Starting phenix.real_space_refine on Thu Mar 5 04:15:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6j0f_9763/03_2026/6j0f_9763.cif Found real_map, /net/cci-nas-00/data/ceres_data/6j0f_9763/03_2026/6j0f_9763.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6j0f_9763/03_2026/6j0f_9763.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6j0f_9763/03_2026/6j0f_9763.map" model { file = "/net/cci-nas-00/data/ceres_data/6j0f_9763/03_2026/6j0f_9763.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6j0f_9763/03_2026/6j0f_9763.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 78 5.16 5 C 12192 2.51 5 N 3222 2.21 5 O 3822 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 234 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19314 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2122 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 9, 'TRANS': 262} Chain breaks: 3 Chain: "a" Number of atoms: 1097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1097 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 7, 'TRANS': 132} Restraints were copied for chains: B, C, D, E, F, b, c, d, e, f Time building chain proxies: 2.47, per 1000 atoms: 0.13 Number of scatterers: 19314 At special positions: 0 Unit cell: (153.577, 167.029, 103.132, 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 78 16.00 O 3822 8.00 N 3222 7.00 C 12192 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 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 837.6 milliseconds 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4680 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 36 sheets defined 21.4% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 6 through 19 removed outlier: 3.608A pdb=" N ALA A 13 " --> pdb=" O ASP A 9 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP A 15 " --> pdb=" O ASN A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 120 removed outlier: 3.561A pdb=" N GLN A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 118 " --> pdb=" O GLN A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 152 removed outlier: 3.521A pdb=" N ASN A 147 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 151 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 152 " --> pdb=" O PHE A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 214 through 220 removed outlier: 4.050A pdb=" N VAL A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 220 " --> pdb=" O ASN A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 267 removed outlier: 4.296A pdb=" N GLU A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG A 264 " --> pdb=" O ASN A 260 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL A 266 " --> pdb=" O PHE A 262 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN A 267 " --> pdb=" O ASP A 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 19 removed outlier: 3.608A pdb=" N ALA B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP B 15 " --> pdb=" O ASN B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 120 removed outlier: 3.561A pdb=" N GLN B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA B 118 " --> pdb=" O GLN B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 152 removed outlier: 3.522A pdb=" N ASN B 147 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU B 152 " --> pdb=" O PHE B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 211 Processing helix chain 'B' and resid 214 through 220 removed outlier: 4.051A pdb=" N VAL B 219 " --> pdb=" O ASP B 215 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 220 " --> pdb=" O ASN B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 267 removed outlier: 4.295A pdb=" N GLU B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL B 266 " --> pdb=" O PHE B 262 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN B 267 " --> pdb=" O ASP B 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 19 removed outlier: 3.608A pdb=" N ALA C 13 " --> pdb=" O ASP C 9 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP C 15 " --> pdb=" O ASN C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 120 removed outlier: 3.560A pdb=" N GLN C 110 " --> pdb=" O ASN C 106 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 118 " --> pdb=" O GLN C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 152 removed outlier: 3.521A pdb=" N ASN C 147 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 151 " --> pdb=" O ASN C 147 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 152 " --> pdb=" O PHE C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 211 Processing helix chain 'C' and resid 214 through 220 removed outlier: 4.050A pdb=" N VAL C 219 " --> pdb=" O ASP C 215 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 220 " --> pdb=" O ASN C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 267 removed outlier: 4.296A pdb=" N GLU C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL C 266 " --> pdb=" O PHE C 262 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN C 267 " --> pdb=" O ASP C 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 19 removed outlier: 3.608A pdb=" N ALA D 13 " --> pdb=" O ASP D 9 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP D 15 " --> pdb=" O ASN D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 120 removed outlier: 3.561A pdb=" N GLN D 110 " --> pdb=" O ASN D 106 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA D 118 " --> pdb=" O GLN D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 152 removed outlier: 3.521A pdb=" N ASN D 147 " --> pdb=" O ASN D 143 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 152 " --> pdb=" O PHE D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 211 Processing helix chain 'D' and resid 214 through 220 removed outlier: 4.051A pdb=" N VAL D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 220 " --> pdb=" O ASN D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 267 removed outlier: 4.297A pdb=" N GLU D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG D 264 " --> pdb=" O ASN D 260 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL D 266 " --> pdb=" O PHE D 262 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN D 267 " --> pdb=" O ASP D 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 19 removed outlier: 3.608A pdb=" N ALA E 13 " --> pdb=" O ASP E 9 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP E 15 " --> pdb=" O ASN E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 120 removed outlier: 3.561A pdb=" N GLN E 110 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA E 118 " --> pdb=" O GLN E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 152 removed outlier: 3.522A pdb=" N ASN E 147 " --> pdb=" O ASN E 143 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER E 151 " --> pdb=" O ASN E 147 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU E 152 " --> pdb=" O PHE E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 211 Processing helix chain 'E' and resid 214 through 220 removed outlier: 4.050A pdb=" N VAL E 219 " --> pdb=" O ASP E 215 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E 220 " --> pdb=" O ASN E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 267 removed outlier: 4.296A pdb=" N GLU E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG E 264 " --> pdb=" O ASN E 260 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL E 266 " --> pdb=" O PHE E 262 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN E 267 " --> pdb=" O ASP E 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 19 removed outlier: 3.609A pdb=" N ALA F 13 " --> pdb=" O ASP F 9 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP F 15 " --> pdb=" O ASN F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 120 removed outlier: 3.562A pdb=" N GLN F 110 " --> pdb=" O ASN F 106 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA F 118 " --> pdb=" O GLN F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 152 removed outlier: 3.521A pdb=" N ASN F 147 " --> pdb=" O ASN F 143 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER F 151 " --> pdb=" O ASN F 147 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU F 152 " --> pdb=" O PHE F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 211 Processing helix chain 'F' and resid 214 through 220 removed outlier: 4.050A pdb=" N VAL F 219 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU F 220 " --> pdb=" O ASN F 216 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 267 removed outlier: 4.296A pdb=" N GLU F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG F 264 " --> pdb=" O ASN F 260 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL F 266 " --> pdb=" O PHE F 262 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN F 267 " --> pdb=" O ASP F 263 " (cutoff:3.500A) Processing helix chain 'a' and resid 76 through 82 Processing helix chain 'b' and resid 76 through 82 Processing helix chain 'c' and resid 76 through 82 Processing helix chain 'd' and resid 76 through 82 Processing helix chain 'e' and resid 76 through 82 