Starting phenix.real_space_refine on Thu Sep 26 23:44:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6m_23700/09_2024/7m6m_23700.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6m_23700/09_2024/7m6m_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6m_23700/09_2024/7m6m_23700.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6m_23700/09_2024/7m6m_23700.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6m_23700/09_2024/7m6m_23700.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m6m_23700/09_2024/7m6m_23700.cif" } resolution = 3.09 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5461/modules/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: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "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: C, B, E, D, F, I, H, J Time building chain proxies: 6.34, per 1000 atoms: 0.45 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: 3.34 Conformation dependent library (CDL) restraints added in 1.7 seconds 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: 1.90 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: 4.64 Time building geometry restraints manager: 3.85 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.57 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: 1.260 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.450 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.940 ------------------------------------------------------------------------------- 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 14545 Z= 0.528 Angle : 1.312 10.359 19745 Z= 0.728 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.026 0.003 TRP D 263 HIS 0.003 0.001 HIS A 133 PHE 0.041 0.004 PHE A 192 TYR 0.029 0.004 TYR C 152 ARG 0.008 0.001 ARG B 51 *********************** 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 fitting. rotamer outliers: 0 poor density : 543 time to evaluate : 1.615 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: 0.7665 (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: 0.8580 (p0) cc_final: 0.8345 (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: 0.8063 (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: 0.8730 (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: 0.7904 (t80) REVERT: D 277 VAL cc_start: 0.8821 (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: 0.8541 (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: 0.2758 time to fit residues: 210.0242 Evaluate side-chains 420 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 420 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 133 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 81 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 154 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS B 290 GLN C 133 HIS C 174 GLN E 290 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14545 Z= 0.254 Angle : 0.693 12.474 19745 Z= 0.364 Chirality : 0.049 0.221 2240 Planarity : 0.005 0.044 2435 Dihedral : 4.972 34.924 2220 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.85 % Allowed : 12.94 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.21), residues: 1700 helix: 2.34 (0.21), residues: 575 sheet: 0.92 (0.27), residues: 420 loop : -1.48 (0.21), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 263 HIS 0.002 0.000 HIS D 133 PHE 0.021 0.002 PHE C 192 TYR 0.018 0.002 TYR D 325 ARG 0.006 0.001 ARG D 53 *********************** 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 504 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 460 time to evaluate : 1.702 Fit side-chains revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8257 (t80) cc_final: 0.8030 (t80) REVERT: A 77 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7953 (pt0) REVERT: A 121 ASP cc_start: 0.8577 (p0) cc_final: 0.8305 (p0) REVERT: A 141 LEU cc_start: 0.8646 (tp) cc_final: 0.8356 (tt) REVERT: A 193 GLU cc_start: 0.8702 (pm20) cc_final: 0.8058 (pm20) REVERT: A 235 GLU cc_start: 0.7463 (tt0) cc_final: 0.7211 (tt0) REVERT: A 249 ILE cc_start: 0.8695 (tt) cc_final: 0.8452 (tp) REVERT: A 268 ILE cc_start: 0.7620 (mm) cc_final: 0.7258 (mt) REVERT: A 311 MET cc_start: 0.8333 (mmm) cc_final: 0.8032 (mmm) REVERT: A 409 ARG cc_start: 0.7895 (tpp80) cc_final: 0.7389 (tpt90) REVERT: B 38 LEU cc_start: 0.8845 (mt) cc_final: 0.8375 (mt) REVERT: B 42 MET cc_start: 0.7623 (mpp) cc_final: 0.6686 (mpp) REVERT: B 49 ASP cc_start: 0.8097 (t0) cc_final: 0.7892 (t0) REVERT: B 104 ASP cc_start: 0.7455 (t0) cc_final: 0.7235 (t0) REVERT: B 243 GLN cc_start: 0.8631 (mt0) cc_final: 0.8262 (mt0) REVERT: B 300 LYS cc_start: 0.8092 (mmtm) cc_final: 0.7788 (mptt) REVERT: B 308 ASP cc_start: 0.8347 (m-30) cc_final: 0.8111 (m-30) REVERT: B 408 LYS cc_start: 0.7903 (mmmm) cc_final: 0.7655 (mmtm) REVERT: B 409 ARG cc_start: 0.8347 (tpp80) cc_final: 0.7881 (tpt90) REVERT: C 89 ARG cc_start: 0.8282 (ttt-90) cc_final: 