Starting phenix.real_space_refine on Fri Jul 3 13:35:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m6m_23700/07_2026/7m6m_23700.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6m_23700/07_2026/7m6m_23700.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7m6m_23700/07_2026/7m6m_23700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6m_23700/07_2026/7m6m_23700.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m6m_23700/07_2026/7m6m_23700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6m_23700/07_2026/7m6m_23700.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7m6m_23700/07_2026/7m6m_23700.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m6m_23700/07_2026/7m6m_23700.cif" } resolution = 3.09 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= 0.003 sd= 0.041 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 95 5.16 5 C 9275 2.51 5 N 2275 2.21 5 O 2545 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14190 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2787 Classifications: {'peptide': 344} Link IDs: {'PTRANS': 16, 'TRANS': 327} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 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 chiralities: 2 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'TCI': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, E, D, G, H, I, J Time building chain proxies: 2.12, per 1000 atoms: 0.15 Number of scatterers: 14190 At special positions: 0 Unit cell: (100.7, 100.7, 132.5, 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 95 16.00 O 2545 8.00 N 2275 7.00 C 9275 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 F 1 " - " ASN A 62 " " NAG G 1 " - " ASN B 62 " " NAG H 1 " - " ASN C 62 " " NAG I 1 " - " ASN E 62 " " NAG J 1 " - " ASN D 62 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 527.7 milliseconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3300 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 20 sheets defined 37.5% alpha, 43.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 33 through 43 removed outlier: 3.566A pdb=" N PHE A 37 " --> pdb=" O PRO A 33 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU A 38 " --> pdb=" O PRO A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 250 Processing helix chain 'A' and resid 251 through 263 Processing helix chain 'A' and resid 263 through 268 removed outlier: 4.130A pdb=" N TRP A 267 " --> pdb=" O TRP A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 298 removed outlier: 4.203A pdb=" N ALA A 296 " --> pdb=" O SER A 292 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 329 removed outlier: 3.700A pdb=" N ILE A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N TYR A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 441 Proline residue: A 419 - end of helix Processing helix chain 'B' and resid 33 through 43 removed outlier: 3.566A pdb=" N PHE B 37 " --> pdb=" O PRO B 33 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B 38 " --> pdb=" O PRO B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 250 Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 263 through 268 removed outlier: 4.130A pdb=" N TRP B 267 " --> pdb=" O TRP B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 298 removed outlier: 4.202A pdb=" N ALA B 296 " --> pdb=" O SER B 292 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER B 297 " --> pdb=" O GLY B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 329 removed outlier: 3.700A pdb=" N ILE B 309 " --> pdb=" O LYS B 305 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 441 Proline residue: B 419 - end of helix Processing helix chain 'C' and resid 33 through 43 removed outlier: 3.565A pdb=" N PHE C 37 " --> pdb=" O PRO C 33 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU C 38 " --> pdb=" O PRO C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 250 Processing helix chain 'C' and resid 251 through 263 Processing helix chain 'C' and resid 263 through 268 removed outlier: 4.129A pdb=" N TRP C 267 " --> pdb=" O TRP C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 298 removed outlier: 4.202A pdb=" N ALA C 296 " --> pdb=" O SER C 292 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER C 297 " --> pdb=" O GLY C 293 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 329 removed outlier: 3.701A pdb=" N ILE C 309 " --> pdb=" O LYS C 305 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR C 325 " --> pdb=" O ALA C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 441 Proline residue: C 419 - end of helix Processing helix chain 'E' and resid 33 through 43 removed outlier: 3.566A pdb=" N PHE E 37 " --> pdb=" O PRO E 33 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU E 38 " --> pdb=" O PRO E 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 244 through 250 Processing helix chain 'E' and resid 251 through 263 Processing helix chain 'E' and resid 263 through 268 removed outlier: 4.130A pdb=" N TRP E 267 " --> pdb=" O TRP E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 298 removed outlier: 4.203A pdb=" N ALA E 296 " --> pdb=" O SER E 292 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER E 297 " --> pdb=" O GLY E 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 329 removed outlier: 3.700A pdb=" N ILE E 309 " --> pdb=" O LYS E 305 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR E 325 " --> pdb=" O ALA E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 402 through 441 Proline residue: E 419 - end of helix Processing helix chain 'D' and resid 33 through 43 removed outlier: 3.566A pdb=" N PHE D 37 " --> pdb=" O PRO D 33 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU D 38 " --> pdb=" O PRO D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 250 Processing helix chain 'D' and resid 251 through 263 Processing helix chain 'D' and resid 263 through 268 removed outlier: 4.130A pdb=" N TRP D 267 " --> pdb=" O TRP D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 298 removed outlier: 4.203A pdb=" N ALA D 296 " --> pdb=" O SER D 292 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N SER D 297 " --> pdb=" O GLY D 293 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 329 removed outlier: 3.700A pdb=" N ILE D 309 " --> pdb=" O LYS D 305 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR D 325 " --> pdb=" O ALA D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 402 through 441 Proline residue: D 419 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 106 through 109 removed outlier: 4.758A pdb=" N LEU A 142 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 68 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL A 61 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU A 193 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL A 63 " --> pdb=" O GLU A 193 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 127 through 132 removed outlier: 6.810A pdb=" N VAL A 159 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA A 130 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR A 157 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N PHE A 132 " --> pdb=" O ARG A 155 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N ARG A 155 " --> pdb=" O PHE A 132 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP A 81 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N SER A 74 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ARG A 83 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN A 85 " --> pdb=" O ASN A 70 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A 68 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN A 93 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASN A 62 " --> pdb=" O ASN A 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.069A pdb=" N THR A 232 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 122 through 124 removed outlier: 6.069A pdb=" N THR A 232 " --> pdb=" O SER A 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 106 through 109 removed