Starting phenix.real_space_refine on Sat Aug 23 15:45:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yx8_39650/08_2025/8yx8_39650.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yx8_39650/08_2025/8yx8_39650.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yx8_39650/08_2025/8yx8_39650.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yx8_39650/08_2025/8yx8_39650.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yx8_39650/08_2025/8yx8_39650.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yx8_39650/08_2025/8yx8_39650.map" } resolution = 2.8 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= 0.001 sd= 0.024 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: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 8485 2.51 5 N 2190 2.21 5 O 2340 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13070 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2572 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 306} Chain breaks: 1 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2572 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 306} Chain breaks: 1 Chain: "C" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2572 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 306} Chain breaks: 1 Chain: "D" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2572 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 306} Chain breaks: 1 Chain: "E" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2572 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 306} Chain breaks: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" C1 NAG F 2 " occ=0.60 ... (12 atoms not shown) pdb=" O7 NAG F 2 " occ=0.60 residue: pdb=" C1 NAG G 2 " occ=0.60 ... (12 atoms not shown) pdb=" O7 NAG G 2 " occ=0.60 residue: pdb=" C1 NAG H 2 " occ=0.60 ... (12 atoms not shown) pdb=" O7 NAG H 2 " occ=0.60 residue: pdb=" C1 NAG I 2 " occ=0.60 ... (12 atoms not shown) pdb=" O7 NAG I 2 " occ=0.60 residue: pdb=" C1 NAG J 2 " occ=0.60 ... (12 atoms not shown) pdb=" O7 NAG J 2 " occ=0.60 Time building chain proxies: 3.37, per 1000 atoms: 0.26 Number of scatterers: 13070 At special positions: 0 Unit cell: (93, 93, 121.83, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 2340 8.00 N 2190 7.00 C 8485 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 157 " - pdb=" SG CYS A 171 " distance=2.03 Simple disulfide: pdb=" SG CYS A 289 " - pdb=" SG CYS A 394 " distance=2.03 Simple disulfide: pdb=" SG CYS B 157 " - pdb=" SG CYS B 171 " distance=2.03 Simple disulfide: pdb=" SG CYS B 289 " - pdb=" SG CYS B 394 " distance=2.03 Simple disulfide: pdb=" SG CYS C 157 " - pdb=" SG CYS C 171 " distance=2.03 Simple disulfide: pdb=" SG CYS C 289 " - pdb=" SG CYS C 394 " distance=2.03 Simple disulfide: pdb=" SG CYS D 157 " - pdb=" SG CYS D 171 " distance=2.03 Simple disulfide: pdb=" SG CYS D 289 " - pdb=" SG CYS D 394 " distance=2.03 Simple disulfide: pdb=" SG CYS E 157 " - pdb=" SG CYS E 171 " distance=2.03 Simple disulfide: pdb=" SG CYS E 289 " - pdb=" SG CYS E 394 " 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 BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " NAG-ASN " NAG A 501 " - " ASN A 170 " " NAG B 501 " - " ASN B 170 " " NAG C 501 " - " ASN C 170 " " NAG D 501 " - " ASN D 170 " " NAG E 501 " - " ASN E 170 " " NAG F 1 " - " ASN A 55 " " NAG G 1 " - " ASN B 55 " " NAG H 1 " - " ASN C 55 " " NAG I 1 " - " ASN D 55 " " NAG J 1 " - " ASN E 55 " Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 672.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3140 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 15 sheets defined 36.7% alpha, 32.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 94 through 97 Processing helix chain 'A' and resid 231 through 252 removed outlier: 4.465A pdb=" N VAL A 239 " --> pdb=" O ILE A 235 " (cutoff:3.500A) Proline residue: A 240 - end of helix Processing helix chain 'A' and resid 259 through 283 removed outlier: 4.175A pdb=" N GLY A 263 " --> pdb=" O ILE A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 320 removed outlier: 3.998A pdb=" N TYR A 295 " --> pdb=" O PRO A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 392 Processing helix chain 'A' and resid 399 through 404 Processing helix chain 'B' and resid 94 through 97 Processing helix chain 'B' and resid 231 through 252 removed outlier: 4.463A pdb=" N VAL B 239 " --> pdb=" O ILE B 235 " (cutoff:3.500A) Proline residue: B 240 - end of helix Processing helix chain 'B' and resid 259 through 283 removed outlier: 4.175A pdb=" N GLY B 263 " --> pdb=" O ILE B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 320 removed outlier: 3.998A pdb=" N TYR B 295 " --> pdb=" O PRO B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 392 Processing helix chain 'B' and resid 399 through 404 Processing helix chain 'C' and resid 94 through 97 Processing helix chain 'C' and resid 231 through 252 removed outlier: 4.463A pdb=" N VAL C 239 " --> pdb=" O ILE C 235 " (cutoff:3.500A) Proline residue: C 240 - end of helix Processing helix chain 'C' and resid 259 through 283 removed outlier: 4.175A pdb=" N GLY C 263 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 291 through 320 removed outlier: 3.998A pdb=" N TYR C 295 " --> pdb=" O PRO C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 392 Processing helix chain 'C' and resid 399 through 404 Processing helix chain 'D' and resid 94 through 97 Processing helix chain 'D' and resid 231 through 252 removed outlier: 4.465A pdb=" N VAL D 239 " --> pdb=" O ILE D 235 " (cutoff:3.500A) Proline residue: D 240 - end of helix Processing helix chain 'D' and resid 259 through 283 removed outlier: 4.175A pdb=" N GLY D 263 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 291 through 320 removed outlier: 3.998A pdb=" N TYR D 295 " --> pdb=" O PRO D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 392 Processing helix chain 'D' and resid 399 through 404 Processing helix chain 'E' and resid 94 through 97 Processing helix chain 'E' and resid 231 through 252 removed outlier: 4.464A pdb=" N VAL E 239 " --> pdb=" O ILE E 235 " (cutoff:3.500A) Proline residue: E 240 - end of helix Processing helix chain 'E' and resid 259 through 283 removed outlier: 4.175A pdb=" N GLY E 263 " --> pdb=" O ILE E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 320 removed outlier: 3.998A pdb=" N TYR E 295 " --> pdb=" O PRO E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 392 Processing helix chain 'E' and resid 399 through 404 Processing sheet with id=AA1, first strand: chain 'A' and resid 107 through 111 removed outlier: 5.688A pdb=" N GLN A 136 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N HIS A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ALA A 150 " --> pdb=" O TRP A 130 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TRP A 130 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA A 152 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL A 128 " --> pdb=" O ALA A 152 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU A 154 " --> pdb=" O LEU A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 111 removed outlier: 5.688A pdb=" N GLN A 136 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN A 148 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N HIS A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN A 73 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N MET A 84 " --> pdb=" O VAL A 71 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL A 71 " --> pdb=" O MET A 84 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N LEU A 86 " --> pdb=" O SER A 69 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER A 69 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ARG A 88 " --> pdb=" O PHE A 67 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N PHE A 67 " --> pdb=" O ARG A 88 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER A 90 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ARG A 65 " --> pdb=" O SER A 90 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N LEU A 92 " --> pdb=" O ASP A 63 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N ASP A 63 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 121 through 122 removed outlier: 4.115A pdb=" N ASP A 206 " --> pdb=" O ARG A 225 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS A 227 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL A 204 " --> pdb=" O LYS A 227 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 111 removed outlier: 5.687A pdb=" N GLN B 136 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN B 148 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N HIS B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA B 150 " --> pdb=" O TRP B 130 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TRP B 130 " --> pdb=" O ALA B 150 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA B 152 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL B 128 " --> pdb=" O ALA B 152 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLU B 154 " --> pdb=" O LEU B 126 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 107 through 111 removed outlier: 5.687A pdb=" N GLN B 136 " --> pdb=" O ASN B 148 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN B 148 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N HIS B 144 " --> pdb=" O ASP B 140 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN B 73 " --> pdb=" O SER B 82 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N MET B 84 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL B 71 " --> pdb=" O MET B 84 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N LEU B 86 " --> pdb=" O SER B 69 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER B 69 " --> pdb=" O LEU B 86 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ARG B 88 " --> pdb=" O PHE B 67 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N PHE B 67 " --> pdb=" O ARG B 88 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER B 90 " --> pdb=" O ARG B 65 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ARG B 65 " --> pdb=" O SER B 90 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N LEU B 92 " --> pdb=" O ASP B 63 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N ASP B 63 " --> pdb=" O LEU B 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 121 through 122 removed outlier: 4.115A pdb=" N ASP B 206 " --> pdb=" O ARG B 225 