 TYR D 121 PHE 0.012 0.002 PHE A 354 TRP 0.015 0.002 TRP C 178 HIS 0.003 0.001 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00322 (13004) covalent geometry : angle 0.66791 (17644) SS BOND : bond 0.00307 ( 36) SS BOND : angle 0.94252 ( 72) hydrogen bonds : bond 0.04016 ( 367) hydrogen bonds : angle 6.89886 ( 1026) link_ALPHA1-2 : bond 0.01367 ( 4) link_ALPHA1-2 : angle 2.04223 ( 12) link_ALPHA1-3 : bond 0.00509 ( 8) link_ALPHA1-3 : angle 4.74119 ( 24) link_ALPHA1-6 : bond 0.00529 ( 4) link_ALPHA1-6 : angle 1.37304 ( 12) link_BETA1-4 : bond 0.01068 ( 20) link_BETA1-4 : angle 3.28582 ( 60) link_NAG-ASN : bond 0.00346 ( 24) link_NAG-ASN : angle 3.19273 ( 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 161 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7965 (m-30) cc_final: 0.7642 (m-30) REVERT: A 304 ASP cc_start: 0.8076 (m-30) cc_final: 0.7857 (m-30) REVERT: A 381 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7466 (mp0) REVERT: A 415 LYS cc_start: 0.8508 (tttp) cc_final: 0.7623 (mtmt) REVERT: B 128 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8291 (ptpp) REVERT: C 103 ASP cc_start: 0.8083 (p0) cc_final: 0.7830 (p0) REVERT: C 150 ARG cc_start: 0.7290 (ttt180) cc_final: 0.6808 (mtm180) REVERT: C 261 LYS cc_start: 0.8463 (ttmm) cc_final: 0.8248 (tptp) REVERT: C 415 LYS cc_start: 0.8685 (tttt) cc_final: 0.8363 (tttp) REVERT: C 432 GLU cc_start: 0.7256 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: D 309 ASP cc_start: 0.7491 (OUTLIER) cc_final: 0.7224 (m-30) REVERT: D 435 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7708 (mp0) REVERT: D 465 ASN cc_start: 0.8405 (m-40) cc_final: 0.7870 (p0) outliers start: 26 outliers final: 11 residues processed: 154 average time/residue: 0.6276 time to fit residues: 105.3085 Evaluate side-chains 139 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 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 C residue 83 GLU Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain D residue 309 ASP Chi-restraints excluded: chain D residue 314 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 68 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 3 optimal weight: 0.1980 chunk 122 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN A 336 HIS ** B 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.135105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.110710 restraints weight = 12840.125| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.61 r_work: 0.3194 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2666 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= 0.134 Angle : 0.766 23.620 17896 Z= 0.354 Chirality : 0.060 1.409 2100 Planarity : 0.004 0.046 2196 Dihedral : 11.129 97.371 2896 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.25 % Favored : 96.69 % Rotamer: Outliers : 1.71 % Allowed : 18.71 % 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 aren not related in a simple way. whole: -0.58 (0.20), residues: 1540 helix: 0.36 (0.97), residues: 28 sheet: 0.04 (0.22), residues: 556 loop : -0.65 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 85 TYR 0.014 0.002 TYR D 121 PHE 0.012 0.002 PHE D 410 TRP 0.023 0.001 TRP A 87 HIS 0.004 0.001 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00273 (13004) covalent geometry : angle 0.68857 (17644) SS BOND : bond 0.00271 ( 36) SS BOND : angle 0.83381 ( 72) hydrogen bonds : bond 0.03660 ( 367) hydrogen bonds : angle 6.72617 ( 1026) link_ALPHA1-2 : bond 0.01418 ( 4) link_ALPHA1-2 : angle 2.13112 ( 12) link_ALPHA1-3 : bond 0.00495 ( 8) link_ALPHA1-3 : angle 4.60522 ( 24) link_ALPHA1-6 : bond 0.00563 ( 4) link_ALPHA1-6 : angle 1.26954 ( 12) link_BETA1-4 : bond 0.01063 ( 20) link_BETA1-4 : angle 3.18300 ( 60) link_NAG-ASN : bond 0.00330 ( 24) link_NAG-ASN : angle 3.51713 ( 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 150 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7941 (m-30) cc_final: 0.7656 (m-30) REVERT: A 304 ASP cc_start: 0.8081 (m-30) cc_final: 0.7850 (m-30) REVERT: A 381 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7443 (mp0) REVERT: A 415 LYS cc_start: 0.8488 (tttp) cc_final: 0.7609 (mtmt) REVERT: B 128 