Starting phenix.real_space_refine on Sun Feb 8 01:17:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oql_70765/02_2026/9oql_70765_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oql_70765/02_2026/9oql_70765.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9oql_70765/02_2026/9oql_70765_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oql_70765/02_2026/9oql_70765_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9oql_70765/02_2026/9oql_70765.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oql_70765/02_2026/9oql_70765.map" } resolution = 2.77 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= 0.001 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: 6 Type Number sf(0) Gaussians P 10 5.49 5 S 77 5.16 5 C 12764 2.51 5 N 2903 2.21 5 O 3247 1.98 5 H 17927 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36928 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 5159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5159 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "B" Number of atoms: 5159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5159 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "C" Number of atoms: 5159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5159 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "D" Number of atoms: 5159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5159 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "E" Number of atoms: 5159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5159 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "F" Number of atoms: 5159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5159 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "G" Number of atoms: 5159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 5159 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Unresolved non-hydrogen bonds: 164 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 134 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'ASP:plan': 6, 'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ARG:plan': 1, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 89 Chain: "A" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 143 Unusual residues: {'ATP': 1, 'CLR': 2, 'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 2, 'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 2, 'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 2, 'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 2, 'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 2, 'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 112 Unusual residues: {'CLR': 2, 'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.88, per 1000 atoms: 0.21 Number of scatterers: 36928 At special positions: 0 Unit cell: (109.65, 109.65, 122.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 77 16.00 P 10 15.00 O 3247 8.00 N 2903 7.00 C 12764 6.00 H 17927 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 66 " - pdb=" SG CYS A 265 " distance=2.03 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS A 246 " distance=2.03 Simple disulfide: pdb=" SG CYS B 66 " - pdb=" SG CYS B 265 " distance=2.03 Simple disulfide: pdb=" SG CYS B 84 " - pdb=" SG CYS B 246 " distance=2.03 Simple disulfide: pdb=" SG CYS C 66 " - pdb=" SG CYS C 265 " distance=2.03 Simple disulfide: pdb=" SG CYS C 84 " - pdb=" SG CYS C 246 " distance=2.03 Simple disulfide: pdb=" SG CYS D 66 " - pdb=" SG CYS D 265 " distance=2.03 Simple disulfide: pdb=" SG CYS D 84 " - pdb=" SG CYS D 246 " distance=2.03 Simple disulfide: pdb=" SG CYS E 66 " - pdb=" SG CYS E 265 " distance=2.03 Simple disulfide: pdb=" SG CYS E 84 " - pdb=" SG CYS E 246 " distance=2.03 Simple disulfide: pdb=" SG CYS F 66 " - pdb=" SG CYS F 265 " distance=2.03 Simple disulfide: pdb=" SG CYS F 84 " - pdb=" SG CYS F 246 " distance=2.03 Simple disulfide: pdb=" SG CYS G 66 " - pdb=" SG CYS G 265 " distance=2.03 Simple disulfide: pdb=" SG CYS G 84 " - pdb=" SG CYS G 246 " 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 NAG-ASN " NAG A 504 " - " ASN A 255 " " NAG B 504 " - " ASN B 255 " " NAG C 504 " - " ASN C 255 " " NAG D 504 " - " ASN D 255 " " NAG E 504 " - " ASN E 255 " " NAG F 504 " - " ASN F 255 " " NAG G 504 " - " ASN G 255 " Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 1.7 seconds 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4662 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 7 sheets defined 70.1% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 32 through 54 Proline residue: A 46 - end of helix removed outlier: 3.609A pdb=" N PHE A 54 " --> pdb=" O ILE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 88 Processing helix chain 'A' and resid 100 through 131 Proline residue: A 110 - end of helix Proline residue: A 123 - end of helix Processing helix chain 'A' and resid 131 through 162 removed outlier: 3.534A pdb=" N ILE A 135 " --> pdb=" O ALA A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 removed outlier: 3.795A pdb=" N ASN A 205 " --> pdb=" O LYS A 201 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 236 Processing helix chain 'A' and resid 250 through 254 removed outlier: 4.214A pdb=" N LEU A 253 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 296 Proline residue: A 289 - end of helix Processing helix chain 'A' and resid 296 through 301 Processing helix chain 'A' and resid 305 through 312 removed outlier: 3.617A pdb=" N VAL A 308 " --> pdb=" O VAL A 305 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 311 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 339 removed outlier: 3.901A pdb=" N LEU A 330 " --> pdb=" O ASN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 356 Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.659A pdb=" N LEU A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 