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LYS B 227 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL B 204 " --> pdb=" O LYS B 227 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 107 through 111 removed outlier: 5.687A pdb=" N GLN C 136 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN C 148 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N HIS C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ALA C 150 " --> pdb=" O TRP C 130 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TRP C 130 " --> pdb=" O ALA C 150 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA C 152 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL C 128 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU C 154 " --> pdb=" O LEU C 126 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 107 through 111 removed outlier: 5.687A pdb=" N GLN C 136 " --> pdb=" O ASN C 148 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN C 148 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N HIS C 144 " --> pdb=" O ASP C 140 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN C 73 " --> pdb=" O SER C 82 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N MET C 84 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL C 71 " --> pdb=" O MET C 84 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N LEU C 86 " --> pdb=" O SER C 69 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER C 69 " --> pdb=" O LEU C 86 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ARG C 88 " --> pdb=" O PHE C 67 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N PHE C 67 " --> pdb=" O ARG C 88 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER C 90 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 7.784A pdb=" N ARG C 65 " --> pdb=" O SER C 90 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N LEU C 92 " --> pdb=" O ASP C 63 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N ASP C 63 " --> pdb=" O LEU C 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 121 through 122 removed outlier: 4.114A pdb=" N ASP C 206 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS C 227 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL C 204 " --> pdb=" O LYS C 227 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 107 through 111 removed outlier: 5.688A pdb=" N GLN D 136 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N HIS D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA D 150 " --> pdb=" O TRP D 130 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N TRP D 130 " --> pdb=" O ALA D 150 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ALA D 152 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL D 128 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N GLU D 154 " --> pdb=" O LEU D 126 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 107 through 111 removed outlier: 5.688A pdb=" N GLN D 136 " --> pdb=" O ASN D 148 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN D 148 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N HIS D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN D 73 " --> pdb=" O SER D 82 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N MET D 84 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL D 71 " --> pdb=" O MET D 84 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N LEU D 86 " --> pdb=" O SER D 69 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER D 69 " --> pdb=" O LEU D 86 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ARG D 88 " --> pdb=" O PHE D 67 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N PHE D 67 " --> pdb=" O ARG D 88 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER D 90 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ARG D 65 " --> pdb=" O SER D 90 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N LEU D 92 " --> pdb=" O ASP D 63 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N ASP D 63 " --> pdb=" O LEU D 92 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 121 through 122 removed outlier: 4.115A pdb=" N ASP D 206 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS D 227 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL D 204 " --> pdb=" O LYS D 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 107 through 111 removed outlier: 5.687A pdb=" N GLN E 136 " --> pdb=" O ASN E 148 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN E 148 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N HIS E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N ALA E 150 " --> pdb=" O TRP E 130 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N TRP E 130 " --> pdb=" O ALA E 150 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA E 152 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N VAL E 128 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU E 154 " --> pdb=" O LEU E 126 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 107 through 111 removed outlier: 5.687A pdb=" N GLN E 136 " --> pdb=" O ASN E 148 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ASN E 148 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N HIS E 144 " --> pdb=" O ASP E 140 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASN E 73 " --> pdb=" O SER E 82 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N MET E 84 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL E 71 " --> pdb=" O MET E 84 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N LEU E 86 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N SER E 69 " --> pdb=" O LEU E 86 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N ARG E 88 " --> pdb=" O PHE E 67 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N PHE E 67 " --> pdb=" O ARG E 88 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER E 90 " --> pdb=" O ARG E 65 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ARG E 65 " --> pdb=" O SER E 90 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N LEU E 92 " --> pdb=" O ASP E 63 " (cutoff:3.500A) removed outlier: 9.645A pdb=" N ASP E 63 " --> pdb=" O LEU E 92 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 121 through 122 removed outlier: 4.114A pdb=" N ASP E 206 " --> pdb=" O ARG E 225 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LYS E 227 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N VAL E 204 " --> pdb=" O LYS E 227 " (cutoff:3.500A) 715 hydrogen bonds defined for protein. 2100 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 1.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2020 1.31 - 1.44: 3605 1.44 - 1.56: 7685 1.56 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 13385 Sorted by residual: bond pdb=" C7 NAG J 1 " pdb=" N2 NAG J 1 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.42e+01 bond pdb=" C7 NAG H 2 " pdb=" N2 NAG H 2 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C7 NAG H 1 " pdb=" N2 NAG H 1 " ideal model delta sigma weight residual 1.346 1.463 -0.117 2.00e-02 2.50e+03 3.40e+01 bond pdb=" C7 NAG J 2 " pdb=" N2 NAG J 2 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.39e+01 bond pdb=" C7 NAG F 2 " pdb=" N2 NAG F 2 " ideal model delta sigma weight residual 1.346 1.462 -0.116 2.00e-02 2.50e+03 3.39e+01 ... (remaining 13380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 17547 1.10 - 2.20: 461 2.20 - 3.30: 169 3.30 - 4.40: 81 4.40 - 5.50: 47 Bond angle restraints: 18305 Sorted by residual: angle pdb=" C4 NAG H 2 " pdb=" C5 NAG H 2 " pdb=" C6 NAG H 2 " ideal model delta sigma weight residual 113.89 108.79 5.10 3.00e+00 1.11e-01 2.89e+00 angle pdb=" C4 NAG G 2 " pdb=" C5 NAG G 2 " pdb=" C6 NAG G 2 " ideal model delta sigma weight residual 113.89 108.81 5.08 3.00e+00 1.11e-01 2.87e+00 angle pdb=" C4 NAG F 2 " pdb=" C5 NAG F 2 " pdb=" C6 NAG F 2 " ideal model delta sigma weight residual 113.89 108.81 5.08 3.00e+00 1.11e-01 2.87e+00 angle pdb=" C4 NAG I 2 " pdb=" C5 NAG I 2 " pdb=" C6 NAG I 2 " ideal model delta sigma weight residual 113.89 108.82 5.07 3.00e+00 1.11e-01 2.86e+00 angle pdb=" C4 NAG J 2 " pdb=" C5 NAG J 2 " pdb=" C6 NAG J 2 " ideal model delta sigma weight residual 113.89 108.84 5.05 3.00e+00 1.11e-01 2.84e+00 ... (remaining 18300 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7582 17.97 - 35.94: 523 35.94 - 53.91: 60 53.91 - 71.87: 5 71.87 - 89.84: 10 Dihedral angle restraints: 8180 sinusoidal: 3385 harmonic: 4795 Sorted by residual: dihedral pdb=" CA VAL B 71 " pdb=" C VAL B 71 " pdb=" N PHE B 72 " pdb=" CA PHE B 72 " ideal model delta harmonic sigma weight residual -180.00 -165.58 -14.42 0 5.00e+00 4.00e-02 8.31e+00 dihedral pdb=" CA VAL D 71 " pdb=" C VAL D 71 " pdb=" N PHE D 72 " pdb=" CA PHE D 72 " ideal model delta harmonic sigma weight residual -180.00 -165.60 -14.40 0 5.00e+00 4.00e-02 8.29e+00 dihedral pdb=" CA VAL A 71 " pdb=" C VAL A 71 " pdb=" N PHE A 72 " pdb=" CA PHE A 72 " ideal model delta harmonic sigma weight residual 180.00 -165.62 -14.38 0 5.00e+00 4.00e-02 8.27e+00 ... (remaining 8177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1462 0.031 - 0.063: 539 0.063 - 0.094: 129 0.094 - 0.126: 80 0.126 - 0.157: 25 Chirality restraints: 2235 Sorted by residual: chirality pdb=" CA PHE A 72 " pdb=" N PHE A 72 " pdb=" C PHE A 72 " pdb=" CB PHE A 72 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CA PHE E 72 " pdb=" N PHE E 72 " pdb=" C PHE E 72 " pdb=" CB PHE E 72 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.01e-01 chirality pdb=" CA PHE B 72 " pdb=" N PHE B 72 " pdb=" C PHE B 72 " pdb=" CB PHE B 72 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.96e-01 ... (remaining 2232 not shown) Planarity restraints: 2260 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 72 " -0.010 2.00e-02 2.50e+03 8.91e-03 1.39e+00 pdb=" CG PHE B 72 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE B 72 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE B 72 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 72 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 72 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE B 72 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 72 " 0.010 2.00e-02 2.50e+03 8.88e-03 1.38e+00 pdb=" CG PHE C 72 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE C 72 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 72 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 72 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE C 72 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 72 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 72 " 0.010 2.00e-02 2.50e+03 8.72e-03 1.33e+00 pdb=" CG PHE D 72 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 72 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE D 72 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE D 72 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 72 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE D 72 " 0.003 2.00e-02 2.50e+03 ... (remaining 2257 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2871 2.80 - 3.33: 11982 3.33 - 3.85: 22222 3.85 - 4.38: 25474 4.38 - 4.90: 44314 Nonbonded interactions: 106863 Sorted by model distance: nonbonded pdb=" OE2 GLU D 242 " pdb=" OH TYR D 296 " model vdw 2.281 3.040 nonbonded pdb=" OE2 GLU B 242 " pdb=" OH TYR B 296 " model vdw 2.281 3.040 nonbonded pdb=" OE2 GLU A 242 " pdb=" OH TYR A 296 " model vdw 2.281 3.040 nonbonded pdb=" OE2 GLU C 242 " pdb=" OH TYR C 296 " model vdw 2.281 3.040 nonbonded pdb=" NE1 TRP B 127 " pdb=" OE1 GLU B 154 " model vdw 2.282 3.120 ... (remaining 106858 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.60 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.020 Find NCS groups from input model: 0.150 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:9.