Processing helix chain 'f' and resid 76 through 82 Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29 removed outlier: 6.796A pdb=" N ALA A 27 " --> pdb=" O VAL A 44 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ILE A 46 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG A 29 " --> pdb=" O ILE A 46 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU A 48 " --> pdb=" O ARG A 29 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASN A 82 " --> pdb=" O TYR A 49 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 51 " --> pdb=" O LYS A 80 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS A 80 " --> pdb=" O ILE A 51 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR A 162 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 132 " --> pdb=" O THR A 165 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 66 removed outlier: 3.550A pdb=" N ARG A 71 " --> pdb=" O ASP A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 223 through 230 removed outlier: 3.619A pdb=" N SER A 247 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 243 " --> pdb=" O VAL A 228 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE A 241 " --> pdb=" O GLU A 230 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE A 242 " --> pdb=" O GLU A 283 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE A 285 " --> pdb=" O ILE A 242 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU A 244 " --> pdb=" O ILE A 285 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 287 " --> pdb=" O LEU A 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 27 through 29 removed outlier: 6.796A pdb=" N ALA B 27 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE B 46 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG B 29 " --> pdb=" O ILE B 46 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU B 48 " --> pdb=" O ARG B 29 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASN B 82 " --> pdb=" O TYR B 49 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE B 51 " --> pdb=" O LYS B 80 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS B 80 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR B 162 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR B 132 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 65 through 66 removed outlier: 3.550A pdb=" N ARG B 71 " --> pdb=" O ASP B 66 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 223 through 230 removed outlier: 3.619A pdb=" N SER B 247 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU B 243 " --> pdb=" O VAL B 228 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE B 241 " --> pdb=" O GLU B 230 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N ILE B 242 " --> pdb=" O GLU B 283 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE B 285 " --> pdb=" O ILE B 242 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU B 244 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS B 287 " --> pdb=" O LEU B 244 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 27 through 29 removed outlier: 6.795A pdb=" N ALA C 27 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE C 46 " --> pdb=" O ALA C 27 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG C 29 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N LEU C 48 " --> pdb=" O ARG C 29 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASN C 82 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE C 51 " --> pdb=" O LYS C 80 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS C 80 " --> pdb=" O ILE C 51 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR C 162 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR C 132 " --> pdb=" O THR C 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 65 through 66 removed outlier: 3.550A pdb=" N ARG C 71 " --> pdb=" O ASP C 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 223 through 230 removed outlier: 3.619A pdb=" N SER C 247 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 243 " --> pdb=" O VAL C 228 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 241 " --> pdb=" O GLU C 230 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE C 242 " --> pdb=" O GLU C 283 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE C 285 " --> pdb=" O ILE C 242 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU C 244 " --> pdb=" O ILE C 285 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS C 287 " --> pdb=" O LEU C 244 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 27 through 29 removed outlier: 6.796A pdb=" N ALA D 27 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE D 46 " --> pdb=" O ALA D 27 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG D 29 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU D 48 " --> pdb=" O ARG D 29 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASN D 82 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE D 51 " --> pdb=" O LYS D 80 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS D 80 " --> pdb=" O ILE D 51 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR D 162 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TYR D 132 " --> pdb=" O THR D 165 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 65 through 66 removed outlier: 3.549A pdb=" N ARG D 71 " --> pdb=" O ASP D 66 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 223 through 230 removed outlier: 3.619A pdb=" N SER D 247 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 243 " --> pdb=" O VAL D 228 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE D 241 " --> pdb=" O GLU D 230 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE D 242 " --> pdb=" O GLU D 283 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE D 285 " --> pdb=" O ILE D 242 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU D 244 " --> pdb=" O ILE D 285 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS D 287 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 27 through 29 removed outlier: 6.795A pdb=" N ALA E 27 " --> pdb=" O VAL E 44 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE E 46 " --> pdb=" O ALA E 27 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG E 29 " --> pdb=" O ILE E 46 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU E 48 " --> pdb=" O ARG E 29 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N ASN E 82 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ILE E 51 " --> pdb=" O LYS E 80 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS E 80 " --> pdb=" O ILE E 51 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR E 162 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR E 132 " --> pdb=" O THR E 165 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 65 through 66 removed outlier: 3.549A pdb=" N ARG E 71 " --> pdb=" O ASP E 66 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 223 through 230 removed outlier: 3.619A pdb=" N SER E 247 " --> pdb=" O GLU E 224 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU E 243 " --> pdb=" O VAL E 228 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE E 241 " --> pdb=" O GLU E 230 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE E 242 " --> pdb=" O GLU E 283 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE E 285 " --> pdb=" O ILE E 242 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU E 244 " --> pdb=" O ILE E 285 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS E 287 " --> pdb=" O LEU E 244 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 27 through 29 removed outlier: 6.796A pdb=" N ALA F 27 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE F 46 " --> pdb=" O ALA F 27 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ARG F 29 " --> pdb=" O ILE F 46 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N LEU F 48 " --> pdb=" O ARG F 29 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASN F 82 " --> pdb=" O TYR F 49 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE F 51 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS F 80 " --> pdb=" O ILE F 51 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR F 162 " --> pdb=" O TYR F 83 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR F 132 " --> pdb=" O THR F 165 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 65 through 66 removed outlier: 3.550A pdb=" N ARG F 71 " --> pdb=" O ASP F 66 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 223 through 230 removed outlier: 3.619A pdb=" N SER F 247 " --> pdb=" O GLU F 224 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU F 243 " --> pdb=" O VAL F 228 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE F 241 " --> pdb=" O GLU F 230 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N ILE F 242 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N ILE F 285 " --> pdb=" O ILE F 242 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LEU F 244 " --> pdb=" O ILE F 285 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS F 287 " --> pdb=" O LEU F 244 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'a' and resid 26 through 27 removed outlier: 