0.8069 (ttt-90) REVERT: C 268 ILE cc_start: 0.7445 (mm) cc_final: 0.7102 (mt) REVERT: C 311 MET cc_start: 0.8607 (mmt) cc_final: 0.8390 (mmm) REVERT: E 38 LEU cc_start: 0.8788 (mt) cc_final: 0.8559 (mt) REVERT: E 42 MET cc_start: 0.7757 (mpp) cc_final: 0.7137 (mpp) REVERT: E 49 ASP cc_start: 0.8152 (t0) cc_final: 0.7938 (t0) REVERT: E 121 ASP cc_start: 0.8458 (p0) cc_final: 0.8163 (p0) REVERT: E 171 MET cc_start: 0.7391 (mpp) cc_final: 0.7084 (mtm) REVERT: E 248 LEU cc_start: 0.8985 (tp) cc_final: 0.8665 (tp) REVERT: E 300 LYS cc_start: 0.7954 (mmtm) cc_final: 0.7566 (mmtt) REVERT: E 308 ASP cc_start: 0.8283 (m-30) cc_final: 0.7956 (m-30) REVERT: E 323 LEU cc_start: 0.8024 (mt) cc_final: 0.7720 (mt) REVERT: E 409 ARG cc_start: 0.8151 (tpp80) cc_final: 0.7867 (tpt90) REVERT: D 37 PHE cc_start: 0.8182 (t80) cc_final: 0.7819 (t80) REVERT: D 91 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.8319 (mt0) REVERT: D 141 LEU cc_start: 0.8690 (tp) cc_final: 0.8397 (tt) REVERT: D 147 ASN cc_start: 0.8566 (p0) cc_final: 0.8360 (p0) REVERT: D 246 TYR cc_start: 0.8321 (t80) cc_final: 0.7965 (t80) REVERT: D 268 ILE cc_start: 0.7613 (mm) cc_final: 0.7335 (mt) REVERT: D 285 LEU cc_start: 0.8886 (tp) cc_final: 0.8563 (tt) REVERT: D 288 THR cc_start: 0.8789 (m) cc_final: 0.8419 (p) REVERT: D 292 SER cc_start: 0.8717 (m) cc_final: 0.8320 (p) REVERT: D 300 LYS cc_start: 0.8200 (mptt) cc_final: 0.7738 (mptt) REVERT: D 308 ASP cc_start: 0.8225 (m-30) cc_final: 0.7993 (m-30) REVERT: D 324 GLU cc_start: 0.7087 (mt-10) cc_final: 0.6561 (mt-10) outliers start: 44 outliers final: 27 residues processed: 478 average time/residue: 0.2625 time to fit residues: 179.8130 Evaluate side-chains 437 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 408 time to evaluate : 1.623 ------------------------------------------------------------------------------- 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 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 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 85 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 128 optimal weight: 0.0470 chunk 105 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 154 optimal weight: 2.9990 chunk 167 optimal weight: 0.9980 chunk 137 optimal weight: 0.2980 chunk 153 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 225 HIS C 174 GLN C 290 GLN E 290 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14545 Z= 0.211 Angle : 0.644 12.250 19745 Z= 0.333 Chirality : 0.046 0.207 2240 Planarity : 0.005 0.051 2435 Dihedral : 4.581 35.730 2220 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.85 % Allowed : 15.47 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.21), residues: 1700 helix: 2.36 (0.22), residues: 575 sheet: 0.95 (0.28), residues: 395 loop : -1.39 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 263 HIS 0.002 0.000 HIS B 133 PHE 0.019 0.002 PHE B 330 TYR 0.022 0.002 TYR C 246 ARG 0.006 0.001 ARG B 143 *********************** 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 466 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 422 time to evaluate : 1.637 Fit side-chains REVERT: A 37 PHE cc_start: 0.8285 (t80) cc_final: 0.8015 (t80) REVERT: A 121 ASP cc_start: 0.8546 (p0) cc_final: 0.8231 (p0) REVERT: A 141 LEU cc_start: 0.8548 (tp) cc_final: 0.8328 (tt) REVERT: A 235 GLU cc_start: 0.7432 (tt0) cc_final: 0.7096 (tt0) REVERT: A 249 ILE cc_start: 0.8746 (tt) cc_final: 0.8462 (tp) REVERT: A 258 ILE cc_start: 0.8579 (mm) cc_final: 0.8300 (tt) REVERT: A 268 ILE cc_start: 0.7630 (mm) cc_final: 0.7225 (mm) REVERT: A 292 SER cc_start: 0.8916 (m) cc_final: 0.8608 (p) REVERT: A 409 ARG cc_start: 0.7804 (tpp80) cc_final: 0.7397 (tpt90) REVERT: B 38 LEU cc_start: 0.8857 (mt) cc_final: 0.8399 (mt) REVERT: B 104 ASP cc_start: 0.7684 (t0) cc_final: 0.7423 (t0) REVERT: B 121 ASP cc_start: 0.8378 (p0) cc_final: 0.8171 (p0) REVERT: B 206 LEU cc_start: 0.7965 (mt) cc_final: 0.7526 (mp) REVERT: B 243 GLN cc_start: 0.8619 (mt0) cc_final: 0.8407 (mt0) REVERT: B 300 LYS cc_start: 0.8168 (mmtm) cc_final: 0.7729 (mptt) REVERT: B 308 ASP cc_start: 0.8411 (m-30) cc_final: 0.8147 (m-30) REVERT: B 409 ARG cc_start: 0.8219 (tpp80) cc_final: 0.7766 (tpt90) REVERT: C 37 PHE cc_start: 0.8143 (t80) cc_final: 0.7768 (t80) REVERT: C 179 GLN cc_start: 0.8615 (pt0) cc_final: 0.8369 (pt0) REVERT: C 268 ILE cc_start: 0.7501 (mm) cc_final: 0.7205 (mt) REVERT: E 49 ASP cc_start: 0.8126 (t0) cc_final: 0.7906 (t0) REVERT: E 104 ASP cc_start: 0.7990 (t0) cc_final: 0.7748 (t0) REVERT: E 105 ASP cc_start: 0.7129 (p0) cc_final: 0.6827 (p0) REVERT: E 121 ASP cc_start: 0.8406 (p0) cc_final: 0.8030 (p0) REVERT: E 171 MET cc_start: 0.7557 (mpp) cc_final: 0.7254 (mtm) REVERT: E 181 GLU cc_start: 0.7823 (tt0) cc_final: 0.7451 (tt0) REVERT: E 248 LEU cc_start: 0.8973 (tp) cc_final: 0.8655 (tp) REVERT: E 300 LYS cc_start: 0.8064 (mmtm) cc_final: 0.7608 (mmtt) REVERT: E 409 ARG cc_start: 0.8051 (tpp80) cc_final: 0.7706 (tpt90) REVERT: D 147 ASN cc_start: 0.8617 (p0) cc_final: 0.8405 (p0) REVERT: D 189 ASP cc_start: 0.7930 (t0) cc_final: 0.7728 (t70) REVERT: D 246 TYR cc_start: 0.8237 (t80) cc_final: 0.7906 (t80) REVERT: D 288 THR cc_start: 0.8806 (m) cc_final: 0.8410 (p) REVERT: D 292 SER cc_start: 0.8755 (m) cc_final: 0.8375 (p) REVERT: D 300 LYS cc_start: 0.8196 (mptt) cc_final: 0.7797 (mptt) REVERT: D 308 ASP cc_start: 0.8273 (m-30) cc_final: 0.8025 (m-30) REVERT: D 426 ASN cc_start: 0.8304 (m-40) cc_final: 0.8103 (m-40) outliers start: 44 outliers final: 34 residues processed: 436 average time/residue: 0.2398 time to fit residues: 154.1420 Evaluate side-chains 426 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 392 time to evaluate : 1.743 ------------------------------------------------------------------------------- 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 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 215 GLU 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 D residue 157 THR Chi-restraints excluded: chain D residue 177 ILE Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 408 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 chunk 103 optimal weight: 0.5980 chunk 155 optimal weight: 2.9990 chunk 164 optimal weight: 0.9990 chunk 81 optimal weight: 0.0770 chunk 147 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 GLN B 225 HIS B 250 GLN C 174 GLN C 290 GLN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14545 Z= 0.227 Angle : 0.640 11.334 19745 Z= 0.333 Chirality : 0.046 0.203 2240 Planarity : 0.005 0.048 2435 Dihedral : 4.534 35.541 2220 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.56 % Allowed : 17.28 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.21), residues: 1700 helix: 2.35 (0.22), residues: 575 sheet: 0.97 (0.28), residues: 395 loop : -1.42 (0.22), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 263 HIS 0.002 0.000 HIS D 133 PHE 0.018 0.002 PHE B 330 TYR 0.022 0.002 TYR C 246 ARG 0.004 0.001 ARG B 143 *********************** 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 471 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 416 time to evaluate : 1.722 Fit side-chains REVERT: A 94 ASP cc_start: 0.8072 (t0) cc_final: 0.7812 (t0) REVERT: A 105 ASP cc_start: 0.7202 (p0) cc_final: 0.6952 (p0) REVERT: A 121 ASP cc_start: 0.8530 (p0) cc_final: 0.8204 (p0) REVERT: A 235 GLU cc_start: 0.7503 (tt0) cc_final: 0.7204 (tt0) REVERT: A 249 ILE cc_start: 0.8769 (tt) cc_final: 0.8480 (tp) REVERT: A 258 ILE cc_start: 0.8654 (mm) cc_final: 0.8335 (tt) REVERT: A 268 ILE cc_start: 0.7654 (mm) cc_final: 0.7247 (mm) REVERT: A 292 SER cc_start: 0.8929 (m) cc_final: 0.8579 (p) REVERT: A 409 ARG cc_start: 0.7840 (tpp80) cc_final: 0.7434 (tpt90) REVERT: B 121 ASP cc_start: 0.8386 (p0) cc_final: 0.8020 (p0) REVERT: B 193 GLU cc_start: 0.8783 (pm20) cc_final: 0.8546 (pm20) REVERT: B 237 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.8109 (ptp90) REVERT: B 243 GLN cc_start: 0.8621 (mt0) cc_final: 0.8413 (mt0) REVERT: B 300 LYS cc_start: 0.8194 (mmtm) cc_final: 0.7753 (mptt) REVERT: B 308 ASP cc_start: 0.8467 (m-30) cc_final: 0.8186 (m-30) REVERT: B 409 ARG cc_start: 0.8194 (tpp80) cc_final: 0.7762 (tpt90) REVERT: C 37 PHE cc_start: 0.8122 (t80) cc_final: 0.7836 (t80) REVERT: C 268 ILE cc_start: 0.7555 (mm) cc_final: 0.7264 (mt) REVERT: E 121 ASP cc_start: 0.8403 (p0) cc_final: 0.8075 (p0) REVERT: E 127 GLU cc_start: 0.7677 (tt0) cc_final: 0.7408 (tt0) REVERT: E 171 MET cc_start: 0.7579 (mpp) cc_final: 0.7379 (mtm) REVERT: E 181 GLU cc_start: 0.7818 (tt0) cc_final: 0.7435 (tt0) REVERT: E 248 LEU cc_start: 0.8989 (tp) cc_final: 0.8692 (tp) REVERT: E 300 LYS cc_start: 0.8132 (mmtm) cc_final: 0.7825 (mptt) REVERT: E 308 ASP cc_start: 0.8412 (m-30) cc_final: 0.8067 (m-30) REVERT: E 323 LEU cc_start: 0.8172 (mp) cc_final: 0.7956 (mt) REVERT: E 324 GLU cc_start: 0.7333 (mt-10) cc_final: 0.6702 (mt-10) REVERT: E 409 ARG cc_start: 0.8074 (tpp80) cc_final: 0.7729 (tpt90) REVERT: D 147 ASN cc_start: 0.8642 (p0) cc_final: 0.8436 (p0) REVERT: D 243 GLN cc_start: 0.8624 (mt0) cc_final: 0.8411 (mm-40) REVERT: D 246 TYR cc_start: 0.8261 (t80) cc_final: 0.7906 (t80) REVERT: D 268 ILE cc_start: 0.8158 (mm) cc_final: 0.7783 (mt) REVERT: D 288 THR cc_start: 0.8808 (m) cc_final: 0.8442 (p) REVERT: D 292 SER cc_start: 0.8792 (m) cc_final: 0.8403 (p) REVERT: D 308 ASP cc_start: 0.8284 (m-30) cc_final: 0.8052 (m-30) outliers start: 55 outliers final: 39 residues processed: 433 average time/residue: 0.2432 time to fit residues: 155.5338 Evaluate side-chains 431 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 391 time to evaluate : 1.475 ------------------------------------------------------------------------------- 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 