11 Processing helix chain 'B' and resid 32 through 54 Proline residue: B 46 - end of helix removed outlier: 3.610A pdb=" N PHE B 54 " --> pdb=" O ILE B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 88 Processing helix chain 'B' and resid 100 through 131 Proline residue: B 110 - end of helix Proline residue: B 123 - end of helix Processing helix chain 'B' and resid 131 through 162 removed outlier: 3.533A pdb=" N ILE B 135 " --> pdb=" O ALA B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 206 removed outlier: 3.795A pdb=" N ASN B 205 " --> pdb=" O LYS B 201 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 236 Processing helix chain 'B' and resid 250 through 254 removed outlier: 4.216A pdb=" N LEU B 253 " --> pdb=" O SER B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 296 Proline residue: B 289 - end of helix Processing helix chain 'B' and resid 296 through 301 Processing helix chain 'B' and resid 305 through 312 removed outlier: 3.616A pdb=" N VAL B 308 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE B 311 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 339 removed outlier: 3.902A pdb=" N LEU B 330 " --> pdb=" O ASN B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 356 Processing helix chain 'B' and resid 361 through 370 removed outlier: 3.657A pdb=" N LEU B 370 " --> pdb=" O LEU B 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 32 through 54 Proline residue: C 46 - end of helix removed outlier: 3.611A pdb=" N PHE C 54 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 88 Processing helix chain 'C' and resid 100 through 131 Proline residue: C 110 - end of helix Proline residue: C 123 - end of helix Processing helix chain 'C' and resid 131 through 162 removed outlier: 3.534A pdb=" N ILE C 135 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 206 removed outlier: 3.795A pdb=" N ASN C 205 " --> pdb=" O LYS C 201 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 236 Processing helix chain 'C' and resid 250 through 254 removed outlier: 4.215A pdb=" N LEU C 253 " --> pdb=" O SER C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 296 Proline residue: C 289 - end of helix Processing helix chain 'C' and resid 296 through 301 Processing helix chain 'C' and resid 305 through 312 removed outlier: 3.617A pdb=" N VAL C 308 " --> pdb=" O VAL C 305 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE C 311 " --> pdb=" O VAL C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 339 removed outlier: 3.903A pdb=" N LEU C 330 " --> pdb=" O ASN C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 356 Processing helix chain 'C' and resid 361 through 370 removed outlier: 3.659A pdb=" N LEU C 370 " --> pdb=" O LEU C 366 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 11 Processing helix chain 'D' and resid 32 through 54 Proline residue: D 46 - end of helix removed outlier: 3.611A pdb=" N PHE D 54 " --> pdb=" O ILE D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 88 Processing helix chain 'D' and resid 100 through 131 Proline residue: D 110 - end of helix Proline residue: D 123 - end of helix Processing helix chain 'D' and resid 131 through 162 removed outlier: 3.534A pdb=" N ILE D 135 " --> pdb=" O ALA D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 206 removed outlier: 3.797A pdb=" N ASN D 205 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER D 206 " --> pdb=" O THR D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 236 Processing helix chain 'D' and resid 250 through 254 removed outlier: 4.215A pdb=" N LEU D 253 " --> pdb=" O SER D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 296 Proline residue: D 289 - end of helix Processing helix chain 'D' and resid 296 through 301 Processing helix chain 'D' and resid 305 through 312 removed outlier: 3.618A pdb=" N VAL D 308 " --> pdb=" O VAL D 305 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE D 311 " --> pdb=" O VAL D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 339 removed outlier: 3.902A pdb=" N LEU D 330 " --> pdb=" O ASN D 326 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 356 Processing helix chain 'D' and resid 361 through 370 removed outlier: 3.658A pdb=" N LEU D 370 " --> pdb=" O LEU D 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 11 Processing helix chain 'E' and resid 32 through 54 Proline residue: E 46 - end of helix removed outlier: 3.611A pdb=" N PHE E 54 " --> pdb=" O ILE E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 88 Processing helix chain 'E' and resid 100 through 131 Proline residue: E 110 - end of helix Proline residue: E 123 - end of helix Processing helix chain 'E' and resid 131 through 162 removed outlier: 3.534A pdb=" N ILE E 135 " --> pdb=" O ALA E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 206 removed outlier: 3.795A pdb=" N ASN E 205 " --> pdb=" O LYS E 201 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER E 206 " --> pdb=" O THR E 202 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 236 Processing helix chain 'E' and resid 250 through 254 removed outlier: 4.215A pdb=" N LEU E 253 " --> pdb=" O SER E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 296 Proline residue: E 289 - end of helix Processing helix chain 'E' and resid 296 through 301 Processing helix chain 'E' and resid 305 through 312 removed outlier: 3.616A pdb=" N VAL E 308 " --> pdb=" O VAL E 305 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE E 311 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 326 through 339 removed outlier: 3.901A pdb=" N LEU E 330 " --> pdb=" O ASN E 326 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 356 Processing helix chain 'E' and resid 361 through 370 removed outlier: 3.657A pdb=" N LEU E 370 " --> pdb=" O LEU E 366 