5.803A pdb=" N LYS a 92 " --> pdb=" O ASN a 114 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN a 114 " --> pdb=" O LYS a 92 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET a 108 " --> pdb=" O LEU a 98 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ASN a 111 " --> pdb=" O MET a 146 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N MET a 146 " --> pdb=" O ASN a 111 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N SER a 113 " --> pdb=" O VAL a 144 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL a 144 " --> pdb=" O SER a 113 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA a 115 " --> pdb=" O ASP a 142 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP a 142 " --> pdb=" O ALA a 115 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N MET a 140 " --> pdb=" O PRO a 117 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER a 119 " --> pdb=" O THR a 138 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR a 62 " --> pdb=" O ALA a 141 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER a 32 " --> pdb=" O ARG a 67 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'a' and resid 26 through 27 removed outlier: 5.803A pdb=" N LYS a 92 " --> pdb=" O ASN a 114 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN a 114 " --> pdb=" O LYS a 92 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET a 108 " --> pdb=" O LEU a 98 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'a' and resid 37 through 38 removed outlier: 3.715A pdb=" N MET b 108 " --> pdb=" O LEU b 98 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN b 114 " --> pdb=" O LYS b 92 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LYS b 92 " --> pdb=" O ASN b 114 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'a' and resid 37 through 38 removed outlier: 6.890A pdb=" N ASN b 111 " --> pdb=" O MET b 146 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N MET b 146 " --> pdb=" O ASN b 111 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N SER b 113 " --> pdb=" O VAL b 144 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL b 144 " --> pdb=" O SER b 113 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA b 115 " --> pdb=" O ASP b 142 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP b 142 " --> pdb=" O ALA b 115 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N MET b 140 " --> pdb=" O PRO b 117 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER b 119 " --> pdb=" O THR b 138 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR b 62 " --> pdb=" O ALA b 141 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER b 32 " --> pdb=" O ARG b 67 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'a' and resid 40 through 44 removed outlier: 5.014A pdb=" N ASP a 41 " --> pdb=" O GLY a 57 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'a' and resid 125 through 126 removed outlier: 4.104A pdb=" N SER f 32 " --> pdb=" O ARG f 67 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR f 62 " --> pdb=" O ALA f 141 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER f 119 " --> pdb=" O THR f 138 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N MET f 140 " --> pdb=" O PRO f 117 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP f 142 " --> pdb=" O ALA f 115 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA f 115 " --> pdb=" O ASP f 142 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL f 144 " --> pdb=" O SER f 113 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N SER f 113 " --> pdb=" O VAL f 144 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N MET f 146 " --> pdb=" O ASN f 111 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASN f 111 " --> pdb=" O MET f 146 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'a' and resid 125 through 126 removed outlier: 4.104A pdb=" N SER f 32 " --> pdb=" O ARG f 67 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR f 62 " --> pdb=" O ALA f 141 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER f 119 " --> pdb=" O THR f 138 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N MET f 140 " --> pdb=" O PRO f 117 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP f 142 " --> pdb=" O ALA f 115 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA f 115 " --> pdb=" O ASP f 142 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL f 144 " --> pdb=" O SER f 113 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N SER f 113 " --> pdb=" O VAL f 144 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N MET f 146 " --> pdb=" O ASN f 111 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASN f 111 " --> pdb=" O MET f 146 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET f 108 " --> pdb=" O LEU f 98 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN f 114 " --> pdb=" O LYS f 92 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LYS f 92 " --> pdb=" O ASN f 114 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'b' and resid 37 through 38 removed outlier: 3.714A pdb=" N MET c 108 " --> pdb=" O LEU c 98 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN c 114 " --> pdb=" O LYS c 92 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LYS c 92 " --> pdb=" O ASN c 114 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'b' and resid 37 through 38 removed outlier: 6.888A pdb=" N ASN c 111 " --> pdb=" O MET c 146 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N MET c 146 " --> pdb=" O ASN c 111 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N SER c 113 " --> pdb=" O VAL c 144 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL c 144 " --> pdb=" O SER c 113 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA c 115 " --> pdb=" O ASP c 142 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP c 142 " --> pdb=" O ALA c 115 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N MET c 140 " --> pdb=" O PRO c 117 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER c 119 " --> pdb=" O THR c 138 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR c 62 " --> pdb=" O ALA c 141 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER c 32 " --> pdb=" O ARG c 67 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'b' and resid 40 through 44 removed outlier: 5.015A pdb=" N ASP b 41 " --> pdb=" O GLY b 57 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'c' and resid 37 through 38 removed outlier: 3.714A pdb=" N MET d 108 " --> pdb=" O LEU d 98 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN d 114 " --> pdb=" O LYS d 92 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LYS d 92 " --> pdb=" O ASN d 114 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'c' and resid 37 through 38 removed outlier: 6.890A pdb=" N ASN d 111 " --> pdb=" O MET d 146 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N MET d 146 " --> pdb=" O ASN d 111 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N SER d 113 " --> pdb=" O VAL d 144 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL d 144 " --> pdb=" O SER d 113 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ALA d 115 " --> pdb=" O ASP d 142 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP d 142 " --> pdb=" O ALA d 115 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N MET d 140 " --> pdb=" O PRO d 117 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER d 119 " --> pdb=" O THR d 138 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR d 62 " --> pdb=" O ALA d 141 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER d 32 " --> pdb=" O ARG d 67 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'c' and resid 40 through 44 removed outlier: 5.015A pdb=" N ASP c 41 " --> pdb=" O GLY c 57 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'd' and resid 37 through 38 removed outlier: 3.714A pdb=" N MET e 108 " --> pdb=" O LEU e 98 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ASN e 114 " --> pdb=" O LYS e 92 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LYS e 92 " --> pdb=" O ASN e 114 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'd' and resid 37 through 38 removed outlier: 6.890A pdb=" N ASN e 111 " --> pdb=" O MET e 146 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N MET e 146 " --> pdb=" O ASN e 111 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N SER e 113 " --> pdb=" O VAL e 144 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL e 144 " --> pdb=" O SER e 113 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA e 115 " --> pdb=" O ASP e 142 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP e 142 " --> pdb=" O ALA e 115 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N MET e 140 " --> pdb=" O PRO e 117 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER e 119 " --> pdb=" O THR e 138 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N THR e 62 " --> pdb=" O ALA e 141 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N SER e 32 " --> pdb=" O ARG e 67 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'd' and resid 40 through 44 removed outlier: 5.015A pdb=" N ASP d 41 " --> pdb=" O GLY d 57 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'e' and resid 40 through 44 removed outlier: 5.015A pdb=" N ASP e 41 " --> pdb=" O GLY e 57 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'f' and resid 40 through 44 removed outlier: 5.014A pdb=" N ASP f 41 " --> pdb=" O GLY f 57 " (cutoff:3.500A) 606 hydrogen bonds defined for protein. 