outlier: 4.757A pdb=" N LEU B 142 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN B 149 " --> pdb=" O SER B 145 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 68 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL B 61 " --> pdb=" O ILE B 191 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU B 193 " --> pdb=" O VAL B 61 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL B 63 " --> pdb=" O GLU B 193 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 127 through 132 removed outlier: 6.811A pdb=" N VAL B 159 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ALA B 130 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR B 157 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N PHE B 132 " --> pdb=" O ARG B 155 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N ARG B 155 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP B 81 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER B 74 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ARG B 83 " --> pdb=" O PHE B 72 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN B 85 " --> pdb=" O ASN B 70 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE B 68 " --> pdb=" O PHE B 87 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN B 93 " --> pdb=" O ASN B 62 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASN B 62 " --> pdb=" O ASN B 93 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.068A pdb=" N THR B 232 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 122 through 124 removed outlier: 6.068A pdb=" N THR B 232 " --> pdb=" O SER B 182 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 106 through 109 removed outlier: 4.758A pdb=" N LEU C 142 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN C 149 " --> pdb=" O SER C 145 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 68 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL C 61 " --> pdb=" O ILE C 191 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU C 193 " --> pdb=" O VAL C 61 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL C 63 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 127 through 132 removed outlier: 6.810A pdb=" N VAL C 159 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA C 130 " --> pdb=" O THR C 157 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N THR C 157 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N PHE C 132 " --> pdb=" O ARG C 155 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ARG C 155 " --> pdb=" O PHE C 132 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP C 81 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER C 74 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N ARG C 83 " --> pdb=" O PHE C 72 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN C 85 " --> pdb=" O ASN C 70 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE C 68 " --> pdb=" O PHE C 87 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN C 93 " --> pdb=" O ASN C 62 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASN C 62 " --> pdb=" O ASN C 93 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.069A pdb=" N THR C 232 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 122 through 124 removed outlier: 6.069A pdb=" N THR C 232 " --> pdb=" O SER C 182 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 106 through 109 removed outlier: 4.758A pdb=" N LEU E 142 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN E 149 " --> pdb=" O SER E 145 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE E 68 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASN E 93 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASN E 62 " --> pdb=" O ASN E 93 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL E 61 " --> pdb=" O ILE E 191 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU E 193 " --> pdb=" O VAL E 61 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N VAL E 63 " --> pdb=" O GLU E 193 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 127 through 132 removed outlier: 6.811A pdb=" N VAL E 159 " --> pdb=" O LYS E 128 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA E 130 " --> pdb=" O THR E 157 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR E 157 " --> pdb=" O ALA E 130 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N PHE E 132 " --> pdb=" O ARG E 155 " (cutoff:3.500A) removed outlier: 8.448A pdb=" N ARG E 155 " --> pdb=" O PHE E 132 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N ASP E 81 " --> pdb=" O SER E 74 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER E 74 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ARG E 83 " --> pdb=" O PHE E 72 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE E 72 " --> pdb=" O ARG E 83 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ASN E 85 " --> pdb=" O ASN E 70 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE E 68 " --> pdb=" O PHE E 87 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ASN E 93 " --> pdb=" O ASN E 62 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASN E 62 " --> pdb=" O ASN E 93 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 122 through 124 removed outlier: 6.068A pdb=" N THR E 232 " --> pdb=" O SER E 182 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 122 through 124 removed outlier: 6.068A pdb=" N THR E 232 " --> pdb=" O SER E 182 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 106 through 109 removed outlier: 4.758A pdb=" N LEU D 142 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ASN D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE D 68 " --> pdb=" O PHE D 87 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N VAL D 61 " --> pdb=" O ILE D 191 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N GLU D 193 " --> pdb=" O VAL D 61 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N VAL D 63 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 127 through 132 removed outlier: 6.810A pdb=" N VAL D 159 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA D 130 " --> pdb=" O THR D 157 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N THR D 157 " --> pdb=" O ALA D 130 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N PHE D 132 " --> pdb=" O ARG D 155 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N ARG D 155 " --> pdb=" O PHE D 132 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ASP D 81 " --> pdb=" O SER D 74 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N SER D 74 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N ARG D 83 " --> pdb=" O PHE D 72 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE D 72 " --> pdb=" O ARG D 83 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASN D 85 " --> pdb=" O ASN D 70 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE D 68 " --> pdb=" O PHE D 87 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N ASN D 93 " --> pdb=" O ASN D 62 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASN D 62 " --> pdb=" O ASN D 93 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 122 through 124 removed outlier: 6.069A pdb=" N THR D 232 " --> pdb=" O SER D 182 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 122 through 124 removed outlier: 6.069A pdb=" N THR D 232 " --> pdb=" O SER D 182 " (cutoff:3.500A) 840 hydrogen bonds defined for protein. 