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8271 (ptpp) REVERT: B 432 GLU cc_start: 0.6968 (OUTLIER) cc_final: 0.6525 (mp0) REVERT: C 150 ARG cc_start: 0.7233 (ttt180) cc_final: 0.6781 (mtm180) REVERT: C 261 LYS cc_start: 0.8438 (ttmm) cc_final: 0.8136 (tptp) REVERT: C 415 LYS cc_start: 0.8704 (tttt) cc_final: 0.8377 (tttp) REVERT: C 432 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6535 (mp0) REVERT: D 309 ASP cc_start: 0.7519 (OUTLIER) cc_final: 0.7218 (m-30) REVERT: D 435 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7716 (mp0) REVERT: D 465 ASN cc_start: 0.8395 (m-40) cc_final: 0.7829 (p0) outliers start: 23 outliers final: 13 residues processed: 147 average time/residue: 0.6473 time to fit residues: 103.6862 Evaluate side-chains 136 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 432 GLU Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 183 CYS Chi-restraints excluded: chain C residue 309 ASP 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 Chi-restraints excluded: chain D residue 334 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 47 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 72 optimal weight: 0.9980 chunk 139 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN A 336 HIS B 147 ASN ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN D 141 ASN D 347 HIS D 391 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.129734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.104828 restraints weight = 12863.551| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 1.60 r_work: 0.3107 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 13100 Z= 0.278 Angle : 0.855 12.167 17896 Z= 0.408 Chirality : 0.057 0.903 2100 Planarity : 0.005 0.046 2196 Dihedral : 11.649 96.870 2896 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.36 % Rotamer: Outliers : 2.52 % Allowed : 18.11 % Favored : 79.36 % 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 aren not related in a simple way. whole: -0.62 (0.20), residues: 1540 helix: -0.50 (0.92), residues: 24 sheet: 0.09 (0.21), residues: 584 loop : -0.71 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 150 TYR 0.015 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 310 Details of bonding type rmsd covalent geometry : bond 0.00613 (13004) covalent geometry : angle 0.76548 (17644) SS BOND : bond 0.00485 ( 36) SS BOND : angle 1.40164 ( 72) hydrogen bonds : bond 0.04854 ( 367) hydrogen bonds : angle 7.13760 ( 1026) link_ALPHA1-2 : bond 0.01555 ( 4) link_ALPHA1-2 : angle 2.32009 ( 12) link_ALPHA1-3 : bond 0.00420 ( 8) link_ALPHA1-3 : angle 4.93584 ( 24) link_ALPHA1-6 : bond 0.00396 ( 4) link_ALPHA1-6 : angle 1.95652 ( 12) link_BETA1-4 : bond 0.01003 ( 20) link_BETA1-4 : angle 3.53929 ( 60) link_NAG-ASN : bond 0.00524 ( 24) link_NAG-ASN : angle 4.01667 ( 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 161 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 127 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8059 (m-30) cc_final: 0.7747 (m-30) REVERT: A 304 ASP cc_start: 0.8050 (m-30) cc_final: 0.7844 (m-30) REVERT: A 381 GLU cc_start: 0.8017 (mt-10) cc_final: 0.7489 (mp0) REVERT: A 415 LYS cc_start: 0.8590 (tttp) cc_final: 0.7543 (mtmt) REVERT: B 128 LYS cc_start: 0.8616 (OUTLIER) cc_final: 0.8368 (pttm) REVERT: B 416 SER cc_start: 0.7670 (p) cc_final: 0.7448 (m) REVERT: B 432 GLU cc_start: 0.6977 (OUTLIER) cc_final: 0.6576 (mp0) REVERT: C 150 ARG cc_start: 0.7413 (ttt180) cc_final: 0.6823 (mtm180) REVERT: C 261 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8266 (tptp) REVERT: C 415 LYS cc_start: 0.8737 (tttt) cc_final: 0.8396 (tttp) REVERT: C 432 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6658 (mp0) REVERT: D 309 ASP cc_start: 0.7539 (OUTLIER) cc_final: 0.7276 (m-30) REVERT: D 375 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8325 (pt0) REVERT: D 435 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7743 (mp0) REVERT: D 465 ASN cc_start: 0.8422 (m-40) cc_final: 0.7882 (p0) outliers start: 34 outliers final: 19 residues processed: 150 average time/residue: 0.6076 time to fit residues: 99.6722 Evaluate side-chains 142 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 