Starting phenix.real_space_refine on Wed Mar 4 14:55:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7m6m_23700/03_2026/7m6m_23700.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m6m_23700/03_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_23700/03_2026/7m6m_23700.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m6m_23700/03_2026/7m6m_23700.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7m6m_23700/03_2026/7m6m_23700.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m6m_23700/03_2026/7m6m_23700.map" } 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-5986/lib/python3.9/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 dihedrals: 6 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: 2.35, per 1000 atoms: 0.17 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: 1.02 Conformation dependent library (CDL) restraints added in 428.3 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: 0.35 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: 2.17 Time building geometry restraints manager: 1.30 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: 8215 16.26 - 32.52: 515 32.52 - 48.79: 105 48.79 - 65.05: 30 65.05 - 81.31: 10 Dihedral angle restraints: 8875 sinusoidal: 3790 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 8872 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: 0.02 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: 1.640 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 11.630 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 11.549 81.309 5575 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 covalent geometry : bond 0.00811 (14545) covalent geometry : angle 1.31241 (19745) hydrogen bonds : bond 0.13763 ( 695) hydrogen bonds : angle 7.00264 ( 2520) link_BETA1-4 : bond 0.00897 ( 5) link_BETA1-4 : angle 1.88954 ( 15) link_NAG-ASN : bond 0.00242 ( 5) link_NAG-ASN : angle 3.41951 ( 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 : 0.536 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: 0.1226 time to fit residues: 94.6524 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 : 0.449 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3493 r_free = 0.3493 target = 0.098249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.087822 restraints weight = 26764.367| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.71 r_work: 0.3182 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 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 = 0.3186 r_free = 0.3186 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3186 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14555 Z= 0.181 Angle : 0.702 13.294 19775 Z= 0.368 Chirality : 0.049 0.220 2240 Planarity : 0.005 0.044 2435 Dihedral : 5.015 35.117 2220 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.78 % Allowed : 12.88 % Favored : 84.34 % 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: 0.70 (0.21), residues: 1700 helix: 2.33 (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 0.006 0.001 ARG A 409 TYR 0.018 0.002 TYR C 246 PHE 0.022 0.002 PHE C 192 TRP 0.017 0.002 TRP E 263 HIS 0.001 0.000 HIS D 133 Details of bonding type rmsd covalent geometry : bond 0.00416 (14545) covalent geometry : angle 0.70022 (19745) hydrogen bonds : bond 0.05076 ( 695) hydrogen bonds : angle 5.20182 ( 2520) link_BETA1-4 : bond 0.00274 ( 5) link_BETA1-4 : angle 1.36433 ( 15) link_NAG-ASN : bond 0.00174 ( 5) link_NAG-ASN : angle 1.81016 ( 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 502 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 459 time to evaluate : 0.527 Fit side-chains revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8437 (t80) cc_final: 0.8178 (t80) REVERT: A 77 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8357 (pt0) REVERT: A 104 ASP cc_start: 0.8004 (t0) cc_final: 0.7758 (t0) REVERT: A 105 ASP cc_start: 0.7583 (p0) cc_final: 0.7358 (p0) REVERT: A 110 ASP cc_start: 0.8739 (t0) cc_final: 0.8518 (t0) REVERT: A 121 ASP cc_start: 0.8835 (p0) cc_final: 0.8555 (p0) REVERT: A 141 LEU cc_start: 0.8847 (tp) cc_final: 0.8576 (tt) REVERT: A 193 GLU cc_start: 0.8829 (pm20) cc_final: 0.8192 (pm20) REVERT: A 218 ASP cc_start: 0.8956 (p0) cc_final: 0.8722 (p0) REVERT: A 235 GLU cc_start: 0.8151 (tt0) cc_final: 0.7934 (tt0) REVERT: A 249 ILE cc_start: 0.8796 (tt) cc_final: 0.8567 (tp) REVERT: A 268 ILE cc_start: 0.7689 (mm) cc_final: 0.7332 (mt) REVERT: A 311 MET cc_start: 0.8697 (mmm) cc_final: 0.8399 (mmm) REVERT: A 409 ARG cc_start: 0.7901 (tpp80) cc_final: 0.7405 (tpt90) REVERT: B 38 LEU cc_start: 0.8899 (mt) cc_final: 0.8462 (mt) REVERT: B 42 MET cc_start: 0.8057 (mpp) cc_final: 0.7195 (mpp) REVERT: B 49 ASP cc_start: 0.8370 (t0) cc_final: 0.8170 (t0) REVERT: B 104 ASP cc_start: 0.7736 (t0) cc_final: 0.7500 (t0) REVERT: B 121 ASP cc_start: 0.8744 (p0) cc_final: 0.8536 (p0) REVERT: B 243 GLN cc_start: 0.8925 (mt0) cc_final: 0.8585 (mt0) REVERT: B 300 LYS cc_start: 0.8219 (mmtm) cc_final: 0.7919 (mptt) REVERT: B 308 ASP cc_start: 0.8691 (m-30) cc_final: 0.8477 (m-30) REVERT: B 408 LYS cc_start: 0.7945 (mmmm) cc_final: 0.7695 (mmtm) REVERT: B 409 ARG cc_start: 0.8402 (tpp80) cc_final: 0.7905 (tpt90) REVERT: C 268 ILE cc_start: 0.7502 (mm) cc_final: 0.7159 (mt) REVERT: C 311 MET cc_start: 0.8966 (mmt) cc_final: 0.8748 (mmm) REVERT: E 38 LEU cc_start: 0.8870 (mt) cc_final: 0.8449 (mt) REVERT: E 42 MET cc_start: 0.8128 (mpp) cc_final: 0.7278 (mpp) REVERT: E 49 ASP cc_start: 0.8372 (t0) cc_final: 0.8154 (t0) REVERT: E 104 ASP cc_start: 0.8180 (t0) cc_final: 0.7953 (t0) REVERT: E 121 ASP cc_start: 0.8668 (p0) cc_final: 0.8365 (p0) REVERT: E 171 MET cc_start: 0.7775 (mpp) cc_final: 0.7297 (mtm) REVERT: E 248 LEU cc_start: 0.9018 (tp) cc_final: 0.8665 (tp) REVERT: E 300 LYS cc_start: 0.8106 (mmtm) cc_final: 0.7712 (mmtt) REVERT: E 308 ASP cc_start: 0.8721 (m-30) cc_final: 0.8428 (m-30) REVERT: E 323 LEU cc_start: 0.8201 (mt) cc_final: 0.7906 (mp) REVERT: E 409 ARG cc_start: 0.8162 (tpp80) cc_final: 0.7873 (tpt90) REVERT: E 434 LYS cc_start: 0.6073 (OUTLIER) cc_final: 0.5806 (ttpp) REVERT: D 37 PHE cc_start: 0.8369 (t80) cc_final: 0.7992 (t80) REVERT: D 81 ASP cc_start: 0.7304 (p0) cc_final: 0.7094 (p0) REVERT: D 91 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8536 (mt0) REVERT: D 141 LEU cc_start: 0.8870 (tp) cc_final: 0.8592 (tt) REVERT: D 147 ASN cc_start: 0.8758 (p0) cc_final: 0.8549 (p0) REVERT: D 246 TYR cc_start: 0.8550 (t80) cc_final: 0.8223 (t80) REVERT: D 285 LEU cc_start: 0.9005 (tp) cc_final: 0.8707 (tt) REVERT: D 288 THR cc_start: 0.8917 (m) cc_final: 0.8573 (p) REVERT: D 292 SER cc_start: 0.8833 (m) cc_final: 0.8461 (p) REVERT: D 300 LYS cc_start: 0.8322 (mptt) cc_final: 0.7845 (mptt) outliers start: 43 outliers final: 28 residues processed: 477 average time/residue: 0.1128 time to fit residues: 78.4938 Evaluate side-chains 435 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 404 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 269 ASN 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: 0.6980 chunk 160 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 149 optimal weight: 0.0470 chunk 42 optimal weight: 0.0040 chunk 162 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.4490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN C 174 GLN C 290 GLN E 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.098566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.088153 restraints weight = 27070.481| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.71 r_work: 0.3199 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.2838 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= 0.132 Angle : 0.640 12.329 19775 Z= 0.328 Chirality : 0.046 0.208 2240 Planarity : 0.004 0.050 2435 Dihedral : 4.590 35.389 2220 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.78 % Allowed : 15.15 % Favored : 82.07 % 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: 2.33 (0.21), residues: 575 sheet: 0.93 (0.28), residues: 395 loop : -1.38 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 333 TYR 0.021 0.002 TYR C 246 PHE 0.019 0.002 PHE B 330 TRP 0.015 0.001 TRP D 263 HIS 0.002 0.000 HIS B 133 Details of bonding type rmsd covalent geometry : bond 0.00295 (14545) covalent geometry : angle 0.63740 (19745) hydrogen bonds : bond 0.04401 ( 695) hydrogen bonds : angle 4.79106 ( 2520) link_BETA1-4 : bond 0.00212 ( 5) link_BETA1-4 : angle 1.44694 ( 15) link_NAG-ASN : bond 0.00387 ( 5) link_NAG-ASN : angle 1.66272 ( 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 465 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 422 time to evaluate : 0.557 Fit side-chains REVERT: A 37 PHE cc_start: 0.8420 (t80) cc_final: 0.8125 (t80) REVERT: A 104 ASP cc_start: 0.8075 (t0) cc_final: 0.7775 (t0) REVERT: A 121 ASP cc_start: 0.8800 (p0) cc_final: 0.8483 (p0) REVERT: A 141 LEU cc_start: 0.8757 (tp) cc_final: 0.8552 (tt) REVERT: A 193 GLU cc_start: 0.8806 (pm20) cc_final: 0.8185 (pm20) REVERT: A 249 ILE cc_start: 0.8766 (tt) cc_final: 0.8484 (tp) REVERT: A 268 ILE cc_start: 0.7711 (mm) cc_final: 0.7328 (mm) REVERT: A 292 SER cc_start: 0.9034 (m) cc_final: 0.8751 (p) REVERT: A 409 ARG cc_start: 0.7861 (tpp80) cc_final: 0.7421 (tpt90) REVERT: B 38 LEU cc_start: 0.8895 (mt) cc_final: 0.8442 (mt) REVERT: B 42 MET cc_start: 0.8063 (mpp) cc_final: 0.7228 (mpp) REVERT: B 104 ASP cc_start: 0.7847 (t0) cc_final: 0.7520 (t0) REVERT: B 121 ASP cc_start: 0.8716 (p0) cc_final: 0.8473 (p0) REVERT: B 206 LEU cc_start: 0.8027 (mt) cc_final: 0.7515 (mp) REVERT: B 300 LYS cc_start: 0.8308 (mmtm) cc_final: 0.7873 (mptt) REVERT: B 308 ASP cc_start: 0.8761 (m-30) cc_final: 0.8508 (m-30) REVERT: B 408 LYS cc_start: 0.7899 (mmmm) cc_final: 0.7694 (mmtm) REVERT: B 409 ARG cc_start: 0.8295 (tpp80) cc_final: 0.7781 (tpt90) REVERT: C 37 PHE cc_start: 0.8233 (t80) cc_final: 0.7852 (t80) REVERT: C 268 ILE cc_start: 0.7523 (mm) cc_final: 0.7243 (mt) REVERT: E 49 ASP cc_start: 0.8334 (t0) cc_final: 0.8109 (t0) REVERT: E 104 ASP cc_start: 0.8267 (t0) cc_final: 0.8015 (t0) REVERT: E 121 ASP cc_start: 0.8626 (p0) cc_final: 0.8302 (p0) REVERT: E 171 MET cc_start: 0.7972 (mpp) cc_final: 0.7741 (mtm) REVERT: E 181 GLU cc_start: 0.8397 (tt0) cc_final: 0.8029 (tt0) REVERT: E 248 LEU cc_start: 0.9015 (tp) cc_final: 0.8688 (tp) REVERT: E 308 ASP cc_start: 0.8751 (m-30) cc_final: 0.8419 (m-30) REVERT: E 323 LEU cc_start: 0.8236 (mt) cc_final: 0.7892 (mt) REVERT: E 409 ARG cc_start: 0.8124 (tpp80) cc_final: 0.7844 (tpt170) REVERT: E 434 LYS cc_start: 0.5936 (OUTLIER) cc_final: 0.5697 (ttpp) REVERT: D 147 ASN cc_start: 0.8806 (p0) cc_final: 0.8592 (p0) REVERT: D 246 TYR cc_start: 0.8459 (t80) cc_final: 0.8150 (t80) REVERT: D 268 ILE cc_start: 0.8100 (mm) cc_final: 0.7721 (mt) REVERT: D 288 THR cc_start: 0.8907 (m) cc_final: 0.8538 (p) REVERT: D 292 SER cc_start: 0.8817 (m) cc_final: 0.8457 (p) REVERT: D 300 LYS cc_start: 0.8329 (mptt) cc_final: 0.7955 (mptt) outliers start: 43 outliers final: 33 residues processed: 436 average time/residue: 0.1095 time to fit residues: 71.4960 Evaluate side-chains 431 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 397 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 427 ILE 