2520 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: 2.67 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4010 1.34 - 1.46: 3081 1.46 - 1.57: 7294 1.57 - 1.69: 0 1.69 - 1.81: 160 Bond restraints: 14545 Sorted by residual: bond pdb=" CB MET D 244 " pdb=" CG MET D 244 " ideal model delta sigma weight residual 1.520 1.449 0.071 3.00e-02 1.11e+03 5.63e+00 bond pdb=" CB MET A 244 " pdb=" CG MET A 244 " ideal model delta sigma weight residual 1.520 1.449 0.071 3.00e-02 1.11e+03 5.60e+00 bond pdb=" CB MET C 244 " pdb=" CG MET C 244 " ideal model delta sigma weight residual 1.520 1.449 0.071 3.00e-02 1.11e+03 5.56e+00 bond pdb=" CB MET E 244 " pdb=" CG MET E 244 " ideal model delta sigma weight residual 1.520 1.449 0.071 3.00e-02 1.11e+03 5.55e+00 bond pdb=" CB MET B 244 " pdb=" CG MET B 244 " ideal model delta sigma weight residual 1.520 1.450 0.070 3.00e-02 1.11e+03 5.49e+00 ... (remaining 14540 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 17933 2.07 - 4.14: 1470 4.14 - 6.22: 250 6.22 - 8.29: 77 8.29 - 10.36: 15 Bond angle restraints: 19745 Sorted by residual: angle pdb=" N PHE A 418 " pdb=" CA PHE A 418 " pdb=" C PHE A 418 " ideal model delta sigma weight residual 112.75 118.16 -5.41 1.36e+00 5.41e-01 1.58e+01 angle pdb=" N PHE B 418 " pdb=" CA PHE B 418 " pdb=" C PHE B 418 " ideal model delta sigma weight residual 112.75 118.14 -5.39 1.36e+00 5.41e-01 1.57e+01 angle pdb=" N PHE D 418 " pdb=" CA PHE D 418 " pdb=" C PHE D 418 " ideal model delta sigma weight residual 112.75 118.13 -5.38 1.36e+00 5.41e-01 1.56e+01 angle pdb=" N PHE E 418 " pdb=" CA PHE E 418 " pdb=" C PHE E 418 " ideal model delta sigma weight residual 112.75 118.12 -5.37 1.36e+00 5.41e-01 1.56e+01 angle pdb=" N PHE C 418 " pdb=" CA PHE C 418 " pdb=" C PHE C 418 " ideal model delta sigma weight residual 112.75 118.11 -5.36 1.36e+00 5.41e-01 1.55e+01 ... (remaining 19740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 7915 16.26 - 32.52: 510 32.52 - 48.79: 100 48.79 - 65.05: 30 65.05 - 81.31: 10 Dihedral angle restraints: 8565 sinusoidal: 3480 harmonic: 5085 Sorted by residual: dihedral pdb=" CA TYR E 221 " pdb=" C TYR E 221 " pdb=" N CYS E 222 " pdb=" CA CYS E 222 " ideal model delta harmonic sigma weight residual 180.00 161.65 18.35 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA TYR B 221 " pdb=" C TYR B 221 " pdb=" N CYS B 222 " pdb=" CA CYS B 222 " ideal model delta harmonic sigma weight residual 180.00 161.68 18.32 0 5.00e+00 4.00e-02 1.34e+01 dihedral pdb=" CA TYR C 221 " pdb=" C TYR C 221 " pdb=" N CYS C 222 " pdb=" CA CYS C 222 " ideal model delta harmonic sigma weight residual 180.00 161.69 18.31 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 8562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1510 0.064 - 0.129: 459 0.129 - 0.193: 206 0.193 - 0.258: 46 0.258 - 0.322: 19 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA PHE B 418 " pdb=" N PHE B 418 " pdb=" C PHE B 418 " pdb=" CB PHE B 418 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA PHE A 418 " pdb=" N PHE A 418 " pdb=" C PHE A 418 " pdb=" CB PHE A 418 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.56e+00 chirality pdb=" CA PHE C 418 " pdb=" N PHE C 418 " pdb=" C PHE C 418 " pdb=" CB PHE C 418 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 2237 not shown) Planarity restraints: 2440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 247 " -0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C TYR E 247 " 0.060 2.00e-02 2.50e+03 pdb=" O TYR E 247 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU E 248 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR B 247 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C TYR B 247 " 0.060 2.00e-02 2.50e+03 pdb=" O TYR B 247 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU B 248 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 247 " -0.017 2.00e-02 2.50e+03 3.44e-02 1.18e+01 pdb=" C TYR A 247 " 0.060 2.00e-02 2.50e+03 pdb=" O TYR A 247 " -0.022 2.00e-02 2.50e+03 pdb=" N LEU A 248 " -0.020 2.00e-02 2.50e+03 ... (remaining 2437 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.89: 5118 2.89 - 3.39: 13174 3.39 - 3.89: 23077 3.89 - 4.40: 25124 4.40 - 4.90: 44831 Nonbonded interactions: 111324 Sorted by model distance: nonbonded pdb=" OD2 ASP B 49 " pdb=" OG SER C 35 " model vdw 2.383 3.040 nonbonded pdb=" O LEU E 298 " pdb=" NZ LYS E 300 " model vdw 2.401 3.120 nonbonded pdb=" O LEU A 298 " pdb=" NZ LYS A 300 " model vdw 2.401 3.120 nonbonded pdb=" O LEU D 298 " pdb=" NZ LYS D 300 " model vdw 2.402 3.120 nonbonded pdb=" O LEU C 298 " pdb=" NZ LYS C 300 " model vdw 2.402 3.120 ... (remaining 111319 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'D' } 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=0.57 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 11.980 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.072 14555 Z= 0.364 Angle : 1.316 10.359 19775 Z= 0.729 Chirality : 0.080 0.322 2240 Planarity : 0.008 0.056 2435 Dihedral : 11.725 81.309 5265 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.20), residues: 1700 helix: 1.66 (0.20), residues: 570 sheet: 0.66 (0.27), residues: 420 loop : -1.30 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 51 TYR 0.029 0.004 TYR C 152 PHE 0.041 0.004 PHE A 192 TRP 0.026 0.003 TRP D 263 HIS 0.003 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00811 / 0.36 (14545) covalent geometry : angle 1.31241 / 0.73 (19745) hydrogen bonds : bond 0.13763 / 8.78 ( 695) hydrogen bonds : angle 7.00264 / 4.77 ( 2520) link_BETA1-4 : bond 0.00897 / 0.52 ( 5) link_BETA1-4 : angle 1.88954 / 1.06 ( 15) link_NAG-ASN : bond 0.00242 / 0.14 ( 5) link_NAG-ASN : angle 3.41951 / 2.26 ( 15) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 543 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8297 (t80) cc_final: 0.7985 (t80) REVERT: A 66 ASN cc_start: 0.8278 (m-40) cc_final: 0.7856 (m-40) REVERT: A 89 ARG cc_start: 0.8138 (ttt-90) cc_final: 0.7781 (ttt-90) REVERT: A 141 LEU cc_start: 0.8725 (tp) cc_final: 0.8439 (tt) REVERT: A 143 ARG cc_start: 0.8533 (ttp-110) cc_final: 0.8236 (ttm-80) REVERT: A 193 GLU cc_start: 0.8628 (pm20) cc_final: 0.8004 (pm20) REVERT: A 235 GLU cc_start: 0.7664 (tt0) cc_final: 0.7433 (tt0) REVERT: A 249 ILE cc_start: 0.8725 (tt) cc_final: 0.8418 (tp) REVERT: A 292 SER cc_start: 0.8869 (m) cc_final: 0.8561 (p) REVERT: A 402 LEU cc_start: 0.8630 (mt) cc_final: 0.8398 (pp) REVERT: B 37 PHE cc_start: 0.8268 (t80) cc_final: 0.7785 (t80) REVERT: B 49 ASP cc_start: 0.7713 (t0) cc_final: 0.7481 (t0) REVERT: B 121 ASP cc_start: 0.8579 (p0) cc_final: 0.8344 (p0) REVERT: B 141 LEU cc_start: 0.8644 (tp) cc_final: 0.8375 (tt) REVERT: B 143 ARG cc_start: 0.8474 (ttp-110) cc_final: 0.7958 (ttm-80) REVERT: B 218 ASP cc_start: 0.8755 (p0) cc_final: 0.8408 (p0) REVERT: B 263 TRP cc_start: 0.8281 (m-10) cc_final: 0.8064 (m-10) REVERT: B 300 LYS cc_start: 0.7801 (mmtm) cc_final: 0.7497 (mptt) REVERT: B 402 LEU cc_start: 0.8755 (mt) cc_final: 0.8457 (pp) REVERT: C 37 PHE cc_start: 0.8325 (t80) cc_final: 0.8085 (t80) REVERT: C 143 ARG cc_start: 0.8424 (ttp-110) cc_final: 0.8124 (ttm-80) REVERT: C 179 GLN cc_start: 0.8602 (pt0) cc_final: 0.8385 (pt0) REVERT: C 311 MET cc_start: 0.8695 (mmt) cc_final: 0.8494 (mmm) REVERT: C 402 LEU cc_start: 0.8577 (mt) cc_final: 0.8318 (pp) REVERT: E 38 LEU cc_start: 0.8802 (mt) cc_final: 0.8573 (mm) REVERT: E 49 ASP cc_start: 0.7827 (t0) cc_final: 0.7575 (t0) REVERT: E 121 ASP cc_start: 0.8537 (p0) cc_final: 0.8073 (p0) REVERT: E 143 ARG cc_start: 0.8482 (ttp-110) cc_final: 0.8274 (ttm-80) REVERT: E 179 GLN cc_start: 0.8702 (pt0) cc_final: 0.8425 (pt0) REVERT: E 248 LEU cc_start: 0.8922 (tp) cc_final: 0.8580 (tp) REVERT: E 300 LYS cc_start: 0.8002 (mmtm) cc_final: 0.7603 (mmtt) REVERT: E 323 LEU cc_start: 0.7989 (mt) cc_final: 0.7682 (mt) REVERT: D 37 PHE cc_start: 0.8294 (t80) cc_final: 0.7892 (t80) REVERT: D 53 ARG cc_start: 0.8614 (ttp80) cc_final: 0.8387 (ptm160) REVERT: D 66 ASN cc_start: 0.8211 (m-40) cc_final: 0.7963 (m-40) REVERT: D 81 ASP cc_start: 0.6909 (p0) cc_final: 0.6685 (p0) REVERT: D 141 LEU cc_start: 0.8731 (tp) cc_final: 0.8463 (tt) REVERT: D 143 ARG cc_start: 0.8330 (ttp-110) cc_final: 0.8026 (ttm-80) REVERT: D 147 ASN cc_start: 0.8427 (p0) cc_final: 0.8184 (p0) REVERT: D 179 GLN cc_start: 0.8645 (pt0) cc_final: 0.8416 (pt0) REVERT: D 196 GLU cc_start: 0.8090 (tp30) cc_final: 0.7805 (tp30) REVERT: D 246 TYR cc_start: 0.8315 (t80) cc_final: 0.7905 (t80) REVERT: D 277 VAL cc_start: 0.8822 (t) cc_final: 0.8503 (p) REVERT: D 285 LEU cc_start: 0.8815 (tp) cc_final: 0.8485 (tt) REVERT: D 288 THR cc_start: 