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 11 Processing helix chain 'F' and resid 32 through 54 Proline residue: F 46 - end of helix removed outlier: 3.609A pdb=" N PHE F 54 " --> pdb=" O ILE F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 88 Processing helix chain 'F' and resid 100 through 131 Proline residue: F 110 - end of helix Proline residue: F 123 - end of helix Processing helix chain 'F' and resid 131 through 162 removed outlier: 3.534A pdb=" N ILE F 135 " --> pdb=" O ALA F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 206 removed outlier: 3.794A pdb=" N ASN F 205 " --> pdb=" O LYS F 201 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER F 206 " --> pdb=" O THR F 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 236 Processing helix chain 'F' and resid 250 through 254 removed outlier: 4.215A pdb=" N LEU F 253 " --> pdb=" O SER F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 296 Proline residue: F 289 - end of helix Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 305 through 312 removed outlier: 3.614A pdb=" N VAL F 308 " --> pdb=" O VAL F 305 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE F 311 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing helix chain 'F' and resid 326 through 339 removed outlier: 3.902A pdb=" N LEU F 330 " --> pdb=" O ASN F 326 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 356 Processing helix chain 'F' and resid 361 through 370 removed outlier: 3.658A pdb=" N LEU F 370 " --> pdb=" O LEU F 366 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 11 Processing helix chain 'G' and resid 32 through 54 Proline residue: G 46 - end of helix removed outlier: 3.611A pdb=" N PHE G 54 " --> pdb=" O ILE G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 88 Processing helix chain 'G' and resid 100 through 131 Proline residue: G 110 - end of helix Proline residue: G 123 - end of helix Processing helix chain 'G' and resid 131 through 162 removed outlier: 3.533A pdb=" N ILE G 135 " --> pdb=" O ALA G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 206 removed outlier: 3.795A pdb=" N ASN G 205 " --> pdb=" O LYS G 201 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER G 206 " --> pdb=" O THR G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 207 through 236 Processing helix chain 'G' and resid 250 through 254 removed outlier: 4.215A pdb=" N LEU G 253 " --> pdb=" O SER G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 269 through 296 Proline residue: G 289 - end of helix Processing helix chain 'G' and resid 296 through 301 Processing helix chain 'G' and resid 305 through 312 removed outlier: 3.615A pdb=" N VAL G 308 " --> pdb=" O VAL G 305 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ILE G 311 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 339 removed outlier: 3.903A pdb=" N LEU G 330 " --> pdb=" O ASN G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 342 through 356 Processing helix chain 'G' and resid 361 through 370 removed outlier: 3.658A pdb=" N LEU G 370 " --> pdb=" O LEU G 366 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 65 removed outlier: 3.598A pdb=" N VAL A 245 " --> pdb=" O GLN A 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 64 through 65 removed outlier: 3.600A pdb=" N VAL B 245 " --> pdb=" O GLN B 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 64 through 65 removed outlier: 3.597A pdb=" N VAL C 245 " --> pdb=" O GLN C 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 64 through 65 removed outlier: 3.598A pdb=" N VAL D 245 " --> pdb=" O GLN D 95 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 64 through 65 removed outlier: 3.598A pdb=" N VAL E 245 " --> pdb=" O GLN E 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 64 through 65 removed outlier: 3.599A pdb=" N VAL F 245 " --> pdb=" O GLN F 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 64 through 65 removed outlier: 3.600A pdb=" N VAL G 245 " --> pdb=" O GLN G 95 " (cutoff:3.500A) 1212 hydrogen bonds defined for protein. 3531 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: 9.71 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17892 1.03 - 1.23: 56 1.23 - 1.42: 7758 1.42 - 1.61: 11574 1.61 - 1.81: 105 Bond restraints: 37385 Sorted by residual: bond pdb=" O5' ATP A 505 " pdb=" PA ATP A 505 " ideal model delta sigma weight residual 1.579 1.603 -0.024 1.10e-02 8.26e+03 4.63e+00 bond pdb=" O2A ATP A 505 " pdb=" PA ATP A 505 " ideal model delta sigma weight residual 1.529 1.492 0.037 2.20e-02 2.07e+03 2.79e+00 bond pdb=" O2B ATP A 505 " pdb=" PB ATP A 505 " ideal model delta sigma weight residual 1.529 1.493 0.036 2.20e-02 2.07e+03 2.71e+00 bond pdb=" O1A ATP A 505 " pdb=" PA ATP A 505 " ideal model delta sigma weight residual 1.477 1.493 -0.016 1.10e-02 8.26e+03 2.10e+00 bond pdb=" C4 ATP A 505 " pdb=" C5 ATP A 505 " ideal model delta sigma weight residual 1.388 1.377 0.011 1.00e-02 1.00e+04 1.27e+00 ... (remaining 37380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 66792 1.73 - 3.47: 534 3.47 - 5.20: 71 5.20 - 6.93: 1 6.93 - 8.67: 1 Bond angle restraints: 67399 Sorted by residual: angle pdb=" PB ATP A 505 " pdb=" O3B ATP A 505 " pdb=" PG ATP A 505 " ideal model delta sigma weight residual 139.87 131.20 8.67 1.00e+00 1.00e+00 7.51e+01 angle pdb=" PA ATP A 505 " pdb=" O3A ATP A 505 " pdb=" PB ATP A 505 " ideal model delta sigma weight residual 136.83 132.48 4.35 1.00e+00 1.00e+00 1.89e+01 angle pdb=" O1G ATP A 505 " pdb=" PG ATP A 505 " pdb=" O3B ATP A 505 " ideal model delta sigma weight residual 110.47 106.06 4.41 1.64e+00 3.70e-01 7.18e+00 angle pdb=" C5' ATP A 505 " pdb=" O5' ATP A 505 " pdb=" PA ATP A 505 " ideal model delta sigma weight residual 121.27 118.67 2.60 1.00e+00 1.00e+00 6.76e+00 angle pdb=" N ILE