Starting phenix.real_space_refine on Fri Jul 3 09:14:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cyg_46043/07_2026/9cyg_46043.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cyg_46043/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9cyg_46043/07_2026/9cyg_46043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cyg_46043/07_2026/9cyg_46043.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9cyg_46043/07_2026/9cyg_46043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cyg_46043/07_2026/9cyg_46043.map" } 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-dev-6108/lib/python3.11/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, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.13, per 1000 atoms: 0.24 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: 1.41 Conformation dependent library (CDL) restraints added in 470.2 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: 0.22 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: 1.46 Time building geometry restraints manager: 1.77 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: 10.480 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.840 Find NCS groups from input model: 0.280 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: 0.010 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 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/Z covalent geometry : bond 0.00612 / 0.28 (13072) covalent geometry : angle 0.95444 / 0.46 (17724) SS BOND : bond 0.00282 / 0.15 ( 36) SS BOND : angle 2.18220 / 1.50 ( 72) hydrogen bonds : bond 0.23940 / 15.67 ( 328) hydrogen bonds : angle 11.36920 / 7.93 ( 852) link_ALPHA1-2 : bond 0.01762 / 0.88 ( 4) link_ALPHA1-2 : angle 4.76544 / 2.44 ( 12) link_ALPHA1-3 : bond 0.00416 / 0.26 ( 8) link_ALPHA1-3 : angle 1.87958 / 1.13 ( 24) link_ALPHA1-6 : bond 0.00518 / 0.33 ( 8) link_ALPHA1-6 : angle 1.29235 / 0.75 ( 24) link_BETA1-4 : bond 0.00976 / 0.53 ( 16) link_BETA1-4 : angle 2.75292 / 1.92 ( 48) link_BETA1-6 : bond 0.00702 / 0.35 ( 4) link_BETA1-6 : angle 1.00741 / 0.56 ( 12) link_NAG-ASN : bond 0.00826 / 0.55 ( 24) link_NAG-ASN : angle 4.25410 / 2.98 ( 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 : 0.415 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: 0.4288 time to fit residues: 98.8892 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 : 0.300 ------------------------------------------------------------------------------- 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... 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 = 0.3343 r_free = 0.3343 target = 0.098369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.081505 restraints weight = 22019.366| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.00 r_work: 0.2952 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1542 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= 0.169 Angle : 0.733 12.202 17988 Z= 0.351 Chirality : 0.052 0.425 2124 Planarity : 0.005 0.055 2192 Dihedral : 17.351 97.315 2960 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.26 % Allowed : 21.96 % Favored : 74.78 % 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: -4.62 (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 0.009 0.001 ARG D 150 TYR 0.010 0.002 TYR D 281 PHE 0.016 0.002 PHE A 132 TRP 0.012 0.001 TRP A 178 HIS 0.004 0.001 HIS A 468 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (13072) covalent geometry : angle 0.66862 / 0.34 (17724) SS BOND : bond 0.00433 / 0.27 ( 36) SS BOND : angle 0.81424 / 0.54 ( 72) hydrogen bonds : bond 0.04818 / 3.09 ( 328) hydrogen bonds : angle 7.84516 / 5.50 ( 852) link_ALPHA1-2 : bond 0.00923 / 0.46 ( 4) link_ALPHA1-2 : angle 3.47555 / 1.88 ( 12) link_ALPHA1-3 : bond 0.00817 / 0.52 ( 8) link_ALPHA1-3 : angle 1.86989 / 1.12 ( 24) link_ALPHA1-6 : bond 0.00425 / 0.27 ( 8) link_ALPHA1-6 : angle 1.34349 / 0.81 ( 24) link_BETA1-4 : bond 0.00740 / 0.42 ( 16) link_BETA1-4 : angle 2.33992 / 1.51 ( 48) link_BETA1-6 : bond 0.00636 / 0.32 ( 4) link_BETA1-6 : angle 1.90493 / 1.06 ( 12) link_NAG-ASN : bond 0.00638 / 0.42 ( 24) link_NAG-ASN : angle 3.94681 / 2.73 ( 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 193 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 0.500 Fit side-chains REVERT: A 294 ASN cc_start: 0.6950 (t0) cc_final: 0.5835 (t0) REVERT: A 328 LYS cc_start: 0.8711 (mtpt) cc_final: 0.8475 (mtpm) REVERT: A 347 HIS cc_start: 0.8064 (m-70) cc_final: 0.7735 (m-70) REVERT: A 359 ASP cc_start: 0.7978 (OUTLIER) cc_final: 0.7398 (m-30) REVERT: A 399 ASP cc_start: 0.8621 (t0) cc_final: 0.8350 (t70) REVERT: A 415 LYS cc_start: 0.8810 (mtmt) cc_final: 0.8584 (ttmm) REVERT: A 463 ASP cc_start: 0.8860 (t0) cc_final: 0.8471 (t0) REVERT: B 294 ASN cc_start: 0.6942 (t0) cc_final: 0.5826 (t0) REVERT: B 328 LYS cc_start: 0.8713 (mtpt) cc_final: 0.8376 (mtpm) REVERT: B 343 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7291 (mm-30) REVERT: B 347 HIS cc_start: 0.8074 (m-70) cc_final: 0.7749 (m-70) REVERT: B 359 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7404 (m-30) REVERT: B 399 ASP cc_start: 0.8624 (t0) cc_final: 0.8361 (t70) REVERT: B 415 LYS cc_start: 0.8795 (mtmt) cc_final: 0.8574 (ttmm) REVERT: B 463 ASP cc_start: 0.8849 (t0) cc_final: 0.8457 (t0) REVERT: C 294 ASN cc_start: 0.6961 (t0) cc_final: 0.5838 (t0) REVERT: C 328 LYS cc_start: 0.8704 (mtpt) cc_final: 0.8470 (mtpm) REVERT: C 347 HIS cc_start: 0.8082 (m-70) cc_final: 0.7762 (m-70) REVERT: C 359 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7423 (m-30) REVERT: C 399 ASP cc_start: 0.8621 (t0) cc_final: 0.8350 (t70) REVERT: C 415 LYS cc_start: 0.8806 (mtmt) cc_final: 0.8585 (ttmm) REVERT: C 463 ASP cc_start: 0.8841 (t0) cc_final: 0.8446 (t0) REVERT: D 294 ASN cc_start: 0.6953 (t0) cc_final: 0.5837 (t0) REVERT: D 328 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8458 (mtpm) REVERT: D 347 HIS cc_start: 0.8063 (m-70) cc_final: 0.7749 (m-70) REVERT: D 359 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7415 (m-30) REVERT: D 399 ASP cc_start: 0.8619 (t0) cc_final: 0.8343 (t70) REVERT: D 415 LYS cc_start: 0.8803 (mtmt) cc_final: 0.8582 (ttmm) REVERT: D 463 ASP cc_start: 0.8850 (t0) cc_final: 0.8458 (t0) outliers start: 44 outliers final: 12 residues processed: 185 average time/residue: 0.5437 time to fit residues: 110.5606 Evaluate side-chains 143 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 126 time to evaluate : 0.506 ------------------------------------------------------------------------------- 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 A residue 431 LYS Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 160 MET Chi-restraints excluded: chain B residue 343 GLU Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 431 LYS 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 C residue 431 LYS Chi-restraints excluded: chain D residue 92 CYS Chi-restraints excluded: chain D residue 160 MET Chi-restraints excluded: chain D residue 359 ASP Chi-restraints excluded: chain D residue 431 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 129 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 39 optimal weight: 0.0770 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: 2.9990 chunk 97 optimal weight: 0.5980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3364 r_free = 0.3364 target = 0.099409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.083501 restraints weight = 22294.293| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 3.06 r_work: 0.2970 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13172 Z= 0.150 Angle : 0.697 11.276 17988 Z= 0.324 Chirality : 0.051 0.448 2124 Planarity : 0.004 0.042 2192 Dihedral : 14.442 94.847 2960 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.82 % Allowed : 22.18 % Favored : 75.00 % 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: -0.85 (0.20), residues: 1544 helix: -3.24 (0.82), residues: 24 sheet: 0.07 (0.22), residues: 504 loop : -0.84 (0.18), residues: 1016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 150 TYR 0.010 0.002 TYR D 281 PHE 0.015 0.002 PHE B 132 TRP 0.012 0.001 TRP A 178 HIS 0.002 0.001 HIS D 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (13072) covalent geometry : angle 0.63946 / 0.31 (17724) SS BOND : bond 0.00216 / 0.13 ( 36) SS BOND : angle 0.64023 / 0.42 ( 72) hydrogen bonds : bond 0.04084 / 2.65 ( 328) hydrogen bonds : angle 6.99031 / 4.88 ( 852) link_ALPHA1-2 : bond 0.01237 / 0.62 ( 4) link_ALPHA1-2 : angle 3.34777 / 1.84 ( 12) link_ALPHA1-3 : bond 0.00814 / 0.52 ( 8) link_ALPHA1-3 : angle 1.57637 / 0.94 ( 24) link_ALPHA1-6 : bond 0.00511 / 0.32 ( 8) link_ALPHA1-6 : angle 1.40061 / 0.85 ( 24) link_BETA1-4 : bond 0.00846 / 0.46 ( 16) link_BETA1-4 : angle 2.20035 / 1.47 ( 48) link_BETA1-6 : bond 0.00725 / 0.36 ( 4) link_BETA1-6 : angle 1.60533 / 0.90 ( 12) link_NAG-ASN : bond 0.00682 / 0.45 ( 24) link_NAG-ASN : angle 3.66242 / 2.55 ( 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: 38 poor density : 141 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ASN cc_start: 0.6932 (t0) cc_final: 