Starting phenix.real_space_refine on Wed Feb 4 21:34:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cyg_46043/02_2026/9cyg_46043.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cyg_46043/02_2026/9cyg_46043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cyg_46043/02_2026/9cyg_46043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cyg_46043/02_2026/9cyg_46043.map" model { file = "/net/cci-nas-00/data/ceres_data/9cyg_46043/02_2026/9cyg_46043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cyg_46043/02_2026/9cyg_46043.cif" } resolution = 2.75 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= 0.007 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 7884 2.51 5 N 2184 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 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12808 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2999 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 374} Chain: "B" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2999 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 374} Chain: "C" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2999 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 374} Chain: "D" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2999 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 374} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} 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: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: 2.73, per 1000 atoms: 0.21 Number of scatterers: 12808 At special positions: 0 Unit cell: (115.275, 115.275, 73.225, 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 2184 7.00 C 7884 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=2.03 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=2.03 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=2.03 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=2.03 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=2.03 Simple disulfide: pdb=" SG CYS D 175 " - pdb=" SG CYS D 193 " distance=2.03 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 G 4 " - " MAN G 5 " " MAN K 4 " - " MAN K 5 " " MAN O 4 " - " MAN O 5 " " MAN S 4 " - " MAN S 5 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 6 " - " MAN G 7 " " BMA K 3 " - " MAN K 4 " " MAN K 6 " - " MAN K 7 " " BMA O 3 " - " MAN O 4 " " MAN O 6 " - " MAN O 7 " " BMA S 3 " - " MAN S 4 " " MAN S 6 " - " MAN S 7 " ALPHA1-6 " BMA G 3 " - " MAN G 6 " " MAN G 6 " - " MAN G 8 " " BMA K 3 " - " MAN K 6 " " MAN K 6 " - " MAN K 8 " " BMA O 3 " - " MAN O 6 " " MAN O 6 " - " MAN O 8 " " BMA S 3 " - " MAN S 6 " " MAN S 6 " - " MAN S 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " BETA1-6 " NAG E 1 " - " FUC E 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG I 1 " - " FUC I 2 " " NAG M 1 " - " FUC M 2 " " NAG Q 1 " - " FUC Q 2 " NAG-ASN " NAG A 502 " - " ASN A 234 " " NAG A 503 " - " ASN A 86 " " NAG B 502 " - " ASN B 234 " " NAG B 503 " - " ASN B 86 " " NAG C 502 " - " ASN C 234 " " NAG C 503 " - " ASN C 86 " " NAG D 502 " - " ASN D 234 " " NAG D 503 " - " ASN D 86 " " NAG E 1 " - " ASN A 245 " " NAG F 1 " - " ASN A 146 " " NAG G 1 " - " ASN A 200 " " NAG H 1 " - " ASN A 367 " " NAG I 1 " - " ASN B 245 " " NAG J 1 " - " ASN B 146 " " NAG K 1 " - " ASN B 200 " " NAG L 1 " - " ASN B 367 " " NAG M 1 " - " ASN C 245 " " NAG N 1 " - " ASN C 146 " " NAG O 1 " - " ASN C 200 " " NAG P 1 " - " ASN C 367 " " NAG Q 1 " - " ASN D 245 " " NAG R 1 " - " ASN D 146 " " NAG S 1 " - " ASN D 200 " " NAG T 1 " - " ASN D 367 " Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 353.0 milliseconds 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2800 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 24 sheets defined 2.8% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 142 through 146 removed outlier: 4.008A pdb=" N ASN A 146 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 142 through 146 removed outlier: 4.009A pdb=" N ASN B 146 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 142 through 146 removed outlier: 4.008A pdb=" N ASN C 146 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 142 through 146 removed outlier: 4.008A 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: 5.343A pdb=" N PHE A 97 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR A 449 " --> pdb=" O PHE A 97 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N CYS A 447 " --> pdb=" O PRO A 99 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.781A pdb=" N CYS A 175 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET A 160 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 5.789A 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: 6.838A pdb=" N ALA A 203 " --> pdb=" O SER A 214 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER A 214 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 7.208A 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: 3.845A pdb=" N VAL A 231 " --> pdb=" O THR A 238 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS A 264 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.528A 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 281 removed outlier: 5.368A pdb=" N CYS A 278 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N VAL A 290 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N CYS A 280 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ARG A 288 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER A 311 " --> pdb=" O ASN A 306 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 352 through 355 removed outlier: 4.776A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 8.183A pdb=" N LEU A 372 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL A 398 " --> pdb=" O LEU A 372 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N TYR A 374 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N VAL A 396 " --> pdb=" O TYR A 374 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR A 376 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG A 394 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 96 through 102 removed outlier: 5.341A pdb=" N PHE B 97 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR B 449 " --> pdb=" O PHE B 97 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N CYS B 447 " --> pdb=" O PRO B 99 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 121 through 124 removed outlier: 3.782A pdb=" N CYS B 175 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET B 160 " --> pdb=" O GLN B 173 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLN B 173 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 179 through 184 removed outlier: 6.837A pdb=" N ALA B 203 " --> pdb=" O SER B 214 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER B 214 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE B 205 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.845A pdb=" N VAL B 231 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS B 264 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.528A 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 281 removed outlier: 5.366A pdb=" N CYS B 278 " --> pdb=" O VAL B 290 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL B 290 " --> pdb=" O CYS B 278 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N CYS B 280 " --> pdb=" O ARG B 288 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ARG B 288 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 3.578A 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 355 removed outlier: 4.759A pdb=" N TRP B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N GLY B 363 " --> pdb=" O TRP B 352 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N LEU B 372 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N VAL B 398 " --> pdb=" O LEU B 372 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N TYR B 374 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL B 396 " --> pdb=" O TYR B 374 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR B 376 " --> pdb=" O ARG B 394 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG B 394 " --> pdb=" O THR B 376 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 96 through 102 removed outlier: 5.342A pdb=" N PHE C 97 " --> pdb=" O THR C 449 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR C 449 " --> pdb=" O PHE C 97 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N CYS C 447 " --> pdb=" O PRO C 99 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ARG C 420 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 121 through 124 removed outlier: 3.781A pdb=" N CYS C 175 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET C 160 " --> pdb=" O GLN C 173 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N GLN C 173 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 179 through 184 removed outlier: 6.837A pdb=" N ALA C 203 " --> pdb=" O SER C 214 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER C 214 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE C 205 " --> pdb=" O VAL C 212 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 231 through 233 removed outlier: 3.844A pdb=" N VAL C 231 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS C 264 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU C 258 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.528A 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 281 removed outlier: 5.364A pdb=" N CYS C 278 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL C 290 " --> pdb=" O CYS C 278 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N CYS C 280 " --> pdb=" O ARG C 288 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ARG C 288 " --> pdb=" O CYS C 280 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER C 311 " --> pdb=" O ASN C 306 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 352 through 355 removed outlier: 4.757A pdb=" N TRP C 352 " --> pdb=" O GLY C 363 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY C 363 " --> pdb=" O TRP C 352 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LEU C 372 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL C 398 " --> pdb=" O LEU C 372 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N TYR C 374 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N VAL C 396 " --> pdb=" O TYR C 374 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N THR C 376 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG C 394 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 96 through 102 removed outlier: 5.341A pdb=" N PHE D 97 " --> pdb=" O THR D 449 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N THR D 449 " --> pdb=" O PHE D 97 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N CYS D 447 " --> pdb=" O PRO D 99 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N ARG D 420 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 121 through 124 removed outlier: 3.782A pdb=" N CYS D 175 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N MET D 160 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLN D 173 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 179 through 184 removed outlier: 6.837A pdb=" N ALA D 203 " --> pdb=" O SER D 214 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER D 214 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE D 205 " --> pdb=" O VAL D 212 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 231 through 233 removed outlier: 3.845A pdb=" N VAL D 231 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N HIS D 264 " --> pdb=" O PHE D 256 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.528A 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 281 removed outlier: 5.366A pdb=" N CYS D 278 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL D 290 " --> pdb=" O CYS D 278 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N CYS D 280 " --> pdb=" O ARG D 288 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N ARG D 288 " --> pdb=" O CYS D 280 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER D 311 " --> pdb=" O ASN D 306 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 352 through 355 removed outlier: 4.752A pdb=" N TRP D 352 " --> pdb=" O GLY D 363 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY D 363 " --> pdb=" O TRP D 352 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N LEU D 372 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL D 398 " --> pdb=" O LEU D 372 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N TYR D 374 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL D 396 " --> pdb=" O TYR D 374 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR D 376 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG D 394 " --> pdb=" O THR D 376 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 852 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: 1.96 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4068 1.34 - 1.47: 3460 1.47 - 1.60: 5440 1.60 - 1.73: 0 1.73 - 1.86: 104 Bond restraints: 13072 Sorted by residual: bond pdb=" C1 NAG M 1 " pdb=" O5 NAG M 1 " ideal model delta sigma weight residual 1.406 1.476 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" C1 NAG Q 1 " pdb=" O5 NAG Q 1 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1 NAG I 1 " pdb=" O5 NAG I 1 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.475 -0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C1 NAG M 1 " pdb=" C2 NAG M 1 " ideal model delta sigma weight residual 1.532 1.590 -0.058 