G 311 " pdb=" CA ILE G 311 " pdb=" C ILE G 311 " ideal model delta sigma weight residual 112.80 110.08 2.72 1.15e+00 7.56e-01 5.61e+00 ... (remaining 67394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 17349 16.16 - 32.32: 1001 32.32 - 48.48: 305 48.48 - 64.64: 110 64.64 - 80.79: 22 Dihedral angle restraints: 18787 sinusoidal: 10226 harmonic: 8561 Sorted by residual: dihedral pdb=" CA GLU C 9 " pdb=" C GLU C 9 " pdb=" N TYR C 10 " pdb=" CA TYR C 10 " ideal model delta harmonic sigma weight residual -180.00 -163.55 -16.45 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA GLU G 9 " pdb=" C GLU G 9 " pdb=" N TYR G 10 " pdb=" CA TYR G 10 " ideal model delta harmonic sigma weight residual -180.00 -163.57 -16.43 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CA GLU D 9 " pdb=" C GLU D 9 " pdb=" N TYR D 10 " pdb=" CA TYR D 10 " ideal model delta harmonic sigma weight residual 180.00 -163.59 -16.41 0 5.00e+00 4.00e-02 1.08e+01 ... (remaining 18784 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2525 0.040 - 0.079: 537 0.079 - 0.119: 157 0.119 - 0.158: 12 0.158 - 0.198: 7 Chirality restraints: 3238 Sorted by residual: chirality pdb=" C1 NAG D 504 " pdb=" ND2 ASN D 255 " pdb=" C2 NAG D 504 " pdb=" O5 NAG D 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.79e-01 chirality pdb=" C1 NAG G 504 " pdb=" ND2 ASN G 255 " pdb=" C2 NAG G 504 " pdb=" O5 NAG G 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.71e-01 chirality pdb=" C1 NAG A 504 " pdb=" ND2 ASN A 255 " pdb=" C2 NAG A 504 " pdb=" O5 NAG A 504 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.65e-01 ... (remaining 3235 not shown) Planarity restraints: 5433 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU F 122 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO F 123 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO F 123 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 123 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 122 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO D 123 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 122 " -0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO A 123 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " -0.019 5.00e-02 4.00e+02 ... (remaining 5430 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.43: 19396 2.43 - 2.97: 84971 2.97 - 3.52: 101702 3.52 - 4.06: 127405 4.06 - 4.60: 195576 Nonbonded interactions: 529050 Sorted by model distance: nonbonded pdb=" HE1 TYR C 309 " pdb=" HD1 TYR C 345 " model vdw 1.890 2.100 nonbonded pdb=" HE1 TYR A 309 " pdb=" HD1 TYR A 345 " model vdw 1.890 2.100 nonbonded pdb=" HE1 TYR D 309 " pdb=" HD1 TYR D 345 " model vdw 1.891 2.100 nonbonded pdb=" HE1 TYR B 309 " pdb=" HD1 TYR B 345 " model vdw 1.892 2.100 nonbonded pdb=" HE1 TYR E 309 " pdb=" HD1 TYR E 345 " model vdw 1.892 2.100 ... (remaining 529045 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 504) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 0.010 Normalize map: mean=0, sd=1: 2.500 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: 0.200 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 36.480 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 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 : 0.003 0.037 19479 Z= 0.141 Angle : 0.525 8.668 26624 Z= 0.282 Chirality : 0.037 0.198 3238 Planarity : 0.004 0.034 3137 Dihedral : 12.020 80.794 7713 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.76 % Allowed : 4.18 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.79 (0.19), residues: 2380 helix: 2.34 (0.14), residues: 1610 sheet: None (None), residues: 0 loop : -1.43 (0.24), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 300 TYR 0.008 0.001 TYR E 83 PHE 0.007 0.001 PHE F 109 TRP 0.007 0.002 TRP E 104 HIS 0.002 0.001 HIS G 134 Details of bonding type rmsd covalent geometry : bond 0.00310 (19458) covalent geometry : angle 0.52333 (26575) SS BOND : bond 0.00255 ( 14) SS BOND : angle 0.95486 ( 28) hydrogen bonds : bond 0.10206 ( 1212) hydrogen bonds : angle 4.19418 ( 3531) link_NAG-ASN : bond 0.00434 ( 7) link_NAG-ASN : angle 1.37700 ( 21) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 194 time to evaluate : 0.752 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: 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: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 201 average time/residue: 1.3445 time to fit residues: 303.6469 Evaluate side-chains 121 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 114 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 TRP Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain D residue 74 TRP Chi-restraints excluded: chain E residue 74 TRP Chi-restraints excluded: chain F residue 74 TRP Chi-restraints excluded: chain G residue 74 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 235 optimal weight: 10.0000 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN B 280 ASN C 280 ASN D 134 HIS D 280 ASN E 280 ASN F 280 ASN G 134 HIS G 280 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.083883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.067600 restraints weight = 196933.499| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.35 r_work: 0.3182 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 19479 Z= 0.161 Angle : 0.520 5.715 26624 Z= 0.270 Chirality : 0.036 0.185 3238 Planarity : 0.004 0.039 3137 Dihedral : 7.609 65.462 3906 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.68 % Allowed : 7.39 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.87 (0.19), residues: 2380 helix: 2.43 (0.14), residues: 1589 sheet: None (None), residues: 0 loop : -1.36 (0.23), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 75 TYR 0.013 0.001 TYR G 10 PHE 0.007 0.001 PHE G 67 TRP 0.008 0.001 TRP F 74 