221 ASP 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 B residue 432 GLU 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 432 GLU Chi-restraints excluded: chain D residue 148 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 57 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 105 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 128 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 0.0980 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN A 336 HIS B 147 ASN B 391 GLN B 465 ASN ** C 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 HIS D 391 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.134105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.109500 restraints weight = 12790.235| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 1.61 r_work: 0.3176 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13100 Z= 0.145 Angle : 0.735 10.870 17896 Z= 0.346 Chirality : 0.051 0.712 2100 Planarity : 0.003 0.045 2196 Dihedral : 11.034 92.919 2896 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.12 % Favored : 96.82 % Rotamer: Outliers : 1.78 % Allowed : 19.08 % Favored : 79.14 % 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 aren not related in a simple way. whole: -0.62 (0.20), residues: 1540 helix: 0.11 (0.92), residues: 28 sheet: 0.03 (0.22), residues: 556 loop : -0.67 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 150 TYR 0.013 0.002 TYR D 121 PHE 0.013 0.002 PHE A 354 TRP 0.016 0.002 TRP A 87 HIS 0.003 0.001 HIS B 184 Details of bonding type rmsd covalent geometry : bond 0.00301 (13004) covalent geometry : angle 0.66074 (17644) SS BOND : bond 0.00291 ( 36) SS BOND : angle 0.90043 ( 72) hydrogen bonds : bond 0.03829 ( 367) hydrogen bonds : angle 6.74145 ( 1026) link_ALPHA1-2 : bond 0.01426 ( 4) link_ALPHA1-2 : angle 2.19210 ( 12) link_ALPHA1-3 : bond 0.00469 ( 8) link_ALPHA1-3 : angle 4.62331 ( 24) link_ALPHA1-6 : bond 0.00466 ( 4) link_ALPHA1-6 : angle 1.36261 ( 12) link_BETA1-4 : bond 0.01043 ( 20) link_BETA1-4 : angle 3.11728 ( 60) link_NAG-ASN : bond 0.00295 ( 24) link_NAG-ASN : angle 3.18889 ( 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 147 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7956 (m-30) cc_final: 0.7634 (m-30) REVERT: A 304 ASP cc_start: 0.8089 (m-30) cc_final: 0.7865 (m-30) REVERT: A 381 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7455 (mp0) REVERT: A 390 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8390 (mp) REVERT: A 415 LYS cc_start: 0.8555 (tttp) cc_final: 0.7542 (mtmt) REVERT: B 128 LYS cc_start: 0.8536 (OUTLIER) cc_final: 0.8280 (ptpp) REVERT: C 150 ARG cc_start: 0.7299 (ttt180) cc_final: 0.6778 (mtm180) REVERT: C 261 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8070 (tptp) REVERT: C 415 LYS cc_start: 0.8742 (tttt) cc_final: 0.8407 (tttp) REVERT: C 432 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6528 (mp0) REVERT: D 309 ASP cc_start: 0.7476 (OUTLIER) cc_final: 0.7170 (m-30) REVERT: D 435 GLU cc_start: 0.8040 (mt-10) cc_final: 0.7745 (mp0) REVERT: D 465 ASN cc_start: 0.8422 (m-40) cc_final: 0.7887 (p0) outliers start: 24 outliers final: 14 residues processed: 142 average time/residue: 0.6385 time to fit residues: 98.9754 Evaluate side-chains 137 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 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 390 LEU Chi-restraints excluded: chain A residue 435 GLU 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 267 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 34 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 8 optimal weight: 0.0000 chunk 11 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 8.9990 chunk 29 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 overall best weight: 2.