0.6298 (t0) REVERT: A 359 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7657 (m-30) REVERT: A 399 ASP cc_start: 0.8757 (t0) cc_final: 0.8490 (t70) REVERT: A 463 ASP cc_start: 0.8762 (t0) cc_final: 0.8465 (t0) REVERT: B 294 ASN cc_start: 0.6911 (t0) cc_final: 0.6259 (t0) REVERT: B 339 ASN cc_start: 0.9016 (m110) cc_final: 0.8521 (p0) REVERT: B 359 ASP cc_start: 0.8215 (OUTLIER) cc_final: 0.7660 (m-30) REVERT: B 399 ASP cc_start: 0.8773 (t0) cc_final: 0.8539 (t70) REVERT: B 463 ASP cc_start: 0.8760 (t0) cc_final: 0.8462 (t0) REVERT: C 294 ASN cc_start: 0.6954 (t0) cc_final: 0.6313 (t0) REVERT: C 359 ASP cc_start: 0.8206 (OUTLIER) cc_final: 0.7654 (m-30) REVERT: C 399 ASP cc_start: 0.8758 (t0) cc_final: 0.8497 (t70) REVERT: C 463 ASP cc_start: 0.8760 (t0) cc_final: 0.8464 (t0) REVERT: D 294 ASN cc_start: 0.6938 (t0) cc_final: 0.6305 (t0) REVERT: D 359 ASP cc_start: 0.8222 (OUTLIER) cc_final: 0.7674 (m-30) REVERT: D 399 ASP cc_start: 0.8760 (t0) cc_final: 0.8498 (t70) REVERT: D 463 ASP cc_start: 0.8770 (t0) cc_final: 0.8474 (t0) outliers start: 38 outliers final: 16 residues processed: 175 average time/residue: 0.4661 time to fit residues: 91.2692 Evaluate side-chains 151 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.425 ------------------------------------------------------------------------------- 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: 0.6980 chunk 80 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 chunk 136 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 105 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 39 optimal weight: 0.0370 chunk 81 optimal weight: 0.8980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3358 r_free = 0.3358 target = 0.098282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.082372 restraints weight = 22391.618| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 3.06 r_work: 0.2969 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13172 Z= 0.142 Angle : 0.695 11.027 17988 Z= 0.319 Chirality : 0.050 0.375 2124 Planarity : 0.003 0.035 2192 Dihedral : 12.229 87.027 2960 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.37 % Allowed : 24.48 % Favored : 73.15 % 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: -0.60 (0.20), residues: 1544 helix: -1.76 (0.86), residues: 24 sheet: 0.04 (0.22), residues: 564 loop : -0.61 (0.19), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 150 TYR 0.009 0.002 TYR A 281 PHE 0.013 0.002 PHE A 132 TRP 0.010 0.001 TRP D 178 HIS 0.002 0.001 HIS C 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (13072) covalent geometry : angle 0.64210 / 0.31 (17724) SS BOND : bond 0.00219 / 0.13 ( 36) SS BOND : angle 0.56191 / 0.38 ( 72) hydrogen bonds : bond 0.03628 / 2.35 ( 328) hydrogen bonds : angle 6.52379 / 4.55 ( 852) link_ALPHA1-2 : bond 0.01245 / 0.63 ( 4) link_ALPHA1-2 : angle 2.89452 / 1.62 ( 12) link_ALPHA1-3 : bond 0.00785 / 0.50 ( 8) link_ALPHA1-3 : angle 1.91481 / 1.14 ( 24) link_ALPHA1-6 : bond 0.00577 / 0.37 ( 8) link_ALPHA1-6 : angle 1.46439 / 0.89 ( 24) link_BETA1-4 : bond 0.00853 / 0.47 ( 16) link_BETA1-4 : angle 2.25931 / 1.53 ( 48) link_BETA1-6 : bond 0.00769 / 0.38 ( 4) link_BETA1-6 : angle 1.58878 / 0.89 ( 12) link_NAG-ASN : bond 0.00577 / 0.38 ( 24) link_NAG-ASN : angle 3.43407 / 2.36 ( 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 158 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.516 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: 0.8323 (OUTLIER) cc_final: 0.7757 (m-30) REVERT: A 399 ASP cc_start: 0.8770 (t0) cc_final: 0.8481 (t70) REVERT: A 463 ASP cc_start: 0.8750 (t0) cc_final: 0.8407 (t0) REVERT: B 329 THR cc_start: 0.8465 (m) cc_final: 0.7962 (p) REVERT: B 359 ASP cc_start: 0.8316 (OUTLIER) cc_final: 0.7750 (m-30) REVERT: B 399 ASP cc_start: 0.8781 (t0) cc_final: 0.8491 (t70) REVERT: B 463 ASP cc_start: 0.8741 (t0) cc_final: 0.8398 (t0) REVERT: C 359 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7755 (m-30) REVERT: C 399 ASP cc_start: 0.8770 (t0) cc_final: 0.8490 (t70) REVERT: C 463 ASP cc_start: 0.8752 (t0) cc_final: 0.8409 (t0) REVERT: D 359 ASP cc_start: 0.8327 (OUTLIER) cc_final: 0.7765 (m-30) REVERT: D 399 ASP cc_start: 0.8768 (t0) cc_final: 0.8491 (t70) REVERT: D 463 ASP cc_start: 0.8763 (t0) cc_final: 0.8420 (t0) outliers start: 32 outliers final: 16 residues processed: 154 average time/residue: 0.4025 time to fit residues: 70.8339 Evaluate side-chains 150 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.559 ------------------------------------------------------------------------------- 