HIS 0.004 0.001 HIS D 134 Details of bonding type rmsd covalent geometry : bond 0.00352 (19458) covalent geometry : angle 0.51791 (26575) SS BOND : bond 0.00244 ( 14) SS BOND : angle 0.94766 ( 28) hydrogen bonds : bond 0.03675 ( 1212) hydrogen bonds : angle 4.03149 ( 3531) link_NAG-ASN : bond 0.00231 ( 7) link_NAG-ASN : angle 1.27427 ( 21) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 129 time to evaluate : 0.803 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 57 GLU cc_start: 0.8639 (pm20) cc_final: 0.8386 (pm20) REVERT: B 74 TRP cc_start: 0.4074 (m-90) cc_final: 0.3761 (m-90) REVERT: D 29 ARG cc_start: 0.7428 (mmt-90) cc_final: 0.6935 (mmt-90) REVERT: D 31 GLU cc_start: 0.7836 (mp0) cc_final: 0.7543 (mp0) REVERT: G 31 GLU cc_start: 0.7779 (mp0) cc_final: 0.7572 (mp0) REVERT: G 57 GLU cc_start: 0.8564 (pm20) cc_final: 0.8206 (pm20) outliers start: 31 outliers final: 14 residues processed: 154 average time/residue: 1.4213 time to fit residues: 245.2476 Evaluate side-chains 126 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 337 GLU Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 37 MET Chi-restraints excluded: chain C residue 74 TRP Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain G residue 214 ILE Chi-restraints excluded: chain G residue 216 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 chunk 234 optimal weight: 7.9990 chunk 119 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 129 optimal weight: 10.0000 overall best weight: 4.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 134 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.080894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.063904 restraints weight = 199102.149| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.15 r_work: 0.3068 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 19479 Z= 0.312 Angle : 0.606 5.496 26624 Z= 0.320 Chirality : 0.039 0.207 3238 Planarity : 0.004 0.040 3137 Dihedral : 7.782 66.417 3896 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.20 % Allowed : 9.29 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.21 (0.19), residues: 2380 helix: 2.69 (0.14), residues: 1512 sheet: -0.73 (0.55), residues: 84 loop : -0.82 (0.25), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 75 TYR 0.017 0.001 TYR A 10 PHE 0.016 0.001 PHE G 67 TRP 0.010 0.001 TRP F 74 HIS 0.004 0.002 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00666 (19458) covalent geometry : angle 0.60463 (26575) SS BOND : bond 0.00403 ( 14) SS BOND : angle 1.36014 ( 28) hydrogen bonds : bond 0.04019 ( 1212) hydrogen bonds : angle 4.34769 ( 3531) link_NAG-ASN : bond 0.00027 ( 7) link_NAG-ASN : angle 0.99182 ( 21) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.051 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 29 ARG cc_start: 0.7618 (mmt-90) cc_final: 0.7147 (mmt-90) REVERT: D 31 GLU cc_start: 0.7890 (mp0) cc_final: 0.7573 (mp0) REVERT: E 31 GLU cc_start: 0.7915 (mp0) cc_final: 0.7623 (mp0) REVERT: F 37 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8936 (tmm) REVERT: G 31 GLU cc_start: 0.7747 (mp0) cc_final: 0.7486 (mp0) outliers start: 22 outliers final: 9 residues processed: 131 average time/residue: 1.4176 time to fit residues: 206.8924 Evaluate side-chains 125 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain G residue 216 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 227 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 232 optimal weight: 7.9990 chunk 113 optimal weight: 4.9990 chunk 201 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 chunk 163 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.081251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.064423 restraints weight = 197256.617| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 3.13 r_work: 0.3075 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 19479 Z= 0.213 Angle : 0.545 5.666 26624 Z= 0.284 Chirality : 0.037 0.191 3238 Planarity : 0.004 0.040 3137 Dihedral : 7.529 65.598 3891 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.98 % Allowed : 10.97 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.33 (0.19), residues: 2380 helix: 2.78 (0.14), residues: 1498 sheet: -0.41 (0.55), residues: 84 loop : -0.71 (0.25), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 75 TYR 0.012 0.001 TYR C 10 PHE 0.013 0.001 PHE G 67 TRP 0.008 0.001 TRP F 74 HIS 0.003 0.001 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00449 (19458) covalent geometry : angle 0.54308 (26575) SS BOND : bond 0.00290 ( 14) SS BOND : angle 1.12177 ( 28) hydrogen bonds : bond 0.03749 ( 1212) hydrogen bonds : angle 4.22040 ( 3531) link_NAG-ASN : bond 0.00214 ( 7) link_NAG-ASN : angle 1.14564 ( 21) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 0.772 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 29 ARG cc_start: 0.7653 (mmt-90) cc_final: 0.7125 (mmt-90) REVERT: D 31 GLU cc_start: 0.7870 (mp0) cc_final: 0.7534 (mp0) REVERT: E 31 GLU cc_start: 0.7846 (mp0) cc_final: 0.7392 (mp0) REVERT: F 37 MET cc_start: 0.9151 (ttt) cc_final: 0.8944 (tmm) REVERT: G 31 GLU cc_start: 0.7740 (mp0) cc_final: 0.7417 (mp0) outliers start: 18 outliers final: 11 residues processed: 128 average time/residue: 1.3715 time to fit residues: 196.5137 Evaluate side-chains 118 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain G residue 139 LEU Chi-restraints excluded: chain G residue 216 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 98 optimal weight: 9.9990 chunk 112 optimal weight: 4.9990 chunk 210 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 236 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.080674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.064175 restraints weight = 196982.536| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 