2.00e-02 2.50e+03 8.43e+00 ... (remaining 13067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 16316 1.61 - 3.23: 1124 3.23 - 4.84: 198 4.84 - 6.46: 69 6.46 - 8.07: 17 Bond angle restraints: 17724 Sorted by residual: angle pdb=" CA CYS A 230 " pdb=" CB CYS A 230 " pdb=" SG CYS A 230 " ideal model delta sigma weight residual 114.40 122.47 -8.07 2.30e+00 1.89e-01 1.23e+01 angle pdb=" CA CYS B 230 " pdb=" CB CYS B 230 " pdb=" SG CYS B 230 " ideal model delta sigma weight residual 114.40 122.46 -8.06 2.30e+00 1.89e-01 1.23e+01 angle pdb=" CA CYS D 230 " pdb=" CB CYS D 230 " pdb=" SG CYS D 230 " ideal model delta sigma weight residual 114.40 122.45 -8.05 2.30e+00 1.89e-01 1.23e+01 angle pdb=" CA CYS C 230 " pdb=" CB CYS C 230 " pdb=" SG CYS C 230 " ideal model delta sigma weight residual 114.40 122.43 -8.03 2.30e+00 1.89e-01 1.22e+01 angle pdb=" CA GLN C 273 " pdb=" CB GLN C 273 " pdb=" CG GLN C 273 " ideal model delta sigma weight residual 114.10 120.07 -5.97 2.00e+00 2.50e-01 8.92e+00 ... (remaining 17719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.81: 7772 24.81 - 49.62: 568 49.62 - 74.44: 140 74.44 - 99.25: 72 99.25 - 124.06: 48 Dihedral angle restraints: 8600 sinusoidal: 4208 harmonic: 4392 Sorted by residual: dihedral pdb=" CA PRO A 282 " pdb=" C PRO A 282 " pdb=" N ARG A 283 " pdb=" CA ARG A 283 " ideal model delta harmonic sigma weight residual 180.00 154.34 25.66 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA PRO C 282 " pdb=" C PRO C 282 " pdb=" N ARG C 283 " pdb=" CA ARG C 283 " ideal model delta harmonic sigma weight residual 180.00 154.40 25.60 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA PRO B 282 " pdb=" C PRO B 282 " pdb=" N ARG B 283 " pdb=" CA ARG B 283 " ideal model delta harmonic sigma weight residual 180.00 154.40 25.60 0 5.00e+00 4.00e-02 2.62e+01 ... (remaining 8597 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.172: 2108 0.172 - 0.344: 12 0.344 - 0.516: 0 0.516 - 0.688: 0 0.688 - 0.860: 4 Chirality restraints: 2124 Sorted by residual: chirality pdb=" C1 NAG J 1 " pdb=" ND2 ASN B 146 " pdb=" C2 NAG J 1 " pdb=" O5 NAG J 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.54 -0.86 2.00e-01 2.50e+01 1.85e+01 chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN C 146 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.54 -0.86 2.00e-01 2.50e+01 1.85e+01 chirality pdb=" C1 NAG R 1 " pdb=" ND2 ASN D 146 " pdb=" C2 NAG R 1 " pdb=" O5 NAG R 1 " both_signs ideal model delta sigma weight residual False -2.40 -1.54 -0.86 2.00e-01 2.50e+01 1.84e+01 ... (remaining 2121 not shown) Planarity restraints: 2216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 428 " 0.407 9.50e-02 1.11e+02 1.83e-01 2.45e+01 pdb=" NE ARG C 428 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG C 428 " 0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG C 428 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG C 428 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 428 " 0.406 9.50e-02 1.11e+02 1.83e-01 2.44e+01 pdb=" NE ARG B 428 " -0.036 2.00e-02 2.50e+03 pdb=" CZ ARG B 428 " 0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG B 428 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG B 428 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 428 " -0.406 9.50e-02 1.11e+02 1.83e-01 2.44e+01 pdb=" NE ARG A 428 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A 428 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A 428 " 0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 428 " -0.003 2.00e-02 2.50e+03 ... (remaining 2213 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 997 2.74 - 3.28: 12128 3.28 - 3.82: 22363 3.82 - 4.36: 28367 4.36 - 4.90: 49426 Nonbonded interactions: 113281 Sorted by model distance: nonbonded pdb=" OG1 THR A 325 " pdb=" OG1 THR A 365 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR C 325 " pdb=" OG1 THR C 365 " model vdw 2.200 3.040 nonbonded pdb=" OG1 THR B 325 " pdb=" OG1 THR B 365 " model vdw 2.209 3.040 nonbonded pdb=" OG1 THR D 325 " pdb=" OG1 THR D 365 " model vdw 2.222 3.040 nonbonded pdb=" O3 NAG R 1 " pdb=" O7 NAG R 2 " model vdw 2.352 3.040 ... (remaining 113276 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'H' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'L' and resid 1) selection = (chain 'M' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'P' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'R' and resid 1) selection = (chain 'T' and resid 1) } ncs_group { reference = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'S' } 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: 11.960 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.540 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.020 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:5.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 : 0.006 0.070 13172 Z= 0.277 Angle : 1.016 11.786 17988 Z= 0.473 Chirality : 0.068 0.860 2124 Planarity : 0.013 0.183 2192 Dihedral : 21.836 124.059 5692 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.89 % Allowed : 21.07 % Favored : 78.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.19), residues: 1544 helix: -5.06 (0.22), residues: 24 sheet: -0.56 (0.22), residues: 472 loop : -1.22 (0.17), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.035 0.003 ARG C 428 TYR 0.015 0.002 TYR C 281 PHE 0.024 0.002 PHE A 422 TRP 0.011 0.001 TRP A 178 HIS 0.005 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00612 (13072) covalent geometry : angle 0.95444 (17724) SS BOND : bond 0.00282 ( 36) SS BOND : angle 2.18220 ( 72) hydrogen bonds : bond 0.23940 ( 328) hydrogen bonds : angle 11.36920 ( 852) link_ALPHA1-2 : bond 0.01762 ( 4) link_ALPHA1-2 : angle 4.76544 ( 12) link_ALPHA1-3 : bond 0.00416 ( 8) link_ALPHA1-3 : angle 1.87958 ( 24) link_ALPHA1-6 : bond 0.00518 ( 8) link_ALPHA1-6 : angle 1.29235 ( 24) link_BETA1-4 : bond 0.00976 ( 16) link_BETA1-4 : angle 2.75292 ( 48) link_BETA1-6 : bond 0.00702 ( 4) link_BETA1-6 : angle 1.00741 ( 12) link_NAG-ASN : bond 0.00826 ( 24) link_NAG-ASN : angle 4.25410 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 200 time to evaluate : 0.391 Fit side-chains REVERT: A 141 ASN cc_start: 0.9229 (t0) cc_final: 0.9018 (t0) REVERT: A 294 ASN cc_start: 0.6835 (t0) cc_final: 0.5781 (t0) REVERT: A 347 HIS cc_start: 0.8031 (m-70) cc_final: 0.7516 (m-70) REVERT: A 358 ASN cc_start: 0.8128 (t0) cc_final: 0.7461 (t0) REVERT: A 399 ASP cc_start: 0.8551 (t0) cc_final: 0.8263 (t70) REVERT: A 463 ASP cc_start: 0.8894 (t0) cc_final: 0.8503 (t0) REVERT: B 141 ASN cc_start: 0.9235 (t0) cc_final: 0.9024 (t0) REVERT: B 294 ASN cc_start: 0.6818 (t0) cc_final: 0.5727 (t0) REVERT: B 339 ASN cc_start: 0.8808 (m110) cc_final: 