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: 1.9990 chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 122 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 168 HIS ** A 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS B 274 HIS ** B 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 336 HIS ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS C 168 HIS ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 168 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 = 0.3316 r_free = 0.3316 target = 0.095676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.079573 restraints weight = 22527.991| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.10 r_work: 0.2875 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13172 Z= 0.215 Angle : 0.717 12.257 17988 Z= 0.333 Chirality : 0.049 0.320 2124 Planarity : 0.004 0.031 2192 Dihedral : 10.970 68.748 2960 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.85 % Allowed : 25.45 % Favored : 72.70 % 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: -0.58 (0.20), residues: 1544 helix: -0.56 (1.00), residues: 24 sheet: 0.14 (0.23), residues: 528 loop : -0.66 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 150 TYR 0.013 0.002 TYR A 121 PHE 0.011 0.002 PHE C 132 TRP 0.015 0.001 TRP C 295 HIS 0.006 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.21 (13072) covalent geometry : angle 0.65988 / 0.32 (17724) SS BOND : bond 0.00338 / 0.19 ( 36) SS BOND : angle 0.61273 / 0.40 ( 72) hydrogen bonds : bond 0.03753 / 2.44 ( 328) hydrogen bonds : angle 6.52870 / 4.55 ( 852) link_ALPHA1-2 : bond 0.01154 / 0.58 ( 4) link_ALPHA1-2 : angle 2.22620 / 1.23 ( 12) link_ALPHA1-3 : bond 0.00651 / 0.42 ( 8) link_ALPHA1-3 : angle 2.12313 / 1.27 ( 24) link_ALPHA1-6 : bond 0.00420 / 0.27 ( 8) link_ALPHA1-6 : angle 1.53095 / 0.93 ( 24) link_BETA1-4 : bond 0.00740 / 0.40 ( 16) link_BETA1-4 : angle 2.47276 / 1.68 ( 48) link_BETA1-6 : bond 0.00540 / 0.27 ( 4) link_BETA1-6 : angle 1.51719 / 0.87 ( 12) link_NAG-ASN : bond 0.00433 / 0.28 ( 24) link_NAG-ASN : angle 3.63144 / 2.48 ( 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 154 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.506 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: 0.8479 (OUTLIER) cc_final: 0.7903 (m-30) REVERT: A 399 ASP cc_start: 0.8791 (t0) cc_final: 0.8505 (t70) REVERT: A 463 ASP cc_start: 0.8814 (t0) cc_final: 0.8490 (t0) REVERT: B 274 HIS cc_start: 0.8229 (OUTLIER) cc_final: 0.7436 (p90) REVERT: B 359 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.7901 (m-30) REVERT: B 399 ASP cc_start: 0.8794 (t0) cc_final: 0.8534 (t70) REVERT: B 463 ASP cc_start: 0.8813 (t0) cc_final: 0.8490 (t0) REVERT: C 359 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.7911 (m-30) REVERT: C 399 ASP cc_start: 0.8782 (t0) cc_final: 0.8506 (t70) REVERT: C 463 ASP cc_start: 0.8813 (t70) cc_final: 0.8489 (t0) REVERT: D 359 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.7908 (m-30) REVERT: D 399 ASP cc_start: 0.8792 (t0) cc_final: 0.8518 (t70) REVERT: D 463 ASP cc_start: 0.8818 (t0) cc_final: 0.8494 (t0) outliers start: 25 outliers final: 12 residues processed: 149 average time/residue: 0.4210 time to fit residues: 71.2370 Evaluate side-chains 137 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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 274 HIS 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 52 optimal weight: 0.7980 chunk 46 optimal weight: 0.1980 chunk 92 optimal weight: 0.1980 chunk 97 optimal weight: 0.6980 chunk 106 optimal weight: 0.3980 chunk 78 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 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: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS ** D 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.096595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.080744 restraints weight = 22201.507| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 3.05 r_work: 0.2913 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 13172 Z= 0.136 Angle : 0.643 11.074 17988 Z= 0.306 Chirality : 0.046 0.198 2124 Planarity : 0.003 0.029 2192 Dihedral : 9.307 59.330 2960 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.37 % Allowed : 24.93 % Favored : 72.70 % 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: 0.23 (1.15), residues: 24 sheet: 0.09 (0.22), residues: 536 loop : -0.64 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 292 TYR 0.011 0.002 TYR B 121 PHE 0.012 0.002 