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 157 THR Chi-restraints excluded: chain D residue 177 ILE 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 408 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 163 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 151 optimal weight: 3.9990 chunk 133 optimal weight: 0.5980 chunk 81 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 140 optimal weight: 0.0970 chunk 61 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN C 91 GLN 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 D 55 ASN D 426 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.097425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.087134 restraints weight = 27220.854| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.74 r_work: 0.3187 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14555 Z= 0.147 Angle : 0.637 11.592 19775 Z= 0.328 Chirality : 0.046 0.202 2240 Planarity : 0.005 0.047 2435 Dihedral : 4.531 35.527 2220 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.69 % Allowed : 17.28 % Favored : 79.03 % 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: 2.30 (0.22), residues: 575 sheet: 0.98 (0.28), residues: 395 loop : -1.42 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 143 TYR 0.024 0.002 TYR C 246 PHE 0.018 0.002 PHE D 330 TRP 0.014 0.001 TRP B 263 HIS 0.002 0.001 HIS B 133 Details of bonding type rmsd covalent geometry : bond 0.00338 (14545) covalent geometry : angle 0.63213 (19745) hydrogen bonds : bond 0.04236 ( 695) hydrogen bonds : angle 4.79416 ( 2520) link_BETA1-4 : bond 0.00350 ( 5) link_BETA1-4 : angle 1.54785 ( 15) link_NAG-ASN : bond 0.00145 ( 5) link_NAG-ASN : angle 2.39563 ( 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 482 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 425 time to evaluate : 0.548 Fit side-chains REVERT: A 94 ASP cc_start: 0.8234 (t0) cc_final: 0.8017 (t0) REVERT: A 104 ASP cc_start: 0.8174 (t0) cc_final: 0.7940 (t0) REVERT: A 105 ASP cc_start: 0.7631 (p0) cc_final: 0.7327 (p0) REVERT: A 121 ASP cc_start: 0.8770 (p0) cc_final: 0.8435 (p0) REVERT: A 193 GLU cc_start: 0.8862 (pm20) cc_final: 0.8182 (pm20) REVERT: A 218 ASP cc_start: 0.8988 (p0) cc_final: 0.8551 (p0) REVERT: A 235 GLU cc_start: 0.8237 (tt0) cc_final: 0.7991 (tt0) REVERT: A 237 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8305 (mtt90) REVERT: A 249 ILE cc_start: 0.8774 (tt) cc_final: 0.8497 (tp) REVERT: A 258 ILE cc_start: 0.8794 (mm) cc_final: 0.8491 (tt) REVERT: A 268 ILE cc_start: 0.7700 (mm) cc_final: 0.7312 (mm) REVERT: A 300 LYS cc_start: 0.8413 (mptt) cc_final: 0.8116 (mmtt) REVERT: A 409 ARG cc_start: 0.7849 (tpp80) cc_final: 0.7421 (tpt90) REVERT: A 426 ASN cc_start: 0.8458 (m-40) cc_final: 0.8250 (m110) REVERT: B 104 ASP cc_start: 0.7960 (t0) cc_final: 0.7636 (t0) REVERT: B 121 ASP cc_start: 0.8695 (p0) cc_final: 0.8384 (p0) REVERT: B 193 GLU cc_start: 0.8891 (pm20) cc_final: 0.8669 (pm20) REVERT: B 237 ARG cc_start: 0.8513 (OUTLIER) cc_final: 0.8052 (ptp90) REVERT: B 258 ILE cc_start: 0.8983 (mt) cc_final: 0.8658 (tt) REVERT: B 300 LYS cc_start: 0.8304 (mmtm) cc_final: 0.7877 (mptt) REVERT: B 308 ASP cc_start: 0.8833 (m-30) cc_final: 0.8552 (m-30) REVERT: B 408 LYS cc_start: 0.7970 (mmmm) cc_final: 0.7752 (mmtm) REVERT: B 409 ARG cc_start: 0.8291 (tpp80) cc_final: 0.7798 (tpt90) REVERT: C 80 MET cc_start: 0.8698 (mmm) cc_final: 0.8443 (mmm) REVERT: C 179 GLN cc_start: 0.8900 (pt0) cc_final: 0.8676 (pt0) REVERT: C 235 GLU cc_start: 0.8066 (tt0) cc_final: 0.7810 (mp0) REVERT: C 268 ILE cc_start: 0.7556 (mm) cc_final: 0.7287 (mt) REVERT: E 49 ASP cc_start: 0.8446 (t0) cc_final: 0.8235 (t0) REVERT: E 104 ASP cc_start: 0.8351 (t0) cc_final: 0.8118 (t0) REVERT: E 121 ASP cc_start: 0.8603 (p0) cc_final: 0.8272 (p0) REVERT: E 127 GLU cc_start: 0.8086 (tt0) cc_final: 0.7819 (tt0) REVERT: E 171 MET cc_start: 0.7909 (mpp) cc_final: 0.7679 (mtm) REVERT: E 181 GLU cc_start: 0.8383 (tt0) cc_final: 0.7984 (tt0) REVERT: E 248 LEU cc_start: 0.9020 (tp) cc_final: 0.8739 (tp) REVERT: E 308 ASP cc_start: 0.8812 (m-30) cc_final: 0.8470 (m-30) REVERT: E 409 ARG cc_start: 0.8102 (tpp80) cc_final: 0.7723 (tpt90) REVERT: E 434 LYS cc_start: 0.6012 (OUTLIER) cc_final: 0.5784 (ttpp) REVERT: D 147 ASN cc_start: 0.8837 (p0) cc_final: 0.8630 (p0) REVERT: D 174 GLN cc_start: 0.8930 (mm-40) cc_final: 0.8551 (mm-40) REVERT: D 243 GLN cc_start: 0.8905 (mt0) cc_final: 0.8695 (mm-40) REVERT: D 246 TYR cc_start: 0.8433 (t80) cc_final: 0.8020 (t80) REVERT: D 252 TYR cc_start: 0.8422 (m-80) cc_final: 0.8198 (m-80) REVERT: D 268 ILE cc_start: 0.8090 (mm) cc_final: 0.7743 (mt) REVERT: D 288 THR cc_start: 0.8925 (m) cc_final: 0.8573 (p) REVERT: D 292 SER cc_start: 0.8892 (m) cc_final: 0.8531 (p) outliers start: 57 outliers final: 36 residues processed: 445 average time/residue: 0.1050 time to fit residues: 70.2004 Evaluate side-chains 434 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 395 time to evaluate : 0.558 ------------------------------------------------------------------------------- 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 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 157 THR 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 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 100 optimal weight: 0.0770 chunk 5 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 0.0980 chunk 33 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 142 optimal weight: 0.6980 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 0.4980 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN C 174 GLN C 179 GLN ** 