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 177 ILE Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 244 MET Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain C residue 411 ASP Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 316 LEU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 206 LEU Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 322 LEU Chi-restraints excluded: chain D residue 408 LYS Chi-restraints excluded: chain D residue 427 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 113 optimal weight: 0.0770 chunk 0 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- 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 ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 290 GLN E 426 ASN D 426 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14545 Z= 0.264 Angle : 0.655 11.604 19745 Z= 0.340 Chirality : 0.046 0.234 2240 Planarity : 0.005 0.048 2435 Dihedral : 4.524 34.351 2220 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.95 % Allowed : 18.12 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.21), residues: 1700 helix: 2.33 (0.22), residues: 575 sheet: 1.00 (0.28), residues: 395 loop : -1.45 (0.21), residues: 730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 263 HIS 0.002 0.001 HIS D 133 PHE 0.021 0.002 PHE A 192 TYR 0.023 0.002 TYR C 246 ARG 0.007 0.001 ARG B 333 *********************** 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 472 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 411 time to evaluate : 1.506 Fit side-chains REVERT: A 121 ASP cc_start: 0.8531 (p0) cc_final: 0.8195 (p0) REVERT: A 193 GLU cc_start: 0.8728 (pm20) cc_final: 0.8108 (pm20) REVERT: A 237 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8029 (mtt90) REVERT: A 249 ILE cc_start: 0.8828 (tt) cc_final: 0.8515 (tp) REVERT: A 250 GLN cc_start: 0.7606 (mm-40) cc_final: 0.7362 (mm110) REVERT: A 258 ILE cc_start: 0.8731 (mm) cc_final: 0.8521 (mm) REVERT: A 268 ILE cc_start: 0.7684 (mm) cc_final: 0.7274 (mm) REVERT: A 292 SER cc_start: 0.8959 (m) cc_final: 0.8596 (p) REVERT: A 409 ARG cc_start: 0.7874 (tpp80) cc_final: 0.7486 (tpt90) REVERT: A 426 ASN cc_start: 0.8319 (m-40) cc_final: 0.8117 (m110) REVERT: B 121 ASP cc_start: 0.8400 (p0) cc_final: 0.8019 (p0) REVERT: B 193 GLU cc_start: 0.8764 (pm20) cc_final: 0.8525 (pm20) REVERT: B 237 ARG cc_start: 0.8319 (OUTLIER) cc_final: 0.7871 (ptp90) REVERT: B 246 TYR cc_start: 0.8395 (t80) cc_final: 0.8177 (t80) REVERT: B 300 LYS cc_start: 0.8136 (mmtm) cc_final: 0.7713 (mptt) REVERT: B 308 ASP cc_start: 0.8448 (m-30) cc_final: 0.8196 (m-30) REVERT: B 409 ARG cc_start: 0.8146 (tpp80) cc_final: 0.7877 (tpt90) REVERT: C 37 PHE cc_start: 0.8292 (t80) cc_final: 0.8061 (t80) REVERT: C 268 ILE cc_start: 0.7584 (mm) cc_final: 0.7326 (mt) REVERT: E 37 PHE cc_start: 0.8472 (t80) cc_final: 0.8270 (t80) REVERT: E 127 GLU cc_start: 0.7735 (tt0) cc_final: 0.7473 (tt0) REVERT: E 181 GLU cc_start: 0.7813 (tt0) cc_final: 0.7428 (tt0) REVERT: E 248 LEU cc_start: 0.9028 (tp) cc_final: 0.8744 (tp) REVERT: E 300 LYS cc_start: 0.8161 (mmtm) cc_final: 0.7829 (mptt) REVERT: E 308 ASP cc_start: 0.8445 (m-30) cc_final: 0.8108 (m-30) REVERT: E 323 LEU cc_start: 0.8171 (mp) cc_final: 0.7906 (mt) REVERT: E 324 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6811 (mt-10) REVERT: E 409 ARG cc_start: 0.8115 (tpp80) cc_final: 0.7765 (tpt90) REVERT: D 147 ASN cc_start: 0.8643 (p0) cc_final: 0.8427 (p0) REVERT: D 246 TYR cc_start: 0.8262 (t80) cc_final: 0.7898 (t80) REVERT: D 268 ILE cc_start: 0.8154 (mm) cc_final: 0.7787 (mt) REVERT: D 288 THR cc_start: 0.8919 (m) cc_final: 0.8517 (p) REVERT: D 292 SER cc_start: 0.8878 (m) cc_final: 0.8472 (p) REVERT: D 308 ASP cc_start: 0.8297 (m-30) cc_final: 0.8072 (m-30) outliers start: 61 outliers final: 45 residues processed: 434 average time/residue: 0.2398 time to fit residues: 153.3237 Evaluate side-chains 450 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 403 time to evaluate : 1.500 ------------------------------------------------------------------------------- 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 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 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 244 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 177 ILE Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 233 CYS 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 206 LEU Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 228 THR 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 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 408 LYS Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 432 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 96 optimal weight: 0.6980 chunk 40 optimal weight: 0.0970 chunk 164 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 76 optimal weight: 0.2980 chunk 13 