1719 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.68 Time building geometry restraints manager: 2.05 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: 6346 1.34 - 1.46: 3209 1.46 - 1.57: 9921 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 19620 Sorted by residual: bond pdb=" N LEU c 86 " pdb=" CA LEU c 86 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.23e-02 6.61e+03 6.15e+00 bond pdb=" N LEU d 86 " pdb=" CA LEU d 86 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.23e-02 6.61e+03 6.15e+00 bond pdb=" N LEU f 86 " pdb=" CA LEU f 86 " ideal model delta sigma weight residual 1.458 1.489 -0.030 1.23e-02 6.61e+03 6.14e+00 bond pdb=" N LEU a 86 " pdb=" CA LEU a 86 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.23e-02 6.61e+03 5.90e+00 bond pdb=" N LEU e 86 " pdb=" CA LEU e 86 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.23e-02 6.61e+03 5.84e+00 ... (remaining 19615 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.26: 26261 3.26 - 6.52: 331 6.52 - 9.78: 72 9.78 - 13.04: 12 13.04 - 16.29: 6 Bond angle restraints: 26682 Sorted by residual: angle pdb=" C GLN b 85 " pdb=" N LEU b 86 " pdb=" CA LEU b 86 " ideal model delta sigma weight residual 120.82 128.28 -7.46 1.50e+00 4.44e-01 2.47e+01 angle pdb=" C GLN e 85 " pdb=" N LEU e 86 " pdb=" CA LEU e 86 " ideal model delta sigma weight residual 120.82 128.26 -7.44 1.50e+00 4.44e-01 2.46e+01 angle pdb=" C GLN d 85 " pdb=" N LEU d 86 " pdb=" CA LEU d 86 " ideal model delta sigma weight residual 120.82 128.26 -7.44 1.50e+00 4.44e-01 2.46e+01 angle pdb=" C GLN f 85 " pdb=" N LEU f 86 " pdb=" CA LEU f 86 " ideal model delta sigma weight residual 120.82 128.23 -7.41 1.50e+00 4.44e-01 2.44e+01 angle pdb=" C GLN a 85 " pdb=" N LEU a 86 " pdb=" CA LEU a 86 " ideal model delta sigma weight residual 120.82 128.23 -7.41 1.50e+00 4.44e-01 2.44e+01 ... (remaining 26677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 10474 16.56 - 33.13: 1017 33.13 - 49.69: 275 49.69 - 66.25: 78 66.25 - 82.82: 30 Dihedral angle restraints: 11874 sinusoidal: 4680 harmonic: 7194 Sorted by residual: dihedral pdb=" CA GLN c 85 " pdb=" C GLN c 85 " pdb=" N LEU c 86 " pdb=" CA LEU c 86 " ideal model delta harmonic sigma weight residual -180.00 -145.66 -34.34 0 5.00e+00 4.00e-02 4.72e+01 dihedral pdb=" CA GLN f 85 " pdb=" C GLN f 85 " pdb=" N LEU f 86 " pdb=" CA LEU f 86 " ideal model delta harmonic sigma weight residual -180.00 -145.66 -34.34 0 5.00e+00 4.00e-02 4.72e+01 dihedral pdb=" CA GLN b 85 " pdb=" C GLN b 85 " pdb=" N LEU b 86 " pdb=" CA LEU b 86 " ideal model delta harmonic sigma weight residual 180.00 -145.67 -34.33 0 5.00e+00 4.00e-02 4.72e+01 ... (remaining 11871 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 2832 0.089 - 0.179: 300 0.179 - 0.268: 24 0.268 - 0.357: 0 0.357 - 0.447: 6 Chirality restraints: 3162 Sorted by residual: chirality pdb=" CB ILE D 128 " pdb=" CA ILE D 128 " pdb=" CG1 ILE D 128 " pdb=" CG2 ILE D 128 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" CB ILE F 128 " pdb=" CA ILE F 128 " pdb=" CG1 ILE F 128 " pdb=" CG2 ILE F 128 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.98e+00 chirality pdb=" CB ILE E 128 " pdb=" CA ILE E 128 " pdb=" CG1 ILE E 128 " pdb=" CG2 ILE E 128 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.45 2.00e-01 2.50e+01 4.97e+00 ... (remaining 3159 not shown) Planarity restraints: 3438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP b 131 " 0.015 2.00e-02 2.50e+03 3.05e-02 9.32e+00 pdb=" CG ASP b 131 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASP b 131 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP b 131 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP a 131 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.28e+00 pdb=" CG ASP a 131 " 0.053 2.00e-02 2.50e+03 pdb=" OD1 ASP a 131 " -0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP a 131 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP e 131 " 0.015 2.00e-02 2.50e+03 3.03e-02 9.20e+00 pdb=" CG ASP e 131 " -0.052 2.00e-02 2.50e+03 pdb=" OD1 ASP e 131 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP e 131 " 0.019 2.00e-02 2.50e+03 ... (remaining 3435 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 4841 2.79 - 3.32: 16131 3.32 - 3.85: 29723 3.85 - 4.37: 32559 4.37 - 4.90: 58990 Nonbonded interactions: 142244 Sorted by model distance: nonbonded pdb=" OH TYR B 132 " pdb=" O ASN c 130 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR A 132 " pdb=" O ASN b 130 " model vdw 2.274 3.040 nonbonded pdb=" O ARG D 123 " pdb=" OG1 THR D 133 " model vdw 2.278 3.040 nonbonded pdb=" O ARG A 123 " pdb=" OG1 THR A 133 " model vdw 2.278 3.040 nonbonded pdb=" O ARG E 123 " pdb=" OG1 THR E 133 " model vdw 2.278 3.040 ... (remaining 142239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 14.620 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 19620 Z= 0.301 Angle : 1.043 16.294 26682 Z= 0.557 Chirality : 0.058 0.447 3162 Planarity : 0.006 0.057 3438 Dihedral : 15.760 82.817 7194 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.19 % Allowed : 14.25 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.54 (0.13), residues: 2412 helix: -4.47 (0.08), residues: 528 sheet: -1.93 (0.18), residues: 666 loop : -2.95 (0.14), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 58 TYR 0.021 0.002 TYR C 49 PHE 0.026 0.003 PHE A 262 TRP 0.039 0.002 TRP B 265 HIS 0.006 0.003 HIS B 52 Details of bonding type rmsd covalent geometry : bond 0.00683 (19620) covalent geometry : angle 1.04287 (26682) hydrogen bonds : bond 0.31576 ( 576) hydrogen bonds : angle 10.18005 ( 1719) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 553 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.6990 (tmm) cc_final: 0.6665 (tmm) REVERT: A 242 ILE cc_start: 0.6582 (mt) cc_final: 0.6299 (mt) REVERT: A 268 ASN cc_start: 0.5583 (OUTLIER) cc_final: 0.4728 (m-40) REVERT: B 242 ILE cc_start: 0.6815 (mt) cc_final: 0.6603 (mt) REVERT: B 254 TYR cc_start: 0.8458 (m-80) cc_final: 0.8087 (m-80) REVERT: B 268 ASN cc_start: 0.6325 (OUTLIER) cc_final: 0.5182 (m-40) REVERT: C 268 ASN cc_start: 0.6007 (OUTLIER) cc_final: 0.4936 (m-40) REVERT: D 38 MET cc_start: 0.6975 (tmm) cc_final: 0.6610 (tmm) REVERT: D 242 ILE cc_start: 0.6422 (mt) cc_final: 0.6152 (mt) REVERT: D 268 ASN cc_start: 0.5695 (OUTLIER) cc_final: 0.4716 (m-40) REVERT: E 38 MET cc_start: 0.7140 (tmm) cc_final: 0.6920 (tmm) REVERT: E 242 ILE cc_start: 0.6795 (mt) cc_final: 0.6554 (mt) REVERT: E 254 TYR cc_start: 0.8427 (m-80) cc_final: 0.8158 (m-80) REVERT: E 268 ASN cc_start: 0.6386 (OUTLIER) cc_final: 0.4928 (m-40) REVERT: F 5 GLN cc_start: 0.8498 (mm-40) cc_final: 0.8268 (mm-40) REVERT: F 245 SER cc_start: 0.8397 (m) cc_final: 0.7953 (t) REVERT: F 268 ASN cc_start: 0.5915 (OUTLIER) cc_final: 0.4757 (m-40) REVERT: a 16 VAL cc_start: 0.9454 (OUTLIER) cc_final: 0.9197 (p) REVERT: a 31 ASN cc_start: 0.8946 (t0) cc_final: 0.8574 (t0) REVERT: a 41 ASP cc_start: 0.8250 (t0) cc_final: 0.8036 (t70) REVERT: a 46 ARG cc_start: 0.6892 (ptt90) cc_final: 0.5038 (ptt90) REVERT: a 82 ASN cc_start: 0.8659 (t0) cc_final: 0.8371 (t0) REVERT: a 113 SER cc_start: 0.8935 (t) cc_final: 0.8584 (p) REVERT: a 143 ARG cc_start: 0.8236 (ttt-90) cc_final: 0.7334 (ttt180) REVERT: b 31 ASN cc_start: 0.8961 (t0) cc_final: 0.8727 (t0) REVERT: b 46 ARG cc_start: 0.6443 (ptt90) cc_final: 0.4547 (mtp85) REVERT: b 82 ASN cc_start: 0.8729 (t0) cc_final: 0.8433 (t0) REVERT: b 108 MET cc_start: 0.8210 (ttm) cc_final: 0.7965 (ttm) REVERT: b 113 SER cc_start: 0.9002 (t) cc_final: 0.8704 (p) REVERT: b 143 ARG cc_start: 0.8200 (ttt-90) cc_final: 0.7454 (ttt180) REVERT: b 146 MET cc_start: 0.8629 (ttm) cc_final: 0.8404 (ttm) REVERT: c 31 ASN cc_start: 0.9026 (t0) cc_final: 0.8784 (t0) REVERT: c 41 ASP cc_start: 0.8171 (t0) cc_final: 0.7870 (t70) REVERT: c 46 ARG cc_start: 0.6682 (ptt90) cc_final: 0.4519 (mtp85) REVERT: c 82 ASN cc_start: 0.8717 (t0) cc_final: 0.8355 (t0) REVERT: c 143 ARG cc_start: 0.8292 (ttt-90) cc_final: 0.7404 (ttt180) REVERT: d 16 VAL cc_start: 0.9486 (OUTLIER) cc_final: 0.9255 (p) REVERT: d 31 ASN cc_start: 0.8930 (t0) cc_final: 0.8545 (t0) REVERT: d 46 ARG cc_start: 0.6994 (ptt90) cc_final: 0.4902 (mtp85) REVERT: d 82 ASN cc_start: 0.8666 (t0) cc_final: 0.8401 (t0) REVERT: d 113 SER cc_start: 0.8843 (t) cc_final: 0.8424 (p) REVERT: d 143 ARG cc_start: 0.8465 (ttt-90) cc_final: 0.7242 (ttt180) REVERT: e 31 ASN cc_start: 0.8926 (t0) cc_final: 0.8715 (t0) REVERT: e 41 ASP cc_start: 0.8228 (t0) cc_final: 0.8020 (t70) REVERT: e 46 ARG cc_start: 0.6540 (ptt90) cc_final: 0.3817 (mtm110) REVERT: e 82 ASN cc_start: 0.8824 (t0) cc_final: 0.8566 (t0) REVERT: e 108 MET cc_start: 0.8097 (ttm) cc_final: 0.7860 (ttm) REVERT: e 113 SER cc_start: 0.9004 (t) cc_final: 0.8632 (p) REVERT: e 143 ARG cc_start: 0.8141 (ttt-90) cc_final: 0.7318 (ttt180) REVERT: f 31 ASN cc_start: 0.9008 (t0) cc_final: 0.8807 (t0) REVERT: f 41 ASP cc_start: 0.8140 (t0) cc_final: 0.7924 (t70) REVERT: f 46 ARG cc_start: 0.6520 (ptt90) cc_final: 0.4651 (ptt90) REVERT: f 143 ARG cc_start: 0.8194 (ttt-90) cc_final: 0.7394 (ttt180) outliers start: 48 outliers final: 16 residues processed: 589 average time/residue: 0.1396 time to fit residues: 125.3592 Evaluate side-chains 402 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 378 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 268 ASN Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain a residue 16 VAL Chi-restraints excluded: chain a residue 22 SER Chi-restraints excluded: chain b residue 22 SER Chi-restraints excluded: chain c residue 22 SER Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 22 SER Chi-restraints excluded: chain e residue 22 SER Chi-restraints excluded: chain f residue 22 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 0.0170 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 overall best weight: 2.