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 = 0.3492 r_free = 0.3492 target = 0.097844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.087528 restraints weight = 27333.485| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.74 r_work: 0.3197 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3425 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= 0.127 Angle : 0.641 11.703 19775 Z= 0.328 Chirality : 0.045 0.198 2240 Planarity : 0.004 0.047 2435 Dihedral : 4.386 33.026 2220 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 3.56 % Allowed : 18.06 % Favored : 78.38 % 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: 0.70 (0.21), residues: 1700 helix: 2.33 (0.22), residues: 575 sheet: 0.93 (0.27), residues: 405 loop : -1.45 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 237 TYR 0.023 0.002 TYR C 246 PHE 0.019 0.001 PHE C 319 TRP 0.013 0.001 TRP B 263 HIS 0.001 0.000 HIS B 133 Details of bonding type rmsd covalent geometry : bond 0.00282 (14545) covalent geometry : angle 0.63680 (19745) hydrogen bonds : bond 0.03882 ( 695) hydrogen bonds : angle 4.63154 ( 2520) link_BETA1-4 : bond 0.00241 ( 5) link_BETA1-4 : angle 1.40210 ( 15) link_NAG-ASN : bond 0.00561 ( 5) link_NAG-ASN : angle 2.34375 ( 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: 55 poor density : 412 time to evaluate : 0.539 Fit side-chains REVERT: A 121 ASP cc_start: 0.8734 (p0) cc_final: 0.8378 (p0) REVERT: A 237 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8254 (mtt90) REVERT: A 249 ILE cc_start: 0.8780 (tt) cc_final: 0.8499 (tp) REVERT: A 250 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7516 (mm110) REVERT: A 268 ILE cc_start: 0.7689 (mm) cc_final: 0.7296 (mm) REVERT: A 409 ARG cc_start: 0.7857 (tpp80) cc_final: 0.7442 (tpt90) REVERT: B 104 ASP cc_start: 0.7966 (t0) cc_final: 0.7764 (t0) REVERT: B 121 ASP cc_start: 0.8656 (p0) cc_final: 0.8408 (p0) REVERT: B 193 GLU cc_start: 0.8845 (pm20) cc_final: 0.8599 (pm20) REVERT: B 237 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8048 (ptp90) REVERT: B 258 ILE cc_start: 0.8983 (mt) cc_final: 0.8771 (mm) REVERT: B 300 LYS cc_start: 0.8227 (mmtm) cc_final: 0.7813 (mptt) REVERT: B 308 ASP cc_start: 0.8856 (m-30) cc_final: 0.8600 (m-30) REVERT: B 409 ARG cc_start: 0.8195 (tpp80) cc_final: 0.7695 (tpt90) REVERT: C 36 GLU cc_start: 0.8711 (pm20) cc_final: 0.8502 (pm20) REVERT: C 80 MET cc_start: 0.8705 (mmm) cc_final: 0.8433 (mmm) REVERT: C 237 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8420 (ptp90) REVERT: C 268 ILE cc_start: 0.7605 (mm) cc_final: 0.7332 (mt) REVERT: E 49 ASP cc_start: 0.8489 (t0) cc_final: 0.8270 (t0) REVERT: E 104 ASP cc_start: 0.8219 (t0) cc_final: 0.7974 (t0) REVERT: E 121 ASP cc_start: 0.8586 (p0) cc_final: 0.8231 (p0) REVERT: E 127 GLU cc_start: 0.8137 (tt0) cc_final: 0.7868 (tt0) REVERT: E 171 MET cc_start: 0.7827 (mpp) cc_final: 0.7489 (mtm) REVERT: E 181 GLU cc_start: 0.8374 (tt0) cc_final: 0.7965 (tt0) REVERT: E 248 LEU cc_start: 0.9018 (tp) cc_final: 0.8738 (tp) REVERT: E 300 LYS cc_start: 0.8273 (mmtt) cc_final: 0.7917 (mmtt) REVERT: E 308 ASP cc_start: 0.8827 (m-30) cc_final: 0.8482 (m-30) REVERT: E 324 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7484 (mt-10) REVERT: E 409 ARG cc_start: 0.8079 (tpp80) cc_final: 0.7695 (tpt90) REVERT: D 77 GLU cc_start: 0.8210 (pt0) cc_final: 0.7992 (pt0) REVERT: D 147 ASN cc_start: 0.8850 (p0) cc_final: 0.8645 (p0) REVERT: D 246 TYR cc_start: 0.8422 (t80) cc_final: 0.8049 (t80) REVERT: D 252 TYR cc_start: 0.8382 (m-80) cc_final: 0.8139 (m-80) REVERT: D 268 ILE cc_start: 0.8054 (mm) cc_final: 0.7806 (mt) REVERT: D 288 THR cc_start: 0.8967 (m) cc_final: 0.8596 (p) REVERT: D 292 SER cc_start: 0.8889 (m) cc_final: 0.8529 (p) outliers start: 55 outliers final: 35 residues processed: 431 average time/residue: 0.1078 time to fit residues: 69.6954 Evaluate side-chains 447 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 409 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 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 237 ARG Chi-restraints excluded: chain C residue 264 VAL 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 251 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 112 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 chunk 141 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 169 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 121 optimal weight: 0.9980 chunk 165 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN C 174 GLN ** C 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.096719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.086561 restraints weight = 27317.034| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.71 r_work: 0.3171 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14555 Z= 0.158 Angle : 0.644 11.017 19775 Z= 0.333 Chirality : 0.046 0.201 2240 Planarity : 0.005 0.046 2435 Dihedral : 4.387 32.577 2220 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.88 % Allowed : 19.16 % Favored : 76.96 % 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: 2.27 (0.22), residues: 575 sheet: 0.89 (0.26), residues: 425 loop : -1.42 (0.22), residues: 700 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 0.019 0.002 PHE B 330 TRP 0.010 0.001 TRP D 430 HIS 0.002 0.001 HIS D 133 Details of bonding type rmsd covalent geometry : bond 0.00367 (14545) covalent geometry : angle 0.64032 (19745) hydrogen bonds : bond 0.04050 ( 695) hydrogen bonds : angle 4.63369 ( 2520) link_BETA1-4 : bond 0.00130 ( 5) link_BETA1-4 : angle 1.47338 ( 15) link_NAG-ASN : bond 0.00129 ( 5) link_NAG-ASN : angle 