optimal weight: 0.0970 chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 0.1980 overall best weight: 0.2776 ------------------------------------------------------------------------------- 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** E 290 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14545 Z= 0.175 Angle : 0.636 10.913 19745 Z= 0.327 Chirality : 0.045 0.199 2240 Planarity : 0.005 0.048 2435 Dihedral : 4.373 30.333 2220 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.17 % Allowed : 19.29 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1700 helix: 2.37 (0.22), residues: 570 sheet: 0.91 (0.27), residues: 405 loop : -1.49 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 263 HIS 0.001 0.000 HIS B 133 PHE 0.019 0.001 PHE C 319 TYR 0.022 0.002 TYR C 246 ARG 0.006 0.001 ARG E 333 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 428 time to evaluate : 1.659 Fit side-chains REVERT: A 94 ASP cc_start: 0.8078 (t0) cc_final: 0.7846 (t70) REVERT: A 105 ASP cc_start: 0.7252 (p0) cc_final: 0.6984 (p0) REVERT: A 121 ASP cc_start: 0.8435 (p0) cc_final: 0.8079 (p0) REVERT: A 249 ILE cc_start: 0.8803 (tt) cc_final: 0.8504 (tp) REVERT: A 250 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7350 (mm110) REVERT: A 268 ILE cc_start: 0.7645 (mm) cc_final: 0.7244 (mm) REVERT: A 409 ARG cc_start: 0.7780 (tpp80) cc_final: 0.7387 (tpt90) REVERT: B 121 ASP cc_start: 0.8315 (p0) cc_final: 0.8057 (p0) REVERT: B 193 GLU cc_start: 0.8750 (pm20) cc_final: 0.8504 (pm20) REVERT: B 246 TYR cc_start: 0.8364 (t80) cc_final: 0.8146 (t80) REVERT: B 258 ILE cc_start: 0.8831 (mm) cc_final: 0.8398 (tt) REVERT: B 300 LYS cc_start: 0.8086 (mmtm) cc_final: 0.7731 (mptt) REVERT: B 308 ASP cc_start: 0.8428 (m-30) cc_final: 0.8192 (m-30) REVERT: B 409 ARG cc_start: 0.8072 (tpp80) cc_final: 0.7807 (tpt90) REVERT: C 37 PHE cc_start: 0.8213 (t80) cc_final: 0.7852 (t80) REVERT: C 268 ILE cc_start: 0.7594 (mm) cc_final: 0.7160 (mm) REVERT: C 300 LYS cc_start: 0.8076 (mptt) cc_final: 0.7809 (mmtt) REVERT: C 316 LEU cc_start: 0.8526 (mt) cc_final: 0.8324 (mm) REVERT: E 121 ASP cc_start: 0.8365 (p0) cc_final: 0.7971 (p0) REVERT: E 127 GLU cc_start: 0.7751 (tt0) cc_final: 0.7491 (tt0) REVERT: E 181 GLU cc_start: 0.7796 (tt0) cc_final: 0.7380 (tt0) REVERT: E 248 LEU cc_start: 0.8993 (tp) cc_final: 0.8702 (tp) REVERT: E 300 LYS cc_start: 0.8083 (mmtm) cc_final: 0.7831 (mptt) REVERT: E 308 ASP cc_start: 0.8436 (m-30) cc_final: 0.8067 (m-30) REVERT: E 324 GLU cc_start: 0.7426 (mt-10) cc_final: 0.7076 (mt-10) REVERT: E 409 ARG cc_start: 0.8052 (tpp80) cc_final: 0.7704 (tpt90) REVERT: D 37 PHE cc_start: 0.8422 (t80) cc_final: 0.8150 (t80) REVERT: D 147 ASN cc_start: 0.8650 (p0) cc_final: 0.8444 (p0) REVERT: D 246 TYR cc_start: 0.8245 (t80) cc_final: 0.7975 (t80) REVERT: D 268 ILE cc_start: 0.8075 (mm) cc_final: 0.7820 (mt) REVERT: D 288 THR cc_start: 0.8894 (m) cc_final: 0.8509 (p) REVERT: D 292 SER cc_start: 0.8859 (m) cc_final: 0.8468 (p) REVERT: D 300 LYS cc_start: 0.8205 (mptt) cc_final: 0.7846 (mmtt) outliers start: 49 outliers final: 34 residues processed: 440 average time/residue: 0.2454 time to fit residues: 159.4731 Evaluate side-chains 449 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 415 time to evaluate : 1.641 ------------------------------------------------------------------------------- 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 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 244 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 411 ASP 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 179 GLN Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain E residue 177 ILE Chi-restraints excluded: chain E residue 228 THR Chi-restraints excluded: chain E residue 235 GLU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 237 ARG Chi-restraints excluded: chain D residue 244 MET Chi-restraints excluded: chain D residue 264 VAL Chi-restraints excluded: chain D residue 322 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 93 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 138 optimal weight: 0.3980 chunk 91 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14545 Z= 0.240 Angle : 0.659 10.784 19745 Z= 0.341 Chirality : 0.046 0.255 2240 Planarity : 0.005 0.046 2435 Dihedral : 4.414 30.660 2220 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.62 % Allowed : 20.45 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.21), residues: 1700 helix: 2.36 (0.22), residues: 570 sheet: 0.91 (0.27), residues: 405 loop : -1.48 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 263 HIS 0.002 0.000 HIS A 133 PHE 0.019 0.002 PHE A 192 TYR 0.024 0.002 TYR C 246 ARG 0.009 0.001 ARG A 333 *********************** 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 470 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 414 time to evaluate : 1.471 Fit