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 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 : 0.007 0.117 13410 Z= 0.338 Angle : 0.580 5.495 18370 Z= 0.265 Chirality : 0.040 0.157 2235 Planarity : 0.003 0.029 2250 Dihedral : 12.018 89.842 5010 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.24 (0.21), residues: 1600 helix: 3.04 (0.20), residues: 530 sheet: 1.44 (0.25), residues: 495 loop : 0.04 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 200 TYR 0.009 0.001 TYR A 272 PHE 0.021 0.001 PHE C 72 TRP 0.009 0.001 TRP D 91 HIS 0.001 0.000 HIS B 276 Details of bonding type rmsd covalent geometry : bond 0.00674 (13385) covalent geometry : angle 0.57846 (18305) SS BOND : bond 0.00031 ( 10) SS BOND : angle 0.51145 ( 20) hydrogen bonds : bond 0.12231 ( 680) hydrogen bonds : angle 4.99996 ( 2100) link_BETA1-4 : bond 0.00300 ( 5) link_BETA1-4 : angle 0.98132 ( 15) link_NAG-ASN : bond 0.00184 ( 10) link_NAG-ASN : angle 1.11217 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 491 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 GLU cc_start: 0.8389 (mp0) cc_final: 0.8073 (mp0) REVERT: A 176 TYR cc_start: 0.8727 (m-80) cc_final: 0.8425 (m-80) REVERT: A 184 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7873 (mt-10) REVERT: A 206 ASP cc_start: 0.8188 (t0) cc_final: 0.7831 (t0) REVERT: A 208 LYS cc_start: 0.8308 (ptpt) cc_final: 0.8039 (mtmm) REVERT: A 259 ILE cc_start: 0.9299 (pt) cc_final: 0.9050 (pp) REVERT: A 272 TYR cc_start: 0.8625 (t80) cc_final: 0.8103 (t80) REVERT: A 283 LEU cc_start: 0.8421 (mt) cc_final: 0.7824 (mp) REVERT: A 297 PHE cc_start: 0.8570 (m-80) cc_final: 0.8119 (m-80) REVERT: A 364 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7639 (mt-10) REVERT: B 75 ASP cc_start: 0.7925 (t0) cc_final: 0.7032 (t0) REVERT: B 129 ASP cc_start: 0.8050 (t0) cc_final: 0.7833 (t0) REVERT: B 206 ASP cc_start: 0.8133 (t0) cc_final: 0.7629 (t0) REVERT: B 208 LYS cc_start: 0.8348 (ptpt) cc_final: 0.8081 (mtmm) REVERT: B 259 ILE cc_start: 0.9220 (pt) cc_final: 0.8798 (pp) REVERT: B 281 GLN cc_start: 0.8557 (mm110) cc_final: 0.8330 (pt0) REVERT: B 283 LEU cc_start: 0.8378 (mt) cc_final: 0.7797 (mp) REVERT: B 310 GLU cc_start: 0.8661 (tm-30) cc_final: 0.8341 (pp20) REVERT: B 361 SER cc_start: 0.8191 (m) cc_final: 0.7662 (p) REVERT: C 75 ASP cc_start: 0.8016 (t0) cc_final: 0.7071 (t0) REVERT: C 77 LEU cc_start: 0.9344 (mt) cc_final: 0.9127 (mm) REVERT: C 124 GLU cc_start: 0.8371 (mp0) cc_final: 0.7991 (mp0) REVERT: C 129 ASP cc_start: 0.8026 (t0) cc_final: 0.7814 (t0) REVERT: C 208 LYS cc_start: 0.8453 (ptpt) cc_final: 0.8157 (mtmm) REVERT: C 279 LEU cc_start: 0.8964 (tp) cc_final: 0.8611 (tp) REVERT: C 281 GLN cc_start: 0.8559 (mm110) cc_final: 0.8328 (tt0) REVERT: C 283 LEU cc_start: 0.8597 (mt) cc_final: 0.8058 (mp) REVERT: C 297 PHE cc_start: 0.8595 (m-80) cc_final: 0.8258 (m-10) REVERT: C 361 SER cc_start: 0.8129 (m) cc_final: 0.7926 (p) REVERT: D 75 ASP cc_start: 0.8025 (t0) cc_final: 0.7292 (t0) REVERT: D 77 LEU cc_start: 0.9336 (mt) cc_final: 0.9082 (mm) REVERT: D 124 GLU cc_start: 0.8357 (mp0) cc_final: 0.8040 (mp0) REVERT: D 206 ASP cc_start: 0.8104 (t0) cc_final: 0.7884 (t0) REVERT: D 259 ILE cc_start: 0.9437 (pt) cc_final: 0.9156 (pp) REVERT: D 272 TYR cc_start: 0.8495 (t80) cc_final: 0.7830 (t80) REVERT: D 279 LEU cc_start: 0.9006 (tp) cc_final: 0.8733 (tp) REVERT: D 283 LEU cc_start: 0.8620 (mt) cc_final: 0.8065 (mp) REVERT: D 297 PHE cc_start: 0.8572 (m-80) cc_final: 0.7881 (m-10) REVERT: E 75 ASP cc_start: 0.8068 (t0) cc_final: 0.7407 (t0) REVERT: E 77 LEU cc_start: 0.9319 (mt) cc_final: 0.9072 (mm) REVERT: E 206 ASP cc_start: 0.8133 (t0) cc_final: 0.7783 (t0) REVERT: E 208 LYS cc_start: 0.8310 (ptpt) cc_final: 0.7910 (mtmm) REVERT: E 227 LYS cc_start: 0.8278 (ptmt) cc_final: 0.8042 (ptmt) REVERT: E 272 TYR cc_start: 0.8636 (t80) cc_final: 0.8185 (t80) REVERT: E 283 LEU cc_start: 0.8482 (mt) cc_final: 0.7935 (mp) REVERT: E 297 PHE cc_start: 0.8564 (m-80) cc_final: 0.7960 (m-10) outliers start: 0 outliers final: 1 residues processed: 491 average time/residue: 0.5314 time to fit residues: 287.3541 Evaluate side-chains 351 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 350 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 142 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 221 GLN B 215 GLN B 221 GLN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 GLN ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 GLN ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.090914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.077730 restraints weight = 20608.735| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 2.47 r_work: 0.2794 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2671 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2671 r_free = 0.2671 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 13410 Z= 0.305 Angle : 0.619 8.447 18370 Z= 0.305 Chirality : 0.043 0.149 2235 Planarity : 0.005 0.042 2250 Dihedral : 5.819 57.005 2062 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 3.50 % Allowed : 12.80 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.21), residues: 1600 helix: 2.82 (0.19), residues: 530 sheet: 1.13 (0.24), residues: 470 loop : 0.01 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 78 TYR 0.021 0.002 TYR D 176 PHE 0.026 0.002 PHE A 72 TRP 0.009 0.001 TRP E 91 HIS 0.003 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00690 (13385) covalent geometry : angle 0.61316 (18305) SS BOND : bond 0.00750 ( 10) SS BOND : angle 1.42190 ( 20) hydrogen bonds : bond 0.04606 ( 680) hydrogen bonds : angle 4.36165 ( 2100) link_BETA1-4 : bond 0.00194 ( 5) link_BETA1-4 : angle 1.80737 ( 15) link_NAG-ASN : bond 0.00544 ( 10) link_NAG-ASN : angle 1.37300 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 367 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8525 (tp30) cc_final: 0.8116 (mm-30) REVERT: A 75 ASP cc_start: 0.8360 (t0) cc_final: 0.8031 (t0) REVERT: A 78 ARG cc_start: 0.8887 (mtp85) cc_final: 0.8619 (mtp85) REVERT: A 124 GLU cc_start: 0.8973 (mp0) cc_final: 0.8706 (mp0) REVERT: A 146 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8045 (mttp) REVERT: A 160 GLU cc_start: 0.8632 (tt0) cc_final: 0.7767 (tm-30) REVERT: A 176 TYR cc_start: 0.8990 (m-80) cc_final: 0.8473 (m-80) REVERT: A 201 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8469 (mp0) REVERT: A 206 ASP cc_start: 0.8513 (t0) cc_final: 0.8103 (t0) REVERT: A 208 LYS cc_start: 0.8596 (ptpt) cc_final: 0.8302 (mtmm) REVERT: A 221 GLN cc_start: 0.8937 (tt0) cc_final: 0.8725 (tt0) REVERT: A 272 TYR cc_start: 0.8966 (t80) cc_final: 0.8347 (t80) REVERT: A 281 GLN cc_start: 0.8817 (mm110) cc_final: 0.8377 (pt0) REVERT: A 283 LEU cc_start: 0.8716 (mt) cc_final: 0.8317 (mp) REVERT: A 297 PHE cc_start: 0.8929 (m-80) cc_final: 0.8566 (m-10) REVERT: A 364 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8099 (mt-10) REVERT: A 382 GLN cc_start: 0.8749 (tp40) cc_final: 0.8438 (mm110) REVERT: B 54 ASN cc_start: 0.9041 (OUTLIER) cc_final: 0.8578 (m-40) REVERT: B 75 ASP cc_start: 0.8248 (t0) cc_final: 0.7753 (t0) REVERT: B 129 ASP cc_start: 0.8701 (t0) cc_final: 0.8275 (t0) REVERT: B 146 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8042 (mttp) REVERT: B 154 GLU cc_start: 0.8905 (tt0) cc_final: 0.8652 (tt0) REVERT: B 199 LYS cc_start: 0.8377 (ptpt) cc_final: 0.7998 (ptmm) REVERT: B 206 ASP cc_start: 0.8392 (t0) cc_final: 0.7862 (t0) REVERT: B 208 LYS cc_start: 0.8651 (ptpt) cc_final: 0.8315 (mtmm) REVERT: B 281 GLN cc_start: 0.8787 (mm110) cc_final: 0.8382 (pt0) REVERT: B 283 LEU cc_start: 0.8582 (mt) cc_final: 0.8270 (mp) REVERT: B 310 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8718 (pp20) REVERT: C 48 GLU cc_start: 0.8502 (tp30) cc_final: 0.8255 (mm-30) REVERT: C 75 ASP cc_start: 0.8211 (t0) cc_final: 0.7780 (t0) REVERT: C 78 ARG cc_start: 0.8865 (mtp85) cc_final: 0.8612 (mtm110) REVERT: C 124 GLU cc_start: 0.9055 (mp0) cc_final: 0.8728 (mp0) REVERT: C 129 ASP cc_start: 0.8767 (t0) cc_final: 0.8366 (t0) REVERT: C 146 LYS cc_start: 0.8652 (mtpt) cc_final: 0.8013 (mtmp) REVERT: C 160 GLU cc_start: 0.8649 (tt0) cc_final: 0.8129 (tp30) REVERT: C 201 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8500 (mp0) REVERT: C 208 LYS cc_start: 0.8675 (ptpt) cc_final: 0.8407 (mtmm) REVERT: C 233 SER cc_start: 0.8838 (m) cc_final: 0.8611 (p) REVERT: C 281 GLN cc_start: 0.8846 (mm110) cc_final: 0.8311 (pt0) REVERT: C 283 LEU cc_start: 0.8777 (mt) cc_final: 0.8420 (mp) REVERT: C 402 GLU cc_start: 0.8702 (mm-30) cc_final: 0.8442 (mt-10) REVERT: D 75 ASP cc_start: 0.8423 (t0) cc_final: 0.7857 (t0) REVERT: D 77 LEU cc_start: 0.9331 (mt) cc_final: 0.9098 (mm) REVERT: D 124 GLU cc_start: 0.8923 (mp0) cc_final: 0.8518 (mp0) REVERT: D 201 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8470 (mp0) REVERT: D 206 ASP cc_start: 0.8509 (t0) cc_final: 0.8100 (t0) REVERT: D 208 LYS cc_start: 0.8687 (mtmm) cc_final: 0.8388 (mtmm) REVERT: D 214 GLN cc_start: 0.8255 (mm-40) cc_final: 0.8051 (mm-40) REVERT: D 272 TYR cc_start: 0.8941 (t80) cc_final: 0.8106 (t80) REVERT: D 281 GLN cc_start: 0.8804 (mm110) cc_final: 0.8502 (mm-40) REVERT: D 283 LEU cc_start: 0.8791 (mt) cc_final: 0.8453 (mp) REVERT: D 402 GLU cc_start: 0.8535 (mm-30) cc_final: 0.8273 (mt-10) REVERT: E 48 GLU cc_start: 0.8394 (tp30) cc_final: 0.8157 (mm-30) REVERT: E 75 ASP cc_start: 0.8335 (t0) cc_final: 0.7817 (t0) REVERT: E 77 LEU cc_start: 0.9282 (mt) cc_final: 0.9013 (mm) REVERT: E 124 GLU cc_start: 0.8982 (mp0) cc_final: 0.8612 (mp0) REVERT: E 146 LYS cc_start: 0.8716 (mtpt) cc_final: 0.8056 (mttp) REVERT: E 160 GLU cc_start: 0.8772 (tt0) cc_final: 0.7876 (tm-30) REVERT: E 201 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8421 (mp0) REVERT: E 206 ASP cc_start: 0.8532 (t0) cc_final: 0.8149 (t0) REVERT: E 208 LYS cc_start: 0.8611 (ptpt) cc_final: 0.8219 (mtmm) REVERT: E 233 SER cc_start: 0.8691 (m) cc_final: 0.8485 (p) REVERT: E 283 LEU cc_start: 0.8723 (mt) cc_final: 0.8376 (mp) outliers start: 50 outliers final: 23 residues processed: 391 average time/residue: 0.5847 time to fit residues: 249.5544 Evaluate side-chains 378 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 352 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 146 LYS Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 233 SER Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 183 MET Chi-restraints excluded: chain E residue 113 GLU Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 183 MET Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 376 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 12 optimal weight: 2.9990 chunk 139 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 72 optimal weight: 0.0970 chunk 145 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN ** C 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 GLN ** D 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.092387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.079360 restraints weight = 20635.216| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 2.44 r_work: 0.2818 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2682 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2682 r_free = 0.2682 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2682 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13410 Z= 0.129 Angle : 0.514 8.425 18370 Z= 0.251 Chirality : 0.039 0.208 2235 Planarity : 0.004 0.032 2250 Dihedral : 5.651 58.142 2062 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 3.50 % Allowed : 15.94 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.21), residues: 1600 helix: 2.98 (0.20), residues: 530 sheet: 0.64 (0.23), residues: 525 loop : 0.37 (0.28), residues: 545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 78 TYR 0.017 0.002 TYR D 176 PHE 0.018 0.002 PHE B 72 TRP 0.007 0.001 TRP C 112 HIS 0.001 0.000 HIS A 406 Details of bonding type rmsd covalent geometry : bond 0.00277 (13385) covalent geometry : angle 0.51017 (18305) SS BOND : bond 0.00375 ( 10) SS BOND : angle 0.92292 ( 20) hydrogen bonds : bond 0.04110 ( 680) hydrogen bonds : angle 4.18428 ( 2100) link_BETA1-4 : bond 0.00335 ( 5) link_BETA1-4 : angle 1.25892 ( 15) link_NAG-ASN : bond 0.00095 ( 10) link_NAG-ASN : angle 1.19867 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 361 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8582 (tp30) cc_final: 0.8137 (mm-30) REVERT: A 75 ASP cc_start: 0.8422 (t0) cc_final: 0.8090 (t0) REVERT: A 78 ARG cc_start: 0.8869 (mtp85) cc_final: 0.8652 (mtp85) REVERT: A 113 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8529 (mm-30) REVERT: A 141 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8145 (pm20) REVERT: A 160 GLU cc_start: 0.8533 (tt0) cc_final: 0.7796 (pp20) REVERT: A 201 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8471 (mp0) REVERT: A 206 ASP cc_start: 0.8531 (t0) cc_final: 0.8156 (t0) REVERT: A 208 LYS cc_start: 0.8600 (ptpt) cc_final: 0.8305 (mtmm) REVERT: A 272 TYR cc_start: 0.8951 (t80) cc_final: 0.8341 (t80) REVERT: A 281 GLN cc_start: 0.8700 (mm110) cc_final: 0.8330 (pt0) REVERT: A 283 LEU cc_start: 0.8639 (mt) cc_final: 0.8210 (mp) REVERT: A 297 PHE cc_start: 0.8893 (m-80) cc_final: 0.8501 (m-10) REVERT: A 364 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8108 (mt-10) REVERT: B 48 GLU cc_start: 0.8656 (tp30) cc_final: 0.8273 (mm-30) REVERT: B 75 ASP cc_start: 0.8275 (t0) cc_final: 0.7812 (t0) REVERT: B 129 ASP cc_start: 0.8790 (t0) cc_final: 0.8368 (t0) REVERT: B 146 LYS cc_start: 0.8801 (mtmt) cc_final: 0.8088 (mttp) REVERT: B 160 GLU cc_start: 0.8580 (tt0) cc_final: 0.7958 (tm-30) REVERT: B 199 LYS cc_start: 0.8221 (ptpt) cc_final: 0.7863 (ptmm) REVERT: B 201 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8375 (mp0) REVERT: B 206 ASP cc_start: 0.8396 (t0) cc_final: 0.7909 (t0) REVERT: B 208 LYS cc_start: 0.8630 (ptpt) cc_final: 0.8287 (mtmm) REVERT: B 281 GLN cc_start: 0.8746 (mm110) cc_final: 0.8328 (pt0) REVERT: B 283 LEU cc_start: 0.8537 (mt) cc_final: 0.8218 (mp) REVERT: B 310 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8725 (pp20) REVERT: B 364 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8222 (mp0) REVERT: C 75 ASP cc_start: 0.8195 (t0) cc_final: 0.7887 (t0) REVERT: C 77 LEU cc_start: 0.9417 (mt) cc_final: 0.9166 (mm) REVERT: C 129 ASP cc_start: 0.8805 (t0) cc_final: 0.8395 (t0) REVERT: C 146 LYS cc_start: 0.8687 (mtpt) cc_final: 0.8083 (mtmp) REVERT: C 160 GLU cc_start: 0.8575 (tt0) cc_final: 0.8118 (mm-30) REVERT: C 201 GLU cc_start: 0.8779 (mt-10) cc_final: 0.8511 (mp0) REVERT: C 208 LYS cc_start: 0.8689 (ptpt) cc_final: 0.8408 (mtmm) REVERT: C 233 SER cc_start: 0.8865 (m) cc_final: 0.8599 (p) REVERT: C 281 GLN cc_start: 0.8811 (mm110) cc_final: 0.8300 (pt0) REVERT: C 283 LEU cc_start: 0.8714 (mt) cc_final: 0.8350 (mp) REVERT: C 402 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8452 (mt-10) REVERT: D 48 GLU cc_start: 0.8543 (tp30) cc_final: 0.8242 (mm-30) REVERT: D 75 ASP cc_start: 0.8441 (t0) cc_final: 0.7892 (t0) REVERT: D 160 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8311 (tp30) REVERT: D 201 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8440 (mp0) REVERT: D 206 ASP cc_start: 0.8472 (t0) cc_final: 0.8141 (t0) REVERT: D 208 LYS cc_start: 0.8721 (mtmm) cc_final: 0.8457 (mtmm) REVERT: D 272 TYR cc_start: 0.8916 (t80) cc_final: 0.8073 (t80) REVERT: D 281 GLN cc_start: 0.8707 (mm110) cc_final: 0.8292 (pt0) REVERT: D 283 LEU cc_start: 0.8708 (mt) cc_final: 0.8413 (mp) REVERT: D 402 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8329 (mt-10) REVERT: E 75 ASP cc_start: 0.8330 (t0) cc_final: 0.7946 (t0) REVERT: E 77 LEU cc_start: 0.9330 (mt) cc_final: 0.9087 (mm) REVERT: E 146 LYS cc_start: 0.8742 (mtpt) cc_final: 0.8067 (mtmp) REVERT: E 160 GLU cc_start: 0.8795 (tt0) cc_final: 0.8423 (mm-30) REVERT: E 198 VAL cc_start: 0.9333 (OUTLIER) cc_final: 0.9034 (m) REVERT: E 201 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8407 (mp0) REVERT: E 206 ASP cc_start: 0.8428 (t0) cc_final: 0.8094 (t0) REVERT: E 208 LYS cc_start: 0.8622 (ptpt) cc_final: 0.8209 (mtmm) REVERT: E 227 LYS cc_start: 0.8787 (ptmt) cc_final: 0.8446 (ptpp) REVERT: E 233 SER cc_start: 0.8756 (m) cc_final: 0.8534 (p) REVERT: E 272 TYR cc_start: 0.8979 (t80) cc_final: 0.8314 (t80) REVERT: E 283 LEU cc_start: 0.8607 (mt) cc_final: 0.8197 (mp) outliers start: 50 outliers final: 24 residues processed: 385 average time/residue: 0.5497 time to fit residues: 232.5113 Evaluate side-chains 368 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 341 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 141 GLN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 141 GLN Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 277 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 27 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 19 optimal weight: 0.0270 chunk 31 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 221 GLN C 156 ASN C 221 GLN C 382 GLN D 156 ASN D 221 GLN E 156 ASN E 382 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.088578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.075331 restraints weight = 20830.908| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 2.50 r_work: 0.2772 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 13410 Z= 0.276 Angle : 0.584 8.731 18370 Z= 0.286 Chirality : 0.042 0.150 2235 Planarity : 0.004 0.036 2250 Dihedral : 5.426 54.536 2060 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.57 % Allowed : 17.55 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.20), residues: 1600 helix: 2.64 (0.20), residues: 530 sheet: 0.91 (0.24), residues: 430 loop : -0.21 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 257 TYR 0.016 0.002 TYR D 374 PHE 0.025 0.002 PHE A 72 TRP 0.010 0.001 TRP D 112 HIS 0.003 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00622 (13385) covalent geometry : angle 0.57895 (18305) SS BOND : bond 0.00470 ( 10) SS BOND : angle 1.29659 ( 20) hydrogen bonds : bond 0.04327 ( 680) hydrogen bonds : angle 4.33811 ( 2100) link_BETA1-4 : bond 0.00135 ( 5) link_BETA1-4 : angle 1.33773 ( 15) link_NAG-ASN : bond 0.00430 ( 10) link_NAG-ASN : angle 1.49318 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 340 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8551 (tp30) cc_final: 0.8146 (mm-30) REVERT: A 75 ASP cc_start: 0.8395 (t0) cc_final: 0.7990 (t0) REVERT: A 78 ARG cc_start: 0.8865 (mtp85) cc_final: 0.8631 (mtp85) REVERT: A 124 GLU cc_start: 0.8987 (mp0) cc_final: 0.8771 (mp0) REVERT: A 132 ASP cc_start: 0.8385 (m-30) cc_final: 0.8138 (t0) REVERT: A 184 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8455 (mt-10) REVERT: A 206 ASP cc_start: 0.8527 (t0) cc_final: 0.8120 (t0) REVERT: A 208 LYS cc_start: 0.8573 (ptpt) cc_final: 0.8261 (mtmm) REVERT: A 232 LYS cc_start: 0.8738 (ttmt) cc_final: 0.8409 (ttmm) REVERT: A 257 ARG cc_start: 0.8692 (ptp-110) cc_final: 0.8481 (ptp-110) REVERT: A 272 TYR cc_start: 0.8976 (t80) cc_final: 0.8348 (t80) REVERT: A 281 GLN cc_start: 0.8863 (mm110) cc_final: 0.8405 (pt0) REVERT: A 283 LEU cc_start: 0.8731 (mt) cc_final: 0.8383 (mp) REVERT: A 297 PHE cc_start: 0.8922 (m-80) cc_final: 0.8565 (m-10) REVERT: A 364 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8038 (mt-10) REVERT: B 75 ASP cc_start: 0.8252 (t0) cc_final: 0.7715 (t0) REVERT: B 129 ASP cc_start: 0.8780 (t0) cc_final: 0.8291 (t0) REVERT: B 