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN A 336 HIS B 147 ASN ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN ** C 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 ASN D 347 HIS D 391 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.130433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.105504 restraints weight = 12843.680| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.61 r_work: 0.3119 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13100 Z= 0.244 Angle : 0.825 11.691 17896 Z= 0.394 Chirality : 0.054 0.643 2100 Planarity : 0.004 0.046 2196 Dihedral : 11.396 92.207 2896 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.70 % Favored : 96.23 % Rotamer: Outliers : 2.00 % Allowed : 19.01 % Favored : 78.99 % 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 aren not related in a simple way. whole: -0.61 (0.20), residues: 1540 helix: -0.52 (0.92), residues: 24 sheet: 0.09 (0.21), residues: 584 loop : -0.71 (0.19), residues: 932 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 150 TYR 0.015 0.002 TYR D 121 PHE 0.017 0.002 PHE A 410 TRP 0.018 0.002 TRP C 178 HIS 0.003 0.001 HIS C 347 Details of bonding type rmsd covalent geometry : bond 0.00534 (13004) covalent geometry : angle 0.74127 (17644) SS BOND : bond 0.00427 ( 36) SS BOND : angle 1.34525 ( 72) hydrogen bonds : bond 0.04632 ( 367) hydrogen bonds : angle 7.02184 ( 1026) link_ALPHA1-2 : bond 0.01602 ( 4) link_ALPHA1-2 : angle 2.39119 ( 12) link_ALPHA1-3 : bond 0.00404 ( 8) link_ALPHA1-3 : angle 4.81839 ( 24) link_ALPHA1-6 : bond 0.00385 ( 4) link_ALPHA1-6 : angle 1.75194 ( 12) link_BETA1-4 : bond 0.01008 ( 20) link_BETA1-4 : angle 3.44896 ( 60) link_NAG-ASN : bond 0.00482 ( 24) link_NAG-ASN : angle 3.70282 ( 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 147 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 120 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.8039 (m-30) cc_final: 0.7693 (m-30) REVERT: A 304 ASP cc_start: 0.8082 (m-30) cc_final: 0.7871 (m-30) REVERT: A 381 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7484 (mp0) REVERT: A 390 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8408 (mp) REVERT: A 415 LYS cc_start: 0.8559 (tttp) cc_final: 0.7531 (mtmt) REVERT: B 128 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8364 (pttm) REVERT: B 416 SER cc_start: 0.7668 (p) cc_final: 0.7443 (m) REVERT: C 150 ARG cc_start: 0.7424 (ttt180) cc_final: 0.6817 (mtm180) REVERT: C 261 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8255 (tptp) REVERT: C 415 LYS cc_start: 0.8749 (tttt) cc_final: 0.8374 (tttp) REVERT: C 432 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6625 (mp0) REVERT: D 309 ASP cc_start: 0.7521 (OUTLIER) cc_final: 0.7246 (m-30) REVERT: D 375 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8310 (pt0) REVERT: D 435 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7778 (mp0) REVERT: D 465 ASN cc_start: 0.8417 (m-40) cc_final: 0.7908 (p0) outliers start: 27 outliers final: 15 residues processed: 139 average time/residue: 0.6017 time to fit residues: 91.5398 Evaluate side-chains 139 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 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 390 LEU Chi-restraints excluded: chain A residue 435 GLU 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 267 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 390 LEU Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain D residue 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: 2.9990 chunk 16 optimal weight: 8.9990 chunk 7 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 36 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN B 147 ASN ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN C 347 HIS D 347 HIS D 391 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.133059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.108350 restraints weight = 12871.430| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.62 r_work: 0.3159 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13100 Z= 0.159 Angle : 0.754 10.984 17896 Z= 0.358 Chirality : 0.051 0.559 2100 Planarity : 0.003 0.045 2196 Dihedral : 11.081 89.430 2896 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.93 % Allowed : 19.01 % Favored : 79.06 % 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 aren not related in a simple way. whole: -0.56 (0.20), residues: 1540 helix: -0.08 (0.89), residues: 28 sheet: 0.14 (0.21), residues: 584 loop : -0.70 (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 D 121 PHE 0.015 0.002 PHE A 410 TRP 