PHE D 132 TRP 0.011 0.001 TRP B 295 HIS 0.021 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (13072) covalent geometry : angle 0.58580 / 0.29 (17724) SS BOND : bond 0.00198 / 0.12 ( 36) SS BOND : angle 0.53453 / 0.35 ( 72) hydrogen bonds : bond 0.03430 / 2.24 ( 328) hydrogen bonds : angle 6.36437 / 4.44 ( 852) link_ALPHA1-2 : bond 0.01349 / 0.68 ( 4) link_ALPHA1-2 : angle 2.11898 / 1.14 ( 12) link_ALPHA1-3 : bond 0.00890 / 0.57 ( 8) link_ALPHA1-3 : angle 1.75807 / 1.05 ( 24) link_ALPHA1-6 : bond 0.00546 / 0.35 ( 8) link_ALPHA1-6 : angle 1.48902 / 0.90 ( 24) link_BETA1-4 : bond 0.00620 / 0.36 ( 16) link_BETA1-4 : angle 2.38093 / 1.65 ( 48) link_BETA1-6 : bond 0.00645 / 0.32 ( 4) link_BETA1-6 : angle 1.53580 / 0.87 ( 12) link_NAG-ASN : bond 0.00092 / 0.05 ( 24) link_NAG-ASN : angle 3.41972 / 2.20 ( 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 164 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.7854 (m-30) REVERT: A 399 ASP cc_start: 0.8774 (t0) cc_final: 0.8482 (t70) REVERT: A 463 ASP cc_start: 0.8783 (t70) cc_final: 0.8454 (t0) REVERT: B 359 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.7840 (m-30) REVERT: B 399 ASP cc_start: 0.8778 (t0) cc_final: 0.8488 (t70) REVERT: B 463 ASP cc_start: 0.8786 (t70) cc_final: 0.8457 (t0) REVERT: C 359 ASP cc_start: 0.8460 (OUTLIER) cc_final: 0.7853 (m-30) REVERT: C 399 ASP cc_start: 0.8770 (t0) cc_final: 0.8478 (t70) REVERT: C 463 ASP cc_start: 0.8785 (t70) cc_final: 0.8453 (t0) REVERT: D 359 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.7859 (m-30) REVERT: D 399 ASP cc_start: 0.8780 (t0) cc_final: 0.8506 (t70) REVERT: D 463 ASP cc_start: 0.8778 (t70) cc_final: 0.8449 (t0) outliers start: 32 outliers final: 20 residues processed: 156 average time/residue: 0.3975 time to fit residues: 70.8829 Evaluate side-chains 147 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 123 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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 460 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 460 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 460 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 460 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: 2.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 120 optimal weight: 0.0370 chunk 124 optimal weight: 0.0970 chunk 122 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.0260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 294 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS ** D 274 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.095335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.079619 restraints weight = 22320.897| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 3.05 r_work: 0.2891 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2753 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13172 Z= 0.212 Angle : 0.645 7.555 17988 Z= 0.312 Chirality : 0.047 0.208 2124 Planarity : 0.003 0.030 2192 Dihedral : 9.073 58.720 2960 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.30 % Allowed : 25.22 % 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: -0.62 (0.20), residues: 1544 helix: 0.25 (1.11), residues: 24 sheet: 0.09 (0.22), residues: 528 loop : -0.71 (0.18), residues: 992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 292 TYR 0.013 0.002 TYR B 423 PHE 0.011 0.002 PHE D 132 TRP 0.011 0.001 TRP A 178 HIS 0.006 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.21 (13072) covalent geometry : angle 0.59422 / 0.30 (17724) SS BOND : bond 0.00326 / 0.19 ( 36) SS BOND : angle 0.59776 / 0.39 ( 72) hydrogen bonds : bond 0.03555 / 2.33 ( 328) hydrogen bonds : angle 6.39516 / 4.45 ( 852) link_ALPHA1-2 : bond 0.01131 / 0.57 ( 4) link_ALPHA1-2 : angle 2.07464 / 1.12 ( 12) link_ALPHA1-3 : bond 0.00748 / 0.48 ( 8) link_ALPHA1-3 : angle 1.92117 / 1.15 ( 24) link_ALPHA1-6 : bond 0.00451 / 0.29 ( 8) link_ALPHA1-6 : angle 1.53007 / 0.92 ( 24) link_BETA1-4 : bond 0.00426 / 0.24 ( 16) link_BETA1-4 : angle 2.65968 / 1.82 ( 48) link_BETA1-6 : bond 0.00605 / 0.30 ( 4) link_BETA1-6 : angle 1.48862 / 0.84 ( 12) link_NAG-ASN : bond 0.00154 / 0.08 ( 24) link_NAG-ASN : angle 2.96350 / 1.92 ( 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 150 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.425 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: 0.7618 (OUTLIER) cc_final: 0.7176 (t0) REVERT: A 359 ASP cc_start: 0.8613 (OUTLIER) cc_final: 0.8044 (m-30) REVERT: A 399 ASP cc_start: 0.8812 (OUTLIER) cc_final: 0.8556 (t70) REVERT: A 463 ASP cc_start: 0.8818 (t0) cc_final: 0.8500 (t0) REVERT: B 359 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8030 (m-30) REVERT: B 399 ASP cc_start: 0.8829 (t0) cc_final: 0.8586 (t70) REVERT: B 463 ASP cc_start: 0.8824 (t0) cc_final: 0.8507 (t0) REVERT: C 294 ASN cc_start: 0.7653 (OUTLIER) cc_final: 0.7210 (t0) REVERT: C 359 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8037 (m-30) REVERT: C 399 ASP cc_start: 0.8826 (t0) cc_final: 0.8565 (t70) REVERT: C 463 ASP cc_start: 0.8818 (t0) cc_final: 0.8499 (t0) REVERT: D 294 ASN cc_start: 0.7609 (OUTLIER) cc_final: 0.7147 (t0) REVERT: D 359 ASP cc_start: 0.8619 (OUTLIER) cc_final: 0.8049 (m-30) REVERT: D 399 ASP cc_start: 0.8835 (t0) cc_final: 0.8575 (t70) REVERT: D 463 ASP cc_start: 0.8817 (t0) cc_final: 0.8493 (t0) outliers start: 31 outliers final: 16 residues processed: 138 average time/residue: 0.4030 time to fit residues: 63.4338 Evaluate side-chains 143 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.508 ------------------------------------------------------------------------------- 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 294 ASN 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 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 294 ASN 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 162 GLU Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 294 ASN 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: 0.7980 chunk 66 optimal weight: 2.9990 chunk 10 optimal weight: 0.0770 chunk 15 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 121 optimal weight: 0.5980 chunk 113 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 90 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 ASN ** 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 131 GLN ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3332 r_free = 0.3332 target = 0.096415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.080454 restraints weight = 22156.489| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 3.06 r_work: 0.2908 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13172 Z= 0.138 Angle : 0.601 6.585 17988 Z= 0.293 Chirality : 0.046 0.197 2124 Planarity : 0.003 0.034 2192 Dihedral : 8.270 59.745 2960 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.12 % Allowed : 24.18 % Favored : 72.70 % 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: -0.59 (0.20), residues: 1544 helix: 0.35 (1.05), residues: 24 sheet: 0.02 (0.22), residues: 536 loop : -0.63 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 292 TYR 0.014 0.002 TYR C 423 PHE 0.012 0.002 PHE B 132 TRP 0.011 0.001 TRP B 178 HIS 0.005 0.001 HIS B 274 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (13072) covalent geometry : angle 0.55882 / 0.28 (17724) SS BOND : bond 0.00206 / 0.12 ( 36) SS BOND : angle 0.52548 / 0.34 ( 72) hydrogen bonds : bond 0.03333 / 2.18 ( 328) hydrogen bonds : angle 6.26123 / 4.36 ( 852) link_ALPHA1-2 : bond 0.01179 / 0.59 ( 4) link_ALPHA1-2 : angle 2.28483 / 1.21 ( 12) link_ALPHA1-3 : bond 0.00941 / 0.60 ( 8) link_ALPHA1-3 : angle 1.64398 / 0.98 ( 24) link_ALPHA1-6 : bond 0.00555 / 0.35 ( 8) link_ALPHA1-6 : angle 1.47906 / 0.89 ( 24) link_BETA1-4 : bond 0.00518 / 0.30 ( 16) link_BETA1-4 : angle 2.56879 / 1.79 ( 48) link_BETA1-6 : bond 0.00656 / 0.33 ( 4) link_BETA1-6 : angle 1.45965 / 0.82 ( 12) link_NAG-ASN : bond 0.00158 / 0.10 ( 24) link_NAG-ASN : angle 2.44025 / 1.58 ( 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 162 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 120 time to evaluate : 0.536 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 359 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.7941 (m-30) REVERT: A 399 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8531 (t70) REVERT: A 463 ASP cc_start: 0.8762 (t0) cc_final: 0.8431 (t0) REVERT: B 359 ASP cc_start: 0.8547 (OUTLIER) cc_final: 0.8258 (m-30) REVERT: B 399 ASP cc_start: 0.8778 (OUTLIER) cc_final: 0.8506 (t70) REVERT: B 463 ASP cc_start: 0.8761 (t0) cc_final: 0.8428 (t0) REVERT: C 294 ASN cc_start: 0.7398 (OUTLIER) cc_final: 0.6960 (t0) REVERT: C 359 ASP cc_start: 0.8552 (OUTLIER) cc_final: 0.8259 (m-30) REVERT: C 399 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8486 (t70) REVERT: C 463 ASP cc_start: 0.8766 (t0) cc_final: 0.8431 (t0) REVERT: D 359 ASP cc_start: 0.8566 (OUTLIER) cc_final: 0.8278 (m-30) REVERT: D 399 ASP cc_start: 0.8784 (OUTLIER) cc_final: 0.8505 (t70) REVERT: D 463 ASP cc_start: 0.8769 (t0) cc_final: 0.8438 (t0) outliers