146 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8021 (mttp) REVERT: B 201 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8374 (mp0) REVERT: B 206 ASP cc_start: 0.8445 (t0) cc_final: 0.7934 (t0) REVERT: B 208 LYS cc_start: 0.8604 (ptpt) cc_final: 0.8250 (mtmm) REVERT: B 279 LEU cc_start: 0.9023 (tp) cc_final: 0.8709 (tt) REVERT: B 281 GLN cc_start: 0.8811 (mm110) cc_final: 0.8396 (pt0) REVERT: B 283 LEU cc_start: 0.8674 (mt) cc_final: 0.8345 (mp) REVERT: C 75 ASP cc_start: 0.8283 (t0) cc_final: 0.7660 (t0) REVERT: C 77 LEU cc_start: 0.9425 (mt) cc_final: 0.9152 (mm) REVERT: C 78 ARG cc_start: 0.8856 (mtp85) cc_final: 0.8483 (mtm110) REVERT: C 129 ASP cc_start: 0.8771 (t0) cc_final: 0.8305 (t0) REVERT: C 146 LYS cc_start: 0.8663 (mtpt) cc_final: 0.8033 (mtmp) REVERT: C 160 GLU cc_start: 0.8641 (tt0) cc_final: 0.8206 (mm-30) REVERT: C 201 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8505 (mp0) REVERT: C 233 SER cc_start: 0.8820 (m) cc_final: 0.8599 (p) REVERT: C 281 GLN cc_start: 0.8857 (mm110) cc_final: 0.8354 (pt0) REVERT: C 283 LEU cc_start: 0.8799 (mt) cc_final: 0.8390 (mp) REVERT: C 402 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8397 (mt-10) REVERT: D 48 GLU cc_start: 0.8488 (tp30) cc_final: 0.8183 (mm-30) REVERT: D 75 ASP cc_start: 0.8380 (t0) cc_final: 0.7777 (t0) REVERT: D 124 GLU cc_start: 0.8985 (mp0) cc_final: 0.8641 (mp0) REVERT: D 146 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.7980 (mttp) REVERT: D 160 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8313 (tp30) REVERT: D 199 LYS cc_start: 0.8536 (ptpt) cc_final: 0.8180 (ptmm) REVERT: D 201 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8455 (mp0) REVERT: D 206 ASP cc_start: 0.8505 (t0) cc_final: 0.8066 (t0) REVERT: D 208 LYS cc_start: 0.8703 (mtmm) cc_final: 0.8439 (mtmm) REVERT: D 281 GLN cc_start: 0.8787 (mm110) cc_final: 0.8493 (mm-40) REVERT: D 283 LEU cc_start: 0.8770 (mt) cc_final: 0.8322 (mp) REVERT: D 402 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8225 (mt-10) REVERT: E 48 GLU cc_start: 0.8417 (tp30) cc_final: 0.8159 (mm-30) REVERT: E 75 ASP cc_start: 0.8309 (t0) cc_final: 0.7844 (t0) REVERT: E 78 ARG cc_start: 0.8777 (mtp85) cc_final: 0.8490 (mtm110) REVERT: E 124 GLU cc_start: 0.8963 (mp0) cc_final: 0.8647 (mp0) REVERT: E 146 LYS cc_start: 0.8684 (mtpt) cc_final: 0.8009 (mtmp) REVERT: E 160 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: E 201 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8435 (mp0) REVERT: E 206 ASP cc_start: 0.8490 (t0) cc_final: 0.8126 (t0) REVERT: E 208 LYS cc_start: 0.8608 (ptpt) cc_final: 0.8260 (mtmm) REVERT: E 233 SER cc_start: 0.8702 (m) cc_final: 0.8468 (p) REVERT: E 283 LEU cc_start: 0.8726 (mt) cc_final: 0.8504 (mt) outliers start: 51 outliers final: 22 residues processed: 372 average time/residue: 0.5057 time to fit residues: 205.8848 Evaluate side-chains 350 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 324 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 372 LEU Chi-restraints excluded: chain E residue 376 VAL Chi-restraints excluded: chain E residue 379 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 148 optimal weight: 0.0970 chunk 81 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 140 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 51 optimal weight: 0.0970 chunk 125 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN C 156 ASN C 221 GLN E 156 ASN E 382 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.091386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.078191 restraints weight = 20771.383| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.51 r_work: 0.2798 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13410 Z= 0.111 Angle : 0.513 8.892 18370 Z= 0.249 Chirality : 0.039 0.165 2235 Planarity : 0.004 0.034 2250 Dihedral : 5.193 54.377 2060 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 3.92 % Allowed : 18.32 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.21), residues: 1600 helix: 2.87 (0.20), residues: 530 sheet: 0.60 (0.24), residues: 475 loop : 0.15 (0.27), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 78 TYR 0.016 0.002 TYR E 374 PHE 0.018 0.002 PHE B 297 TRP 0.008 0.001 TRP C 112 HIS 0.001 0.000 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00237 (13385) covalent geometry : angle 0.50956 (18305) SS BOND : bond 0.00370 ( 10) SS BOND : angle 0.90342 ( 20) hydrogen bonds : bond 0.03910 ( 680) hydrogen bonds : angle 4.14364 ( 2100) link_BETA1-4 : bond 0.00335 ( 5) link_BETA1-4 : angle 1.22548 ( 15) link_NAG-ASN : bond 0.00193 ( 10) link_NAG-ASN : angle 1.09344 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 345 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8558 (tp30) cc_final: 0.8117 (mm-30) REVERT: A 75 ASP cc_start: 0.8364 (t0) cc_final: 0.7981 (t0) REVERT: A 124 GLU cc_start: 0.8953 (mp0) cc_final: 0.8629 (mp0) REVERT: A 132 ASP cc_start: 0.8352 (m-30) cc_final: 0.8072 (t0) REVERT: A 153 THR cc_start: 0.9292 (p) cc_final: 0.9013 (t) REVERT: A 206 ASP cc_start: 0.8502 (t0) cc_final: 0.8140 (t0) REVERT: A 208 LYS cc_start: 0.8554 (ptpt) cc_final: 0.8224 (mtmm) REVERT: A 232 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8364 (ttmm) REVERT: A 257 ARG cc_start: 0.8725 (ptp-110) cc_final: 0.8524 (ptp-110) REVERT: A 272 TYR cc_start: 0.8887 (t80) cc_final: 0.8201 (t80) REVERT: A 281 GLN cc_start: 0.8766 (mm110) cc_final: 0.8329 (pt0) REVERT: A 283 LEU cc_start: 0.8661 (mt) cc_final: 0.8231 (mp) REVERT: A 297 PHE cc_start: 0.8837 (m-80) cc_final: 0.8426 (m-10) REVERT: A 364 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7984 (mt-10) REVERT: B 75 ASP cc_start: 0.8189 (t0) cc_final: 0.7672 (t0) REVERT: B 77 LEU cc_start: 0.9328 (mt) cc_final: 0.9096 (mm) REVERT: B 129 ASP cc_start: 0.8788 (t0) cc_final: 0.8253 (t0) REVERT: B 146 LYS cc_start: 0.8748 (mtmt) cc_final: 0.8037 (mttp) REVERT: B 160 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8308 (mm-30) REVERT: B 201 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8268 (mp0) REVERT: B 206 ASP cc_start: 0.8378 (t0) cc_final: 0.7873 (t0) REVERT: B 208 LYS cc_start: 0.8564 (ptpt) cc_final: 0.8206 (mtmm) REVERT: B 232 LYS cc_start: 0.8637 (ttmt) cc_final: 0.8303 (ttmm) REVERT: B 279 LEU cc_start: 0.9030 (tp) cc_final: 0.8803 (tt) REVERT: B 281 GLN cc_start: 0.8747 (mm110) cc_final: 0.8372 (pt0) REVERT: B 283 LEU cc_start: 0.8626 (mt) cc_final: 0.8212 (mp) REVERT: C 75 ASP cc_start: 0.8237 (t0) cc_final: 0.7666 (t0) REVERT: C 77 LEU cc_start: 0.9400 (mt) cc_final: 0.9185 (mm) REVERT: C 78 ARG cc_start: 0.8796 (mtp85) cc_final: 0.8545 (mtm110) REVERT: C 129 ASP cc_start: 0.8780 (t0) cc_final: 0.8251 (t0) REVERT: C 146 LYS cc_start: 0.8662 (mtpt) cc_final: 0.8044 (mtmp) REVERT: C 160 GLU cc_start: 0.8602 (tt0) cc_final: 0.8120 (mm-30) REVERT: C 201 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8370 (mp0) REVERT: C 208 LYS cc_start: 0.8596 (mtmm) cc_final: 0.8294 (mtmm) REVERT: C 232 LYS cc_start: 0.8657 (ttmt) cc_final: 0.8415 (ttmt) REVERT: C 233 SER cc_start: 0.8802 (m) cc_final: 0.8515 (p) REVERT: C 238 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8357 (mm) REVERT: C 281 GLN cc_start: 0.8794 (mm110) cc_final: 0.8253 (pt0) REVERT: C 283 LEU cc_start: 0.8704 (mt) cc_final: 0.8310 (mp) REVERT: C 402 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8394 (mt-10) REVERT: D 48 GLU cc_start: 0.8495 (tp30) cc_final: 0.8176 (mm-30) REVERT: D 75 ASP cc_start: 0.8311 (t0) cc_final: 0.7724 (t0) REVERT: D 124 GLU cc_start: 0.8940 (mp0) cc_final: 0.8517 (mp0) REVERT: D 141 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8135 (pm20) REVERT: D 154 GLU cc_start: 0.8992 (tt0) cc_final: 0.8780 (tt0) REVERT: D 160 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.7801 (pp20) REVERT: D 184 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8148 (pt0) REVERT: D 199 LYS cc_start: 0.8382 (ptpt) cc_final: 0.8104 (ptmm) REVERT: D 201 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8431 (mp0) REVERT: D 206 ASP cc_start: 0.8511 (t0) cc_final: 0.8122 (t0) REVERT: D 208 LYS cc_start: 0.8689 (mtmm) cc_final: 0.8457 (mtmm) REVERT: D 281 GLN cc_start: 0.8750 (mm110) cc_final: 0.8301 (pt0) REVERT: D 283 LEU cc_start: 0.8712 (mt) cc_final: 0.8175 (mp) REVERT: D 402 GLU cc_start: 0.8498 (mm-30) cc_final: 0.8225 (mt-10) REVERT: E 75 ASP cc_start: 0.8293 (t0) cc_final: 0.7826 (t0) REVERT: E 78 ARG cc_start: 0.8705 (mtp85) cc_final: 0.8468 (mtm110) REVERT: E 146 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8015 (mttp) REVERT: E 160 GLU cc_start: 0.8782 (tt0) cc_final: 0.8401 (mm-30) REVERT: E 201 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8302 (mp0) REVERT: E 206 ASP cc_start: 0.8442 (t0) cc_final: 0.8141 (t0) REVERT: E 232 LYS cc_start: 0.8773 (ttmt) cc_final: 0.8398 (ttmm) REVERT: E 233 SER cc_start: 0.8697 (m) cc_final: 0.8430 (p) REVERT: E 283 LEU cc_start: 0.8581 (mt) cc_final: 0.8156 (mp) outliers start: 56 outliers final: 23 residues processed: 374 average time/residue: 0.5160 time to fit residues: 211.8701 Evaluate side-chains 361 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 335 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 238 LEU Chi-restraints excluded: chain C residue 304 LEU Chi-restraints excluded: chain D residue 141 GLN Chi-restraints excluded: chain D residue 142 ASP Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain D residue 253 LEU Chi-restraints excluded: chain E residue 142 ASP Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 277 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 110 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN B 382 GLN C 156 ASN D 221 GLN E 156 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.088153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.074918 restraints weight = 20724.708| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.47 r_work: 0.2737 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2628 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2628 r_free = 0.2628 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2628 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 13410 Z= 0.285 Angle : 0.591 9.158 18370 Z= 0.290 Chirality : 0.042 0.161 2235 Planarity : 0.004 0.033 2250 Dihedral : 5.079 49.363 2060 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 3.08 % Allowed : 19.65 