0.8606 (p0) REVERT: B 347 HIS cc_start: 0.8033 (m-70) cc_final: 0.7525 (m-70) REVERT: B 358 ASN cc_start: 0.8126 (t0) cc_final: 0.7477 (t0) REVERT: B 399 ASP cc_start: 0.8546 (t0) cc_final: 0.8258 (t70) REVERT: B 463 ASP cc_start: 0.8896 (t0) cc_final: 0.8508 (t0) REVERT: C 141 ASN cc_start: 0.9232 (t0) cc_final: 0.9021 (t0) REVERT: C 294 ASN cc_start: 0.6828 (t0) cc_final: 0.5733 (t0) REVERT: C 347 HIS cc_start: 0.8034 (m-70) cc_final: 0.7526 (m-70) REVERT: C 358 ASN cc_start: 0.8138 (t0) cc_final: 0.7514 (t0) REVERT: C 399 ASP cc_start: 0.8547 (t0) cc_final: 0.8256 (t70) REVERT: C 463 ASP cc_start: 0.8892 (t0) cc_final: 0.8507 (t0) REVERT: D 141 ASN cc_start: 0.9227 (t0) cc_final: 0.9017 (t0) REVERT: D 294 ASN cc_start: 0.6830 (t0) cc_final: 0.5741 (t0) REVERT: D 347 HIS cc_start: 0.8020 (m-70) cc_final: 0.7516 (m-70) REVERT: D 358 ASN cc_start: 0.8116 (t0) cc_final: 0.7455 (t0) REVERT: D 399 ASP cc_start: 0.8550 (t0) cc_final: 0.8261 (t70) REVERT: D 463 ASP cc_start: 0.8896 (t0) cc_final: 0.8508 (t0) outliers start: 12 outliers final: 4 residues processed: 208 average time/residue: 0.4730 time to fit residues: 108.5940 Evaluate side-chains 145 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 141 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain D residue 92 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.0060 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN A 147 ASN A 468 HIS B 131 GLN B 147 ASN B 468 HIS C 131 GLN C 147 ASN C 468 HIS D 131 GLN D 147 ASN D 468 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.098325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.081543 restraints weight = 21998.793| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.99 r_work: 0.2953 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13172 Z= 0.168 Angle : 0.730 12.030 17988 Z= 0.349 Chirality : 0.052 0.428 2124 Planarity : 0.005 0.055 2192 Dihedral : 17.303 97.094 2960 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.97 % Allowed : 22.55 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.20), residues: 1544 helix: -4.61 (0.31), residues: 24 sheet: 0.20 (0.22), residues: 500 loop : -0.93 (0.18), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 150 TYR 0.010 0.002 TYR B 374 PHE 0.016 0.002 PHE A 132 TRP 0.012 0.001 TRP C 178 HIS 0.004 0.001 HIS D 336 Details of bonding type rmsd covalent geometry : bond 0.00378 (13072) covalent geometry : angle 0.66513 (17724) SS BOND : bond 0.00755 ( 36) SS BOND : angle 0.79974 ( 72) hydrogen bonds : bond 0.04854 ( 328) hydrogen bonds : angle 7.83865 ( 852) link_ALPHA1-2 : bond 0.00875 ( 4) link_ALPHA1-2 : angle 3.39207 ( 12) link_ALPHA1-3 : bond 0.00761 ( 8) link_ALPHA1-3 : angle 1.91345 ( 24) link_ALPHA1-6 : bond 0.00445 ( 8) link_ALPHA1-6 : angle 1.38159 ( 24) link_BETA1-4 : bond 0.00697 ( 16) link_BETA1-4 : angle 2.35684 ( 48) link_BETA1-6 : bond 0.00549 ( 4) link_BETA1-6 : angle 1.96193 ( 12) link_NAG-ASN : bond 0.00621 ( 24) link_NAG-ASN : angle 3.92568 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 150 time to evaluate : 0.519 Fit side-chains REVERT: A 294 ASN cc_start: 0.6938 (t0) cc_final: 0.5835 (t0) REVERT: A 328 LYS cc_start: 0.8722 (mtpt) cc_final: 0.8488 (mtpm) REVERT: A 347 HIS cc_start: 0.8056 (m-70) cc_final: 0.7722 (m-70) REVERT: A 359 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7388 (m-30) REVERT: A 399 ASP cc_start: 0.8618 (t0) cc_final: 0.8352 (t70) REVERT: A 415 LYS cc_start: 0.8811 (mtmt) cc_final: 0.8584 (ttmm) REVERT: A 463 ASP cc_start: 0.8861 (t0) cc_final: 0.8473 (t0) REVERT: B 294 ASN cc_start: 0.6931 (t0) cc_final: 0.5816 (t0) REVERT: B 328 LYS cc_start: 0.8715 (mtpt) cc_final: 0.8482 (mtpm) REVERT: B 347 HIS cc_start: 0.8074 (m-70) cc_final: 0.7748 (m-70) REVERT: B 359 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7403 (m-30) REVERT: B 399 ASP cc_start: 0.8622 (t0) cc_final: 0.8358 (t70) REVERT: B 415 LYS cc_start: 0.8793 (mtmt) cc_final: 0.8571 (ttmm) REVERT: B 463 ASP cc_start: 0.8849 (t0) cc_final: 0.8458 (t0) REVERT: C 294 ASN cc_start: 0.6951 (t0) cc_final: 0.5832 (t0) REVERT: C 328 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8487 (mtpm) REVERT: C 347 HIS cc_start: 0.8082 (m-70) cc_final: 0.7762 (m-70) REVERT: C 359 ASP cc_start: 0.7989 (OUTLIER) cc_final: 0.7424 (m-30) REVERT: C 399 ASP cc_start: 0.8622 (t0) cc_final: 0.8349 (t70) REVERT: C 415 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8584 (ttmm) REVERT: C 463 ASP cc_start: 0.8840 (t0) cc_final: 0.8448 (t0) REVERT: D 294 ASN cc_start: 0.6946 (t0) cc_final: 0.5844 (t0) REVERT: D 328 LYS cc_start: 0.8718 (mtpt) cc_final: 0.8474 (mtpm) REVERT: D 347 HIS cc_start: 0.8063 (m-70) cc_final: 0.7750 (m-70) REVERT: D 359 ASP cc_start: 0.7987 (OUTLIER) cc_final: 0.7411 (m-30) REVERT: D 399 ASP cc_start: 0.8619 (t0) cc_final: 0.8347 (t70) REVERT: D 415 LYS cc_start: 0.8804 (mtmt) cc_final: 0.8583 (ttmm) REVERT: D 463 ASP cc_start: 0.8848 (t0) cc_final: 0.8458 (t0) outliers start: 40 outliers final: 8 residues processed: 186 average time/residue: 0.5589 time to fit residues: 113.9972 Evaluate side-chains 138 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 359 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 129 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 39 optimal weight: 0.0270 chunk 98 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 117 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 441 ASN B 441 ASN C 441 ASN D 441 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.097452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.081513 restraints weight = 22307.582| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 3.06 r_work: 0.2961 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13172 Z= 0.163 Angle : 0.702 11.437 17988 Z= 0.326 Chirality : 0.051 0.445 2124 Planarity : 0.004 0.043 2192 Dihedral : 14.391 95.265 2960 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.67 % Allowed : 22.18 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.84 (0.20), residues: 1544 helix: -3.18 (0.83), residues: 24 sheet: 0.06 (0.22), residues: 504 loop : -0.82 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 150 TYR 0.010 0.002 TYR D 281 PHE 0.016 0.002 PHE D 132 TRP 0.012 0.001 TRP A 178 HIS 0.002 0.001 HIS D 144 Details of bonding type rmsd covalent geometry : bond 0.00367 (13072) covalent geometry : angle 0.64289 (17724) SS BOND : bond 0.00284 ( 36) SS BOND : angle 0.63611 ( 72) hydrogen bonds : bond 0.04086 ( 328) hydrogen bonds : angle 6.97720 ( 852) link_ALPHA1-2 : bond 0.01251 ( 4) link_ALPHA1-2 : angle 3.35279 ( 12) link_ALPHA1-3 : bond 0.00794 ( 8) link_ALPHA1-3 : angle 1.62115 ( 24) link_ALPHA1-6 : bond 0.00507 ( 8) link_ALPHA1-6 : angle 1.41269 ( 24) link_BETA1-4 : bond 0.00831 ( 16) link_BETA1-4 : angle 2.22502 ( 48) link_BETA1-6 : bond 0.00735 ( 4) link_BETA1-6 : angle 1.61238 ( 12) link_NAG-ASN : bond 0.00680 ( 24) link_NAG-ASN : angle 3.69496 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ASN cc_start: 0.6930 (t0) cc_final: 0.6280 (t0) REVERT: A 359 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7743 (m-30) REVERT: A 399 ASP cc_start: 0.8777 (t0) cc_final: 0.8520 (t70) REVERT: A 463 ASP cc_start: 0.8786 (t0) cc_final: 0.8496 (t0) REVERT: B 294 ASN cc_start: 0.6912 (t0) cc_final: 0.6234 (t0) REVERT: B 359 ASP cc_start: 0.8257 (OUTLIER) cc_final: 0.7707 (m-30) REVERT: B 399 ASP cc_start: 0.8789 (t0) cc_final: 0.8526 (t70) REVERT: B 463 ASP cc_start: 0.8788 (t0) cc_final: 0.8501 (t0) REVERT: C 294 ASN cc_start: 0.6948 (t0) cc_final: 0.6277 (t0) REVERT: C 359 ASP cc_start: 0.8261 (OUTLIER) cc_final: 0.7716 (m-30) REVERT: C 399 ASP cc_start: 0.8776 (t0) cc_final: 0.8521 (t70) REVERT: C 463 ASP cc_start: 0.8782 (t0) cc_final: 0.8493 (t0) REVERT: D 294 ASN cc_start: 0.6941 (t0) cc_final: 0.6268 (t0) REVERT: D 359 ASP cc_start: 0.8283 (OUTLIER) cc_final: 0.7740 (m-30) REVERT: D 399 ASP cc_start: 0.8765 (t0) cc_final: 0.8515 (t70) REVERT: D 463 ASP cc_start: 0.8797 (t0) cc_final: 0.8513 (t0) outliers start: 36 outliers final: 16 residues processed: 175 average time/residue: 0.4923 time to fit residues: 95.7617 Evaluate side-chains 153 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 359 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 43 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 136 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 105 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 39 optimal weight: 0.0870 chunk 81 optimal weight: 2.9990 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 347 HIS A 468 HIS B 347 HIS B 468 HIS C 347 HIS C 468 HIS D 347 HIS D 468 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.097433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.081545 restraints weight = 22439.053| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 3.06 r_work: 0.2947 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13172 Z= 0.156 Angle : 0.704 10.861 17988 Z= 0.323 Chirality : 0.050 0.392 2124 Planarity : 0.003 0.035 2192 Dihedral : 12.422 88.631 2960 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.30 % Allowed : 24.78 % Favored : 72.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.20), residues: 1544 helix: -1.61 (0.89), residues: 24 sheet: 0.17 (0.22), residues: 548 loop : -0.64 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.011 0.002 TYR B 121 PHE 0.012 0.002 PHE C 132 TRP 0.010 0.001 TRP D 178 HIS 0.002 0.001 HIS C 144 Details of bonding type rmsd covalent geometry : bond 0.00353 (13072) covalent geometry : angle 0.64874 (17724) SS BOND : bond 0.00246 ( 36) SS BOND : angle 0.56676 ( 72) hydrogen bonds : bond 0.03639 ( 328) hydrogen bonds : angle 6.50509 ( 852) link_ALPHA1-2 : bond 0.01245 ( 4) link_ALPHA1-2 : angle 3.07090 ( 12) link_ALPHA1-3 : bond 0.00772 ( 8) link_ALPHA1-3 : angle 1.97622 ( 24) link_ALPHA1-6 : bond 0.00525 ( 8) link_ALPHA1-6 : angle 1.47502 ( 24) link_BETA1-4 : bond 0.00811 ( 16) link_BETA1-4 : angle 2.30033 ( 48) link_BETA1-6 : bond 0.00664 ( 4) link_BETA1-6 : angle 1.59141 ( 12) link_NAG-ASN : bond 0.00542 ( 24) link_NAG-ASN : angle 3.49115 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 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: 31 poor density : 130 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 ASP cc_start: 0.8368 (OUTLIER) cc_final: 0.7793 (m-30) REVERT: A 399 ASP cc_start: 0.8787 (t0) cc_final: 0.8499 (t70) REVERT: A 463 ASP cc_start: 0.8758 (t0) cc_final: 0.8436 (t0) REVERT: B 339 ASN cc_start: 0.9052 (m110) cc_final: 0.8433 (p0) REVERT: B 359 ASP cc_start: 0.8372 (OUTLIER) cc_final: 0.7791 (m-30) REVERT: B 399 ASP cc_start: 0.8788 (t0) cc_final: 0.8508 (t70) REVERT: B 463 ASP cc_start: 0.8753 (t0) cc_final: 0.8430 (t0) REVERT: C 294 ASN cc_start: 0.7153 (t0) cc_final: 0.6890 (t0) REVERT: C 329 THR cc_start: 0.8517 (m) cc_final: 0.8038 (p) REVERT: C 359 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.7800 (m-30) REVERT: C 399 ASP cc_start: 0.8768 (t0) cc_final: 0.8476 (t70) REVERT: C 463 ASP cc_start: 0.8759 (t0) cc_final: 0.8421 (t0) REVERT: D 294 ASN cc_start: 0.7147 (t0) cc_final: 0.6896 (t0) REVERT: D 359 ASP cc_start: 0.8366 (OUTLIER) cc_final: 0.7801 (m-30) REVERT: D 399 ASP cc_start: 0.8779 (t0) cc_final: 0.8510 (t70) REVERT: D 463 ASP cc_start: 0.8767 (t0) cc_final: 0.8449 (t0) outliers start: 31 outliers final: 16 residues processed: 157 average time/residue: 0.3657 time to fit residues: 65.2641 Evaluate side-chains 144 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 267 LYS Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 267 LYS Chi-restraints excluded: chain D residue 359 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 11 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 48 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 133 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS B 168 HIS B 336 HIS ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS C 168 HIS C 347 HIS ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 HIS D 347 HIS ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.096298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.080299 restraints weight = 22413.099| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.07 r_work: 0.2903 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13172 Z= 0.165 Angle : 0.689 12.200 17988 Z= 0.319 Chirality : 0.048 0.301 2124 Planarity : 0.003 0.031 2192 Dihedral : 10.664 68.139 2960 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.08 % Allowed : 25.59 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.20), residues: 1544 helix: -0.59 (0.98), residues: 24 sheet: 0.19 (0.23), residues: 528 loop : -0.64 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 150 TYR 0.012 0.002 TYR D 121 PHE 0.013 0.002 PHE B 132 TRP 0.011 0.001 TRP A 178 HIS 0.007 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00378 (13072) covalent geometry : angle 0.63466 (17724) SS BOND : bond 0.00252 ( 36) SS BOND : angle 0.60364 ( 72) hydrogen bonds : bond 0.03574 ( 328) hydrogen bonds : angle 6.41214 ( 852) link_ALPHA1-2 : bond 0.01370 ( 4) link_ALPHA1-2 : angle 2.05428 ( 12) link_ALPHA1-3 : bond 0.00762 ( 8) link_ALPHA1-3 : angle 1.94329 ( 24) link_ALPHA1-6 : bond 0.00505 ( 8) link_ALPHA1-6 : angle 1.49864 ( 24) link_BETA1-4 : bond 0.00727 ( 16) link_BETA1-4 : angle 2.36249 ( 48) link_BETA1-6 : bond 0.00674 ( 4) link_BETA1-6 : angle 1.42793 ( 12) link_NAG-ASN : bond 0.00415 ( 24) link_NAG-ASN : angle 3.52659 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.7899 (m-30) REVERT: A 399 ASP cc_start: 0.8794 (t0) cc_final: 0.8500 (t70) REVERT: A 463 ASP cc_start: 0.8774 (t0) cc_final: 0.8449 (t0) REVERT: B 359 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.7881 (m-30) REVERT: B 399 ASP cc_start: 0.8805 (t0) cc_final: 0.8506 (t70) REVERT: B 463 ASP cc_start: 0.8779 (t0) cc_final: 0.8454 (t0) REVERT: C 359 ASP cc_start: 0.8462 (OUTLIER) cc_final: 0.7890 (m-30) REVERT: C 399 ASP cc_start: 0.8783 (t0) cc_final: 0.8493 (t70) REVERT: C 463 ASP cc_start: 0.8784 (t0) cc_final: 0.8459 (t0) REVERT: D 359 ASP cc_start: 0.8480 (OUTLIER) cc_final: 0.7902 (m-30) REVERT: D 399 ASP cc_start: 0.8801 (t0) cc_final: 0.8506 (t70) REVERT: D 463 ASP cc_start: 0.8789 (t0) cc_final: 0.8458 (t0) outliers start: 28 outliers final: 20 residues processed: 153 average time/residue: 0.3623 time to fit residues: 63.3833 Evaluate side-chains 149 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 460 ASP Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 460 ASP Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 247 THR Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 460 ASP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 247 THR Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 460 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 52 optimal weight: 0.8980 chunk 46 optimal weight: 0.3980 chunk 92 optimal weight: 0.1980 chunk 97 optimal weight: 0.6980 chunk 106 optimal weight: 0.0000 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS A 347 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS B 274 HIS B 347 HIS ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS C 274 HIS C 294 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS D 274 HIS D 294 ASN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.097668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.081716 restraints weight = 22101.166| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.05 r_work: 0.2939 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13172 Z= 0.134 Angle : 0.638 11.154 17988 Z= 0.303 Chirality : 0.046 0.200 2124 Planarity : 0.003 0.033 2192 Dihedral : 9.132 58.795 2960 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.45 % Allowed : 25.07 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.20), residues: 1544 helix: 0.14 (1.09), residues: 24 sheet: 0.00 (0.22), residues: 568 loop : -0.64 (0.18), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 150 TYR 0.011 0.001 TYR D 121 PHE 0.012 0.002 PHE A 354 TRP 0.010 0.001 TRP A 178 HIS 0.006 0.001 HIS C 336 Details of bonding type rmsd covalent geometry : bond 0.00301 (13072) covalent geometry : angle 0.58173 (17724) SS BOND : bond 0.00188 ( 36) SS BOND : angle 0.52195 ( 72) hydrogen bonds : bond 0.03345 ( 328) hydrogen bonds : angle 6.29754 ( 852) link_ALPHA1-2 : bond 0.01375 ( 4) link_ALPHA1-2 : angle 2.11080 ( 12) link_ALPHA1-3 : bond 0.00911 ( 8) link_ALPHA1-3 : angle 1.69875 ( 24) link_ALPHA1-6 : bond 0.00584 ( 8) link_ALPHA1-6 : angle 1.48189 ( 24) link_BETA1-4 : bond 0.00594 ( 16) link_BETA1-4 : angle 2.35544 ( 48) link_BETA1-6 : bond 0.00682 ( 4) link_BETA1-6 : angle 1.48033 ( 12) link_NAG-ASN : bond 0.00088 ( 24) link_NAG-ASN : angle 3.41796 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 127 time to evaluate : 0.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 ASP cc_start: 0.8428 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: A 399 ASP cc_start: 0.8737 (t0) cc_final: 0.8482 (t70) REVERT: A 463 ASP cc_start: 0.8715 (t70) cc_final: 0.8387 (t0) REVERT: B 294 ASN cc_start: 0.7414 (t0) cc_final: 0.7190 (t0) REVERT: B 359 ASP cc_start: 0.8423 (OUTLIER) cc_final: 0.7800 (m-30) REVERT: B 399 ASP cc_start: 0.8750 (t0) cc_final: 0.8456 (t70) REVERT: B 463 ASP cc_start: 0.8718 (t70) cc_final: 0.8394 (t0) REVERT: C 359 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.7810 (m-30) REVERT: C 399 ASP cc_start: 0.8740 (t0) cc_final: 0.8450 (t70) REVERT: C 463 ASP cc_start: 0.8725 (t70) cc_final: 0.8398 (t0) REVERT: D 359 ASP cc_start: 0.8429 (OUTLIER) cc_final: 0.7812 (m-30) REVERT: D 399 ASP cc_start: 0.8739 (t0) cc_final: 0.8450 (t70) REVERT: D 463 ASP cc_start: 0.8723 (t70) cc_final: 0.8399 (t0) outliers start: 33 outliers final: 12 residues processed: 152 average time/residue: 0.3732 time to fit residues: 65.0676 Evaluate side-chains 136 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 359 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 93 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 60 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS B 274 HIS B 347 HIS ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS C 274 HIS ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS D 274 HIS ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.096115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.080248 restraints weight = 22298.872| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 3.07 r_work: 0.2908 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13172 Z= 0.182 Angle : 0.626 6.967 17988 Z= 0.304 Chirality : 0.046 0.207 2124 Planarity : 0.003 0.033 2192 Dihedral : 8.641 58.477 2960 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.52 % Allowed : 25.00 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.20), residues: 1544 helix: 0.52 (1.12), residues: 24 sheet: 0.14 (0.22), residues: 528 loop : -0.67 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 300 TYR 0.013 0.002 TYR C 423 PHE 0.011 0.002 PHE A 354 TRP 0.011 0.001 TRP B 178 HIS 0.006 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00418 (13072) covalent geometry : angle 0.57741 (17724) SS BOND : bond 0.00290 ( 36) SS BOND : angle 0.56347 ( 72) hydrogen bonds : bond 0.03484 ( 328) hydrogen bonds : angle 6.34754 ( 852) link_ALPHA1-2 : bond 0.01150 ( 4) link_ALPHA1-2 : angle 2.16496 ( 12) link_ALPHA1-3 : bond 0.00794 ( 8) link_ALPHA1-3 : angle 1.85967 ( 24) link_ALPHA1-6 : bond 0.00497 ( 8) link_ALPHA1-6 : angle 1.54104 ( 24) link_BETA1-4 : bond 0.00424 ( 16) link_BETA1-4 : angle 2.71173 ( 48) link_BETA1-6 : bond 0.00640 ( 4) link_BETA1-6 : angle 1.47037 ( 12) link_NAG-ASN : bond 0.00159 ( 24) link_NAG-ASN : angle 2.74427 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.7953 (m-30) REVERT: A 399 ASP cc_start: 0.8782 (OUTLIER) cc_final: 0.8495 (t70) REVERT: A 463 ASP cc_start: 0.8749 (t70) cc_final: 0.8430 (t0) REVERT: B 359 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.7952 (m-30) REVERT: B 399 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8490 (t70) REVERT: B 463 ASP cc_start: 0.8748 (t70) cc_final: 0.8429 (t0) REVERT: C 294 ASN cc_start: 0.7156 (t0) cc_final: 0.6908 (t0) REVERT: C 359 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: C 399 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8476 (t70) REVERT: C 463 ASP cc_start: 0.8757 (t70) cc_final: 0.8436 (t0) REVERT: D 294 ASN cc_start: 0.7116 (t0) cc_final: 0.6803 (t0) REVERT: D 359 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.7970 (m-30) REVERT: D 399 ASP cc_start: 0.8777 (t0) cc_final: 0.8490 (t70) REVERT: D 463 ASP cc_start: 0.8754 (t70) cc_final: 0.8435 (t0) outliers start: 34 outliers final: 13 residues processed: 137 average time/residue: 0.4137 time to fit residues: 64.2049 Evaluate side-chains 132 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 359 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 11 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 chunk 15 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 113 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 chunk 96 optimal weight: 0.5980 chunk 90 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 GLN A 274 HIS ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 GLN B 274 HIS ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS C 131 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.096527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.080427 restraints weight = 22089.107| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 3.06 r_work: 0.2906 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13172 Z= 0.147 Angle : 0.598 6.622 17988 Z= 0.292 Chirality : 0.046 0.201 2124 Planarity : 0.003 0.034 2192 Dihedral : 8.011 59.913 2960 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.60 % Allowed : 25.07 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.20), residues: 1544 helix: 0.49 (1.07), residues: 24 sheet: 0.10 (0.22), residues: 560 loop : -0.60 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 292 TYR 0.013 0.002 TYR C 423 PHE 0.012 0.002 PHE C 354 TRP 0.011 0.001 TRP C 178 HIS 0.006 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00337 (13072) covalent geometry : angle 0.55475 (17724) SS BOND : bond 0.00220 ( 36) SS BOND : angle 0.51902 ( 72) hydrogen bonds : bond 0.03344 ( 328) hydrogen bonds : angle 6.25426 ( 852) link_ALPHA1-2 : bond 0.01137 ( 4) link_ALPHA1-2 : angle 2.34167 ( 12) link_ALPHA1-3 : bond 0.00907 ( 8) link_ALPHA1-3 : angle 1.65012 ( 24) link_ALPHA1-6 : bond 0.00565 ( 8) link_ALPHA1-6 : angle 1.49512 ( 24) link_BETA1-4 : bond 0.00479 ( 16) link_BETA1-4 : angle 2.54224 ( 48) link_BETA1-6 : bond 0.00643 ( 4) link_BETA1-6 : angle 1.44438 ( 12) link_NAG-ASN : bond 0.00184 ( 24) link_NAG-ASN : angle 2.44737 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 117 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ASN cc_start: 0.7552 (t0) cc_final: 0.7308 (t0) REVERT: A 359 ASP cc_start: 0.8581 (OUTLIER) cc_final: 0.8267 (m-30) REVERT: A 399 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8513 (t70) REVERT: A 463 ASP cc_start: 0.8768 (t70) cc_final: 0.8455 (t0) REVERT: B 274 HIS cc_start: 0.8189 (OUTLIER) cc_final: 0.7491 (p90) REVERT: B 359 ASP cc_start: 0.8570 (OUTLIER) cc_final: 0.8257 (m-30) REVERT: B 399 ASP cc_start: 0.8791 (OUTLIER) cc_final: 0.8504 (t70) REVERT: B 463 ASP cc_start: 0.8766 (t70) cc_final: 0.8424 (t0) REVERT: C 359 ASP cc_start: 0.8555 (OUTLIER) cc_final: 0.8238 (m-30) REVERT: C 399 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8500 (t70) REVERT: C 463 ASP cc_start: 0.8763 (t70) cc_final: 0.8419 (t0) REVERT: D 359 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8282 (m-30) REVERT: D 399 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8508 (t70) REVERT: D 463 ASP cc_start: 0.8768 (t70) cc_final: 0.8455 (t0) outliers start: 35 outliers final: 17 residues processed: 138 average time/residue: 0.4087 time to fit residues: 64.1497 Evaluate side-chains 133 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 107 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 274 HIS Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 399 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 101 optimal weight: 0.5980 chunk 151 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 137 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 63 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 147 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 274 HIS ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS C 274 HIS C 294 ASN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS D 274 HIS ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.096868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.080734 restraints weight = 22393.514| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.09 r_work: 0.2902 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 13172 Z= 0.147 Angle : 0.596 6.502 17988 Z= 0.293 Chirality : 0.046 0.201 2124 Planarity : 0.003 0.035 2192 Dihedral : 7.809 59.040 2960 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.52 % Allowed : 25.45 % Favored : 72.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.21), residues: 1544 helix: 0.66 (1.07), residues: 24 sheet: 0.09 (0.22), residues: 560 loop : -0.54 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 292 TYR 0.016 0.002 TYR C 423 PHE 0.011 0.002 PHE A 354 TRP 0.010 0.001 TRP A 178 HIS 0.011 0.001 HIS B 274 Details of bonding type rmsd covalent geometry : bond 0.00337 (13072) covalent geometry : angle 0.55528 (17724) SS BOND : bond 0.00221 ( 36) SS BOND : angle 0.52573 ( 72) hydrogen bonds : bond 0.03329 ( 328) hydrogen bonds : angle 6.24111 ( 852) link_ALPHA1-2 : bond 0.01082 ( 4) link_ALPHA1-2 : angle 2.35085 ( 12) link_ALPHA1-3 : bond 0.00907 ( 8) link_ALPHA1-3 : angle 1.67543 ( 24) link_ALPHA1-6 : bond 0.00563 ( 8) link_ALPHA1-6 : angle 1.50423 ( 24) link_BETA1-4 : bond 0.00455 ( 16) link_BETA1-4 : angle 2.49382 ( 48) link_BETA1-6 : bond 0.00630 ( 4) link_BETA1-6 : angle 1.42951 ( 12) link_NAG-ASN : bond 0.00165 ( 24) link_NAG-ASN : angle 2.35049 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 108 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ASN cc_start: 0.7534 (t0) cc_final: 0.7283 (t0) REVERT: A 359 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8289 (m-30) REVERT: A 399 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8515 (t70) REVERT: A 463 ASP cc_start: 0.8767 (t70) cc_final: 0.8422 (t0) REVERT: B 273 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8415 (pm20) REVERT: B 359 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8308 (m-30) REVERT: B 399 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8524 (t70) REVERT: B 463 ASP cc_start: 0.8772 (t70) cc_final: 0.8447 (t0) REVERT: C 274 HIS cc_start: 0.8151 (OUTLIER) cc_final: 0.7479 (p90) REVERT: C 359 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8280 (m-30) REVERT: C 399 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8501 (t70) REVERT: C 463 ASP cc_start: 0.8764 (t70) cc_final: 0.8438 (t0) REVERT: D 274 HIS cc_start: 0.8159 (OUTLIER) cc_final: 0.7509 (p90) REVERT: D 359 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8289 (m-30) REVERT: D 399 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8505 (t70) REVERT: D 463 ASP cc_start: 0.8768 (t70) cc_final: 0.8423 (t0) outliers start: 34 outliers final: 19 residues processed: 126 average time/residue: 0.4201 time to fit residues: 59.7713 Evaluate side-chains 137 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 107 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 162 GLU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 267 LYS Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 267 LYS Chi-restraints excluded: chain B residue 273 GLN Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 274 HIS Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 162 GLU Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 274 HIS Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 399 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 55 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 134 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 146 optimal weight: 1.9990 chunk 77 optimal weight: 0.2980 chunk 12 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.096455 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.080351 restraints weight = 22354.953| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 3.09 r_work: 0.2898 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13172 Z= 0.157 Angle : 0.599 6.242 17988 Z= 0.296 Chirality : 0.046 0.205 2124 Planarity : 0.003 0.035 2192 Dihedral : 7.707 58.582 2960 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.00 % Allowed : 25.74 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.21), residues: 1544 helix: 0.73 (1.06), residues: 24 sheet: 0.08 (0.22), residues: 560 loop : -0.51 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 292 TYR 0.017 0.002 TYR C 423 PHE 0.011 0.002 PHE A 354 TRP 0.010 0.001 TRP A 178 HIS 0.010 0.001 HIS C 274 Details of bonding type rmsd covalent geometry : bond 0.00359 (13072) covalent geometry : angle 0.55941 (17724) SS BOND : bond 0.00242 ( 36) SS BOND : angle 0.56502 ( 72) hydrogen bonds : bond 0.03399 ( 328) hydrogen bonds : angle 6.23898 ( 852) link_ALPHA1-2 : bond 0.01055 ( 4) link_ALPHA1-2 : angle 2.35572 ( 12) link_ALPHA1-3 : bond 0.00899 ( 8) link_ALPHA1-3 : angle 1.69109 ( 24) link_ALPHA1-6 : bond 0.00548 ( 8) link_ALPHA1-6 : angle 1.50965 ( 24) link_BETA1-4 : bond 0.00426 ( 16) link_BETA1-4 : angle 2.44871 ( 48) link_BETA1-6 : bond 0.00643 ( 4) link_BETA1-6 : angle 1.39026 ( 12) link_NAG-ASN : bond 0.00167 ( 24) link_NAG-ASN : angle 2.30015 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3088 Ramachandran restraints generated. 1544 Oldfield, 0 Emsley, 1544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 106 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ASN cc_start: 0.7532 (t0) cc_final: 0.7297 (t0) REVERT: A 359 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8310 (m-30) REVERT: A 399 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8511 (t70) REVERT: A 463 ASP cc_start: 0.8776 (t70) cc_final: 0.8452 (t0) REVERT: B 359 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8303 (m-30) REVERT: B 399 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8523 (t70) REVERT: B 463 ASP cc_start: 0.8781 (t70) cc_final: 0.8488 (t0) REVERT: C 359 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8293 (m-30) REVERT: C 399 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8505 (t70) REVERT: C 463 ASP cc_start: 0.8777 (t70) cc_final: 0.8483 (t0) REVERT: D 359 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8303 (m-30) REVERT: D 399 ASP cc_start: 0.8794 (OUTLIER) cc_final: 0.8511 (t70) REVERT: D 463 ASP cc_start: 0.8778 (t70) cc_final: 0.8454 (t0) outliers start: 27 outliers final: 14 residues processed: 121 average time/residue: 0.4340 time to fit residues: 59.0925 Evaluate side-chains 122 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 100 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 160 MET Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain A residue 399 ASP Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 162 GLU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 399 ASP Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 160 MET Chi-restraints excluded: chain C residue 162 GLU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 399 ASP Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 399 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 134 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 128 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 59 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 468 HIS ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS D 131 GLN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.095982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.079989 restraints weight = 22452.837| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 3.07 r_work: 0.2888 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.2975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13172 Z= 0.167 Angle : 0.600 6.177 17988 Z= 0.298 Chirality : 0.046 0.201 2124 Planarity : 0.003 0.035 2192 Dihedral : 7.617 58.204 2960 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.78 % Allowed : 26.41 % Favored : 71.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.21), residues: 1544 helix: 0.73 (1.05), residues: 24 sheet: 0.06 (0.22), residues: 560 loop : -0.53 (0.19), residues: 960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 292 TYR 0.018 0.002 TYR C 423 PHE 0.011 0.002 PHE A 354 TRP 0.011 0.001 TRP D 178 HIS 0.006 0.001 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.00386 (13072) covalent geometry : angle 0.56221 (17724) SS BOND : bond 0.00264 ( 36) SS BOND : angle 0.57418 ( 72) hydrogen bonds : bond 0.03458 ( 328) hydrogen bonds : angle 6.25503 ( 852) link_ALPHA1-2 : bond 0.00941 ( 4) link_ALPHA1-2 : angle 2.37992 ( 12) link_ALPHA1-3 : bond 0.00867 ( 8) link_ALPHA1-3 : angle 1.71760 ( 24) link_ALPHA1-6 : bond 0.00518 ( 8) link_ALPHA1-6 : angle 1.52585 ( 24) link_BETA1-4 : bond 0.00394 ( 16) link_BETA1-4 : angle 2.36947 ( 48) link_BETA1-6 : bond 0.00617 ( 4) link_BETA1-6 : angle 1.36081 ( 12) link_NAG-ASN : bond 0.00183 ( 24) link_NAG-ASN : angle 2.26724 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3082.70 seconds wall clock time: 53 minutes 59.03 seconds (3239.03 seconds total)