3.06 r_work: 0.3065 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 19479 Z= 0.225 Angle : 0.549 5.487 26624 Z= 0.288 Chirality : 0.037 0.191 3238 Planarity : 0.004 0.040 3137 Dihedral : 7.495 64.153 3891 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.58 % Allowed : 11.08 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.32 (0.19), residues: 2380 helix: 2.75 (0.14), residues: 1498 sheet: -0.14 (0.56), residues: 84 loop : -0.72 (0.25), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 75 TYR 0.012 0.001 TYR A 10 PHE 0.014 0.001 PHE G 67 TRP 0.008 0.001 TRP F 74 HIS 0.003 0.001 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00479 (19458) covalent geometry : angle 0.54703 (26575) SS BOND : bond 0.00301 ( 14) SS BOND : angle 1.03791 ( 28) hydrogen bonds : bond 0.03771 ( 1212) hydrogen bonds : angle 4.25359 ( 3531) link_NAG-ASN : bond 0.00169 ( 7) link_NAG-ASN : angle 1.14992 ( 21) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 136 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 107 time to evaluate : 0.798 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: symmetry clash revert: symmetry clash REVERT: D 29 ARG cc_start: 0.7753 (mmt-90) cc_final: 0.7131 (mmt-90) REVERT: D 31 GLU cc_start: 0.7849 (mp0) cc_final: 0.7479 (mp0) REVERT: E 31 GLU cc_start: 0.7837 (mp0) cc_final: 0.7386 (mp0) REVERT: F 37 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8961 (tmm) REVERT: G 31 GLU cc_start: 0.7741 (mp0) cc_final: 0.7417 (mp0) outliers start: 29 outliers final: 15 residues processed: 130 average time/residue: 1.3540 time to fit residues: 197.9230 Evaluate side-chains 119 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 103 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 MET Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 139 LEU Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain G residue 216 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 81 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 98 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 92 optimal weight: 1.9990 chunk 208 optimal weight: 3.9990 chunk 175 optimal weight: 4.9990 chunk 207 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.082091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.065297 restraints weight = 195359.859| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 3.17 r_work: 0.3099 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19479 Z= 0.126 Angle : 0.514 5.211 26624 Z= 0.265 Chirality : 0.036 0.170 3238 Planarity : 0.004 0.038 3137 Dihedral : 7.019 60.859 3891 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 1.03 % Allowed : 11.62 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.43 (0.19), residues: 2380 helix: 2.82 (0.14), residues: 1498 sheet: 0.01 (0.58), residues: 84 loop : -0.66 (0.25), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 75 TYR 0.010 0.001 TYR A 10 PHE 0.008 0.001 PHE G 263 TRP 0.009 0.001 TRP C 74 HIS 0.001 0.000 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00277 (19458) covalent geometry : angle 0.51236 (26575) SS BOND : bond 0.00166 ( 14) SS BOND : angle 0.78794 ( 28) hydrogen bonds : bond 0.03448 ( 1212) hydrogen bonds : angle 4.05402 ( 3531) link_NAG-ASN : bond 0.00360 ( 7) link_NAG-ASN : angle 1.41269 ( 21) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 109 time to evaluate : 1.068 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: D 29 ARG cc_start: 0.7680 (mmt-90) cc_final: 0.7108 (mmt-90) REVERT: D 31 GLU cc_start: 0.7763 (mp0) cc_final: 0.7379 (mp0) REVERT: E 31 GLU cc_start: 0.7779 (mp0) cc_final: 0.7288 (mp0) REVERT: F 37 MET cc_start: 0.9144 (ttt) cc_final: 0.8937 (tmm) REVERT: G 31 GLU cc_start: 0.7654 (mp0) cc_final: 0.7309 (mp0) REVERT: G 57 GLU cc_start: 0.8695 (pm20) cc_final: 0.8469 (pm20) outliers start: 19 outliers final: 15 residues processed: 126 average time/residue: 1.4233 time to fit residues: 200.4563 Evaluate side-chains 121 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 216 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 17 optimal weight: 10.0000 chunk 188 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 26 optimal weight: 0.1980 chunk 194 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 147 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.081197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.064896 restraints weight = 196436.075| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 3.04 r_work: 0.3088 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19479 Z= 0.182 Angle : 0.542 5.497 26624 Z= 0.282 Chirality : 0.036 0.177 3238 Planarity : 0.004 0.040 3137 Dihedral : 7.040 60.072 3891 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.14 % Allowed : 12.11 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.44 (0.19), residues: 2380 helix: 2.84 (0.14), residues: 1498 sheet: 0.16 (0.57), residues: 84 loop : -0.68 (0.25), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 75 TYR 0.015 0.001 TYR G 10 PHE 0.012 0.001 PHE G 67 TRP 0.007 0.001 TRP C 74 HIS 0.002 0.001 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00395 (19458) covalent geometry : angle 0.54065 (26575) SS BOND : bond 0.00232 ( 14) SS BOND : angle 0.78246 ( 28) hydrogen bonds : bond 0.03524 ( 1212) hydrogen bonds : angle 4.11718 ( 3531) link_NAG-ASN : bond 0.00226 ( 7) link_NAG-ASN : angle 1.32888 ( 21) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 104 time to evaluate : 1.031 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: D 29 ARG cc_start: 0.7749 (mmt-90) cc_final: 0.7168 (mmt-90) REVERT: D 31 GLU cc_start: 0.7785 (mp0) cc_final: 0.7402 (mp0) REVERT: E 31 GLU cc_start: 0.7790 (mp0) cc_final: 0.7302 (mp0) REVERT: F 37 MET cc_start: 0.9149 (ttt) cc_final: 0.8942 (tmm) REVERT: G 31 GLU