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.21), residues: 1600 helix: 2.67 (0.20), residues: 525 sheet: 0.46 (0.23), residues: 475 loop : 0.00 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 257 TYR 0.018 0.002 TYR E 374 PHE 0.026 0.002 PHE A 385 TRP 0.018 0.001 TRP C 112 HIS 0.003 0.001 HIS E 103 Details of bonding type rmsd covalent geometry : bond 0.00640 (13385) covalent geometry : angle 0.58594 (18305) SS BOND : bond 0.00670 ( 10) SS BOND : angle 1.45863 ( 20) hydrogen bonds : bond 0.04255 ( 680) hydrogen bonds : angle 4.31945 ( 2100) link_BETA1-4 : bond 0.00037 ( 5) link_BETA1-4 : angle 1.27308 ( 15) link_NAG-ASN : bond 0.00420 ( 10) link_NAG-ASN : angle 1.48645 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 345 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8550 (tp30) cc_final: 0.8142 (mm-30) REVERT: A 75 ASP cc_start: 0.8379 (t0) cc_final: 0.7969 (t0) REVERT: A 124 GLU cc_start: 0.8949 (mp0) cc_final: 0.8692 (mp0) REVERT: A 132 ASP cc_start: 0.8389 (m-30) cc_final: 0.8117 (t0) REVERT: A 146 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8062 (mttp) REVERT: A 206 ASP cc_start: 0.8529 (t0) cc_final: 0.8160 (t0) REVERT: A 272 TYR cc_start: 0.8960 (t80) cc_final: 0.8321 (t80) REVERT: A 281 GLN cc_start: 0.8894 (mm110) cc_final: 0.8383 (pt0) REVERT: A 283 LEU cc_start: 0.8635 (mt) cc_final: 0.8284 (mp) REVERT: A 297 PHE cc_start: 0.8860 (m-80) cc_final: 0.8475 (m-10) REVERT: A 364 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8069 (mt-10) REVERT: B 48 GLU cc_start: 0.8636 (tp30) cc_final: 0.8155 (mm-30) REVERT: B 75 ASP cc_start: 0.8242 (t0) cc_final: 0.7693 (t0) REVERT: B 129 ASP cc_start: 0.8794 (t0) cc_final: 0.8266 (t0) REVERT: B 146 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8072 (mttp) REVERT: B 201 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8374 (mp0) REVERT: B 206 ASP cc_start: 0.8406 (t0) cc_final: 0.8035 (t0) REVERT: B 279 LEU cc_start: 0.9035 (tp) cc_final: 0.8739 (tt) REVERT: B 281 GLN cc_start: 0.8759 (mm110) cc_final: 0.8338 (pt0) REVERT: B 283 LEU cc_start: 0.8623 (mt) cc_final: 0.8278 (mp) REVERT: C 75 ASP cc_start: 0.8308 (t0) cc_final: 0.7650 (t0) REVERT: C 77 LEU cc_start: 0.9435 (mt) cc_final: 0.9167 (mm) REVERT: C 78 ARG cc_start: 0.8873 (mtp85) cc_final: 0.8537 (mtm110) REVERT: C 129 ASP cc_start: 0.8804 (t0) cc_final: 0.8245 (t0) REVERT: C 146 LYS cc_start: 0.8679 (mtpt) cc_final: 0.8077 (mtmp) REVERT: C 160 GLU cc_start: 0.8655 (tt0) cc_final: 0.8187 (mm-30) REVERT: C 201 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8519 (mp0) REVERT: C 233 SER cc_start: 0.8803 (m) cc_final: 0.8591 (p) REVERT: C 281 GLN cc_start: 0.8816 (mm110) cc_final: 0.8311 (pt0) REVERT: C 283 LEU cc_start: 0.8644 (mt) cc_final: 0.8305 (mp) REVERT: C 402 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8412 (mt-10) REVERT: D 48 GLU cc_start: 0.8487 (tp30) cc_final: 0.8193 (mm-30) REVERT: D 75 ASP cc_start: 0.8369 (t0) cc_final: 0.7731 (t0) REVERT: D 146 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.7972 (mttp) REVERT: D 154 GLU cc_start: 0.9080 (tt0) cc_final: 0.8813 (tt0) REVERT: D 160 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.8345 (tp30) REVERT: D 199 LYS cc_start: 0.8534 (ptpt) cc_final: 0.8172 (ptmm) REVERT: D 201 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8456 (mp0) REVERT: D 206 ASP cc_start: 0.8526 (t0) cc_final: 0.8095 (t0) REVERT: D 208 LYS cc_start: 0.8705 (mtmm) cc_final: 0.8440 (mtmm) REVERT: D 281 GLN cc_start: 0.8798 (mm110) cc_final: 0.8493 (mm-40) REVERT: D 283 LEU cc_start: 0.8746 (mt) cc_final: 0.8344 (mp) REVERT: D 402 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8237 (mt-10) REVERT: E 48 GLU cc_start: 0.8448 (tp30) cc_final: 0.8175 (mm-30) REVERT: E 75 ASP cc_start: 0.8325 (t0) cc_final: 0.7790 (t0) REVERT: E 78 ARG cc_start: 0.8782 (mtp85) cc_final: 0.8528 (mtm110) REVERT: E 124 GLU cc_start: 0.9014 (mp0) cc_final: 0.8548 (mp0) REVERT: E 132 ASP cc_start: 0.7954 (t0) cc_final: 0.7658 (t0) REVERT: E 146 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8017 (mtmp) REVERT: E 156 ASN cc_start: 0.9352 (OUTLIER) cc_final: 0.9115 (t0) REVERT: E 160 GLU cc_start: 0.8823 (OUTLIER) cc_final: 0.7982 (tm-30) REVERT: E 201 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8447 (mp0) REVERT: E 206 ASP cc_start: 0.8455 (t0) cc_final: 0.8096 (t0) REVERT: E 208 LYS cc_start: 0.8630 (ptpp) cc_final: 0.7863 (pttp) REVERT: E 233 SER cc_start: 0.8680 (m) cc_final: 0.8474 (p) REVERT: E 283 LEU cc_start: 0.8694 (mt) cc_final: 0.8423 (mp) REVERT: E 364 GLU cc_start: 0.8297 (mp0) cc_final: 0.8037 (mt-10) outliers start: 44 outliers final: 17 residues processed: 371 average time/residue: 0.6039 time to fit residues: 244.1342 Evaluate side-chains 349 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 327 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 146 LYS Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 156 ASN Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 198 VAL Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 277 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 112 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 18 optimal weight: 6.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN C 156 ASN E 156 ASN E 382 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.088961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.075815 restraints weight = 20788.069| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 2.46 r_work: 0.2757 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13410 Z= 0.196 Angle : 0.565 9.353 18370 Z= 0.278 Chirality : 0.041 0.201 2235 Planarity : 0.004 0.034 2250 Dihedral : 4.942 46.555 2060 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 3.15 % Allowed : 20.77 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.21), residues: 1600 helix: 2.61 (0.20), residues: 530 sheet: 0.39 (0.23), residues: 475 loop : 0.08 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 257 TYR 0.024 0.002 TYR D 176 PHE 0.026 0.002 PHE C 297 TRP 0.016 0.001 TRP C 112 HIS 0.002 0.000 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00437 (13385) covalent geometry : angle 0.56074 (18305) SS BOND : bond 0.00431 ( 10) SS BOND : angle 1.39158 ( 20) hydrogen bonds : bond 0.04129 ( 680) hydrogen bonds : angle 4.31741 ( 2100) link_BETA1-4 : bond 0.00153 ( 5) link_BETA1-4 : angle 1.20043 ( 15) link_NAG-ASN : bond 0.00151 ( 10) link_NAG-ASN : angle 1.29045 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 347 time to evaluate : 0.614 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: A 48 GLU cc_start: 0.8567 (tp30) cc_final: 0.8163 (mm-30) REVERT: A 75 ASP cc_start: 0.8345 (t0) cc_final: 0.7939 (t0) REVERT: A 81 MET cc_start: 0.9051 (ttp) cc_final: 0.8765 (ptt) REVERT: A 124 GLU cc_start: 0.8887 (mp0) cc_final: 0.8630 (mp0) REVERT: A 132 ASP cc_start: 0.8385 (m-30) cc_final: 0.8107 (t0) REVERT: A 146 LYS cc_start: 0.8663 (mtpt) cc_final: 0.8063 (mttp) REVERT: A 184 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8180 (pt0) REVERT: A 199 LYS cc_start: 0.8473 (ptmt) cc_final: 0.8136 (ptmm) REVERT: A 206 ASP cc_start: 0.8551 (t0) cc_final: 0.8196 (t0) REVERT: A 208 LYS cc_start: 0.8693 (ptpp) cc_final: 0.7849 (pttp) REVERT: A 232 LYS cc_start: 0.8665 (ttmt) cc_final: 0.8349 (ttmm) REVERT: A 272 TYR cc_start: 0.8952 (t80) cc_final: 0.8318 (t80) REVERT: A 281 GLN cc_start: 0.8852 (mm110) cc_final: 0.8378 (pt0) REVERT: A 283 LEU cc_start: 0.8655 (mt) cc_final: 0.8337 (mp) REVERT: A 297 PHE cc_start: 0.8858 (m-80) cc_final: 0.8485 (m-10) REVERT: A 364 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8057 (mt-10) REVERT: B 75 ASP cc_start: 0.8220 (t0) cc_final: 0.7687 (t0) REVERT: B 77 LEU cc_start: 0.9371 (mt) cc_final: 0.9093 (mm) REVERT: B 129 ASP cc_start: 0.8800 (t0) cc_final: 0.8391 (t0) REVERT: B 146 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8057 (mttp) REVERT: B 201 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8350 (mp0) REVERT: B 206 ASP cc_start: 0.8369 (t0) cc_final: 0.7995 (t0) REVERT: B 260 GLU cc_start: 0.8867 (pm20) cc_final: 0.8314 (pm20) REVERT: B 279 LEU cc_start: 0.9053 (tp) cc_final: 0.8789 (tt) REVERT: B 281 GLN cc_start: 0.8789 (mm110) cc_final: 0.8380 (pt0) REVERT: B 283 LEU cc_start: 0.8595 (mt) cc_final: 0.8273 (mp) REVERT: C 75 ASP cc_start: 0.8306 (t0) cc_final: 0.7709 (t0) REVERT: C 77 LEU cc_start: 0.9417 (mt) cc_final: 0.9163 (mm) REVERT: C 78 ARG cc_start: 0.8873 (mtp85) cc_final: 0.8567 (mtm110) REVERT: C 129 ASP cc_start: 0.8776 (t0) cc_final: 0.8147 (t0) REVERT: C 146 LYS cc_start: 0.8692 (mtpt) cc_final: 0.8078 (mtmp) REVERT: C 160 GLU cc_start: 0.8647 (tt0) cc_final: 0.8183 (mm-30) REVERT: C 201 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8495 (mp0) REVERT: C 233 SER cc_start: 0.8836 (m) cc_final: 0.8573 (p) REVERT: C 281 GLN cc_start: 0.8835 (mm110) cc_final: 0.8343 (pt0) REVERT: C 402 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8408 (mt-10) REVERT: D 48 GLU cc_start: 0.8498 (tp30) cc_final: 0.8207 (mm-30) REVERT: D 75 ASP cc_start: 0.8367 (t0) cc_final: 0.7717 (t0) REVERT: D 154 GLU cc_start: 0.9100 (tt0) cc_final: 0.8822 (tt0) REVERT: D 160 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8322 (tp30) REVERT: D 184 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8180 (pt0) REVERT: D 199 LYS cc_start: 0.8533 (ptpt) cc_final: 0.8188 (ptmm) REVERT: D 201 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8458 (mp0) REVERT: D 206 ASP cc_start: 0.8508 (t0) cc_final: 0.8086 (t0) REVERT: D 208 LYS cc_start: 0.8689 (mtmm) cc_final: 0.8412 (mtmm) REVERT: D 281 GLN cc_start: 0.8793 (mm110) cc_final: 0.8339 (pt0) REVERT: D 402 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8265 (mt-10) REVERT: E 48 GLU cc_start: 0.8496 (tp30) cc_final: 0.8238 (mm-30) REVERT: E 75 ASP cc_start: 0.8332 (t0) cc_final: 0.7788 (t0) REVERT: E 78 ARG cc_start: 0.8768 (mtp85) cc_final: 0.8520 (mtm110) REVERT: E 124 GLU cc_start: 0.8946 (mp0) cc_final: 0.8631 (mp0) REVERT: E 132 ASP cc_start: 0.7976 (t0) cc_final: 0.7692 (t0) REVERT: E 146 LYS cc_start: 0.8686 (mtpt) cc_final: 0.7997 (mttp) REVERT: E 160 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.7968 (tm-30) REVERT: E 167 ASP cc_start: 0.9439 (p0) cc_final: 0.9103 (p0) REVERT: E 201 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8378 (mp0) REVERT: E 206 ASP