0.016 0.002 TRP C 178 HIS 0.005 0.001 HIS C 347 Details of bonding type rmsd covalent geometry : bond 0.00333 (13004) covalent geometry : angle 0.67826 (17644) SS BOND : bond 0.00309 ( 36) SS BOND : angle 1.10848 ( 72) hydrogen bonds : bond 0.03996 ( 367) hydrogen bonds : angle 6.78861 ( 1026) link_ALPHA1-2 : bond 0.01420 ( 4) link_ALPHA1-2 : angle 2.27953 ( 12) link_ALPHA1-3 : bond 0.00474 ( 8) link_ALPHA1-3 : angle 4.66594 ( 24) link_ALPHA1-6 : bond 0.00440 ( 4) link_ALPHA1-6 : angle 1.39414 ( 12) link_BETA1-4 : bond 0.01030 ( 20) link_BETA1-4 : angle 3.16928 ( 60) link_NAG-ASN : bond 0.00338 ( 24) link_NAG-ASN : angle 3.22674 ( 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 144 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 251 ASP cc_start: 0.7972 (m-30) cc_final: 0.7653 (m-30) REVERT: A 304 ASP cc_start: 0.8073 (m-30) cc_final: 0.7862 (m-30) REVERT: A 381 GLU cc_start: 0.7983 (mt-10) cc_final: 0.7486 (mp0) REVERT: A 390 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8410 (mp) REVERT: A 415 LYS cc_start: 0.8522 (tttp) cc_final: 0.7518 (mtmt) REVERT: B 128 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8298 (ptpp) REVERT: C 150 ARG cc_start: 0.7363 (ttt180) cc_final: 0.6784 (mtm180) REVERT: C 261 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8218 (tptp) REVERT: C 415 LYS cc_start: 0.8741 (tttt) cc_final: 0.8464 (tttp) REVERT: C 432 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6565 (mp0) REVERT: D 309 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7162 (m-30) REVERT: D 375 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8229 (pt0) REVERT: D 435 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7758 (mp0) REVERT: D 465 ASN cc_start: 0.8398 (m-40) cc_final: 0.7897 (p0) outliers start: 26 outliers final: 14 residues processed: 138 average time/residue: 0.6510 time to fit residues: 97.9082 Evaluate side-chains 133 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 113 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 390 LEU Chi-restraints excluded: chain A residue 435 GLU 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 267 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 309 ASP Chi-restraints excluded: chain C residue 432 GLU Chi-restraints excluded: chain D residue 148 THR 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: 0.6980 chunk 110 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 87 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 82 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 147 ASN ** B 391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN ** C 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3641 r_free = 0.3641 target = 0.137242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.114480 restraints weight = 13606.776| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.52 r_work: 0.3256 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2835 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= 0.162 Angle : 0.749 10.644 17896 Z= 0.357 Chirality : 0.051 0.472 2100 Planarity : 0.004 0.045 2196 Dihedral : 11.009 86.836 2896 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.93 % Allowed : 18.86 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.20), residues: 1540 helix: 0.09 (0.91), residues: 28 sheet: 0.15 (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 0.014 0.002 TYR D 121 PHE 0.017 0.002 PHE A 410 TRP 0.015 0.002 TRP C 178 HIS 0.006 0.001 HIS C 347 Details of bonding type rmsd covalent geometry : bond 0.00344 (13004) covalent geometry : angle 0.67577 (17644) SS BOND : bond 0.00324 ( 36) SS BOND : angle 1.08487 ( 72) hydrogen bonds : bond 0.03965 ( 367) hydrogen bonds : angle 6.74002 ( 1026) link_ALPHA1-2 : bond 0.01519 ( 4) link_ALPHA1-2 : angle 2.38780 ( 12) link_ALPHA1-3 : bond 0.00408 ( 8) link_ALPHA1-3 : angle 4.62500 ( 24) link_ALPHA1-6 : bond 0.00455 ( 4) link_ALPHA1-6 : angle 1.42241 ( 12) link_BETA1-4 : bond 0.01015 ( 20) link_BETA1-4 : angle 3.17049 ( 60) link_NAG-ASN : bond 0.00345 ( 24) link_NAG-ASN : angle 3.11954 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4476.34 seconds wall clock time: 77 minutes 31.71 seconds (4651.71 seconds total)