side-chains REVERT: A 121 ASP cc_start: 0.8472 (p0) cc_final: 0.8107 (p0) REVERT: A 193 GLU cc_start: 0.8736 (pm20) cc_final: 0.8155 (pm20) REVERT: A 237 ARG cc_start: 0.8401 (OUTLIER) cc_final: 0.7974 (mtt90) REVERT: A 249 ILE cc_start: 0.8842 (tt) cc_final: 0.8521 (tp) REVERT: A 250 GLN cc_start: 0.7653 (mm-40) cc_final: 0.7420 (mm110) REVERT: A 268 ILE cc_start: 0.7708 (mm) cc_final: 0.7280 (mm) REVERT: A 409 ARG cc_start: 0.7830 (tpp80) cc_final: 0.7452 (tpt90) REVERT: B 121 ASP cc_start: 0.8378 (p0) cc_final: 0.7954 (p0) REVERT: B 193 GLU cc_start: 0.8793 (pm20) cc_final: 0.8536 (pm20) REVERT: B 246 TYR cc_start: 0.8411 (t80) cc_final: 0.8180 (t80) REVERT: B 258 ILE cc_start: 0.8865 (mm) cc_final: 0.8433 (tt) REVERT: B 300 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7765 (mptt) REVERT: B 308 ASP cc_start: 0.8443 (m-30) cc_final: 0.8202 (m-30) REVERT: B 409 ARG cc_start: 0.8098 (tpp80) cc_final: 0.7866 (tpt90) REVERT: C 232 THR cc_start: 0.8715 (OUTLIER) cc_final: 0.8472 (t) REVERT: C 268 ILE cc_start: 0.7613 (mm) cc_final: 0.7186 (mm) REVERT: C 316 LEU cc_start: 0.8525 (mt) cc_final: 0.8309 (mm) REVERT: E 127 GLU cc_start: 0.7785 (tt0) cc_final: 0.7506 (tt0) REVERT: E 248 LEU cc_start: 0.9029 (tp) cc_final: 0.8773 (tp) REVERT: E 300 LYS cc_start: 0.8143 (mmtm) cc_final: 0.7881 (mptt) REVERT: E 308 ASP cc_start: 0.8468 (m-30) cc_final: 0.8117 (m-30) REVERT: E 323 LEU cc_start: 0.8186 (mt) cc_final: 0.7769 (mt) REVERT: E 324 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7166 (mt-10) REVERT: E 409 ARG cc_start: 0.8070 (tpp80) cc_final: 0.7723 (tpt90) REVERT: D 89 ARG cc_start: 0.8501 (ttt-90) cc_final: 0.8262 (ttt-90) REVERT: D 147 ASN cc_start: 0.8654 (p0) cc_final: 0.8450 (p0) REVERT: D 246 TYR cc_start: 0.8309 (t80) cc_final: 0.7950 (t80) REVERT: D 268 ILE cc_start: 0.8083 (mm) cc_final: 0.7825 (mt) REVERT: D 288 THR cc_start: 0.8977 (m) cc_final: 0.8589 (p) REVERT: D 292 SER cc_start: 0.8879 (m) cc_final: 0.8485 (p) outliers start: 56 outliers final: 42 residues processed: 432 average time/residue: 0.2339 time to fit residues: 149.5371 Evaluate side-chains 451 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 407 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ASP 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 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 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 179 GLN Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 3.9990 chunk 97 optimal weight: 0.1980 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 104 optimal weight: 0.5980 chunk 111 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 128 optimal weight: 2.9990 chunk 149 optimal weight: 0.2980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 174 GLN C 334 GLN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14545 Z= 0.190 Angle : 0.667 10.286 19745 Z= 0.341 Chirality : 0.046 0.252 2240 Planarity : 0.005 0.046 2435 Dihedral : 4.353 28.325 2220 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.85 % Allowed : 22.20 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.21), residues: 1700 helix: 2.29 (0.22), residues: 570 sheet: 0.92 (0.27), residues: 405 loop : -1.49 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 263 HIS 0.001 0.000 HIS D 133 PHE 0.024 0.001 PHE D 37 TYR 0.022 0.002 TYR C 246 ARG 0.006 0.001 ARG B 237 *********************** 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 fitting. rotamer outliers: 44 poor density : 415 time to evaluate : 1.580 Fit side-chains REVERT: A 121 ASP cc_start: 0.8428 (p0) cc_final: 0.8045 (p0) REVERT: A 249 ILE cc_start: 0.8833 (tt) cc_final: 0.8524 (tp) REVERT: A 250 GLN cc_start: 0.7608 (mm-40) cc_final: 0.7344 (mm110) REVERT: A 268 ILE cc_start: 0.7674 (mm) cc_final: 0.7285 (mm) REVERT: A 409 ARG cc_start: 0.7770 (tpp80) cc_final: 0.7340 (tpt90) REVERT: B 121 ASP cc_start: 0.8320 (p0) cc_final: 0.7885 (p0) REVERT: B 193 GLU cc_start: 0.8784 (pm20) cc_final: 0.8522 (pm20) REVERT: B 246 TYR cc_start: 0.8401 (t80) cc_final: 0.8176 (t80) REVERT: B 258 ILE cc_start: 0.8855 (mm) cc_final: 0.8424 (tt) REVERT: B 300 LYS cc_start: 0.8109 (mmtm) cc_final: 0.7738 (mptt) REVERT: B 308 ASP cc_start: 0.8455 (m-30) cc_final: 0.8177 (m-30) REVERT: B 409 ARG cc_start: 0.8086 (tpp80) cc_final: 0.7816 (tpt90) REVERT: C 232 THR cc_start: 0.8668 (OUTLIER) cc_final: 0.8404 (t) REVERT: C 268 ILE cc_start: 0.7586 (mm) cc_final: 0.7168 (mm) REVERT: C 316 LEU cc_start: 0.8482 (mt) cc_final: 0.8257 (mm) REVERT: E 121 ASP cc_start: 0.8406 (p0) cc_final: 0.7976 (p0) REVERT: E 127 GLU cc_start: 0.7774 (tt0) cc_final: 0.7505 (tt0) REVERT: E 248 LEU cc_start: 0.9010 (tp) cc_final: 0.8763 (tp) REVERT: E 300 LYS cc_start: 0.8103 (mmtm) cc_final: 0.7831 (mptt) REVERT: E 308 ASP cc_start: 0.8463 (m-30) cc_final: 0.8095 (m-30) REVERT: E 323 LEU cc_start: 0.8144 (mt) cc_final: 0.7815 (mt) REVERT: E 324 GLU cc_start: 0.7411 (mt-10) cc_final: 0.7171 (mt-10) REVERT: E 409 ARG cc_start: 0.8048 (tpp80) cc_final: 0.7704 (tpt90) REVERT: D 89 ARG cc_start: 0.8475 (ttt-90) cc_final: 0.8238 (ttt-90) REVERT: D 147 ASN cc_start: 0.8658 (p0) cc_final: 0.8453 (p0) REVERT: D 246 TYR cc_start: 0.8308 (t80) cc_final: 0.8013 (t80) REVERT: D 292 SER cc_start: 0.8876 (m) cc_final: 0.8482 (p) REVERT: D 300 LYS cc_start: 0.8241 (mptt) cc_final: 0.7890 (mmtt) outliers start: 44 outliers final: 34 residues processed: 426 average time/residue: 0.2350 time to fit residues: 148.7771 Evaluate side-chains 445 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 410 time to evaluate : 1.696 ------------------------------------------------------------------------------- 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 264 VAL Chi-restraints excluded: chain A residue 270 MET 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 244 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 152 optimal weight: 1.9990 chunk 91 optimal weight: 0.2980 chunk 66 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 137 optimal weight: 3.9990 chunk 144 optimal weight: 2.9990 chunk 100 optimal weight: 0.7980 chunk 161 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN C 174 GLN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14545 Z= 0.221 Angle : 0.676 10.408 19745 Z= 0.347 Chirality : 0.046 0.259 2240 Planarity : 0.005 0.044 2435 Dihedral : 4.344 28.146 2220 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.78 % Allowed : 23.11 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1700 helix: 2.25 (0.22), residues: 570 sheet: 0.94 (0.27), residues: 405 loop : -1.48 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 263 HIS 0.002 0.000 HIS D 133 PHE 0.022 0.002 PHE B 330 TYR 0.023 0.002 TYR C 246 ARG 0.011 0.001 ARG C 333 *********************** 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 453 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 410 time to evaluate : 1.509 Fit side-chains REVERT: A 121 ASP cc_start: 0.8439 (p0) cc_final: 0.8056 (p0) REVERT: A 193 GLU cc_start: 0.8747 (pm20) cc_final: 0.8211 (pm20) REVERT: A 249 ILE cc_start: 0.8835 (tt) cc_final: 0.8574 (tp) REVERT: A 268 ILE cc_start: 0.7674 (mm) cc_final: 0.7267 (mm) REVERT: A 409 ARG cc_start: 0.7782 (tpp80) cc_final: 0.7393 (tpt90) REVERT: B 121 ASP cc_start: 0.8366 (p0) cc_final: 0.7937 (p0) REVERT: B 193 GLU cc_start: 0.8825 (pm20) cc_final: 0.8548 (pm20) REVERT: B 241 GLU cc_start: 0.7839 (tt0) cc_final: 0.7622 (tt0) REVERT: B 246 TYR cc_start: 0.8419 (t80) cc_final: 0.8195 (t80) REVERT: B 258 ILE cc_start: 0.8870 (mm) cc_final: 0.8418 (tt) REVERT: B 300 LYS cc_start: 0.8117 (mmtm) cc_final: 0.7714 (mptt) REVERT: B 308 ASP cc_start: 0.8461 (m-30) cc_final: 0.8170 (m-30) REVERT: B 409 ARG cc_start: 0.8085 (tpp80) cc_final: 0.7679 (tpt90) REVERT: C 232 THR cc_start: 0.8667 (OUTLIER) cc_final: 0.8391 (t) REVERT: C 268 ILE cc_start: 0.7610 (mm) cc_final: 0.7189 (mm) REVERT: C 316 LEU cc_start: 0.8478 (mt) cc_final: 0.8221 (mm) REVERT: C 409 ARG cc_start: 0.7823 (ttm-80) cc_final: 0.6972 (tpt90) REVERT: E 127 GLU cc_start: 0.7794 (tt0) cc_final: 0.7521 (tt0) REVERT: E 248 LEU cc_start: 0.9036 (tp) cc_final: 0.8790 (tp) REVERT: E 300 LYS cc_start: 0.8107 (mmtm) cc_final: 0.7830 (mptt) REVERT: E 308 ASP cc_start: 0.8476 (m-30) cc_final: 0.8098 (m-30) REVERT: E 323 LEU cc_start: 0.8192 (mt) cc_final: 0.7872 (mt) REVERT: E 324 GLU cc_start: 0.7403 (mt-10) cc_final: 0.7172 (mt-10) REVERT: E 409 ARG cc_start: 0.8054 (tpp80) cc_final: 0.7711 (tpt90) REVERT: D 89 ARG cc_start: 0.8487 (ttt-90) cc_final: 0.8234 (ttt-90) REVERT: D 147 ASN cc_start: 0.8660 (p0) cc_final: 0.8451 (p0) REVERT: D 246 TYR cc_start: 0.8355 (t80) cc_final: 0.8010 (t80) REVERT: D 268 ILE cc_start: 0.8125 (mm) cc_final: 0.7663 (mt) REVERT: D 292 SER cc_start: 0.8828 (m) cc_final: 0.8463 (p) REVERT: D 300 LYS cc_start: 0.8241 (mptt) cc_final: 0.7870 (mmtt) outliers start: 43 outliers final: 35 residues processed: 426 average time/residue: 0.2438 time to fit residues: 152.1455 Evaluate side-chains 444 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 408 time to evaluate : 1.650 ------------------------------------------------------------------------------- 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 264 VAL Chi-restraints excluded: chain A residue 270 MET 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 234 ILE Chi-restraints excluded: chain B residue 235 GLU Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 192 PHE Chi-restraints excluded: chain C residue 232 THR Chi-restraints excluded: chain C residue 233 CYS Chi-restraints excluded: chain C residue 264 VAL Chi-restraints excluded: chain C residue 408 LYS Chi-restraints excluded: chain C residue 428 PHE Chi-restraints excluded: chain E residue 