cc_start: 0.8449 (t0) cc_final: 0.8103 (t0) REVERT: E 208 LYS cc_start: 0.8630 (ptpp) cc_final: 0.7862 (pttp) REVERT: E 233 SER cc_start: 0.8696 (m) cc_final: 0.8434 (p) REVERT: E 283 LEU cc_start: 0.8691 (mt) cc_final: 0.8316 (mp) REVERT: E 364 GLU cc_start: 0.8305 (mp0) cc_final: 0.8050 (mt-10) outliers start: 45 outliers final: 20 residues processed: 372 average time/residue: 0.5907 time to fit residues: 240.1251 Evaluate side-chains 342 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 320 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain C residue 379 LEU Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 123 LEU Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 379 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 67 optimal weight: 0.7980 chunk 118 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN B 382 GLN C 156 ASN ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.091119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.077946 restraints weight = 20370.491| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 2.47 r_work: 0.2806 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13410 Z= 0.126 Angle : 0.545 9.463 18370 Z= 0.266 Chirality : 0.039 0.141 2235 Planarity : 0.004 0.044 2250 Dihedral : 4.573 40.475 2060 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.31 % Allowed : 21.26 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.21), residues: 1600 helix: 2.85 (0.20), residues: 525 sheet: 0.42 (0.24), residues: 475 loop : 0.09 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 257 TYR 0.022 0.002 TYR D 176 PHE 0.024 0.002 PHE C 297 TRP 0.016 0.001 TRP C 112 HIS 0.001 0.000 HIS C 276 Details of bonding type rmsd covalent geometry : bond 0.00277 (13385) covalent geometry : angle 0.54174 (18305) SS BOND : bond 0.00342 ( 10) SS BOND : angle 1.06394 ( 20) hydrogen bonds : bond 0.03928 ( 680) hydrogen bonds : angle 4.17590 ( 2100) link_BETA1-4 : bond 0.00282 ( 5) link_BETA1-4 : angle 1.20961 ( 15) link_NAG-ASN : bond 0.00070 ( 10) link_NAG-ASN : angle 1.15594 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 332 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8587 (tp30) cc_final: 0.8176 (mm-30) REVERT: A 75 ASP cc_start: 0.8343 (t0) cc_final: 0.7948 (t0) REVERT: A 81 MET cc_start: 0.9026 (ttp) cc_final: 0.8742 (ptt) REVERT: A 132 ASP cc_start: 0.8353 (m-30) cc_final: 0.8008 (t0) REVERT: A 146 LYS cc_start: 0.8644 (mtpt) cc_final: 0.7994 (mttp) REVERT: A 153 THR cc_start: 0.9323 (p) cc_final: 0.9017 (t) REVERT: A 184 GLU cc_start: 0.8621 (mt-10) cc_final: 0.8183 (pt0) REVERT: A 199 LYS cc_start: 0.8416 (ptmt) cc_final: 0.8172 (ptmm) REVERT: A 206 ASP cc_start: 0.8509 (t0) cc_final: 0.8234 (t0) REVERT: A 232 LYS cc_start: 0.8647 (ttmt) cc_final: 0.8338 (ttmm) REVERT: A 272 TYR cc_start: 0.8884 (t80) cc_final: 0.8267 (t80) REVERT: A 281 GLN cc_start: 0.8805 (mm110) cc_final: 0.8333 (pt0) REVERT: A 283 LEU cc_start: 0.8624 (mt) cc_final: 0.8279 (mp) REVERT: A 297 PHE cc_start: 0.8839 (m-80) cc_final: 0.8544 (m-80) REVERT: A 364 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8184 (mt-10) REVERT: B 75 ASP cc_start: 0.8199 (t0) cc_final: 0.7703 (t0) REVERT: B 129 ASP cc_start: 0.8786 (t0) cc_final: 0.8233 (t0) REVERT: B 201 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8315 (mp0) REVERT: B 206 ASP cc_start: 0.8352 (t0) cc_final: 0.7863 (t0) REVERT: B 208 LYS cc_start: 0.8671 (ptpp) cc_final: 0.7782 (pttp) REVERT: B 260 GLU cc_start: 0.8863 (pm20) cc_final: 0.8322 (pm20) REVERT: B 281 GLN cc_start: 0.8744 (mm110) cc_final: 0.8378 (pt0) REVERT: B 283 LEU cc_start: 0.8563 (mt) cc_final: 0.8241 (mp) REVERT: C 75 ASP cc_start: 0.8313 (t0) cc_final: 0.7761 (t0) REVERT: C 77 LEU cc_start: 0.9388 (mt) cc_final: 0.9147 (mm) REVERT: C 81 MET cc_start: 0.9093 (ttp) cc_final: 0.8827 (ptm) REVERT: C 129 ASP cc_start: 0.8792 (t0) cc_final: 0.8159 (t0) REVERT: C 146 LYS cc_start: 0.8676 (mtpt) cc_final: 0.8061 (mtmp) REVERT: C 160 GLU cc_start: 0.8592 (tt0) cc_final: 0.8140 (mm-30) REVERT: C 201 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8374 (mp0) REVERT: C 232 LYS cc_start: 0.8621 (ttmt) cc_final: 0.8346 (tppp) REVERT: C 233 SER cc_start: 0.8761 (m) cc_final: 0.8535 (p) REVERT: C 281 GLN cc_start: 0.8783 (mm110) cc_final: 0.8274 (pt0) REVERT: C 283 LEU cc_start: 0.8538 (mt) cc_final: 0.8244 (mp) REVERT: C 402 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8408 (mt-10) REVERT: D 75 ASP cc_start: 0.8396 (t0) cc_final: 0.7719 (t0) REVERT: D 146 LYS cc_start: 0.8616 (mtmt) cc_final: 0.7975 (mttp) REVERT: D 160 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8537 (mm-30) REVERT: D 184 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8180 (pt0) REVERT: D 199 LYS cc_start: 0.8474 (ptpt) cc_final: 0.8140 (ptmm) REVERT: D 201 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8427 (mp0) REVERT: D 206 ASP cc_start: 0.8494 (t0) cc_final: 0.8119 (t0) REVERT: D 208 LYS cc_start: 0.8670 (mtmm) cc_final: 0.8414 (mtmm) REVERT: D 281 GLN cc_start: 0.8723 (mm110) cc_final: 0.8319 (pt0) REVERT: D 402 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8252 (mt-10) REVERT: E 75 ASP cc_start: 0.8329 (t0) cc_final: 0.7799 (t0) REVERT: E 78 ARG cc_start: 0.8712 (mtp85) cc_final: 0.8499 (mtm110) REVERT: E 132 ASP cc_start: 0.7898 (t0) cc_final: 0.7626 (t0) REVERT: E 146 LYS cc_start: 0.8695 (mtpt) cc_final: 0.8008 (mttp) REVERT: E 160 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8424 (mm-30) REVERT: E 167 ASP cc_start: 0.9443 (p0) cc_final: 0.9118 (p0) REVERT: E 201 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8347 (mp0) REVERT: E 206 ASP cc_start: 0.8407 (t0) cc_final: 0.8066 (t0) REVERT: E 208 LYS cc_start: 0.8575 (ptpp) cc_final: 0.7808 (pttp) REVERT: E 232 LYS cc_start: 0.8758 (ttmt) cc_final: 0.8333 (ttmm) REVERT: E 233 SER cc_start: 0.8669 (m) cc_final: 0.8457 (p) REVERT: E 283 LEU cc_start: 0.8657 (mt) cc_final: 0.8352 (mp) outliers start: 33 outliers final: 16 residues processed: 349 average time/residue: 0.5431 time to fit residues: 208.3764 Evaluate side-chains 337 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 319 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ASN Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 277 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 25 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 88 optimal weight: 1.9990 chunk 149 optimal weight: 0.7980 chunk 147 optimal weight: 0.0050 chunk 84 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 158 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN A 290 ASN C 156 ASN D 221 GLN D 382 GLN ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.091681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.078409 restraints weight = 20476.067| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.47 r_work: 0.2805 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2689 r_free = 0.2689 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13410 Z= 0.121 Angle : 0.545 9.584 18370 Z= 0.265 Chirality : 0.039 0.177 2235 Planarity : 0.004 0.032 2250 Dihedral : 4.305 33.872 2060 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.82 % Allowed : 21.82 % Favored : 76.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.66 (0.21), residues: 1600 helix: 2.83 (0.20), residues: 530 sheet: 0.66 (0.25), residues: 430 loop : -0.02 (0.26), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 257 TYR 0.030 0.002 TYR B 176 PHE 0.023 0.002 PHE C 297 TRP 0.013 0.001 TRP C 112 HIS 0.001 0.000 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00268 (13385) covalent geometry : angle 0.54085 (18305) SS BOND : bond 0.00405 ( 10) SS BOND : angle 1.31699 ( 20) hydrogen bonds : bond 0.03879 ( 680) hydrogen bonds : angle 4.13555 ( 2100) link_BETA1-4 : bond 0.00258 ( 5) link_BETA1-4 : angle 1.23005 ( 15) link_NAG-ASN : bond 0.00122 ( 10) link_NAG-ASN : angle 1.18203 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 327 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8603 (tp30) cc_final: 0.8182 (mm-30) REVERT: A 75 ASP cc_start: 0.8350 (t0) cc_final: 0.7952 (t0) REVERT: A 81 MET cc_start: 0.8998 (ttp) cc_final: 0.8711 (ptt) REVERT: A 132 ASP cc_start: 0.8374 (m-30) cc_final: 0.7943 (t0) REVERT: A 146 LYS cc_start: 0.8660 (mtpt) cc_final: 0.8014 (mttp) REVERT: A 153 THR cc_start: 0.9315 (p) cc_final: 0.8983 (t) REVERT: A 184 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8223 (pt0) REVERT: A 199 LYS cc_start: 0.8399 (ptmt) cc_final: 0.8180 (ptmm) REVERT: A 206 ASP cc_start: 0.8504 (t0) cc_final: 0.8170 (t0) REVERT: A 208 LYS cc_start: 0.8695 (ptpp) cc_final: 0.7840 (pttp) REVERT: A 232 LYS cc_start: 0.8666 (ttmt) cc_final: 0.8310 (ttmm) REVERT: A 272 TYR cc_start: 0.8873 (t80) cc_final: 0.8232 (t80) REVERT: A 283 LEU cc_start: 0.8633 (mt) cc_final: 0.8302 (mp) REVERT: A 297 PHE cc_start: 0.8803 (m-80) cc_final: 0.8405 (m-10) REVERT: A 364 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8240 (mt-10) REVERT: B 75 ASP cc_start: 0.8185 (t0) cc_final: 0.7696 (t0) REVERT: B 129 ASP cc_start: 0.8794 (t0) cc_final: 0.8359 (t0) REVERT: B 146 LYS cc_start: 0.8715 (mtmt) cc_final: 0.8014 (mttp) REVERT: B 201 GLU cc_start: 0.8640 (mt-10) cc_final: 0.8269 (mp0) REVERT: B 206 ASP cc_start: 0.8368 (t0) cc_final: 0.7898 (t0) REVERT: B 208 LYS cc_start: 0.8659 (ptpp) cc_final: 0.7780 (pttp) REVERT: B 232 LYS cc_start: 0.8636 (ttmt) cc_final: 0.8356 (ttmm) REVERT: B 260 GLU cc_start: 0.8862 (pm20) cc_final: 0.8324 (pm20) REVERT: B 281 GLN cc_start: 0.8706 (mm110) cc_final: 0.8353 (pt0) REVERT: B 283 LEU cc_start: 0.8539 (mt) cc_final: 0.8141 (mp) REVERT: C 75 ASP cc_start: 0.8335 (t0) cc_final: 0.7754 (t0) REVERT: C 77 LEU cc_start: 0.9382 (mt) cc_final: 0.9138 (mm) REVERT: C 78 ARG cc_start: 0.8857 (mtp85) cc_final: 0.8632 (mtm110) REVERT: C 81 MET cc_start: 0.9090 (ttp) cc_final: 0.8832 (ptm) REVERT: C 129 ASP cc_start: 0.8801 (t0) cc_final: 0.8168 (t0) REVERT: C 146 LYS cc_start: 0.8677 (mtpt) cc_final: 0.8061 (mtmp) REVERT: C 160 GLU cc_start: 0.8583 (tt0) cc_final: 0.8134 (mm-30) REVERT: C 201 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8366 (mp0) REVERT: C 232 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8078 (ttmm) REVERT: C 233 SER cc_start: 0.8753 (m) cc_final: 0.8497 (p) REVERT: C 260 GLU cc_start: 0.8869 (pm20) cc_final: 0.8454 (pm20) REVERT: C 281 GLN cc_start: 