start: 42 outliers final: 16 residues processed: 147 average time/residue: 0.4144 time to fit residues: 69.5033 Evaluate side-chains 134 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 109 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 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 294 ASN 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: 3.9990 chunk 151 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 137 optimal weight: 0.5980 chunk 74 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 147 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS ** D 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.095889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.079863 restraints weight = 22543.481| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 3.07 r_work: 0.2891 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.2913 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= 0.161 Angle : 0.608 6.342 17988 Z= 0.299 Chirality : 0.046 0.204 2124 Planarity : 0.003 0.034 2192 Dihedral : 7.854 59.152 2960 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.45 % Allowed : 25.22 % 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: 0.78 (1.06), residues: 24 sheet: 0.02 (0.22), residues: 536 loop : -0.57 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 292 TYR 0.016 0.002 TYR A 423 PHE 0.011 0.002 PHE A 354 TRP 0.010 0.001 TRP C 178 HIS 0.005 0.001 HIS D 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (13072) covalent geometry : angle 0.56558 / 0.29 (17724) SS BOND : bond 0.00253 / 0.15 ( 36) SS BOND : angle 0.55434 / 0.36 ( 72) hydrogen bonds : bond 0.03416 / 2.24 ( 328) hydrogen bonds : angle 6.26887 / 4.36 ( 852) link_ALPHA1-2 : bond 0.01021 / 0.51 ( 4) link_ALPHA1-2 : angle 2.32092 / 1.23 ( 12) link_ALPHA1-3 : bond 0.00844 / 0.54 ( 8) link_ALPHA1-3 : angle 1.77579 / 1.06 ( 24) link_ALPHA1-6 : bond 0.00522 / 0.34 ( 8) link_ALPHA1-6 : angle 1.53471 / 0.92 ( 24) link_BETA1-4 : bond 0.00409 / 0.24 ( 16) link_BETA1-4 : angle 2.53303 / 1.76 ( 48) link_BETA1-6 : bond 0.00622 / 0.31 ( 4) link_BETA1-6 : angle 1.42662 / 0.81 ( 12) link_NAG-ASN : bond 0.00175 / 0.10 ( 24) link_NAG-ASN : angle 2.42704 / 1.60 ( 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 143 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 110 time to evaluate : 0.531 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 359 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8269 (m-30) REVERT: A 399 ASP cc_start: 0.8792 (t0) cc_final: 0.8511 (t70) REVERT: A 463 ASP cc_start: 0.8787 (t0) cc_final: 0.8504 (t0) REVERT: B 359 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8291 (m-30) REVERT: B 399 ASP cc_start: 0.8796 (OUTLIER) cc_final: 0.8514 (t70) REVERT: B 463 ASP cc_start: 0.8784 (t0) cc_final: 0.8499 (t0) REVERT: C 294 ASN cc_start: 0.7499 (OUTLIER) cc_final: 0.7024 (t0) REVERT: C 359 ASP cc_start: 0.8598 (OUTLIER) cc_final: 0.8287 (m-30) REVERT: C 399 ASP cc_start: 0.8780 (OUTLIER) cc_final: 0.8494 (t70) REVERT: C 463 ASP cc_start: 0.8780 (t0) cc_final: 0.8490 (t0) REVERT: D 359 ASP cc_start: 0.8614 (OUTLIER) cc_final: 0.8305 (m-30) REVERT: D 399 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8501 (t70) REVERT: D 463 ASP cc_start: 0.8788 (t0) cc_final: 0.8503 (t0) outliers start: 33 outliers final: 18 residues processed: 131 average time/residue: 0.4438 time to fit residues: 65.7479 Evaluate side-chains 131 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 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 275 VAL 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 294 ASN 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 55 optimal weight: 0.2980 chunk 53 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 chunk 77 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 294 ASN ** 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 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 468 HIS ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.096458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.080411 restraints weight = 22388.402| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 3.07 r_work: 0.2896 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2955 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= 0.154 Angle : 0.596 6.236 17988 Z= 0.295 Chirality : 0.046 0.201 2124 Planarity : 0.003 0.035 2192 Dihedral : 7.629 57.915 2960 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.00 % Allowed : 25.67 % 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: -0.52 (0.20), residues: 1544 helix: 0.62 (1.01), residues: 24 sheet: 0.06 (0.22), residues: 536 loop : -0.58 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 292 TYR 0.018 0.002 TYR D 423 PHE 0.011 0.002 PHE B 354 TRP 0.011 0.001 TRP C 178 HIS 0.005 0.001 HIS D 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (13072) covalent geometry : angle 0.55782 / 0.29 (17724) SS BOND : bond 0.00233 / 0.14 ( 36) SS BOND : angle 0.56831 / 0.37 ( 72) hydrogen bonds : bond 0.03431 / 2.24 ( 328) hydrogen bonds : angle 6.24467 / 4.35 ( 852) link_ALPHA1-2 : bond 0.00987 / 0.49 ( 4) link_ALPHA1-2 : angle 2.40980 / 1.28 ( 12) link_ALPHA1-3 : bond 0.00897 / 0.57 ( 8) link_ALPHA1-3 : angle 1.66644 / 0.99 ( 24) link_ALPHA1-6 : bond 0.00550 / 0.35 ( 8) link_ALPHA1-6 : angle 1.50352 / 0.90 ( 24) link_BETA1-4 : bond 0.00427 / 0.25 ( 16) link_BETA1-4 : angle 2.39600 / 1.67 ( 48) link_BETA1-6 : bond 0.00628 / 0.31 ( 4) link_BETA1-6 : angle 1.40570 / 0.79 ( 12) link_NAG-ASN : bond 0.00173 / 0.11 ( 24) link_NAG-ASN : angle 2.26592 / 1.49 ( 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 129 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.509 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 359 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8261 (m-30) REVERT: A 399 ASP cc_start: 0.8792 (OUTLIER) cc_final: 0.8516 (t70) REVERT: A 463 ASP cc_start: 0.8803 (t0) cc_final: 0.8496 (t0) REVERT: B 359 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8298 (m-30) REVERT: B 399 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8501 (t70) REVERT: B 463 ASP cc_start: 0.8796 (t0) cc_final: 0.8483 (t0) REVERT: C 294 ASN cc_start: 0.7496 (OUTLIER) cc_final: 0.7012 (t0) REVERT: C 359 ASP cc_start: 0.8586 (OUTLIER) cc_final: 0.8266 (m-30) REVERT: C 399 ASP cc_start: 0.8786 (OUTLIER) cc_final: 0.8501 (t70) REVERT: C 463 ASP cc_start: 0.8803 (t0) cc_final: 0.8491 (t0) REVERT: D 359 ASP cc_start: 0.8601 (OUTLIER) cc_final: 0.8310 (m-30) REVERT: D 399 ASP cc_start: 0.8785 (OUTLIER) cc_final: 0.8505 (t70) REVERT: D 463 ASP cc_start: 0.8802 (t0) cc_final: 0.8492 (t0) outliers start: 27 outliers final: 16 residues processed: 116 average time/residue: 0.4033 time to fit residues: 53.4527 Evaluate side-chains 126 residues out of total 1348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 230 CYS Chi-restraints excluded: chain B residue 247 THR Chi-restraints excluded: chain B residue 275 VAL 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 294 ASN 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: 0.9980 chunk 24 optimal weight: 2.9990 chunk 140 optimal weight: 0.9990 chunk 123 optimal weight: 0.2980 chunk 53 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 134 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3294 r_free = 0.3294 target = 0.095453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.078580 restraints weight = 22046.752| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.05 r_work: 0.2868 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.2988 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= 0.173 Angle : 0.602 6.237 17988 Z= 0.299 Chirality : 0.046 0.203 2124 Planarity : 0.003 0.035 2192 Dihedral : 7.603 58.091 2960 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.93 % Allowed : 26.04 % 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: -0.52 (0.20), residues: 1544 helix: 0.73 (1.04), residues: 24 sheet: 0.02 (0.22), residues: 536 loop : -0.55 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 292 TYR 0.017 0.002 TYR D 423 PHE 0.011 0.002 PHE A 354 TRP 0.011 0.001 TRP B 178 HIS 0.005 0.001 HIS D 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.17 (13072) covalent geometry : angle 0.56306 / 0.29 (17724) SS BOND : bond 0.00277 / 0.16 ( 36) SS BOND : angle 0.59086 / 0.39 ( 72) hydrogen bonds : bond 0.03462 / 2.27 ( 328) hydrogen bonds : angle 6.25205 / 4.35 ( 852) link_ALPHA1-2 : bond 0.00887 / 0.44 ( 4) link_ALPHA1-2 : angle 2.38109 / 1.27 ( 12) link_ALPHA1-3 : bond 0.00846 / 0.54 ( 8) link_ALPHA1-3 : angle 1.74561 / 1.04 ( 24) link_ALPHA1-6 : bond 0.00494 / 0.32 ( 8) link_ALPHA1-6 : angle 1.53676 / 0.92 ( 24) link_BETA1-4 : bond 0.00371 / 0.22 ( 16) link_BETA1-4 : angle 2.33666 / 1.61 ( 48) link_BETA1-6 : bond 0.00599 / 0.30 ( 4) link_BETA1-6 : angle 1.39949 / 0.79 ( 12) link_NAG-ASN : bond 0.00184 / 0.11 ( 24) link_NAG-ASN : angle 2.29942 / 1.53 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3249.34 seconds wall clock time: 56 minutes 57.01 seconds (3417.01 seconds total)