0.8548 (m) cc_final: 0.8194 (p) REVERT: D 316 LEU cc_start: 0.8542 (mt) cc_final: 0.8255 (mt) REVERT: D 323 LEU cc_start: 0.8083 (mt) cc_final: 0.7774 (pp) REVERT: D 402 LEU cc_start: 0.8779 (mt) cc_final: 0.8569 (pp) outliers start: 0 outliers final: 0 residues processed: 543 average time/residue: 0.1060 time to fit residues: 82.7126 Evaluate side-chains 420 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 133 HIS B 290 GLN C 133 HIS C 174 GLN E 290 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.098192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.087783 restraints weight = 26707.025| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.71 r_work: 0.3183 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3186 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14555 Z= 0.180 Angle : 0.701 12.885 19775 Z= 0.367 Chirality : 0.049 0.204 2240 Planarity : 0.005 0.044 2435 Dihedral : 4.802 35.101 1910 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.78 % Allowed : 13.01 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.21), residues: 1700 helix: 2.31 (0.21), residues: 575 sheet: 0.91 (0.27), residues: 420 loop : -1.49 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 53 TYR 0.019 0.002 TYR C 246 PHE 0.021 0.002 PHE C 192 TRP 0.017 0.001 TRP E 263 HIS 0.002 0.001 HIS D 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 (14545) covalent geometry : angle 0.69900 / 0.37 (19745) hydrogen bonds : bond 0.05050 / 3.22 ( 695) hydrogen bonds : angle 5.17724 / 3.54 ( 2520) link_BETA1-4 : bond 0.00090 / 0.05 ( 5) link_BETA1-4 : angle 1.20812 / 0.71 ( 15) link_NAG-ASN : bond 0.00341 / 0.20 ( 5) link_NAG-ASN : angle 1.74638 / 1.03 ( 15) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 457 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8439 (t80) cc_final: 0.8175 (t80) REVERT: A 77 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8344 (pt0) REVERT: A 104 ASP cc_start: 0.8007 (t0) cc_final: 0.7763 (t0) REVERT: A 105 ASP cc_start: 0.7602 (p0) cc_final: 0.7382 (p0) REVERT: A 110 ASP cc_start: 0.8735 (t0) cc_final: 0.8510 (t0) REVERT: A 121 ASP cc_start: 0.8836 (p0) cc_final: 0.8553 (p0) REVERT: A 141 LEU cc_start: 0.8847 (tp) cc_final: 0.8577 (tt) REVERT: A 193 GLU cc_start: 0.8829 (pm20) cc_final: 0.8193 (pm20) REVERT: A 218 ASP cc_start: 0.8957 (p0) cc_final: 0.8721 (p0) REVERT: A 235 GLU cc_start: 0.8170 (tt0) cc_final: 0.7958 (tt0) REVERT: A 249 ILE cc_start: 0.8781 (tt) cc_final: 0.8561 (tp) REVERT: A 268 ILE cc_start: 0.7684 (mm) cc_final: 0.7329 (mt) REVERT: A 311 MET cc_start: 0.8690 (mmm) cc_final: 0.8400 (mmm) REVERT: A 409 ARG cc_start: 0.7904 (tpp80) cc_final: 0.7412 (tpt90) REVERT: B 38 LEU cc_start: 0.8893 (mt) cc_final: 0.8472 (mt) REVERT: B 42 MET cc_start: 0.8044 (mpp) cc_final: 0.7215 (mpp) REVERT: B 49 ASP cc_start: 0.8380 (t0) cc_final: 0.8180 (t0) REVERT: B 104 ASP cc_start: 0.7766 (t0) cc_final: 0.7527 (t0) REVERT: B 121 ASP cc_start: 0.8744 (p0) cc_final: 0.8537 (p0) REVERT: B 243 GLN cc_start: 0.8926 (mt0) cc_final: 0.8586 (mt0) REVERT: B 300 LYS cc_start: 0.8227 (mmtm) cc_final: 0.7909 (mptt) REVERT: B 308 ASP cc_start: 0.8694 (m-30) cc_final: 0.8478 (m-30) REVERT: B 408 LYS cc_start: 0.7951 (mmmm) cc_final: 0.7715 (mmtm) REVERT: B 409 ARG cc_start: 0.8357 (tpp80) cc_final: 0.7870 (tpt90) REVERT: C 89 ARG cc_start: 0.8698 (ttt-90) cc_final: 0.8488 (ttt-90) REVERT: C 268 ILE cc_start: 0.7510 (mm) cc_final: 0.7167 (mt) REVERT: C 311 MET cc_start: 0.8968 (mmt) cc_final: 0.8739 (mmm) REVERT: E 38 LEU cc_start: 0.8865 (mt) cc_final: 0.8652 (mt) REVERT: E 42 MET cc_start: 0.8125 (mpp) cc_final: 0.7555 (mpp) REVERT: E 49 ASP cc_start: 0.8378 (t0) cc_final: 0.8158 (t0) REVERT: E 104 ASP cc_start: 0.8204 (t0) cc_final: 0.7976 (t0) REVERT: E 121 ASP cc_start: 0.8672 (p0) cc_final: 0.8369 (p0) REVERT: E 181 GLU cc_start: 0.8398 (tt0) cc_final: 0.8113 (tt0) REVERT: E 248 LEU cc_start: 0.9018 (tp) cc_final: 0.8713 (tp) REVERT: E 300 LYS cc_start: 0.8126 (mmtm) cc_final: 0.7773 (mmtt) REVERT: E 308 ASP cc_start: 0.8722 (m-30) cc_final: 0.8425 (m-30) REVERT: E 323 LEU cc_start: 0.8193 (mt) cc_final: 0.7957 (mt) REVERT: E 409 ARG cc_start: 0.8167 (tpp80) cc_final: 0.7869 (tpt90) REVERT: E 434 LYS cc_start: 0.6065 (OUTLIER) cc_final: 0.5821 (ttpp) REVERT: D 37 PHE cc_start: 0.8364 (t80) cc_final: 0.7975 (t80) REVERT: D 81 ASP cc_start: 0.7308 (p0) cc_final: 0.7093 (p0) REVERT: D 91 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8544 (mt0) REVERT: D 141 LEU cc_start: 0.8868 (tp) cc_final: 0.8588 (tt) REVERT: D 147 ASN cc_start: 0.8764 (p0) cc_final: 0.8556 (p0) REVERT: D 246 TYR cc_start: 0.8550 (t80) cc_final: 0.8214 (t80) REVERT: D 268 ILE cc_start: 0.7661 (mm) cc_final: 0.7391 (mt) REVERT: D 285 LEU cc_start: 0.9007 (tp) cc_final: 0.8708 (tt) REVERT: D 288 THR cc_start: 0.8921 (m) cc_final: 0.8575 (p) REVERT: D 292 SER cc_start: 0.8837 (m) cc_final: 0.8464 (p) REVERT: D 300 LYS cc_start: 0.8326 (mptt) cc_final: 0.7848 (mptt) outliers start: 43 outliers final: 27 residues processed: 474 average time/residue: 0.0969 time to fit residues: 67.3297 Evaluate side-chains 435 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 405 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 269 ASN Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 270 MET Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 269 ASN Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 406 ARG Chi-restraints excluded: chain D residue 408 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 24 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 81 optimal weight: 0.3980 chunk 103 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 149 optimal weight: 0.0980 chunk 42 optimal weight: 0.0030 chunk 162 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 overall best weight: 0.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 139 ASN C 174 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 290 GLN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.098786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.088354 restraints weight = 27131.330| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.72 r_work: 0.3208 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14555 Z= 0.128 Angle : 0.632 12.059 19775 Z= 0.323 Chirality : 0.046 0.189 2240 Planarity : 0.004 0.051 2435 Dihedral : 4.418 35.226 1910 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.65 % Allowed : 15.21 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.21), residues: 1700 helix: 2.36 (0.22), residues: 575 sheet: 0.91 (0.28), residues: 395 loop : -1.36 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 333 TYR 0.021 0.002 TYR C 246 PHE 0.019 0.001 PHE B 330 TRP 0.015 0.001 TRP D 263 HIS 0.002 0.000 HIS B 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (14545) covalent geometry : angle 0.63016 / 0.32 (19745) hydrogen bonds : bond 0.04262 / 2.71 ( 695) hydrogen bonds : angle 4.74659 / 3.25 ( 2520) link_BETA1-4 : bond 0.00363 / 0.20 ( 5) link_BETA1-4 : angle 1.04728 / 0.67 ( 15) link_NAG-ASN : bond 0.00280 / 0.14 ( 5) link_NAG-ASN : angle 1.65323 / 0.90 ( 15) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 427 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8461 (t80) cc_final: 0.8165 (t80) REVERT: A 104 ASP cc_start: 0.8090 (t0) cc_final: 0.7779 (t0) REVERT: A 121 ASP cc_start: 0.8788 (p0) cc_final: 0.8465 (p0) REVERT: A 141 LEU cc_start: 0.8729 (tp) cc_final: 0.8528 (tt) REVERT: A 193 GLU cc_start: 0.8805 (pm20) cc_final: 0.8138 (pm20) REVERT: A 249 ILE cc_start: 0.8748 (tt) cc_final: 0.8470 (tp) REVERT: A 258 ILE cc_start: 0.8703 (mm) cc_final: 0.8443 (tt) REVERT: A 268 ILE cc_start: 0.7663 (mm) cc_final: 0.7277 (mm) REVERT: A 292 SER cc_start: 0.9034 (m) cc_final: 0.8750 (p) REVERT: A 409 ARG cc_start: 0.7856 (tpp80) cc_final: 0.7416 (tpt90) REVERT: B 38 LEU cc_start: 0.8887 (mt) cc_final: 0.8433 (mt) REVERT: B 42 MET cc_start: 0.8054 (mpp) cc_final: 0.7226 (mpp) REVERT: B 104 ASP cc_start: 0.7975 (t0) cc_final: 0.7638 (t0) REVERT: B 121 ASP cc_start: 0.8704 (p0) cc_final: 0.8455 (p0) REVERT: B 206 LEU cc_start: 0.8031 (mt) cc_final: 0.7522 (mp) REVERT: B 300 LYS cc_start: 0.8305 (mmtm) cc_final: 0.7865 (mptt) REVERT: B 308 ASP cc_start: 0.8745 (m-30) cc_final: 0.8488 (m-30) REVERT: B 408 LYS cc_start: 0.7885 (mmmm) cc_final: 0.7678 (mmtm) REVERT: B 409 ARG cc_start: 0.8297 (tpp80) cc_final: 0.7787 (tpt90) REVERT: C 37 PHE cc_start: 0.8239 (t80) cc_final: 0.7875 (t80) REVERT: C 179 GLN cc_start: 0.8847 (pt0) cc_final: 0.8615 (pt0) REVERT: C 268 ILE cc_start: 0.7489 (mm) cc_final: 0.7191 (mt) REVERT: E 49 ASP cc_start: 0.8333 (t0) cc_final: 0.8111 (t0) REVERT: E 104 ASP cc_start: 0.8321 (t0) cc_final: 0.8062 (t0) REVERT: E 121 ASP cc_start: 0.8624 (p0) cc_final: 0.8291 (p0) REVERT: E 181 GLU cc_start: 0.8394 (tt0) cc_final: 0.8032 (tt0) REVERT: E 248 LEU cc_start: 0.9004 (tp) cc_final: 0.8687 (tp) REVERT: E 300 LYS cc_start: 0.8211 (mmtm) cc_final: 0.7679 (mmtt) REVERT: E 308 ASP cc_start: 0.8752 (m-30) cc_final: 0.8451 (m-30) REVERT: E 409 ARG cc_start: 0.8121 (tpp80) cc_final: 0.7843 (tpt170) REVERT: E 434 LYS cc_start: 0.5988 (OUTLIER) cc_final: 0.5711 (ttpp) REVERT: D 147 ASN cc_start: 0.8835 (p0) cc_final: 0.8631 (p0) REVERT: D 189 ASP cc_start: 0.8169 (t0) cc_final: 0.7961 (t70) REVERT: D 246 TYR cc_start: 0.8411 (t80) cc_final: 0.8092 (t80) REVERT: D 288 THR cc_start: 0.8895 (m) cc_final: 0.8527 (p) REVERT: D 292 SER cc_start: 0.8820 (m) cc_final: 0.8463 (p) REVERT: D 300 LYS cc_start: 0.8338 (mptt) cc_final: 0.7998 (mptt) outliers start: 41 outliers final: 30 residues processed: 439 average time/residue: 0.1137 time to fit residues: 74.9260 Evaluate side-chains 418 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 387 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 32 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 298 LEU Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 298 LEU Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 408 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 163 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 133 optimal weight: 0.6980 chunk 81 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 140 optimal weight: 0.0000 chunk 61 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 139 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN C 174 GLN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 GLN D 55 ASN D 426 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.098049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.087708 restraints weight = 27272.284| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.73 r_work: 0.3191 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14555 Z= 0.145 Angle : 0.637 11.252 19775 Z= 0.328 Chirality : 0.046 0.185 2240 Planarity : 0.004 0.047 2435 Dihedral : 4.443 35.162 1910 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.69 % Allowed : 17.09 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.21), residues: 1700 helix: 2.32 (0.22), residues: 575 sheet: 0.97 (0.28), residues: 395 loop : -1.40 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 143 TYR 0.023 0.002 TYR C 246 PHE 0.018 0.002 PHE B 330 TRP 0.014 0.001 TRP B 263 HIS 0.002 0.001 HIS D 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (14545) covalent geometry : angle 0.63331 / 0.33 (19745) hydrogen bonds : bond 0.04194 / 2.68 ( 695) hydrogen bonds : angle 4.76212 / 3.23 ( 2520) link_BETA1-4 : bond 0.00294 / 0.16 ( 5) link_BETA1-4 : angle 1.33070 / 0.85 ( 15) link_NAG-ASN : bond 0.00843 / 0.44 ( 5) link_NAG-ASN : angle 2.09475 / 1.15 ( 15) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 413 time to evaluate : 0.489 Fit side-chains REVERT: A 104 ASP cc_start: 0.8156 (t0) cc_final: 0.7935 (t0) REVERT: A 121 ASP cc_start: 0.8761 (p0) cc_final: 0.8474 (p0) REVERT: A 193 GLU cc_start: 0.8839 (pm20) cc_final: 0.8177 (pm20) REVERT: A 237 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8184 (mtt90) REVERT: A 249 ILE cc_start: 0.8776 (tt) cc_final: 0.8497 (tp) REVERT: A 258 ILE cc_start: 0.8785 (mm) cc_final: 0.8478 (tt) REVERT: A 268 ILE cc_start: 0.7683 (mm) cc_final: 0.7291 (mm) REVERT: A 300 LYS cc_start: 0.8392 (mptt) cc_final: 0.8083 (mmtt) REVERT: A 409 ARG cc_start: 0.7881 (tpp80) cc_final: 0.7471 (tpt90) REVERT: A 426 ASN cc_start: 0.8464 (m-40) cc_final: 0.8261 (m110) REVERT: B 104 ASP cc_start: 0.7988 (t0) cc_final: 0.7709 (t0) REVERT: B 121 ASP cc_start: 0.8699 (p0) cc_final: 0.8388 (p0) REVERT: B 193 GLU cc_start: 0.8882 (pm20) cc_final: 0.8679 (pm20) REVERT: B 196 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8239 (mm-30) REVERT: B 237 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8057 (ptp90) REVERT: B 258 ILE cc_start: 0.8982 (mt) cc_final: 0.8656 (tt) REVERT: B 270 MET cc_start: 0.7920 (pmm) cc_final: 0.7660 (pmm) REVERT: B 300 LYS cc_start: 0.8317 (mmtm) cc_final: 0.7875 (mptt) REVERT: B 308 ASP cc_start: 0.8820 (m-30) cc_final: 0.8547 (m-30) REVERT: B 408 LYS cc_start: 0.7880 (mmmm) cc_final: 0.7651 (mmtm) REVERT: B 409 ARG cc_start: 0.8256 (tpp80) cc_final: 0.7759 (tpt90) REVERT: C 268 ILE cc_start: 0.7561 (mm) cc_final: 0.7295 (mt) REVERT: E 49 ASP cc_start: 0.8447 (t0) cc_final: 0.8246 (t0) REVERT: E 104 ASP cc_start: 0.8324 (t0) cc_final: 0.8115 (t0) REVERT: E 121 ASP cc_start: 0.8606 (p0) cc_final: 0.8213 (p0) REVERT: E 127 GLU cc_start: 0.8098 (tt0) cc_final: 0.7830 (tt0) REVERT: E 181 GLU cc_start: 0.8390 (tt0) cc_final: 0.8010 (tt0) REVERT: E 248 LEU cc_start: 0.9009 (tp) cc_final: 0.8680 (tp) REVERT: E 300 LYS cc_start: 0.8328 (mmtm) cc_final: 0.8047 (mptt) REVERT: E 308 ASP cc_start: 0.8814 (m-30) cc_final: 0.8476 (m-30) REVERT: E 323 LEU cc_start: 0.8299 (mp) cc_final: 0.8085 (mt) REVERT: E 324 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7324 (mt-10) REVERT: E 409 ARG cc_start: 0.8095 (tpp80) cc_final: 0.7718 (tpt90) REVERT: E 434 LYS cc_start: 0.6050 (OUTLIER) cc_final: 0.5785 (ttpp) REVERT: D 147 ASN cc_start: 0.8834 (p0) cc_final: 0.8628 (p0) REVERT: D 243 GLN cc_start: 0.8903 (mt0) cc_final: 0.8688 (mm-40) REVERT: D 246 TYR cc_start: 0.8444 (t80) cc_final: 0.8074 (t80) REVERT: D 268 ILE cc_start: 0.8152 (mm) cc_final: 0.7794 (mt) REVERT: D 288 THR cc_start: 0.8917 (m) cc_final: 0.8569 (p) REVERT: D 292 SER cc_start: 0.8883 (m) cc_final: 0.8525 (p) outliers start: 57 outliers final: 35 residues processed: 433 average time/residue: 0.1122 time to fit residues: 72.7550 Evaluate side-chains 435 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 397 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 431 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 100 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 22 optimal weight: 0.4980 chunk 33 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 142 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 290 GLN C 91 GLN C 174 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 GLN E 426 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.097430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.087145 restraints weight = 27434.852| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.73 r_work: 0.3182 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14555 Z= 0.145 Angle : 0.654 11.763 19775 Z= 0.335 Chirality : 0.046 0.195 2240 Planarity : 0.005 0.046 2435 Dihedral : 4.441 33.455 1910 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.50 % Allowed : 18.32 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.21), residues: 1700 helix: 2.29 (0.22), residues: 575 sheet: 0.98 (0.28), residues: 395 loop : -1.40 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 53 TYR 0.023 0.002 TYR C 246 PHE 0.018 0.002 PHE A 37 TRP 0.013 0.001 TRP B 263 HIS 0.002 0.000 HIS D 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (14545) covalent geometry : angle 0.64842 / 0.33 (19745) hydrogen bonds : bond 0.04021 / 2.56 ( 695) hydrogen bonds : angle 4.64728 / 3.15 ( 2520) link_BETA1-4 : bond 0.00171 / 0.10 ( 5) link_BETA1-4 : angle 1.38139 / 1.00 ( 15) link_NAG-ASN : bond 0.00164 / 0.09 ( 5) link_NAG-ASN : angle 2.92979 / 1.61 ( 15) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 413 time to evaluate : 0.478 Fit side-chains REVERT: A 105 ASP cc_start: 0.7636 (p0) cc_final: 0.7338 (p0) REVERT: A 110 ASP cc_start: 0.8654 (t0) cc_final: 0.8422 (t0) REVERT: A 121 ASP cc_start: 0.8754 (p0) cc_final: 0.8408 (p0) REVERT: A 218 ASP cc_start: 0.8970 (p0) cc_final: 0.8545 (p0) REVERT: A 237 ARG cc_start: 0.8618 (OUTLIER) cc_final: 0.8276 (mtt90) REVERT: A 249 ILE cc_start: 0.8818 (tt) cc_final: 0.8486 (tp) REVERT: A 268 ILE cc_start: 0.7758 (mm) cc_final: 0.7367 (mm) REVERT: A 292 SER cc_start: 0.9061 (m) cc_final: 0.8730 (p) REVERT: A 409 ARG cc_start: 0.7875 (tpp80) cc_final: 0.7473 (tpt90) REVERT: B 121 ASP cc_start: 0.8676 (p0) cc_final: 0.8352 (p0) REVERT: B 193 GLU cc_start: 0.8855 (pm20) cc_final: 0.8610 (pm20) REVERT: B 196 GLU cc_start: 0.8491 (mm-30) cc_final: 0.8278 (mm-30) REVERT: B 237 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8083 (ptp90) REVERT: B 258 ILE cc_start: 0.8999 (mt) cc_final: 0.8787 (mm) REVERT: B 300 LYS cc_start: 0.8252 (mmtm) cc_final: 0.7832 (mptt) REVERT: B 308 ASP cc_start: 0.8833 (m-30) cc_final: 0.8590 (m-30) REVERT: B 409 ARG cc_start: 0.8240 (tpp80) cc_final: 0.7749 (tpt90) REVERT: C 235 GLU cc_start: 0.7102 (mp0) cc_final: 0.6887 (mp0) REVERT: C 268 ILE cc_start: 0.7623 (mm) cc_final: 0.7351 (mt) REVERT: E 37 PHE cc_start: 0.8525 (t80) cc_final: 0.8183 (t80) REVERT: E 49 ASP cc_start: 0.8486 (t0) cc_final: 0.8282 (t0) REVERT: E 104 ASP cc_start: 0.8231 (t0) cc_final: 0.7997 (t0) REVERT: E 127 GLU cc_start: 0.8155 (tt0) cc_final: 0.7876 (tt0) REVERT: E 181 GLU cc_start: 0.8374 (tt0) cc_final: 0.7955 (tt0) REVERT: E 248 LEU cc_start: 0.8998 (tp) cc_final: 0.8685 (tp) REVERT: E 300 LYS cc_start: 0.8325 (mmtm) cc_final: 0.8037 (mptt) REVERT: E 308 ASP cc_start: 0.8832 (m-30) cc_final: 0.8497 (m-30) REVERT: E 323 LEU cc_start: 0.8314 (mp) cc_final: 0.8062 (mt) REVERT: E 324 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7434 (mt-10) REVERT: E 409 ARG cc_start: 0.8110 (tpp80) cc_final: 0.7731 (tpt90) REVERT: D 147 ASN cc_start: 0.8847 (p0) cc_final: 0.8643 (p0) REVERT: D 246 TYR cc_start: 0.8440 (t80) cc_final: 0.8114 (t80) REVERT: D 252 TYR cc_start: 0.8389 (m-80) cc_final: 0.8102 (m-80) REVERT: D 288 THR cc_start: 0.8987 (m) cc_final: 0.8616 (p) REVERT: D 292 SER cc_start: 0.8904 (m) cc_final: 0.8547 (p) outliers start: 54 outliers final: 38 residues processed: 434 average time/residue: 0.1116 time to fit residues: 72.6644 Evaluate side-chains 445 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 405 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 427 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 112 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 169 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 426 ASN C 174 GLN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 GLN D 243 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.095421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 20)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.085205 restraints weight = 27604.296| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.72 r_work: 0.3148 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14555 Z= 0.186 Angle : 0.672 10.960 19775 Z= 0.347 Chirality : 0.047 0.201 2240 Planarity : 0.005 0.046 2435 Dihedral : 4.612 33.180 1910 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 4.08 % Allowed : 19.09 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.21), residues: 1700 helix: 2.28 (0.22), residues: 570 sheet: 0.82 (0.26), residues: 425 loop : -1.45 (0.22), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 333 TYR 0.024 0.002 TYR C 246 PHE 0.022 0.002 PHE A 192 TRP 0.010 0.001 TRP C 263 HIS 0.002 0.001 HIS A 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00437 / 0.19 (14545) covalent geometry : angle 0.66566 / 0.35 (19745) hydrogen bonds : bond 0.04256 / 2.71 ( 695) hydrogen bonds : angle 4.66598 / 3.17 ( 2520) link_BETA1-4 : bond 0.00166 / 0.08 ( 5) link_BETA1-4 : angle 1.33885 / 0.92 ( 15) link_NAG-ASN : bond 0.00228 / 0.15 ( 5) link_NAG-ASN : angle 3.18441 / 1.79 ( 15) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 414 time to evaluate : 0.557 Fit side-chains REVERT: A 121 ASP cc_start: 0.8752 (p0) cc_final: 0.8402 (p0) REVERT: A 193 GLU cc_start: 0.8840 (pm20) cc_final: 0.8378 (pm20) REVERT: A 237 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8022 (mtt90) REVERT: A 268 ILE cc_start: 0.7771 (mm) cc_final: 0.7386 (mm) REVERT: A 409 ARG cc_start: 0.7909 (tpp80) cc_final: 0.7508 (tpt90) REVERT: B 121 ASP cc_start: 0.8695 (p0) cc_final: 0.8361 (p0) REVERT: B 193 GLU cc_start: 0.8907 (pm20) cc_final: 0.8665 (pm20) REVERT: B 196 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8346 (mm-30) REVERT: B 237 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8133 (ptp90) REVERT: B 300 LYS cc_start: 0.8299 (mmtm) cc_final: 0.7888 (mptt) REVERT: B 308 ASP cc_start: 0.8843 (m-30) cc_final: 0.8610 (m-30) REVERT: B 409 ARG cc_start: 0.8188 (tpp80) cc_final: 0.7903 (tpt90) REVERT: C 268 ILE cc_start: 0.7646 (mm) cc_final: 0.7372 (mt) REVERT: C 290 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8853 (tt0) REVERT: C 300 LYS cc_start: 0.8335 (mmtt) cc_final: 0.8094 (mmtt) REVERT: E 104 ASP cc_start: 0.8292 (t0) cc_final: 0.8072 (t0) REVERT: E 121 ASP cc_start: 0.8646 (p0) cc_final: 0.8273 (p0) REVERT: E 127 GLU cc_start: 0.8206 (tt0) cc_final: 0.7937 (tt0) REVERT: E 181 GLU cc_start: 0.8385 (tt0) cc_final: 0.7988 (tt0) REVERT: E 248 LEU cc_start: 0.9055 (tp) cc_final: 0.8766 (tp) REVERT: E 300 LYS cc_start: 0.8344 (mmtm) cc_final: 0.8044 (mptt) REVERT: E 308 ASP cc_start: 0.8856 (m-30) cc_final: 0.8526 (m-30) REVERT: E 323 LEU cc_start: 0.8358 (mp) cc_final: 0.8091 (mt) REVERT: E 324 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7529 (mt-10) REVERT: E 409 ARG cc_start: 0.8150 (tpp80) cc_final: 0.7774 (tpt90) REVERT: D 37 PHE cc_start: 0.8633 (t80) cc_final: 0.8395 (t80) REVERT: D 147 ASN cc_start: 0.8849 (p0) cc_final: 0.8640 (p0) REVERT: D 246 TYR cc_start: 0.8456 (t80) cc_final: 0.8154 (t80) REVERT: D 268 ILE cc_start: 0.8229 (mm) cc_final: 0.7852 (mt) REVERT: D 288 THR cc_start: 0.9071 (m) cc_final: 0.8700 (p) REVERT: D 292 SER cc_start: 0.8958 (m) cc_final: 0.8586 (p) REVERT: D 300 LYS cc_start: 0.8391 (mptt) cc_final: 0.8075 (mmtt) outliers start: 63 outliers final: 46 residues processed: 436 average time/residue: 0.1130 time to fit residues: 73.7309 Evaluate side-chains 453 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 404 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 289 THR Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 434 LYS Chi-restraints excluded: chain D residue 110 ASP Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 270 MET Chi-restraints excluded: chain D residue 427 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 103 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 152 optimal weight: 0.6980 chunk 165 optimal weight: 0.9980 chunk 166 optimal weight: 0.0470 chunk 145 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 56 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.097169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.086853 restraints weight = 27256.545| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.73 r_work: 0.3178 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14555 Z= 0.139 Angle : 0.672 12.615 19775 Z= 0.343 Chirality : 0.046 0.316 2240 Planarity : 0.005 0.046 2435 Dihedral : 4.541 30.388 1910 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.56 % Allowed : 21.10 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.21), residues: 1700 helix: 2.26 (0.22), residues: 570 sheet: 0.89 (0.27), residues: 405 loop : -1.47 