0.8744 (mm110) cc_final: 0.8234 (pt0) REVERT: C 402 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8395 (mt-10) REVERT: D 75 ASP cc_start: 0.8408 (t0) cc_final: 0.7727 (t0) REVERT: D 146 LYS cc_start: 0.8626 (mtmt) cc_final: 0.7983 (mttp) REVERT: D 160 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8534 (mm-30) REVERT: D 184 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8187 (pt0) REVERT: D 199 LYS cc_start: 0.8433 (ptpt) cc_final: 0.8094 (ptmm) REVERT: D 201 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8426 (mp0) REVERT: D 206 ASP cc_start: 0.8484 (t0) cc_final: 0.8112 (t0) REVERT: D 208 LYS cc_start: 0.8666 (mtmm) cc_final: 0.8410 (mtmm) REVERT: D 283 LEU cc_start: 0.8631 (mt) cc_final: 0.8238 (mp) REVERT: D 402 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8242 (mt-10) REVERT: E 75 ASP cc_start: 0.8318 (t0) cc_final: 0.7793 (t0) REVERT: E 132 ASP cc_start: 0.7820 (t0) cc_final: 0.7568 (t0) REVERT: E 146 LYS cc_start: 0.8701 (mtpt) cc_final: 0.8010 (mttp) REVERT: E 160 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8427 (mm-30) REVERT: E 167 ASP cc_start: 0.9436 (p0) cc_final: 0.9117 (p0) REVERT: E 201 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8352 (mp0) REVERT: E 206 ASP cc_start: 0.8373 (t0) cc_final: 0.8054 (t0) REVERT: E 208 LYS cc_start: 0.8589 (ptpp) cc_final: 0.7834 (pttp) REVERT: E 232 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8331 (ttmm) REVERT: E 233 SER cc_start: 0.8765 (m) cc_final: 0.8496 (p) REVERT: E 272 TYR cc_start: 0.8911 (t80) cc_final: 0.8167 (t80) outliers start: 26 outliers final: 17 residues processed: 344 average time/residue: 0.5486 time to fit residues: 207.4996 Evaluate side-chains 342 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 323 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 112 TRP Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 277 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 16 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 81 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 152 optimal weight: 0.3980 chunk 38 optimal weight: 5.9990 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 156 ASN B 221 GLN C 156 ASN C 382 GLN ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.091186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.077820 restraints weight = 20558.195| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.50 r_work: 0.2808 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13410 Z= 0.150 Angle : 0.554 9.669 18370 Z= 0.272 Chirality : 0.040 0.153 2235 Planarity : 0.004 0.035 2250 Dihedral : 4.140 25.821 2060 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.68 % Allowed : 22.24 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.62 (0.21), residues: 1600 helix: 2.85 (0.20), residues: 525 sheet: 0.65 (0.25), residues: 430 loop : -0.08 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 257 TYR 0.035 0.002 TYR B 176 PHE 0.025 0.002 PHE C 297 TRP 0.014 0.001 TRP C 112 HIS 0.002 0.000 HIS B 276 Details of bonding type rmsd covalent geometry : bond 0.00334 (13385) covalent geometry : angle 0.55042 (18305) SS BOND : bond 0.00396 ( 10) SS BOND : angle 1.26040 ( 20) hydrogen bonds : bond 0.03941 ( 680) hydrogen bonds : angle 4.16184 ( 2100) link_BETA1-4 : bond 0.00213 ( 5) link_BETA1-4 : angle 1.23115 ( 15) link_NAG-ASN : bond 0.00065 ( 10) link_NAG-ASN : angle 1.25229 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3200 Ramachandran restraints generated. 1600 Oldfield, 0 Emsley, 1600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 331 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 GLU cc_start: 0.8590 (tp30) cc_final: 0.8166 (mm-30) REVERT: A 75 ASP cc_start: 0.8368 (t0) cc_final: 0.7966 (t0) REVERT: A 81 MET cc_start: 0.9037 (ttp) cc_final: 0.8778 (ptt) REVERT: A 146 LYS cc_start: 0.8645 (mtpt) cc_final: 0.8000 (mttp) REVERT: A 153 THR cc_start: 0.9306 (p) cc_final: 0.8980 (t) REVERT: A 184 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8233 (pt0) REVERT: A 199 LYS cc_start: 0.8413 (ptmt) cc_final: 0.8068 (ptmm) REVERT: A 206 ASP cc_start: 0.8503 (t0) cc_final: 0.8154 (t0) REVERT: A 208 LYS cc_start: 0.8712 (ptpp) cc_final: 0.8124 (mtmm) REVERT: A 232 LYS cc_start: 0.8634 (ttmt) cc_final: 0.8298 (ttmm) REVERT: A 272 TYR cc_start: 0.8881 (t80) cc_final: 0.8284 (t80) REVERT: A 283 LEU cc_start: 0.8564 (mt) cc_final: 0.8210 (mp) REVERT: A 297 PHE cc_start: 0.8842 (m-80) cc_final: 0.8474 (m-10) REVERT: A 364 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8173 (mp0) REVERT: B 75 ASP cc_start: 0.8214 (t0) cc_final: 0.7710 (t0) REVERT: B 129 ASP cc_start: 0.8812 (t0) cc_final: 0.8506 (t0) REVERT: B 146 LYS cc_start: 0.8716 (mtmt) cc_final: 0.8005 (mttp) REVERT: B 160 GLU cc_start: 0.8937 (mm-30) cc_final: 0.8434 (mm-30) REVERT: B 201 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8307 (mp0) REVERT: B 206 ASP cc_start: 0.8371 (t0) cc_final: 0.7896 (t0) REVERT: B 208 LYS cc_start: 0.8669 (ptpp) cc_final: 0.7789 (pttp) REVERT: B 232 LYS cc_start: 0.8649 (ttmt) cc_final: 0.8373 (ttmm) REVERT: B 260 GLU cc_start: 0.8871 (pm20) cc_final: 0.8333 (pm20) REVERT: B 283 LEU cc_start: 0.8472 (mt) cc_final: 0.8234 (mt) REVERT: C 75 ASP cc_start: 0.8369 (t0) cc_final: 0.7737 (t0) REVERT: C 77 LEU cc_start: 0.9396 (mt) cc_final: 0.9151 (mm) REVERT: C 78 ARG cc_start: 0.8925 (mtp85) cc_final: 0.8688 (mtm110) REVERT: C 81 MET cc_start: 0.9113 (ttp) cc_final: 0.8854 (ptm) REVERT: C 129 ASP cc_start: 0.8802 (t0) cc_final: 0.8227 (t0) REVERT: C 146 LYS cc_start: 0.8678 (mtpt) cc_final: 0.8069 (mtmp) REVERT: C 160 GLU cc_start: 0.8568 (tt0) cc_final: 0.8129 (mm-30) REVERT: C 201 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8384 (mp0) REVERT: C 232 LYS cc_start: 0.8588 (ttmt) cc_final: 0.8085 (ttmm) REVERT: C 233 SER cc_start: 0.8746 (m) cc_final: 0.8490 (p) REVERT: C 281 GLN cc_start: 0.8740 (mm110) cc_final: 0.8218 (pt0) REVERT: C 306 LEU cc_start: 0.8976 (tp) cc_final: 0.8770 (tp) REVERT: C 402 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8387 (mt-10) REVERT: D 75 ASP cc_start: 0.8430 (t0) cc_final: 0.7749 (t0) REVERT: D 146 LYS cc_start: 0.8624 (mtmt) cc_final: 0.8033 (mttp) REVERT: D 160 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8520 (mm-30) REVERT: D 199 LYS cc_start: 0.8457 (ptpt) cc_final: 0.8106 (ptmm) REVERT: D 201 GLU cc_start: 0.8729 (mt-10) cc_final: 0.8430 (mp0) REVERT: D 206 ASP cc_start: 0.8489 (t0) cc_final: 0.8111 (t0) REVERT: D 208 LYS cc_start: 0.8673 (mtmm) cc_final: 0.8411 (mtmm) REVERT: D 402 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8286 (mt-10) REVERT: E 48 GLU cc_start: 0.8504 (tp30) cc_final: 0.8222 (mm-30) REVERT: E 75 ASP cc_start: 0.8322 (t0) cc_final: 0.7872 (t0) REVERT: E 124 GLU cc_start: 0.8920 (mp0) cc_final: 0.8513 (mp0) REVERT: E 132 ASP cc_start: 0.7849 (t0) cc_final: 0.7579 (t0) REVERT: E 146 LYS cc_start: 0.8697 (mtpt) cc_final: 0.8016 (mtmp) REVERT: E 160 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.7957 (tm-30) REVERT: E 167 ASP cc_start: 0.9440 (p0) cc_final: 0.9113 (p0) REVERT: E 184 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8067 (pt0) REVERT: E 201 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8369 (mp0) REVERT: E 206 ASP cc_start: 0.8378 (t0) cc_final: 0.8058 (t0) REVERT: E 208 LYS cc_start: 0.8583 (ptpp) cc_final: 0.7831 (pttp) REVERT: E 232 LYS cc_start: 0.8768 (ttmt) cc_final: 0.8345 (ttmm) REVERT: E 233 SER cc_start: 0.8676 (m) cc_final: 0.8458 (p) REVERT: E 272 TYR cc_start: 0.8893 (t80) cc_final: 0.8194 (t80) REVERT: E 297 PHE cc_start: 0.8511 (m-10) cc_final: 0.8305 (m-10) REVERT: E 364 GLU cc_start: 0.8271 (mp0) cc_final: 0.8048 (mt-10) outliers start: 24 outliers final: 19 residues processed: 350 average time/residue: 0.5564 time to fit residues: 213.5728 Evaluate side-chains 341 residues out of total 1430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 320 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 179 SER Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain B residue 54 ASN Chi-restraints excluded: chain B residue 179 SER Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 235 ILE Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 160 GLU Chi-restraints excluded: chain D residue 179 SER Chi-restraints excluded: chain D residue 235 ILE Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 160 GLU Chi-restraints excluded: chain E residue 277 SER Chi-restraints excluded: chain E residue 305 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 116 optimal weight: 2.9990 chunk 135 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 136 optimal weight: 0.5980 chunk 145 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN C 156 ASN D 382 GLN ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 382 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.089499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.076058 restraints weight = 20644.822| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.49 r_work: 0.2777 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2632 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2634 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2634 r_free = 0.2634 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2634 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13410 Z= 0.223 Angle : 0.594 9.704 18370 Z= 0.294 Chirality : 0.041 0.164 2235 Planarity : 0.004 0.035 2250 Dihedral : 4.226 22.316 2060 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.75 % Allowed : 22.38 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.21), residues: 1600 helix: 2.69 (0.20), residues: 525 sheet: 0.55 (0.24), residues: 430 loop : -0.10 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 257 TYR 0.038 0.003 TYR B 176 PHE 0.027 0.002 PHE C 297 TRP 0.014 0.001 TRP C 112 HIS 0.002 0.001 HIS E 276 Details of bonding type rmsd covalent geometry : bond 0.00499 (13385) covalent geometry : angle 0.58884 (18305) SS BOND : bond 0.00544 ( 10) SS BOND : angle 1.50469 ( 20) hydrogen bonds : bond 0.04141 ( 680) hydrogen bonds : angle 4.27924 ( 2100) link_BETA1-4 : bond 0.00124 ( 5) link_BETA1-4 : angle 1.20505 ( 15) link_NAG-ASN : bond 0.00271 ( 10) link_NAG-ASN : angle 1.41082 ( 30) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5052.51 seconds wall clock time: 86 minutes 52.75 seconds (5212.75 seconds total)