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 52 HIS A 122 ASN A 268 ASN B 39 GLN B 52 HIS B 122 ASN B 268 ASN C 5 GLN C 39 GLN C 52 HIS C 122 ASN C 268 ASN D 39 GLN D 52 HIS ** D 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 ASN D 268 ASN E 39 GLN E 52 HIS E 122 ASN E 154 ASN E 268 ASN F 39 GLN F 52 HIS F 122 ASN F 268 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.124369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.094832 restraints weight = 28374.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.096184 restraints weight = 20046.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.097104 restraints weight = 15606.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.097637 restraints weight = 13095.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.098078 restraints weight = 11627.228| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19620 Z= 0.178 Angle : 0.691 15.385 26682 Z= 0.345 Chirality : 0.045 0.166 3162 Planarity : 0.005 0.056 3438 Dihedral : 6.556 46.501 2652 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 4.47 % Allowed : 19.04 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.14), residues: 2412 helix: -2.39 (0.17), residues: 516 sheet: -1.39 (0.18), residues: 672 loop : -2.60 (0.15), residues: 1224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 203 TYR 0.020 0.002 TYR b 45 PHE 0.032 0.002 PHE A 262 TRP 0.023 0.001 TRP B 265 HIS 0.002 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00418 (19620) covalent geometry : angle 0.69068 (26682) hydrogen bonds : bond 0.04252 ( 576) hydrogen bonds : angle 5.30719 ( 1719) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 426 time to evaluate : 0.766 Fit side-chains REVERT: A 30 PHE cc_start: 0.8775 (m-80) cc_final: 0.8522 (m-80) REVERT: A 38 MET cc_start: 0.7192 (tmm) cc_final: 0.6705 (tmm) REVERT: A 202 LEU cc_start: 0.9207 (mm) cc_final: 0.8984 (mm) REVERT: A 240 MET cc_start: 0.3086 (mtp) cc_final: 0.2854 (mtm) REVERT: A 256 LYS cc_start: 0.8751 (mptt) cc_final: 0.8448 (tppt) REVERT: A 268 ASN cc_start: 0.5162 (OUTLIER) cc_final: 0.4297 (m-40) REVERT: B 73 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.9051 (mt) REVERT: B 202 LEU cc_start: 0.9206 (mm) cc_final: 0.8997 (mm) REVERT: B 254 TYR cc_start: 0.8262 (m-80) cc_final: 0.7820 (m-80) REVERT: B 256 LYS cc_start: 0.8531 (mptt) cc_final: 0.8325 (tppt) REVERT: B 268 ASN cc_start: 0.6160 (OUTLIER) cc_final: 0.4608 (m-40) REVERT: C 256 LYS cc_start: 0.8676 (mptt) cc_final: 0.8344 (tppt) REVERT: C 268 ASN cc_start: 0.5769 (OUTLIER) cc_final: 0.4658 (m110) REVERT: D 30 PHE cc_start: 0.8811 (m-80) cc_final: 0.8459 (m-80) REVERT: D 38 MET cc_start: 0.7082 (tmm) cc_final: 0.6643 (tmm) REVERT: D 240 MET cc_start: 0.2910 (mtp) cc_final: 0.2677 (mtm) REVERT: D 256 LYS cc_start: 0.8844 (mptt) cc_final: 0.8411 (tppt) REVERT: D 268 ASN cc_start: 0.5147 (OUTLIER) cc_final: 0.4242 (m110) REVERT: E 254 TYR cc_start: 0.8233 (m-80) cc_final: 0.7845 (m-80) REVERT: E 256 LYS cc_start: 0.8605 (mptt) cc_final: 0.8257 (tppt) REVERT: E 268 ASN cc_start: 0.6029 (OUTLIER) cc_final: 0.4279 (m-40) REVERT: F 256 LYS cc_start: 0.8696 (mptt) cc_final: 0.8308 (tppt) REVERT: F 268 ASN cc_start: 0.5763 (OUTLIER) cc_final: 0.4535 (m110) REVERT: F 287 LYS cc_start: 0.7748 (tmtt) cc_final: 0.7517 (tttp) REVERT: a 31 ASN cc_start: 0.8967 (t0) cc_final: 0.8592 (t0) REVERT: a 81 ILE cc_start: 0.9329 (tt) cc_final: 0.9086 (tt) REVERT: a 82 ASN cc_start: 0.8797 (t0) cc_final: 0.8559 (t0) REVERT: a 108 MET cc_start: 0.8250 (ttm) cc_final: 0.8040 (ttt) REVERT: a 113 SER cc_start: 0.8975 (t) cc_final: 0.8642 (p) REVERT: a 143 ARG cc_start: 0.8540 (ttt-90) cc_final: 0.7098 (ttt180) REVERT: b 31 ASN cc_start: 0.8964 (t0) cc_final: 0.8721 (t0) REVERT: b 46 ARG cc_start: 0.6367 (ptt90) cc_final: 0.4411 (ptt90) REVERT: b 77 LEU cc_start: 0.9265 (mt) cc_final: 0.8900 (mt) REVERT: b 82 ASN cc_start: 0.8925 (t0) cc_final: 0.8635 (t0) REVERT: b 113 SER cc_start: 0.9053 (t) cc_final: 0.8841 (p) REVERT: b 143 ARG cc_start: 0.8389 (ttt-90) cc_final: 0.7464 (ttt180) REVERT: c 46 ARG cc_start: 0.6409 (ptt90) cc_final: 0.4438 (ptt90) REVERT: c 81 ILE cc_start: 0.9378 (tt) cc_final: 0.9154 (tt) REVERT: c 140 MET cc_start: 0.8274 (ttt) cc_final: 0.8055 (ttt) REVERT: c 143 ARG cc_start: 0.8325 (ttt-90) cc_final: 0.7230 (ttt180) REVERT: d 16 VAL cc_start: 0.9497 (OUTLIER) cc_final: 0.9260 (p) REVERT: d 31 ASN cc_start: 0.8953 (t0) cc_final: 0.8601 (t0) REVERT: d 81 ILE cc_start: 0.9343 (tt) cc_final: 0.9096 (tt) REVERT: d 82 ASN cc_start: 0.8886 (t0) cc_final: 0.8645 (t0) REVERT: d 113 SER cc_start: 0.8943 (t) cc_final: 0.8579 (p) REVERT: d 143 ARG cc_start: 0.8571 (ttt-90) cc_final: 0.7111 (ttt180) REVERT: e 31 ASN cc_start: 0.8971 (t0) cc_final: 0.8710 (t0) REVERT: e 46 ARG cc_start: 0.6445 (ptt90) cc_final: 0.4472 (ptt90) REVERT: e 77 LEU cc_start: 0.9257 (mt) cc_final: 0.8823 (mt) REVERT: e 82 ASN cc_start: 0.8951 (t0) cc_final: 0.8737 (t0) REVERT: e 113 SER cc_start: 0.9056 (t) cc_final: 0.8769 (p) REVERT: e 143 ARG cc_start: 0.8337 (ttt-90) cc_final: 0.7443 (ttt180) REVERT: f 31 ASN cc_start: 0.9022 (t0) cc_final: 0.8814 (t0) REVERT: f 46 ARG cc_start: 0.6388 (ptt90) cc_final: 0.4500 (ptt90) REVERT: f 81 ILE cc_start: 0.9367 (tt) cc_final: 0.9164 (tt) REVERT: f 143 ARG cc_start: 0.8261 (ttt-90) cc_final: 0.7221 (ttt180) outliers start: 98 outliers final: 55 residues processed: 499 average time/residue: 0.1345 time to fit residues: 104.4576 Evaluate side-chains 449 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 386 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 268 ASN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 85 GLN Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain c residue 27 LYS Chi-restraints excluded: chain c residue 113 SER Chi-restraints excluded: chain c residue 130 ASN Chi-restraints excluded: chain d residue 16 VAL Chi-restraints excluded: chain d residue 27 LYS Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain e residue 27 LYS Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain f residue 27 LYS Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 113 SER Chi-restraints excluded: chain f residue 130 ASN Chi-restraints excluded: chain f residue 145 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 80 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN b 58 GLN c 58 GLN e 58 GLN f 58 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.130490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.103240 restraints weight = 28097.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.102147 restraints weight = 24244.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.102263 restraints weight = 23898.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.102782 restraints weight = 21212.