2.03915 ( 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 469 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 409 time to evaluate : 0.438 Fit side-chains REVERT: A 121 ASP cc_start: 0.8730 (p0) cc_final: 0.8369 (p0) REVERT: A 237 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8039 (mtt90) REVERT: A 249 ILE cc_start: 0.8863 (tt) cc_final: 0.8567 (tp) REVERT: A 250 GLN cc_start: 0.7918 (mm-40) cc_final: 0.7697 (mm110) REVERT: A 268 ILE cc_start: 0.7743 (mm) cc_final: 0.7367 (mm) REVERT: A 409 ARG cc_start: 0.7874 (tpp80) cc_final: 0.7474 (tpt90) REVERT: B 121 ASP cc_start: 0.8673 (p0) cc_final: 0.8327 (p0) REVERT: B 193 GLU cc_start: 0.8877 (pm20) cc_final: 0.8637 (pm20) REVERT: B 237 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.8094 (ptp90) REVERT: B 300 LYS cc_start: 0.8250 (mmtm) cc_final: 0.7868 (mptt) REVERT: B 308 ASP cc_start: 0.8830 (m-30) cc_final: 0.8598 (m-30) REVERT: B 409 ARG cc_start: 0.8165 (tpp80) cc_final: 0.7880 (tpt90) REVERT: C 105 ASP cc_start: 0.7655 (p0) cc_final: 0.7399 (p0) REVERT: C 218 ASP cc_start: 0.9185 (p0) cc_final: 0.8850 (p0) REVERT: C 237 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.8403 (ptp90) REVERT: C 268 ILE cc_start: 0.7637 (mm) cc_final: 0.7328 (mt) REVERT: C 300 LYS cc_start: 0.8331 (mmtt) cc_final: 0.8091 (mmtt) REVERT: C 323 LEU cc_start: 0.8168 (mt) cc_final: 0.7959 (mp) REVERT: E 49 ASP cc_start: 0.8495 (t0) cc_final: 0.8291 (t0) REVERT: E 104 ASP cc_start: 0.8276 (t0) cc_final: 0.8035 (t0) REVERT: E 121 ASP cc_start: 0.8610 (p0) cc_final: 0.8244 (p0) REVERT: E 127 GLU cc_start: 0.8169 (tt0) cc_final: 0.7892 (tt0) REVERT: E 171 MET cc_start: 0.7935 (mpp) cc_final: 0.7629 (mtm) REVERT: E 181 GLU cc_start: 0.8372 (tt0) cc_final: 0.7993 (tt0) REVERT: E 248 LEU cc_start: 0.9044 (tp) cc_final: 0.8770 (tp) REVERT: E 300 LYS cc_start: 0.8284 (mmtt) cc_final: 0.7975 (mmtt) REVERT: E 308 ASP cc_start: 0.8851 (m-30) cc_final: 0.8504 (m-30) REVERT: E 323 LEU cc_start: 0.8320 (mp) cc_final: 0.7937 (mt) REVERT: E 324 GLU cc_start: 0.7902 (mt-10) cc_final: 0.7598 (mt-10) REVERT: E 409 ARG cc_start: 0.8094 (tpp80) cc_final: 0.7718 (tpt90) REVERT: D 37 PHE cc_start: 0.8622 (t80) cc_final: 0.8367 (t80) REVERT: D 147 ASN cc_start: 0.8864 (p0) cc_final: 0.8657 (p0) REVERT: D 246 TYR cc_start: 0.8422 (t80) cc_final: 0.8028 (t80) REVERT: D 252 TYR cc_start: 0.8447 (m-80) cc_final: 0.8158 (m-80) REVERT: D 268 ILE cc_start: 0.8078 (mm) cc_final: 0.7815 (mt) REVERT: D 288 THR cc_start: 0.9035 (m) cc_final: 0.8666 (p) REVERT: D 292 SER cc_start: 0.8962 (m) cc_final: 0.8608 (p) REVERT: D 300 LYS cc_start: 0.8378 (mptt) cc_final: 0.8089 (mmtt) outliers start: 60 outliers final: 45 residues processed: 432 average time/residue: 0.1030 time to fit residues: 66.7212 Evaluate side-chains 445 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 397 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU 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 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 237 ARG 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 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 E residue 420 LEU Chi-restraints excluded: chain D residue 110 ASP 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 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 Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 431 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: 0.5980 chunk 152 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 166 optimal weight: 2.9990 chunk 145 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 174 GLN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.096507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.086253 restraints weight = 27201.829| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.71 r_work: 0.3167 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14555 Z= 0.158 Angle : 0.662 10.614 19775 Z= 0.340 Chirality : 0.046 0.238 2240 Planarity : 0.005 0.048 2435 Dihedral : 4.398 31.226 2220 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.62 % Allowed : 21.04 % 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: 0.67 (0.21), residues: 1700 helix: 2.25 (0.22), residues: 575 sheet: 0.83 (0.26), residues: 425 loop : -1.42 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 333 TYR 0.023 0.002 TYR C 246 PHE 0.021 0.002 PHE B 330 TRP 0.011 0.001 TRP B 263 HIS 0.002 0.000 HIS D 133 Details of bonding type rmsd covalent geometry : bond 0.00366 (14545) covalent geometry : angle 0.65930 (19745) hydrogen bonds : bond 0.04007 ( 695) hydrogen bonds : angle 4.61962 ( 2520) link_BETA1-4 : bond 0.00168 ( 5) link_BETA1-4 : angle 1.44302 ( 15) link_NAG-ASN : bond 0.00048 ( 5) link_NAG-ASN : angle 1.79924 ( 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 464 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 408 time to evaluate : 0.550 Fit side-chains REVERT: A 121 ASP cc_start: 0.8730 (p0) cc_final: 0.8362 (p0) REVERT: A 193 GLU cc_start: 0.8870 (pm20) cc_final: 0.8297 (pm20) REVERT: A 249 ILE cc_start: 0.8883 (tt) cc_final: 0.8596 (tp) REVERT: A 250 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7715 (mm110) REVERT: A 268 ILE cc_start: 0.7780 (mm) cc_final: 0.7390 (mm) REVERT: A 409 ARG cc_start: 0.7875 (tpp80) cc_final: 0.7481 (tpt90) REVERT: B 121 ASP cc_start: 0.8661 (p0) cc_final: 0.8309 (p0) REVERT: B 193 GLU cc_start: 0.8902 (pm20) cc_final: 0.8650 (pm20) REVERT: B 237 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8084 (ptp90) REVERT: B 300 LYS cc_start: 0.8273 (mmtm) cc_final: 0.7910 (mptt) REVERT: B 308 ASP cc_start: 0.8842 (m-30) cc_final: 0.8613 (m-30) REVERT: B 409 ARG cc_start: 0.8149 (tpp80) cc_final: 0.7875 (tpt90) REVERT: C 80 MET cc_start: 0.8783 (mmm) cc_final: 0.8491 (mmm) REVERT: C 237 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.8372 (ptp90) REVERT: C 268 ILE cc_start: 0.7617 (mm) cc_final: 0.7229 (mm) REVERT: C 300 LYS cc_start: 0.8296 (mmtt) cc_final: 0.8092 (mmtt) REVERT: C 323 LEU cc_start: 0.8184 (mt) cc_final: 0.7961 (mp) REVERT: E 77 GLU cc_start: 0.8200 (pt0) cc_final: 0.7999 (pt0) REVERT: E 104 ASP cc_start: 0.8321 (t0) cc_final: 0.8109 (t0) REVERT: E 127 GLU cc_start: 0.8176 (tt0) cc_final: 0.7894 (tt0) REVERT: E 171 MET cc_start: 0.7933 (mpp) cc_final: 0.7618 (mtm) REVERT: E 181 GLU cc_start: 0.8360 (tt0) cc_final: 0.7961 (tt0) REVERT: E 248 LEU cc_start: 0.9077 (tp) cc_final: 0.8835 (tp) REVERT: E 300 LYS cc_start: 0.8332 (mmtt) cc_final: 0.8014 (mmtt) REVERT: E 308 ASP cc_start: 0.8857 (m-30) cc_final: 0.8497 (m-30) REVERT: E 323 LEU cc_start: 0.8385 (mp) cc_final: 0.7997 (mt) REVERT: E 324 GLU cc_start: 0.7903 (mt-10) cc_final: 0.7631 (mt-10) REVERT: E 409 ARG cc_start: 0.8092 (tpp80) cc_final: 0.7720 (tpt90) REVERT: D 89 ARG cc_start: 0.8830 (ttt-90) cc_final: 0.8585 (ttt-90) REVERT: D 147 ASN cc_start: 0.8869 (p0) cc_final: 0.8661 (p0) REVERT: D 246 TYR cc_start: 0.8440 (t80) cc_final: 0.8042 (t80) REVERT: D 268 ILE cc_start: 0.8057 (mm) cc_final: 0.7804 (mt) REVERT: D 288 THR cc_start: 0.9085 (m) cc_final: 0.8707 (p) REVERT: D 292 SER cc_start: 0.8972 (m) cc_final: 0.8600 (p) REVERT: D 300 LYS cc_start: 0.8416 (mptt) cc_final: 0.8046 (mmtt) outliers start: 56 outliers final: 44 residues processed: 428 average time/residue: 0.1090 time to fit residues: 69.9313 Evaluate side-chains 447 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 401 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LEU 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 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 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 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 237 ARG 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 228 THR Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 237 ARG 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 206 LEU 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 Chi-restraints excluded: chain D residue 428 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 98 optimal weight: 0.5980 chunk 94 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 119 optimal weight: 0.2980 chunk 36 optimal weight: 0.0060 chunk 158 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 174 GLN C 179 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.096800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.086526 restraints weight = 27373.377| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.74 r_work: 0.3180 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14555 Z= 0.138 Angle : 0.668 12.226 19775 Z= 0.339 Chirality : 0.046 0.327 2240 Planarity : 0.005 0.044 2435 Dihedral : 4.352 29.279 2220 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.37 % Allowed : 22.01 % Favored : 74.63 % 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: 0.61 (0.21), residues: 1700 helix: 2.21 (0.22), residues: 575 sheet: 0.90 (0.27), residues: 405 loop : -1.48 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 333 TYR 0.023 0.002 TYR C 246 PHE 0.023 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 covalent geometry : bond 0.00314 (14545) covalent geometry : angle 0.66591 (19745) hydrogen bonds : bond 0.03867 ( 695) hydrogen bonds : angle 4.58916 ( 2520) link_BETA1-4 : bond 0.00188 ( 5) link_BETA1-4 : angle 1.41657 ( 15) link_NAG-ASN : bond 0.00027 ( 5) link_NAG-ASN : angle 1.59580 ( 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 459 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 407 time to evaluate : 0.532 Fit side-chains REVERT: A 121 ASP cc_start: 0.8716 (p0) cc_final: 0.8329 (p0) REVERT: A 193 GLU cc_start: 0.8894 (pm20) cc_final: 0.8308 (pm20) REVERT: A 249 ILE cc_start: 0.8864 (tt) cc_final: 0.8610 (tp) REVERT: A 268 ILE cc_start: 0.7750 (mm) cc_final: 0.7378 (mm) REVERT: A 409 ARG cc_start: 0.7836 (tpp80) cc_final: 0.7431 (tpt90) REVERT: B 121 ASP cc_start: 0.8619 (p0) cc_final: 0.8255 (p0) REVERT: B 193 GLU cc_start: 0.8919 (pm20) cc_final: 0.8658 (pm20) REVERT: B 237 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8028 (ptp90) REVERT: B 300 LYS cc_start: 0.8274 (mmtm) cc_final: 0.7892 (mptt) REVERT: B 308 ASP cc_start: 0.8841 (m-30) cc_final: 0.8596 (m-30) REVERT: B 409 ARG cc_start: 0.8140 (tpp80) cc_final: 0.7840 (tpt90) REVERT: C 80 MET cc_start: 0.8753 (mmm) cc_final: 0.8477 (mmm) REVERT: C 237 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8337 (ptp90) REVERT: C 268 ILE cc_start: 0.7608 (mm) cc_final: 0.7201 (mm) REVERT: C 323 LEU cc_start: 0.8189 (mt) cc_final: 0.7974 (mp) REVERT: C 409 ARG cc_start: 0.7923 (ttm-80) cc_final: 0.6936 (tpt90) REVERT: E 77 GLU cc_start: 0.8231 (pt0) cc_final: 0.8019 (pt0) REVERT: E 104 ASP cc_start: 0.8365 (t0) cc_final: 0.8164 (t0) REVERT: E 121 ASP cc_start: 0.8620 (p0) cc_final: 0.8220 (p0) REVERT: E 127 GLU cc_start: 0.8206 (tt0) cc_final: 0.7920 (tt0) REVERT: E 248 LEU cc_start: 0.9078 (tp) cc_final: 0.8848 (tp) REVERT: E 251 MET cc_start: 0.7684 (OUTLIER) cc_final: 0.7175 (ptp) REVERT: E 300 LYS cc_start: 0.8296 (mmtt) cc_final: 0.7939 (mmtt) REVERT: E 308 ASP cc_start: 0.8867 (m-30) cc_final: 0.8526 (m-30) REVERT: E 323 LEU cc_start: 0.8357 (mp) cc_final: 0.8138 (mt) REVERT: E 324 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7646 (mt-10) REVERT: E 409 ARG cc_start: 0.8079 (tpp80) cc_final: 0.7705 (tpt90) REVERT: D 89 ARG cc_start: 0.8827 (ttt-90) cc_final: 0.8571 (ttt-90) REVERT: D 147 ASN cc_start: 0.8873 (p0) cc_final: 0.8670 (p0) REVERT: D 246 TYR cc_start: 0.8484 (t80) cc_final: 0.8195 (t80) REVERT: D 288 THR cc_start: 0.9097 (m) cc_final: 0.8723 (p) REVERT: D 292 SER cc_start: 0.8989 (m) cc_final: 0.8613 (p) REVERT: D 300 LYS cc_start: 0.8455 (mptt) cc_final: 0.8084 (mmtt) outliers start: 52 outliers final: 37 residues processed: 425 average time/residue: 0.1104 time to fit residues: 69.6886 Evaluate side-chains 440 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 400 time to evaluate : 0.434 ------------------------------------------------------------------------------- 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 304 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 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 192 PHE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 237 ARG 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 235 GLU Chi-restraints excluded: chain E residue 251 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 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 Chi-restraints excluded: chain D residue 428 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 160 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 144 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 GLN C 174 GLN C 334 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.094486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.084319 restraints weight = 27485.324| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 2.71 r_work: 0.3134 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14555 Z= 0.211 Angle : 0.716 12.060 19775 Z= 0.368 Chirality : 0.048 0.339 2240 Planarity : 0.005 0.071 2435 Dihedral : 4.515 30.585 2220 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.98 % Allowed : 22.59 % Favored : 74.43 % 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: 0.56 (0.21), residues: 1700 helix: 2.16 (0.22), residues: 575 sheet: 0.90 (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 D 333 TYR 0.024 0.002 TYR C 246 PHE 0.025 0.002 PHE A 192 TRP 0.009 0.001 TRP A 430 HIS 0.002 0.001 HIS D 133 Details of bonding type rmsd covalent geometry : bond 0.00501 (14545) covalent geometry : angle 0.71307 (19745) hydrogen bonds : bond 0.04234 ( 695) hydrogen bonds : angle 4.66280 ( 2520) link_BETA1-4 : bond 0.00050 ( 5) link_BETA1-4 : angle 1.58716 ( 15) link_NAG-ASN : bond 0.00241 ( 5) link_NAG-ASN : angle 1.99515 ( 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 454 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 408 time to evaluate : 0.549 Fit side-chains REVERT: A 121 ASP cc_start: 0.8740 (p0) cc_final: 0.8378 (p0) REVERT: A 193 GLU cc_start: 0.8929 (pm20) cc_final: 0.8346 (pm20) REVERT: A 268 ILE cc_start: 0.7792 (mm) cc_final: 0.7415 (mm) REVERT: A 409 ARG cc_start: 0.7915 (tpp80) cc_final: 0.7532 (tpt90) REVERT: B 121 ASP cc_start: 0.8686 (p0) cc_final: 0.8323 (p0) REVERT: B 127 GLU cc_start: 0.8167 (tp30) cc_final: 0.7877 (tp30) REVERT: B 193 GLU cc_start: 0.8955 (pm20) cc_final: 0.8698 (pm20) REVERT: B 237 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.8127 (ptp90) REVERT: B 241 GLU cc_start: 0.8397 (tt0) cc_final: 0.8188 (tt0) REVERT: B 300 LYS cc_start: 0.8301 (mmtm) cc_final: 0.7879 (mptt) REVERT: B 308 ASP cc_start: 0.8842 (m-30) cc_final: 0.8616 (m-30) REVERT: B 409 ARG cc_start: 0.8179 (tpp80) cc_final: 0.7720 (tpt90) REVERT: C 80 MET cc_start: 0.8813 (mmm) cc_final: 0.8518 (mmm) REVERT: C 237 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8462 (ptp90) REVERT: C 268 ILE cc_start: 0.7675 (mm) cc_final: 0.7294 (mm) REVERT: C 409 ARG cc_start: 0.8027 (ttm-80) cc_final: 0.7114 (tpt90) REVERT: E 80 MET cc_start: 0.8738 (mmt) cc_final: 0.8237 (mmt) REVERT: E 127 GLU cc_start: 0.8207 (tt0) cc_final: 0.7936 (tt0) REVERT: E 171 MET cc_start: 0.7992 (mtm) cc_final: 0.7448 (mtp) REVERT: E 248 LEU cc_start: 0.9095 (tp) cc_final: 0.8893 (tp) REVERT: E 300 LYS cc_start: 0.8355 (mmtt) cc_final: 0.8052 (mmtt) REVERT: E 308 ASP cc_start: 0.8857 (m-30) cc_final: 0.8555 (m-30) REVERT: E 323 LEU cc_start: 0.8414 (mp) cc_final: 0.8029 (mt) REVERT: E 324 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7528 (mt-10) REVERT: E 409 ARG cc_start: 0.8126 (tpp80) cc_final: 0.7760 (tpt90) REVERT: D 147 ASN cc_start: 0.8876 (p0) cc_final: 0.8648 (p0) REVERT: D 171 MET cc_start: 0.8272 (mtm) cc_final: 0.8002 (mtp) REVERT: D 246 TYR cc_start: 0.8517 (t80) cc_final: 0.8176 (t80) REVERT: D 292 SER cc_start: 0.9066 (m) cc_final: 0.8788 (p) REVERT: D 300 LYS cc_start: 0.8467 (mptt) cc_final: 0.8118 (mmtt) outliers start: 46 outliers final: 36 residues processed: 425 average time/residue: 0.1115 time to fit residues: 70.3030 Evaluate side-chains 443 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 405 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 304 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 206 LEU Chi-restraints excluded: chain C residue 237 ARG 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 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 264 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 316 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 427 ILE Chi-restraints excluded: chain D residue 428 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 71 optimal weight: 0.0050 chunk 95 optimal weight: 0.5980 chunk 139 optimal weight: 1.9990 chunk 143 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 