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 333 TYR 0.021 0.002 TYR C 246 PHE 0.021 0.001 PHE B 330 TRP 0.011 0.001 TRP A 263 HIS 0.001 0.000 HIS D 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (14545) covalent geometry : angle 0.66924 / 0.34 (19745) hydrogen bonds : bond 0.03976 / 2.53 ( 695) hydrogen bonds : angle 4.60838 / 3.12 ( 2520) link_BETA1-4 : bond 0.00216 / 0.13 ( 5) link_BETA1-4 : angle 1.14673 / 0.77 ( 15) link_NAG-ASN : bond 0.00034 / 0.03 ( 5) link_NAG-ASN : angle 2.20154 / 1.25 ( 15) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 417 time to evaluate : 0.719 Fit side-chains REVERT: A 105 ASP cc_start: 0.7567 (p0) cc_final: 0.7224 (p0) REVERT: A 110 ASP cc_start: 0.8626 (t0) cc_final: 0.8377 (t0) REVERT: A 121 ASP cc_start: 0.8723 (p0) cc_final: 0.8352 (p0) REVERT: A 218 ASP cc_start: 0.8985 (p0) cc_final: 0.8695 (p0) REVERT: A 268 ILE cc_start: 0.7763 (mm) cc_final: 0.7388 (mm) REVERT: A 409 ARG cc_start: 0.7874 (tpp80) cc_final: 0.7474 (tpt90) REVERT: B 121 ASP cc_start: 0.8648 (p0) cc_final: 0.8297 (p0) REVERT: B 193 GLU cc_start: 0.8936 (pm20) cc_final: 0.8682 (pm20) REVERT: B 237 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.8068 (ptp90) REVERT: B 300 LYS cc_start: 0.8275 (mmtm) cc_final: 0.7918 (mptt) REVERT: B 308 ASP cc_start: 0.8848 (m-30) cc_final: 0.8603 (m-30) REVERT: B 409 ARG cc_start: 0.8132 (tpp80) cc_final: 0.7857 (tpt90) REVERT: C 232 THR cc_start: 0.8750 (OUTLIER) cc_final: 0.8447 (t) REVERT: C 268 ILE cc_start: 0.7623 (mm) cc_final: 0.7241 (mm) REVERT: C 290 GLN cc_start: 0.9078 (OUTLIER) cc_final: 0.8856 (tt0) REVERT: C 409 ARG cc_start: 0.7862 (ttm-80) cc_final: 0.6923 (tpt90) REVERT: E 127 GLU cc_start: 0.8188 (tt0) cc_final: 0.7917 (tt0) REVERT: E 248 LEU cc_start: 0.9046 (tp) cc_final: 0.8779 (tp) REVERT: E 300 LYS cc_start: 0.8316 (mmtm) cc_final: 0.8018 (mptt) REVERT: E 308 ASP cc_start: 0.8823 (m-30) cc_final: 0.8513 (m-30) REVERT: E 324 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7582 (mt-10) REVERT: E 409 ARG cc_start: 0.8118 (tpp80) cc_final: 0.7741 (tpt90) REVERT: D 89 ARG cc_start: 0.8829 (ttt-90) cc_final: 0.8592 (ttt-90) REVERT: D 147 ASN cc_start: 0.8864 (p0) cc_final: 0.8652 (p0) REVERT: D 246 TYR cc_start: 0.8418 (t80) cc_final: 0.8110 (t80) REVERT: D 292 SER cc_start: 0.8976 (m) cc_final: 0.8609 (p) REVERT: D 300 LYS cc_start: 0.8470 (mptt) cc_final: 0.8107 (mmtt) outliers start: 55 outliers final: 41 residues processed: 436 average time/residue: 0.1152 time to fit residues: 75.2186 Evaluate side-chains 451 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 407 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 270 MET Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 322 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 71 optimal weight: 4.9990 chunk 60 optimal weight: 0.0050 chunk 98 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 chunk 36 optimal weight: 0.0770 chunk 158 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.5352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 174 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.097553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.087290 restraints weight = 27373.941| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.72 r_work: 0.3190 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14555 Z= 0.138 Angle : 0.683 11.898 19775 Z= 0.347 Chirality : 0.047 0.316 2240 Planarity : 0.005 0.045 2435 Dihedral : 4.484 28.744 1910 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.37 % Allowed : 22.14 % Favored : 74.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.21), residues: 1700 helix: 2.20 (0.22), residues: 570 sheet: 0.85 (0.27), residues: 405 loop : -1.46 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 89 TYR 0.022 0.002 TYR C 246 PHE 0.024 0.002 PHE D 37 TRP 0.011 0.001 TRP A 263 HIS 0.001 0.000 HIS D 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (14545) covalent geometry : angle 0.68034 / 0.35 (19745) hydrogen bonds : bond 0.03889 / 2.48 ( 695) hydrogen bonds : angle 4.56064 / 3.09 ( 2520) link_BETA1-4 : bond 0.00217 / 0.13 ( 5) link_BETA1-4 : angle 1.19111 / 0.77 ( 15) link_NAG-ASN : bond 0.00066 / 0.05 ( 5) link_NAG-ASN : angle 1.89303 / 1.06 ( 15) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 419 time to evaluate : 0.588 Fit side-chains REVERT: A 121 ASP cc_start: 0.8687 (p0) cc_final: 0.8301 (p0) REVERT: A 193 GLU cc_start: 0.8863 (pm20) cc_final: 0.8359 (pm20) REVERT: A 268 ILE cc_start: 0.7779 (mm) cc_final: 0.7374 (mm) REVERT: A 409 ARG cc_start: 0.7833 (tpp80) cc_final: 0.7432 (tpt90) REVERT: B 121 ASP cc_start: 0.8634 (p0) cc_final: 0.8267 (p0) REVERT: B 193 GLU cc_start: 0.8950 (pm20) cc_final: 0.8696 (pm20) REVERT: B 237 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.8021 (ptp90) REVERT: B 300 LYS cc_start: 0.8283 (mmtm) cc_final: 0.7899 (mptt) REVERT: B 308 ASP cc_start: 0.8848 (m-30) cc_final: 0.8596 (m-30) REVERT: B 409 ARG cc_start: 0.8142 (tpp80) cc_final: 0.7842 (tpt90) REVERT: C 232 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8386 (t) REVERT: C 268 ILE cc_start: 0.7636 (mm) cc_final: 0.7232 (mm) REVERT: C 290 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8838 (tt0) REVERT: C 409 ARG cc_start: 0.7841 (ttm-80) cc_final: 0.6919 (tpt90) REVERT: E 80 MET cc_start: 0.8667 (mmt) cc_final: 0.8201 (mmt) REVERT: E 121 ASP cc_start: 0.8632 (p0) cc_final: 0.8219 (p0) REVERT: E 127 GLU cc_start: 0.8206 (tt0) cc_final: 0.7924 (tt0) REVERT: E 248 LEU cc_start: 0.9066 (tp) cc_final: 0.8814 (tp) REVERT: E 300 LYS cc_start: 0.8310 (mmtm) cc_final: 0.7968 (mptt) REVERT: E 308 ASP cc_start: 0.8792 (m-30) cc_final: 0.8533 (m-30) REVERT: E 324 GLU cc_start: 0.7877 (mt-10) cc_final: 0.7661 (mt-10) REVERT: E 409 ARG cc_start: 0.8101 (tpp80) cc_final: 0.7726 (tpt90) REVERT: D 89 ARG cc_start: 0.8832 (ttt-90) cc_final: 0.8579 (ttt-90) REVERT: D 94 ASP cc_start: 0.8316 (t0) cc_final: 0.8096 (t0) REVERT: D 147 ASN cc_start: 0.8837 (p0) cc_final: 0.8623 (p0) REVERT: D 246 TYR cc_start: 0.8472 (t80) cc_final: 0.8185 (t80) REVERT: D 268 ILE cc_start: 0.8143 (mm) cc_final: 0.7688 (mt) REVERT: D 292 SER cc_start: 0.8919 (m) cc_final: 0.8591 (p) REVERT: D 300 LYS cc_start: 0.8463 (mptt) cc_final: 0.8097 (mmtt) outliers start: 52 outliers final: 38 residues processed: 435 average time/residue: 0.1130 time to fit residues: 73.4858 Evaluate side-chains 447 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 406 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 290 GLN Chi-restraints excluded: chain D residue 322 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 160 optimal weight: 0.8980 chunk 137 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 174 GLN D 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.094999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.084800 restraints weight = 27581.562| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 2.72 r_work: 0.3141 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14555 Z= 0.197 Angle : 0.722 12.255 19775 Z= 0.372 Chirality : 0.048 0.333 2240 Planarity : 0.005 0.046 2435 Dihedral : 4.697 29.972 1910 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.04 % Allowed : 23.17 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.21), residues: 1700 helix: 2.14 (0.22), residues: 570 sheet: 0.82 (0.27), residues: 405 loop : -1.48 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 333 TYR 0.023 0.002 TYR C 246 PHE 0.024 0.002 PHE A 192 TRP 0.010 0.001 TRP A 430 HIS 0.002 0.001 HIS D 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.20 (14545) covalent geometry : angle 0.71428 / 0.37 (19745) hydrogen bonds : bond 0.04246 / 2.71 ( 695) hydrogen bonds : angle 4.63013 / 3.13 ( 2520) link_BETA1-4 : bond 0.00175 / 0.10 ( 5) link_BETA1-4 : angle 1.44302 / 1.01 ( 15) link_NAG-ASN : bond 0.00370 / 0.22 ( 5) link_NAG-ASN : angle 3.63350 / 2.16 ( 15) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 413 time to evaluate : 0.600 Fit side-chains REVERT: A 105 ASP cc_start: 0.7523 (p0) cc_final: 0.7221 (p0) REVERT: A 110 ASP cc_start: 0.8600 (t0) cc_final: 0.8302 (t0) REVERT: A 121 ASP cc_start: 0.8724 (p0) cc_final: 0.8356 (p0) REVERT: A 218 ASP cc_start: 0.9057 (p0) cc_final: 0.8749 (p0) REVERT: A 268 ILE cc_start: 0.7817 (mm) cc_final: 0.7435 (mm) REVERT: A 409 ARG cc_start: 0.7904 (tpp80) cc_final: 0.7528 (tpt90) REVERT: B 121 ASP cc_start: 0.8708 (p0) cc_final: 0.8339 (p0) REVERT: B 193 GLU cc_start: 0.8979 (pm20) cc_final: 0.8729 (pm20) REVERT: B 237 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.8110 (ptp90) REVERT: B 300 LYS cc_start: 0.8294 (mmtm) cc_final: 0.7862 (mptt) REVERT: B 308 ASP cc_start: 0.8857 (m-30) cc_final: 0.8611 (m-30) REVERT: B 409 ARG cc_start: 0.8173 (tpp80) cc_final: 0.7717 (tpt90) REVERT: C 232 THR cc_start: 0.8813 (OUTLIER) cc_final: 0.8552 (t) REVERT: C 268 ILE cc_start: 0.7647 (mm) cc_final: 0.7246 (mm) REVERT: C 290 GLN cc_start: 0.9127 (OUTLIER) cc_final: 0.8919 (tt0) REVERT: C 409 ARG cc_start: 0.7950 (ttm-80) cc_final: 0.7082 (tpt90) REVERT: E 127 GLU cc_start: 0.8209 (tt0) cc_final: 0.7933 (tt0) REVERT: E 248 LEU cc_start: 0.9136 (tp) cc_final: 0.8913 (tp) REVERT: E 300 LYS cc_start: 0.8345 (mmtm) cc_final: 0.7972 (mptt) REVERT: E 308 ASP cc_start: 0.8797 (m-30) cc_final: 0.8539 (m-30) REVERT: E 323 LEU cc_start: 0.8376 (mp) cc_final: 0.8108 (mt) REVERT: E 324 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7529 (mt-10) REVERT: E 409 ARG cc_start: 0.8191 (tpp80) cc_final: 0.7823 (tpt90) REVERT: D 89 ARG cc_start: 0.8851 (ttt-90) cc_final: 0.8565 (ttt-90) REVERT: D 147 ASN cc_start: 0.8852 (p0) cc_final: 0.8617 (p0) REVERT: D 246 TYR cc_start: 0.8499 (t80) cc_final: 0.8172 (t80) REVERT: D 292 SER cc_start: 0.8950 (m) cc_final: 0.8586 (p) outliers start: 47 outliers final: 36 residues processed: 429 average time/residue: 0.1124 time to fit residues: 72.3361 Evaluate side-chains 443 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 404 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 192 PHE Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 237 ARG Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 244 MET Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 290 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 71 optimal weight: 0.9980 chunk 95 optimal weight: 0.0570 chunk 139 optimal weight: 0.9980 chunk 143 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 chunk 113 optimal weight: 2.9990 chunk 132 optimal weight: 0.0020 chunk 77 optimal weight: 0.0010 chunk 54 optimal weight: 3.9990 overall best weight: 0.3112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 GLN B 334 GLN C 91 GLN C 174 GLN C 334 GLN D 168 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.097847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.087554 restraints weight = 27253.987| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.73 r_work: 0.3191 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14555 Z= 0.137 Angle : 0.714 12.557 19775 Z= 0.362 Chirality : 0.047 0.342 2240 Planarity : 0.005 0.055 2435 Dihedral : 4.547 27.812 1910 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.27 % Allowed : 24.01 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.21), residues: 1700 helix: 2.12 (0.22), residues: 575 sheet: 0.81 (0.27), residues: 405 loop : -1.50 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 242 TYR 0.023 0.002 TYR C 246 PHE 0.024 0.001 PHE B 330 TRP 0.012 0.001 TRP A 263 HIS 0.001 0.000 HIS D 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (14545) covalent geometry : angle 0.70837 / 0.36 (19745) hydrogen bonds : bond 0.03839 / 2.46 ( 695) hydrogen bonds : angle 4.57544 / 3.10 ( 2520) link_BETA1-4 : bond 0.00284 / 0.16 ( 5) link_BETA1-4 : angle 1.17050 / 0.81 ( 15) link_NAG-ASN : bond 0.00116 / 0.06 ( 5) link_NAG-ASN : angle 3.25885 / 1.96 ( 15) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 405 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 121 ASP cc_start: 0.8681 (p0) cc_final: 0.8290 (p0) REVERT: A 193 GLU cc_start: 0.8814 (pm20) cc_final: 0.8420 (pm20) REVERT: A 268 ILE cc_start: 0.7807 (mm) cc_final: 0.7414 (mm) REVERT: A 409 ARG cc_start: 0.7836 (tpp80) cc_final: 0.7515 (tpt90) REVERT: B 121 ASP cc_start: 0.8640 (p0) cc_final: 0.8246 (p0) REVERT: B 193 GLU cc_start: 0.8975 (pm20) cc_final: 0.8747 (pm20) REVERT: B 300 LYS cc_start: 0.8268 (mmtm) cc_final: 0.7834 (mptt) REVERT: B 308 ASP cc_start: 0.8866 (m-30) cc_final: 0.8587 (m-30) REVERT: B 409 ARG cc_start: 0.8140 (tpp80) cc_final: 0.7668 (tpt90) REVERT: C 80 MET cc_start: 0.8759 (mmm) cc_final: 0.8518 (mmm) REVERT: C 232 THR cc_start: 0.8701 (OUTLIER) cc_final: 0.8345 (t) REVERT: C 268 ILE cc_start: 0.7597 (mm) cc_final: 0.7201 (mm) REVERT: C 290 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8857 (tt0) REVERT: C 409 ARG cc_start: 0.7891 (ttm-80) cc_final: 0.7019 (tpt90) REVERT: E 121 ASP cc_start: 0.8650 (p0) cc_final: 0.8225 (p0) REVERT: E 127 GLU cc_start: 0.8181 (tt0) cc_final: 0.7916 (tt0) REVERT: E 248 LEU cc_start: 0.9098 (tp) cc_final: 0.8875 (tp) REVERT: E 300 LYS cc_start: 0.8324 (mmtm) cc_final: 0.7973 (mptt) REVERT: E 308 ASP cc_start: 0.8781 (m-30) cc_final: 0.8528 (m-30) REVERT: E 323 LEU cc_start: 0.8345 (mp) cc_final: 0.8067 (mt) REVERT: E 324 GLU cc_start: 0.7755 (mt-10) cc_final: 0.7547 (mt-10) REVERT: E 409 ARG cc_start: 0.8133 (tpp80) cc_final: 0.7762 (tpt90) REVERT: D 37 PHE cc_start: 0.8814 (t80) cc_final: 0.8565 (t80) REVERT: D 89 ARG cc_start: 0.8832 (ttt-90) cc_final: 0.8584 (ttt-90) REVERT: D 147 ASN cc_start: 0.8841 (p0) cc_final: 0.8622 (p0) REVERT: D 246 TYR cc_start: 0.8494 (t80) cc_final: 0.8213 (t80) REVERT: D 268 ILE cc_start: 0.8125 (mm) cc_final: 0.7671 (mt) REVERT: D 292 SER cc_start: 0.8928 (m) cc_final: 0.8573 (p) REVERT: D 300 LYS cc_start: 0.8415 (mptt) cc_final: 0.8016 (mmtt) outliers start: 35 outliers final: 30 residues processed: 416 average time/residue: 0.1027 time to fit residues: 64.2314 Evaluate side-chains 434 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 402 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 237 ARG Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 290 GLN Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 206 LEU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 264 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 149 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 136 optimal weight: 0.2980 chunk 101 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 chunk 156 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 GLN B 334 GLN C 91 GLN C 174 GLN C 334 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.097533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.087293 restraints weight = 27269.629| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.73 r_work: 0.3186 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 14555 Z= 0.192 Angle : 0.906 59.196 19775 Z= 0.502 Chirality : 0.049 0.627 2240 Planarity : 0.005 0.051 2435 Dihedral : 4.640 42.725 1910 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.14 % Allowed : 24.01 % Favored : 73.85 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.21), residues: 1700 helix: 2.09 (0.22), residues: 575 sheet: 0.81 (0.27), residues: 405 loop : -1.52 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 237 TYR 0.022 0.002 TYR C 246 PHE 0.022 0.001 PHE B 330 TRP 0.011 0.001 TRP A 263 HIS 0.001 0.000 HIS D 133 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.19 (14545) covalent geometry : angle 0.90134 / 0.50 (19745) hydrogen bonds : bond 0.03873 / 2.48 ( 695) hydrogen bonds : angle 4.57420 / 3.10 ( 2520) link_BETA1-4 : bond 0.00316 / 0.18 ( 5) link_BETA1-4 : angle 1.19818 / 0.82 ( 15) link_NAG-ASN : bond 0.00089 / 0.04 ( 5) link_NAG-ASN : angle 3.22076 / 1.94 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2819.93 seconds wall clock time: 49 minutes 18.37 seconds (2958.37 seconds total)