cc_start: 0.7672 (mp0) cc_final: 0.7363 (mp0) REVERT: G 57 GLU cc_start: 0.8751 (pm20) cc_final: 0.8468 (pm20) outliers start: 21 outliers final: 19 residues processed: 124 average time/residue: 1.4472 time to fit residues: 200.7962 Evaluate side-chains 122 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 136 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 139 LEU Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 115 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 147 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 190 optimal weight: 0.0970 chunk 217 optimal weight: 9.9990 chunk 146 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 124 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.081656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.064851 restraints weight = 195954.777| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 3.14 r_work: 0.3097 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19479 Z= 0.156 Angle : 0.535 5.663 26624 Z= 0.278 Chirality : 0.036 0.172 3238 Planarity : 0.004 0.039 3137 Dihedral : 6.921 58.806 3891 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.58 % Allowed : 11.95 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.36 (0.19), residues: 2380 helix: 2.72 (0.14), residues: 1519 sheet: 0.21 (0.58), residues: 84 loop : -0.71 (0.25), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 75 TYR 0.014 0.001 TYR E 10 PHE 0.010 0.001 PHE E 67 TRP 0.008 0.001 TRP C 74 HIS 0.001 0.000 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00340 (19458) covalent geometry : angle 0.53345 (26575) SS BOND : bond 0.00205 ( 14) SS BOND : angle 0.88694 ( 28) hydrogen bonds : bond 0.03446 ( 1212) hydrogen bonds : angle 4.07419 ( 3531) link_NAG-ASN : bond 0.00278 ( 7) link_NAG-ASN : angle 1.39254 ( 21) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.940 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 337 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8656 (pp20) REVERT: D 29 ARG cc_start: 0.7748 (mmt-90) cc_final: 0.7249 (mmt90) REVERT: D 31 GLU cc_start: 0.7780 (mp0) cc_final: 0.7390 (mp0) REVERT: E 31 GLU cc_start: 0.7780 (mp0) cc_final: 0.7325 (mp0) REVERT: E 37 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8871 (ttp) REVERT: F 37 MET cc_start: 0.9176 (ttt) cc_final: 0.8971 (tmm) REVERT: G 31 GLU cc_start: 0.7672 (mp0) cc_final: 0.7356 (mp0) REVERT: G 57 GLU cc_start: 0.8762 (pm20) cc_final: 0.8443 (pm20) REVERT: G 75 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8828 (mmt-90) outliers start: 29 outliers final: 16 residues processed: 135 average time/residue: 1.4183 time to fit residues: 214.8187 Evaluate side-chains 123 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 210 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 208 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 216 optimal weight: 0.5980 chunk 11 optimal weight: 4.9990 chunk 223 optimal weight: 0.7980 chunk 15 optimal weight: 20.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.082112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.065882 restraints weight = 195444.798| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 3.06 r_work: 0.3110 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19479 Z= 0.119 Angle : 0.528 6.569 26624 Z= 0.273 Chirality : 0.035 0.162 3238 Planarity : 0.004 0.038 3137 Dihedral : 6.561 55.619 3891 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.09 % Allowed : 12.38 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.44 (0.19), residues: 2380 helix: 2.77 (0.14), residues: 1519 sheet: 0.50 (0.60), residues: 84 loop : -0.70 (0.26), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 75 TYR 0.013 0.001 TYR F 10 PHE 0.008 0.001 PHE G 263 TRP 0.010 0.001 TRP C 74 HIS 0.001 0.000 HIS C 134 Details of bonding type rmsd covalent geometry : bond 0.00267 (19458) covalent geometry : angle 0.52603 (26575) SS BOND : bond 0.00129 ( 14) SS BOND : angle 0.77826 ( 28) hydrogen bonds : bond 0.03244 ( 1212) hydrogen bonds : angle 3.97504 ( 3531) link_NAG-ASN : bond 0.00361 ( 7) link_NAG-ASN : angle 1.52307 ( 21) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 138 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 1.083 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: symmetry clash REVERT: D 29 ARG cc_start: 0.7703 (mmt-90) cc_final: 0.7115 (mmt-90) REVERT: D 31 GLU cc_start: 0.7709 (mp0) cc_final: 0.7306 (mp0) REVERT: E 31 GLU cc_start: 0.7706 (mp0) cc_final: 0.7218 (mp0) REVERT: E 37 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8872 (ttp) REVERT: F 37 MET cc_start: 0.9187 (ttt) cc_final: 0.8981 (tmm) REVERT: G 29 ARG cc_start: 0.7833 (mmt90) cc_final: 0.7460 (mmt-90) REVERT: G 31 GLU cc_start: 0.7608 (mp0) cc_final: 0.7294 (mp0) REVERT: G 57 GLU cc_start: 0.8640 (pm20) cc_final: 0.8376 (pm20) REVERT: G 75 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8772 (mmt-90) outliers start: 20 outliers final: 16 residues processed: 136 average time/residue: 1.4535 time to fit residues: 221.6244 Evaluate side-chains 130 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 75 ARG Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 23 optimal weight: 2.9990 chunk 181 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 chunk 137 optimal weight: 7.9990 chunk 62 optimal weight: 9.9990 chunk 193 optimal weight: 3.9990 chunk 227 optimal weight: 0.0980 chunk 195 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 126 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.082097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.065381 restraints weight = 195782.692| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.11 r_work: 0.3110 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19479 Z= 0.141 Angle : 0.543 6.793 26624 Z= 0.280 