174 GLN D 168 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.096279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.086001 restraints weight = 27277.691| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.72 r_work: 0.3163 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.4011 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= 0.149 Angle : 0.702 12.608 19775 Z= 0.359 Chirality : 0.047 0.342 2240 Planarity : 0.005 0.045 2435 Dihedral : 4.430 28.700 2220 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.59 % Allowed : 23.30 % Favored : 74.11 % 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: 2.12 (0.22), residues: 580 sheet: 0.88 (0.27), residues: 405 loop : -1.55 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 333 TYR 0.022 0.002 TYR B 246 PHE 0.024 0.002 PHE B 330 TRP 0.011 0.001 TRP A 263 HIS 0.001 0.000 HIS D 133 Details of bonding type rmsd covalent geometry : bond 0.00346 (14545) covalent geometry : angle 0.69996 (19745) hydrogen bonds : bond 0.03948 ( 695) hydrogen bonds : angle 4.61113 ( 2520) link_BETA1-4 : bond 0.00185 ( 5) link_BETA1-4 : angle 1.41692 ( 15) link_NAG-ASN : bond 0.00037 ( 5) link_NAG-ASN : angle 1.62972 ( 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: 40 poor density : 400 time to evaluate : 0.339 Fit side-chains REVERT: A 121 ASP cc_start: 0.8710 (p0) cc_final: 0.8327 (p0) REVERT: A 193 GLU cc_start: 0.8920 (pm20) cc_final: 0.8323 (pm20) REVERT: A 250 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7662 (mm110) REVERT: A 268 ILE cc_start: 0.7817 (mm) cc_final: 0.7428 (mm) REVERT: A 409 ARG cc_start: 0.7880 (tpp80) cc_final: 0.7544 (tpt90) REVERT: B 121 ASP cc_start: 0.8648 (p0) cc_final: 0.8262 (p0) REVERT: B 193 GLU cc_start: 0.8971 (pm20) cc_final: 0.8704 (pm20) REVERT: B 237 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8187 (ptp90) REVERT: B 300 LYS cc_start: 0.8282 (mmtm) cc_final: 0.7831 (mptt) REVERT: B 308 ASP cc_start: 0.8860 (m-30) cc_final: 0.8588 (m-30) REVERT: B 409 ARG cc_start: 0.8170 (tpp80) cc_final: 0.7711 (tpt90) REVERT: C 42 MET cc_start: 0.8098 (mtp) cc_final: 0.7894 (ttt) REVERT: C 80 MET cc_start: 0.8793 (mmm) cc_final: 0.8522 (mmm) REVERT: C 237 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8387 (ptp90) REVERT: C 268 ILE cc_start: 0.7662 (mm) cc_final: 0.7247 (mm) REVERT: E 80 MET cc_start: 0.8747 (mmt) cc_final: 0.8276 (mmt) REVERT: E 89 ARG cc_start: 0.8827 (ttt-90) cc_final: 0.8604 (ttt-90) REVERT: E 121 ASP cc_start: 0.8675 (p0) cc_final: 0.8255 (p0) REVERT: E 127 GLU cc_start: 0.8172 (tt0) cc_final: 0.7897 (tt0) REVERT: E 171 MET cc_start: 0.7901 (mtm) cc_final: 0.7406 (mtp) REVERT: E 300 LYS cc_start: 0.8322 (mmtt) cc_final: 0.8024 (mmtt) REVERT: E 308 ASP cc_start: 0.8834 (m-30) cc_final: 0.8577 (m-30) REVERT: E 323 LEU cc_start: 0.8408 (mp) cc_final: 0.8013 (mt) REVERT: E 324 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7681 (mt-10) REVERT: E 409 ARG cc_start: 0.8145 (tpp80) cc_final: 0.7784 (tpt90) REVERT: D 89 ARG cc_start: 0.8840 (ttt-90) cc_final: 0.8618 (ttt-90) REVERT: D 147 ASN cc_start: 0.8874 (p0) cc_final: 0.8651 (p0) REVERT: D 246 TYR cc_start: 0.8551 (t80) cc_final: 0.8196 (t80) REVERT: D 292 SER cc_start: 0.9073 (m) cc_final: 0.8682 (p) REVERT: D 300 LYS cc_start: 0.8453 (mptt) cc_final: 0.8053 (mmtt) outliers start: 40 outliers final: 36 residues processed: 415 average time/residue: 0.1057 time to fit residues: 65.7039 Evaluate side-chains 434 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 396 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 304 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 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 237 ARG 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 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 264 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 206 LEU 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 Chi-restraints excluded: chain D residue 428 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 149 optimal weight: 0.0470 chunk 14 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 169 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 156 optimal weight: 3.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 174 GLN C 179 GLN C 290 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.096091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.085847 restraints weight = 27317.708| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.71 r_work: 0.3159 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.112 14555 Z= 0.186 Angle : 0.887 59.182 19775 Z= 0.493 Chirality : 0.048 0.530 2240 Planarity : 0.005 0.045 2435 Dihedral : 4.501 40.239 2220 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.65 % Allowed : 23.56 % Favored : 73.79 % Cbeta Deviations : 0.00 % 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: 0.50 (0.21), residues: 1700 helix: 2.10 (0.21), residues: 580 sheet: 0.87 (0.27), residues: 405 loop : -1.58 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 333 TYR 0.023 0.002 TYR D 99 PHE 0.021 0.002 PHE B 330 TRP 0.010 0.001 TRP A 263 HIS 0.001 0.000 HIS D 133 Details of bonding type rmsd covalent geometry : bond 0.00405 (14545) covalent geometry : angle 0.88591 (19745) hydrogen bonds : bond 0.03952 ( 695) hydrogen bonds : angle 4.61033 ( 2520) link_BETA1-4 : bond 0.00339 ( 5) link_BETA1-4 : angle 1.43430 ( 15) link_NAG-ASN : bond 0.00038 ( 5) link_NAG-ASN : angle 1.62551 ( 15) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2719.91 seconds wall clock time: 47 minutes 36.24 seconds (2856.24 seconds total)