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.102974 restraints weight = 18345.666| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19620 Z= 0.132 Angle : 0.639 14.952 26682 Z= 0.312 Chirality : 0.044 0.164 3162 Planarity : 0.004 0.055 3438 Dihedral : 5.756 46.350 2643 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 5.43 % Allowed : 20.09 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.51 (0.15), residues: 2412 helix: -0.92 (0.21), residues: 528 sheet: -1.25 (0.18), residues: 720 loop : -2.28 (0.16), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 19 TYR 0.024 0.002 TYR c 17 PHE 0.029 0.002 PHE A 262 TRP 0.016 0.001 TRP B 265 HIS 0.002 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00308 (19620) covalent geometry : angle 0.63891 (26682) hydrogen bonds : bond 0.03520 ( 576) hydrogen bonds : angle 4.76949 ( 1719) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 428 time to evaluate : 0.739 Fit side-chains revert: symmetry clash REVERT: A 38 MET cc_start: 0.7344 (tmm) cc_final: 0.6880 (tmm) REVERT: A 105 ASP cc_start: 0.8223 (t0) cc_final: 0.7560 (p0) REVERT: A 268 ASN cc_start: 0.5448 (OUTLIER) cc_final: 0.4170 (m-40) REVERT: B 58 ARG cc_start: 0.9421 (OUTLIER) cc_final: 0.9043 (ttm170) REVERT: B 73 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8945 (mt) REVERT: B 254 TYR cc_start: 0.8144 (m-80) cc_final: 0.7770 (m-80) REVERT: B 256 LYS cc_start: 0.8611 (mptt) cc_final: 0.8380 (tppt) REVERT: B 268 ASN cc_start: 0.6202 (OUTLIER) cc_final: 0.4574 (m-40) REVERT: C 31 ASP cc_start: 0.8149 (t0) cc_final: 0.7768 (t0) REVERT: C 256 LYS cc_start: 0.8634 (mptt) cc_final: 0.8370 (tppt) REVERT: C 268 ASN cc_start: 0.5407 (OUTLIER) cc_final: 0.4410 (m-40) REVERT: D 30 PHE cc_start: 0.8826 (m-80) cc_final: 0.8561 (m-80) REVERT: D 38 MET cc_start: 0.7270 (tmm) cc_final: 0.6738 (tmm) REVERT: D 105 ASP cc_start: 0.8136 (t0) cc_final: 0.7481 (p0) REVERT: D 268 ASN cc_start: 0.5376 (OUTLIER) cc_final: 0.4180 (m-40) REVERT: E 31 ASP cc_start: 0.8089 (t0) cc_final: 0.7833 (t0) REVERT: E 51 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8946 (pt) REVERT: E 58 ARG cc_start: 0.9335 (OUTLIER) cc_final: 0.9108 (ttm170) REVERT: E 254 TYR cc_start: 0.8121 (m-80) cc_final: 0.7767 (m-80) REVERT: E 256 LYS cc_start: 0.8591 (mptt) cc_final: 0.8252 (tppt) REVERT: E 268 ASN cc_start: 0.6028 (OUTLIER) cc_final: 0.4388 (m-40) REVERT: F 31 ASP cc_start: 0.8104 (t0) cc_final: 0.7718 (t0) REVERT: F 171 ASN cc_start: 0.6984 (p0) cc_final: 0.6768 (p0) REVERT: F 256 LYS cc_start: 0.8683 (mptt) cc_final: 0.8350 (tppt) REVERT: F 268 ASN cc_start: 0.5389 (OUTLIER) cc_final: 0.4313 (m-40) REVERT: a 31 ASN cc_start: 0.8967 (t0) cc_final: 0.8661 (t0) REVERT: a 46 ARG cc_start: 0.6837 (ptt90) cc_final: 0.5514 (ptt90) REVERT: a 82 ASN cc_start: 0.8765 (t0) cc_final: 0.8527 (t0) REVERT: a 113 SER cc_start: 0.8929 (t) cc_final: 0.8667 (p) REVERT: a 143 ARG cc_start: 0.8537 (ttt-90) cc_final: 0.7133 (ttt180) REVERT: b 31 ASN cc_start: 0.8973 (t0) cc_final: 0.8721 (t0) REVERT: b 46 ARG cc_start: 0.6344 (ptt90) cc_final: 0.4264 (ptt90) REVERT: b 77 LEU cc_start: 0.9182 (mt) cc_final: 0.8737 (mt) REVERT: b 82 ASN cc_start: 0.8866 (t0) cc_final: 0.8629 (t0) REVERT: b 143 ARG cc_start: 0.8394 (ttt-90) cc_final: 0.7427 (ttt180) REVERT: c 46 ARG cc_start: 0.6467 (ptt90) cc_final: 0.4519 (ptt90) REVERT: c 140 MET cc_start: 0.8272 (ttt) cc_final: 0.7965 (ttt) REVERT: c 143 ARG cc_start: 0.8469 (ttt-90) cc_final: 0.7252 (ttt180) REVERT: d 31 ASN cc_start: 0.8934 (t0) cc_final: 0.8563 (t0) REVERT: d 82 ASN cc_start: 0.8823 (t0) cc_final: 0.8591 (t0) REVERT: d 113 SER cc_start: 0.8899 (t) cc_final: 0.8597 (p) REVERT: d 143 ARG cc_start: 0.8556 (ttt-90) cc_final: 0.7119 (ttt180) REVERT: e 31 ASN cc_start: 0.8938 (t0) cc_final: 0.8686 (t0) REVERT: e 46 ARG cc_start: 0.6431 (ptt90) cc_final: 0.4435 (ptt90) REVERT: e 77 LEU cc_start: 0.9148 (mt) cc_final: 0.8763 (mt) REVERT: e 82 ASN cc_start: 0.8856 (t0) cc_final: 0.8626 (t0) REVERT: e 85 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7924 (mt0) REVERT: e 113 SER cc_start: 0.8992 (t) cc_final: 0.8789 (p) REVERT: e 143 ARG cc_start: 0.8342 (ttt-90) cc_final: 0.7316 (ttt180) REVERT: e 145 ILE cc_start: 0.8986 (pt) cc_final: 0.8773 (pt) REVERT: f 31 ASN cc_start: 0.9025 (t0) cc_final: 0.8803 (t0) REVERT: f 46 ARG cc_start: 0.6416 (ptt90) cc_final: 0.4514 (ptt90) REVERT: f 132 ILE cc_start: 0.8671 (pt) cc_final: 0.8444 (pt) REVERT: f 143 ARG cc_start: 0.8354 (ttt-90) cc_final: 0.7176 (ttt180) outliers start: 119 outliers final: 65 residues processed: 524 average time/residue: 0.1387 time to fit residues: 112.0687 Evaluate side-chains 469 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 393 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 128 ILE Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 128 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 58 ARG Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 268 ASN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 130 ASN Chi-restraints excluded: chain b residue 27 LYS Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 85 GLN Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain c residue 27 LYS Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 145 ILE Chi-restraints excluded: chain d residue 27 LYS Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 130 ASN Chi-restraints excluded: chain e residue 27 LYS Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 85 GLN Chi-restraints excluded: chain f residue 27 LYS Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 145 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 109 optimal weight: 0.9980 chunk 205 optimal weight: 0.0870 chunk 55 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 178 optimal weight: 0.2980 chunk 104 optimal weight: 10.0000 chunk 49 optimal weight: 20.0000 chunk 105 optimal weight: 6.9990 chunk 106 optimal weight: 7.9990 overall best weight: 1.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 ASN D 121 ASN b 58 GLN e 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.125911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.096715 restraints weight = 28117.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.098009 restraints weight = 20488.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.098487 restraints weight = 14877.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.098787 restraints weight = 13163.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.099062 restraints weight = 12618.648| |-----------------------------------------------------------------------------| r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19620 Z= 0.136 Angle : 0.626 14.799 26682 Z= 0.304 Chirality : 0.044 0.159 3162 Planarity : 0.004 0.054 3438 Dihedral : 5.355 31.838 2640 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 6.03 % Allowed : 21.64 % Favored : 72.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.16), residues: 2412 helix: -0.25 (0.22), residues: 528 sheet: -1.08 (0.19), residues: 720 loop : -2.18 (0.16), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 123 TYR 0.019 0.002 TYR c 17 PHE 0.027 0.002 PHE B 262 TRP 0.013 0.001 TRP B 265 HIS 0.002 0.001 HIS C 200 Details of bonding type rmsd covalent geometry : bond 0.00321 (19620) covalent geometry : angle 0.62627 (26682) hydrogen bonds : bond 0.03207 ( 576) hydrogen bonds : angle 4.58360 ( 1719) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 563 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 431 time to evaluate : 0.717 Fit side-chains REVERT: A 5 GLN cc_start: 0.7961 (mm-40) cc_final: 0.7738 (mm-40) REVERT: A 38 MET cc_start: 0.7309 (tmm) cc_final: 0.6895 (tmm) REVERT: A 105 ASP cc_start: 0.8024 (t0) cc_final: 0.7604 (p0) REVERT: A 193 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7718 (pp) REVERT: A 268 ASN cc_start: 0.5280 (OUTLIER) cc_final: 0.4040 (m-40) REVERT: B 58 ARG cc_start: 0.9392 (OUTLIER) cc_final: 0.8947 (ttm170) REVERT: B 73 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8927 (mt) REVERT: B 193 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.7468 (pp) REVERT: B 254 TYR cc_start: 0.8178 (m-80) cc_final: 0.7794 (m-80) REVERT: B 256 LYS cc_start: 0.8660 (mptt) cc_final: 0.8380 (tppt) REVERT: B 268 ASN cc_start: 0.5928 (OUTLIER) cc_final: 0.4487 (m-40) REVERT: C 31 ASP cc_start: 0.8102 (t0) cc_final: 0.7703 (t0) REVERT: C 256 LYS cc_start: 0.8716 (mptt) cc_final: 0.8340 (tppt) REVERT: C 268 ASN cc_start: 0.5105 (OUTLIER) cc_final: 0.4096 (m-40) REVERT: D 5 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7700 (mm-40) REVERT: D 14 MET cc_start: 0.8729 (mmm) cc_final: 0.8480 (tpp) REVERT: D 30 PHE cc_start: 0.8771 (m-80) cc_final: 0.8402 (m-80) REVERT: D 38 MET cc_start: 0.7222 (tmm) cc_final: 0.6650 (tmm) REVERT: D 105 ASP cc_start: 0.7894 (t0) cc_final: 0.7472 (p0) REVERT: D 193 LEU cc_start: 0.8237 (OUTLIER) cc_final: 0.7581 (pp) REVERT: D 256 LYS cc_start: 0.8792 (mptt) cc_final: 0.8395 (tppt) REVERT: D 268 ASN cc_start: 0.5234 (OUTLIER) cc_final: 0.4084 (m-40) REVERT: E 193 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.7412 (pp) REVERT: E 254 TYR cc_start: 0.8111 (m-80) cc_final: 0.7747 (m-80) REVERT: E 256 LYS cc_start: 0.8560 (mptt) cc_final: 0.8251 (tppt) REVERT: E 262 PHE cc_start: 0.7112 (p90) cc_final: 0.6817 (p90) REVERT: E 268 ASN cc_start: 0.5894 (OUTLIER) cc_final: 0.4350 (m-40) REVERT: F 17 MET cc_start: 0.8907 (ttp) cc_final: 0.8657 (ttp) REVERT: F 31 ASP cc_start: 0.8053 (t0) cc_final: 0.7643 (t0) REVERT: F 256 LYS cc_start: 0.8698 (mptt) cc_final: 0.8218 (tppt) REVERT: F 268 ASN cc_start: 0.5446 (OUTLIER) cc_final: 0.4162 (m-40) REVERT: a 31 ASN cc_start: 0.8931 (t0) cc_final: 0.8630 (t0) REVERT: a 46 ARG cc_start: 0.6826 (ptt90) cc_final: 0.5497 (ptt90) REVERT: a 82 ASN cc_start: 0.8811 (t0) cc_final: 0.8582 (t0) REVERT: a 113 SER cc_start: 0.8935 (t) cc_final: 0.8672 (p) REVERT: a 143 ARG cc_start: 