Chirality : 0.036 0.162 3238 Planarity : 0.004 0.039 3137 Dihedral : 6.492 54.135 3891 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.98 % Allowed : 12.66 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.54 (0.19), residues: 2380 helix: 2.88 (0.14), residues: 1505 sheet: 0.59 (0.61), residues: 84 loop : -0.65 (0.25), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 75 TYR 0.019 0.001 TYR B 10 PHE 0.009 0.001 PHE G 67 TRP 0.009 0.001 TRP C 74 HIS 0.001 0.000 HIS G 106 Details of bonding type rmsd covalent geometry : bond 0.00313 (19458) covalent geometry : angle 0.54102 (26575) SS BOND : bond 0.00159 ( 14) SS BOND : angle 0.77941 ( 28) hydrogen bonds : bond 0.03252 ( 1212) hydrogen bonds : angle 3.98061 ( 3531) link_NAG-ASN : bond 0.00312 ( 7) link_NAG-ASN : angle 1.50664 ( 21) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4760 Ramachandran restraints generated. 2380 Oldfield, 0 Emsley, 2380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Residue THR 21 is missing expected H atoms. Skipping. Residue LYS 24 is missing expected H atoms. Skipping. Residue LYS 26 is missing expected H atoms. Skipping. Residue SER 98 is missing expected H atoms. Skipping. Residue LYS 155 is missing expected H atoms. Skipping. Residue LYS 158 is missing expected H atoms. Skipping. Residue SER 159 is missing expected H atoms. Skipping. Residue LYS 192 is missing expected H atoms. Skipping. Residue LYS 302 is missing expected H atoms. Skipping. Residue THR 303 is missing expected H atoms. Skipping. Residue THR 314 is missing expected H atoms. Skipping. Residue VAL 317 is missing expected H atoms. Skipping. Residue LEU 318 is missing expected H atoms. Skipping. Residue LYS 321 is missing expected H atoms. Skipping. Residue SER 322 is missing expected H atoms. Skipping. Residue SER 356 is missing expected H atoms. Skipping. Residue SER 357 is missing expected H atoms. Skipping. Residue ILE 361 is missing expected H atoms. Skipping. Residue MET 364 is missing expected H atoms. Skipping. Residue LEU 365 is missing expected H atoms. Skipping. Residue LEU 366 is missing expected H atoms. Skipping. Residue LEU 367 is missing expected H atoms. Skipping. Residue THR 368 is missing expected H atoms. Skipping. Residue LEU 370 is missing expected H atoms. Skipping. Residue MET 372 is missing expected H atoms. Skipping. Evaluate side-chains 134 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 116 time to evaluate : 0.874 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 337 GLU cc_start: 0.8772 (tm-30) cc_final: 0.8524 (pp20) REVERT: B 337 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8502 (pp20) REVERT: D 29 ARG cc_start: 0.7724 (mmt-90) cc_final: 0.7361 (mmt-90) REVERT: D 31 GLU cc_start: 0.7730 (mp0) cc_final: 0.7332 (mp0) REVERT: D 337 GLU cc_start: 0.8739 (tm-30) cc_final: 0.8505 (pp20) REVERT: E 31 GLU cc_start: 0.7739 (mp0) cc_final: 0.7257 (mp0) REVERT: E 37 MET cc_start: 0.9120 (OUTLIER) cc_final: 0.8892 (ttp) REVERT: F 37 MET cc_start: 0.9179 (ttt) cc_final: 0.8975 (tmm) REVERT: G 29 ARG cc_start: 0.7834 (mmt90) cc_final: 0.7570 (mmt-90) REVERT: G 31 GLU cc_start: 0.7609 (mp0) cc_final: 0.7274 (mp0) REVERT: G 337 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8450 (pp20) outliers start: 18 outliers final: 16 residues processed: 132 average time/residue: 1.5415 time to fit residues: 226.7898 Evaluate side-chains 124 residues out of total 2177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 CYS Chi-restraints excluded: chain A residue 246 CYS Chi-restraints excluded: chain B residue 216 CYS Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 216 CYS Chi-restraints excluded: chain D residue 246 CYS Chi-restraints excluded: chain E residue 37 MET Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 216 CYS Chi-restraints excluded: chain E residue 246 CYS Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 216 CYS Chi-restraints excluded: chain F residue 246 CYS Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 216 CYS Chi-restraints excluded: chain G residue 246 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 31 optimal weight: 9.9990 chunk 194 optimal weight: 0.5980 chunk 138 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 74 optimal weight: 0.7980 chunk 103 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 135 optimal weight: 7.9990 chunk 131 optimal weight: 7.9990 chunk 192 optimal weight: 4.9990 overall best weight: 3.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.080533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.063664 restraints weight = 198294.035| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.05 r_work: 0.3067 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.3383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 19479 Z= 0.251 Angle : 0.597 8.145 26624 Z= 0.312 Chirality : 0.037 0.187 3238 Planarity : 0.004 0.052 3137 Dihedral : 7.086 57.550 3891 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.98 % Allowed : 12.93 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.44 (0.19), residues: 2380 helix: 2.82 (0.14), residues: 1505 sheet: 0.21 (0.55), residues: 84 loop : -0.68 (0.25), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 75 TYR 0.028 0.001 TYR E 10 PHE 0.016 0.001 PHE G 67 TRP 0.008 0.001 TRP E 74 HIS 0.003 0.001 HIS E 106 Details of bonding type rmsd covalent geometry : bond 0.00541 (19458) covalent geometry : angle 0.59518 (26575) SS BOND : bond 0.00360 ( 14) SS BOND : angle 1.10434 ( 28) hydrogen bonds : bond 0.03666 ( 1212) hydrogen bonds : angle 4.19847 ( 3531) link_NAG-ASN : bond 0.00120 ( 7) link_NAG-ASN : angle 1.28889 ( 21) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8646.38 seconds wall clock time: 147 minutes 29.10 seconds (8849.10 seconds total)