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 0.5980 chunk 76 optimal weight: 0.0470 chunk 112 optimal weight: 2.9990 chunk 169 optimal weight: 0.2980 chunk 155 optimal weight: 2.9990 chunk 134 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 104 optimal weight: 0.0870 chunk 82 optimal weight: 0.7980 chunk 107 optimal weight: 0.6980 chunk 143 optimal weight: 0.6980 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 426 ASN B 334 GLN C 174 GLN E 334 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14545 Z= 0.193 Angle : 0.690 10.229 19745 Z= 0.352 Chirality : 0.046 0.270 2240 Planarity : 0.005 0.045 2435 Dihedral : 4.284 26.782 2220 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.39 % Allowed : 23.62 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1700 helix: 2.19 (0.22), residues: 570 sheet: 0.95 (0.27), residues: 405 loop : -1.50 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 263 HIS 0.001 0.000 HIS D 133 PHE 0.024 0.001 PHE B 330 TYR 0.022 0.002 TYR C 246 ARG 0.006 0.001 ARG D 333 ********************** 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 456 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 419 time to evaluate : 1.708 Fit side-chains REVERT: A 105 ASP cc_start: 0.7327 (p0) cc_final: 0.7055 (p0) REVERT: A 121 ASP cc_start: 0.8400 (p0) cc_final: 0.8009 (p0) REVERT: A 193 GLU cc_start: 0.8744 (pm20) cc_final: 0.8201 (pm20) REVERT: A 250 GLN cc_start: 0.7589 (mm-40) cc_final: 0.7318 (mm110) REVERT: A 268 ILE cc_start: 0.7699 (mm) cc_final: 0.7273 (mm) REVERT: A 409 ARG cc_start: 0.7758 (tpp80) cc_final: 0.7326 (tpt90) REVERT: B 121 ASP cc_start: 0.8319 (p0) cc_final: 0.8087 (p0) REVERT: B 246 TYR cc_start: 0.8423 (t80) cc_final: 0.8202 (t80) REVERT: B 258 ILE cc_start: 0.8859 (mm) cc_final: 0.8409 (tt) REVERT: B 300 LYS cc_start: 0.8091 (mmtm) cc_final: 0.7661 (mptt) REVERT: B 308 ASP cc_start: 0.8440 (m-30) cc_final: 0.8142 (m-30) REVERT: B 409 ARG cc_start: 0.8072 (tpp80) cc_final: 0.7657 (tpt90) REVERT: C 268 ILE cc_start: 0.7560 (mm) cc_final: 0.7323 (mm) REVERT: C 316 LEU cc_start: 0.8474 (mt) cc_final: 0.8212 (mm) REVERT: E 121 ASP cc_start: 0.8423 (p0) cc_final: 0.7986 (p0) REVERT: E 127 GLU cc_start: 0.7774 (tt0) cc_final: 0.7497 (tt0) REVERT: E 248 LEU cc_start: 0.9019 (tp) cc_final: 0.8771 (tp) REVERT: E 300 LYS cc_start: 0.8084 (mmtm) cc_final: 0.7838 (mptt) REVERT: E 308 ASP cc_start: 0.8466 (m-30) cc_final: 0.8118 (m-30) REVERT: E 323 LEU cc_start: 0.8205 (mt) cc_final: 0.7809 (mt) REVERT: E 409 ARG cc_start: 0.8031 (tpp80) cc_final: 0.7690 (tpt90) REVERT: D 89 ARG cc_start: 0.8476 (ttt-90) cc_final: 0.8235 (ttt-90) REVERT: D 147 ASN cc_start: 0.8658 (p0) cc_final: 0.8451 (p0) REVERT: D 246 TYR cc_start: 0.8376 (t80) cc_final: 0.8047 (t80) REVERT: D 268 ILE cc_start: 0.8063 (mm) cc_final: 0.7615 (mt) REVERT: D 292 SER cc_start: 0.8799 (m) cc_final: 0.8441 (p) REVERT: D 300 LYS cc_start: 0.8229 (mptt) cc_final: 0.7852 (mmtt) outliers start: 37 outliers final: 32 residues processed: 431 average time/residue: 0.2400 time to fit residues: 153.6436 Evaluate side-chains 439 residues out of total 1545 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 407 time to evaluate : 1.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 428 PHE Chi-restraints excluded: chain B residue 157 THR Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 230 LYS Chi-restraints excluded: chain B residue 234 ILE Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain B residue 264 VAL Chi-restraints excluded: chain B residue 411 ASP Chi-restraints excluded: chain B residue 428 PHE Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 179 GLN Chi-restraints excluded: chain C residue 192 PHE 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 4.9990 chunk 124 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 135 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 138 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 118 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.097635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.087356 restraints weight = 27200.162| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.70 r_work: 0.3190 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 14545 Z= 0.222 Angle : 0.690 10.416 19745 Z= 0.352 Chirality : 0.046 0.256 2240 Planarity : 0.005 0.043 2435 Dihedral : 4.255 27.453 2220 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.39 % Allowed : 24.08 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.21), residues: 1700 helix: 2.18 (0.22), residues: 570 sheet: 0.97 (0.27), residues: 405 loop : -1.51 (0.21), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 263 HIS 0.002 0.000 HIS D 133 PHE 0.023 0.002 PHE B 330 TYR 0.022 0.002 TYR C 246 ARG 0.010 0.001 ARG E 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3569.00 seconds wall clock time: 64 minutes 0.63 seconds (3840.63 seconds total)