0.8532 (ttt-90) cc_final: 0.7168 (ttt180) REVERT: b 31 ASN cc_start: 0.8985 (t0) cc_final: 0.8748 (t0) REVERT: b 46 ARG cc_start: 0.6368 (ptt90) cc_final: 0.4297 (ptt90) REVERT: b 77 LEU cc_start: 0.9065 (mt) cc_final: 0.8735 (mt) REVERT: b 82 ASN cc_start: 0.8822 (t0) cc_final: 0.8581 (t0) REVERT: b 143 ARG cc_start: 0.8390 (ttt-90) cc_final: 0.7423 (ttt180) REVERT: c 46 ARG cc_start: 0.6491 (ptt90) cc_final: 0.4476 (ptt90) REVERT: c 82 ASN cc_start: 0.8746 (t0) cc_final: 0.8238 (t0) REVERT: c 140 MET cc_start: 0.8250 (ttt) cc_final: 0.7882 (ttt) REVERT: c 143 ARG cc_start: 0.8515 (ttt-90) cc_final: 0.7340 (ttt180) REVERT: d 17 TYR cc_start: 0.9279 (p90) cc_final: 0.9070 (p90) REVERT: d 31 ASN cc_start: 0.8930 (t0) cc_final: 0.8622 (t0) REVERT: d 82 ASN cc_start: 0.8787 (t0) cc_final: 0.8567 (t0) REVERT: d 113 SER cc_start: 0.8882 (t) cc_final: 0.8615 (p) REVERT: d 143 ARG cc_start: 0.8549 (ttt-90) cc_final: 0.7201 (ttt180) REVERT: e 31 ASN cc_start: 0.8943 (t0) cc_final: 0.8693 (t0) REVERT: e 46 ARG cc_start: 0.6626 (ptt90) cc_final: 0.4646 (ptt90) REVERT: e 77 LEU cc_start: 0.9090 (mt) cc_final: 0.8732 (mt) REVERT: e 113 SER cc_start: 0.9011 (t) cc_final: 0.8789 (p) REVERT: e 143 ARG cc_start: 0.8324 (ttt-90) cc_final: 0.7289 (ttt180) REVERT: e 145 ILE cc_start: 0.8939 (OUTLIER) cc_final: 0.8715 (pt) REVERT: f 46 ARG cc_start: 0.6442 (ptt90) cc_final: 0.4485 (ptt90) REVERT: f 143 ARG cc_start: 0.8403 (ttt-90) cc_final: 0.7214 (ttt180) outliers start: 132 outliers final: 98 residues processed: 532 average time/residue: 0.1311 time to fit residues: 108.6275 Evaluate side-chains 519 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 408 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 231 THR Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 73 LEU Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 161 ASN Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 268 ASN Chi-restraints excluded: chain E residue 287 LYS Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 268 ASN Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 60 GLN Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 130 ASN Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain b residue 27 LYS Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 120 LEU Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 27 LYS Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain c residue 130 ASN Chi-restraints excluded: chain c residue 137 ILE Chi-restraints excluded: chain c residue 145 ILE Chi-restraints excluded: chain d residue 10 VAL Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 70 VAL Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 130 ASN Chi-restraints excluded: chain d residue 137 ILE Chi-restraints excluded: chain d residue 139 LEU Chi-restraints excluded: chain e residue 27 LYS Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 106 LEU Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain e residue 145 ILE Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 27 LYS Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain f residue 130 ASN Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 145 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 242 optimal weight: 5.9990 chunk 218 optimal weight: 3.9990 chunk 196 optimal weight: 0.2980 chunk 186 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 153 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 224 optimal weight: 7.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.125882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.095519 restraints weight = 28414.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.097136 restraints weight = 19580.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.098190 restraints weight = 14933.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.098933 restraints weight = 12251.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.099355 restraints weight = 10726.057| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 19620 Z= 0.292 Angle : 0.737 14.821 26682 Z= 0.364 Chirality : 0.048 0.187 3162 Planarity : 0.005 0.053 3438 Dihedral : 5.859 34.168 2640 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Rotamer: Outliers : 7.21 % Allowed : 22.79 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.12 (0.16), residues: 2412 helix: -0.16 (0.23), residues: 534 sheet: -1.11 (0.20), residues: 618 loop : -2.16 (0.16), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 123 TYR 0.022 0.002 TYR e 45 PHE 0.028 0.003 PHE B 262 TRP 0.009 0.001 TRP B 265 HIS 0.004 0.002 HIS F 200 Details of bonding type rmsd covalent geometry : bond 0.00699 (19620) covalent geometry : angle 0.73722 (26682) hydrogen bonds : bond 0.03811 ( 576) hydrogen bonds : angle 4.95272 ( 1719) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 409 time to evaluate : 0.732 Fit side-chains REVERT: A 38 MET cc_start: 0.7435 (tmm) cc_final: 0.6963 (tmm) REVERT: A 105 ASP cc_start: 0.8199 (t0) cc_final: 0.7718 (p0) REVERT: A 193 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7809 (pp) REVERT: A 268 ASN cc_start: 0.5218 (OUTLIER) cc_final: 0.4931 (p0) REVERT: B 38 MET cc_start: 0.7292 (tmm) cc_final: 0.6854 (tmm) REVERT: B 58 ARG cc_start: 0.9537 (OUTLIER) cc_final: 0.9176 (ttm170) REVERT: B 193 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.7567 (pp) REVERT: B 230 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7616 (pm20) REVERT: B 254 TYR cc_start: 0.8377 (m-80) cc_final: 0.7959 (m-80) REVERT: B 256 LYS cc_start: 0.8711 (mptt) cc_final: 0.8504 (tppt) REVERT: B 268 ASN cc_start: 0.5698 (OUTLIER) cc_final: 0.5429 (p0) REVERT: C 31 ASP cc_start: 0.8188 (t0) cc_final: 0.7770 (t0) REVERT: C 121 ASN cc_start: 0.8804 (OUTLIER) cc_final: 0.8397 (m-40) REVERT: C 230 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7535 (pm20) REVERT: C 256 LYS cc_start: 0.8737 (mptt) cc_final: 0.8429 (tppt) REVERT: C 268 ASN cc_start: 0.5068 (OUTLIER) cc_final: 0.4862 (p0) REVERT: D 30 PHE cc_start: 0.8820 (m-80) cc_final: 0.8547 (m-80) REVERT: D 38 MET cc_start: 0.7360 (tmm) cc_final: 0.7024 (tmm) REVERT: D 55 LEU cc_start: 0.9185 (OUTLIER) cc_final: 0.8979 (mt) REVERT: D 193 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.7882 (pp) REVERT: D 254 TYR cc_start: 0.8451 (m-80) cc_final: 0.7940 (m-80) REVERT: D 256 LYS cc_start: 0.8746 (mptt) cc_final: 0.8436 (tppt) REVERT: D 268 ASN cc_start: 0.4953 (OUTLIER) cc_final: 0.4664 (p0) REVERT: E 38 MET cc_start: 0.7352 (tmm) cc_final: 0.6866 (tmm) REVERT: E 193 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7481 (pp) REVERT: E 254 TYR cc_start: 0.8330 (m-80) cc_final: 0.7930 (m-80) REVERT: E 256 LYS cc_start: 0.8750 (mptt) cc_final: 0.8456 (tppt) REVERT: E 262 PHE cc_start: 0.7029 (p90) cc_final: 0.6628 (p90) REVERT: E 268 ASN cc_start: 0.5724 (OUTLIER) cc_final: 0.5468 (p0) REVERT: F 31 ASP cc_start: 0.8139 (t0) cc_final: 0.7758 (t0) REVERT: F 121 ASN cc_start: 0.8794 (OUTLIER) cc_final: 0.8471 (m-40) REVERT: F 193 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7558 (pp) REVERT: F 230 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7700 (pm20) REVERT: F 256 LYS cc_start: 0.8654 (mptt) cc_final: 0.8307 (tppt) REVERT: a 31 ASN cc_start: 0.8990 (t0) cc_final: 0.8584 (t0) REVERT: a 46 ARG cc_start: 0.7089 (ptt90) cc_final: 0.4899 (ptt90) REVERT: a 82 ASN cc_start: 0.8945 (t0) cc_final: 0.8449 (t0) REVERT: a 113 SER cc_start: 0.8921 (t) cc_final: 0.8484 (p) REVERT: a 143 ARG cc_start: 0.8775 (ttt-90) cc_final: 0.7405 (ttt180) REVERT: b 31 ASN cc_start: 0.9045 (t0) cc_final: 0.8788 (t0) REVERT: b 46 ARG cc_start: 0.6848 (ptt90) cc_final: 0.4575 (ptt90) REVERT: b 77 LEU cc_start: 0.9247 (mt) cc_final: 0.8983 (mt) REVERT: b 82 ASN cc_start: 0.9033 (t0) cc_final: 0.8823 (t0) REVERT: b 143 ARG cc_start: 0.8727 (ttt-90) cc_final: 0.7382 (ttt180) REVERT: c 46 ARG cc_start: 0.6547 (ptt90) cc_final: 0.4450 (ptt90) REVERT: c 82 ASN cc_start: 0.8897 (t0) cc_final: 0.8488 (t0) REVERT: c 140 MET cc_start: 0.8448 (ttt) cc_final: 0.8068 (ttt) REVERT: c 143 ARG cc_start: 0.8749 (ttt-90) cc_final: 0.7573 (ttt180) REVERT: d 31 ASN cc_start: 0.8955 (t0) cc_final: 0.8603 (t0) REVERT: d 46 ARG cc_start: 0.7125 (ptt90) cc_final: 0.4933 (ptt90) REVERT: d 82 ASN cc_start: 0.8929 (t0) cc_final: 0.8397 (t0) REVERT: d 113 SER cc_start: 0.8944 (t) cc_final: 0.8550 (p) REVERT: e 31 ASN cc_start: 0.8989 (t0) cc_final: 0.8744 (t0) REVERT: e 46 ARG cc_start: 0.7008 (ptt90) cc_final: 0.4574 (mtp85) REVERT: e 77 LEU cc_start: 0.9231 (mt) cc_final: 0.8981 (mt) REVERT: e 113 SER cc_start: 0.8977 (t) cc_final: 0.8649 (p) REVERT: e 143 ARG cc_start: 0.8724 (ttt-90) cc_final: 0.7406 (ttt180) REVERT: f 46 ARG cc_start: 0.6686 (ptt90) cc_final: 0.4443 (ptt90) REVERT: f 82 ASN cc_start: 0.8863 (t0) cc_final: 0.8517 (t0) REVERT: f 143 ARG cc_start: 0.8727 (ttt-90) cc_final: 0.7577 (ttt180) outliers start: 158 outliers final: 101 residues processed: 535 average time/residue: 0.1294 time to fit residues: 109.0323 Evaluate side-chains 503 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 385 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 185 SER Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 247 SER Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 58 ARG Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 128 ILE Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 161 ASN Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 247 SER Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 161 ASN Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 185 SER Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 161 ASN Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 247 SER Chi-restraints excluded: chain E residue 268 ASN Chi-restraints excluded: chain E residue 287 LYS Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 185 SER Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 60 GLN Chi-restraints excluded: chain a residue 65 THR Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 130 ASN Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain b residue 27 LYS Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 120 LEU Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 14 ILE Chi-restraints excluded: chain c residue 27 LYS Chi-restraints excluded: chain c residue 65 THR Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain c residue 130 ASN Chi-restraints excluded: chain c residue 137 ILE Chi-restraints excluded: chain d residue 10 VAL Chi-restraints excluded: chain d residue 60 GLN Chi-restraints excluded: chain d residue 65 THR Chi-restraints excluded: chain d residue 89 VAL Chi-restraints excluded: chain d residue 137 ILE Chi-restraints excluded: chain d residue 139 LEU Chi-restraints excluded: chain e residue 27 LYS Chi-restraints excluded: chain e residue 65 THR Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 106 LEU Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 27 LYS Chi-restraints excluded: chain f residue 65 THR Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain f residue 130 ASN Chi-restraints excluded: chain f residue 137 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 180 optimal weight: 0.6980 chunk 220 optimal weight: 2.9990 chunk 242 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 40 optimal weight: 0.1980 chunk 0 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 97 optimal weight: 0.0980 chunk 54 optimal weight: 5.9990 chunk 128 optimal weight: 0.0370 chunk 226 optimal weight: 3.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN d 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.133338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.105899 restraints weight = 27733.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.104804 restraints weight = 23296.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.105416 restraints weight = 21430.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.105752 restraints weight = 17884.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.105911 restraints weight = 16646.738| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 19620 Z= 0.095 Angle : 0.627 14.880 26682 Z= 0.299 Chirality : 0.044 0.181 3162 Planarity : 0.004 0.054 3438 Dihedral : 5.145 28.944 2638 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 5.66 % Allowed : 23.93 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.16), residues: 2412 helix: 0.30 (0.23), residues: 528 sheet: -0.93 (0.20), residues: 666 loop : -2.08 (0.16), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 123 TYR 0.021 0.002 TYR e 45 PHE 0.028 0.002 PHE C 262 TRP 0.012 0.001 TRP A 265 HIS 0.001 0.000 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00207 (19620) covalent geometry : angle 0.62735 (26682) hydrogen bonds : bond 0.02885 ( 576) hydrogen bonds : angle 4.43408 ( 1719) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 448 time to evaluate : 0.679 Fit side-chains REVERT: A 38 MET cc_start: 0.7456 (tmm) cc_final: 0.6890 (tmm) REVERT: A 121 ASN cc_start: 0.7861 (m-40) cc_final: 0.7444 (m-40) REVERT: A 193 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8207 (pp) REVERT: A 268 ASN cc_start: 0.5388 (OUTLIER) cc_final: 0.5095 (p0) REVERT: B 152 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8780 (pp) REVERT: B 193 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7440 (pp) REVERT: B 254 TYR cc_start: 0.8282 (m-80) cc_final: 0.7901 (m-80) REVERT: B 268 ASN cc_start: 0.5592 (OUTLIER) cc_final: 0.5336 (p0) REVERT: C 31 ASP cc_start: 0.8103 (t0) cc_final: 0.7735 (t0) REVERT: C 121 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.8114 (m-40) REVERT: C 171 ASN cc_start: 0.7261 (p0) cc_final: 0.7035 (p0) REVERT: C 193 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.7310 (pp) REVERT: C 230 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7565 (pm20) REVERT: C 256 LYS cc_start: 0.8725 (mptt) cc_final: 0.8244 (tppt) REVERT: C 268 ASN cc_start: 0.5129 (OUTLIER) cc_final: 0.4152 (m-40) REVERT: D 105 ASP cc_start: 0.7934 (t0) cc_final: 0.7319 (p0) REVERT: D 193 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8145 (pp) REVERT: D 254 TYR cc_start: 0.8319 (m-80) cc_final: 0.7912 (m-80) REVERT: D 256 LYS cc_start: 0.8742 (mptt) cc_final: 0.8361 (tppt) REVERT: D 268 ASN cc_start: 0.5284 (OUTLIER) cc_final: 0.4954 (p0) REVERT: D 287 LYS cc_start: 0.7344 (pttp) cc_final: 0.7091 (pttp) REVERT: E 152 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8795 (pp) REVERT: E 193 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7375 (pp) REVERT: E 230 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7693 (pm20) REVERT: E 254 TYR cc_start: 0.8225 (m-80) cc_final: 0.7803 (m-80) REVERT: E 256 LYS cc_start: 0.8574 (mptt) cc_final: 0.8304 (tppt) REVERT: E 262 PHE cc_start: 0.7064 (p90) cc_final: 0.6761 (p90) REVERT: E 268 ASN cc_start: 0.5680 (OUTLIER) cc_final: 0.5425 (p0) REVERT: F 31 ASP cc_start: 0.8099 (t0) cc_final: 0.7659 (t0) REVERT: F 105 ASP cc_start: 0.8138 (t0) cc_final: 0.7652 (p0) REVERT: F 121 ASN cc_start: 0.8536 (OUTLIER) cc_final: 0.8178 (m-40) REVERT: F 193 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.7336 (pp) REVERT: F 230 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7532 (pm20) REVERT: F 256 LYS cc_start: 0.8638 (mptt) cc_final: 0.8241 (tppt) REVERT: a 31 ASN cc_start: 0.8969 (t0) cc_final: 0.8616 (t0) REVERT: a 46 ARG cc_start: 0.6984 (ptt90) cc_final: 0.4747 (ptt90) REVERT: a 111 ASN cc_start: 0.9020 (p0) cc_final: 0.8782 (p0) REVERT: a 113 SER cc_start: 0.8956 (t) cc_final: 0.8644 (p) REVERT: a 143 ARG cc_start: 0.8445 (ttt-90) cc_final: 0.7196 (ttt180) REVERT: b 31 ASN cc_start: 0.9017 (t0) cc_final: 0.8703 (t0) REVERT: b 46 ARG cc_start: 0.6686 (ptt90) cc_final: 0.4426 (ptt90) REVERT: b 82 ASN cc_start: 0.8829 (t0) cc_final: 0.8619 (t0) REVERT: b 143 ARG cc_start: 0.8358 (ttt-90) cc_final: 0.7160 (ttt180) REVERT: c 27 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8360 (mtmm) REVERT: c 46 ARG cc_start: 0.6412 (ptt90) cc_final: 0.4390 (ptt90) REVERT: c 82 ASN cc_start: 0.8737 (t0) cc_final: 0.8339 (t0) REVERT: c 108 MET cc_start: 0.8130 (ttm) cc_final: 0.7891 (tpp) REVERT: c 140 MET cc_start: 0.8212 (ttt) cc_final: 0.7863 (ttt) REVERT: c 143 ARG cc_start: 0.8379 (ttt-90) cc_final: 0.7255 (ttt180) REVERT: d 31 ASN cc_start: 0.8931 (t0) cc_final: 0.8598 (t0) REVERT: d 46 ARG cc_start: 0.7000 (ptt90) cc_final: 0.4863 (ptt90) REVERT: d 111 ASN cc_start: 0.8999 (p0) cc_final: 0.8744 (p0) REVERT: d 113 SER cc_start: 0.8916 (t) cc_final: 0.8608 (p) REVERT: d 143 ARG cc_start: 0.8462 (ttt-90) cc_final: 0.7188 (ttt180) REVERT: e 31 ASN cc_start: 0.8961 (t0) cc_final: 0.8633 (t0) REVERT: e 46 ARG cc_start: 0.6867 (ptt90) cc_final: 0.4605 (ptt90) REVERT: e 143 ARG cc_start: 0.8556 (ttt-90) cc_final: 0.7443 (ttt180) REVERT: f 46 ARG cc_start: 0.6391 (ptt90) cc_final: 0.4421 (ptt90) REVERT: f 82 ASN cc_start: 0.8675 (t0) cc_final: 0.8343 (t0) REVERT: f 143 ARG cc_start: 0.8335 (ttt-90) cc_final: 0.7178 (ttt180) outliers start: 124 outliers final: 69 residues processed: 544 average time/residue: 0.1369 time to fit residues: 114.9882 Evaluate side-chains 493 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 405 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 115 VAL Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 230 GLU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 268 ASN Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 128 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 268 ASN Chi-restraints excluded: chain E residue 287 LYS Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 130 ASN Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain b residue 16 VAL Chi-restraints excluded: chain b residue 27 LYS Chi-restraints excluded: chain b residue 120 LEU Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 27 LYS Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain c residue 145 ILE Chi-restraints excluded: chain d residue 10 VAL Chi-restraints excluded: chain d residue 27 LYS Chi-restraints excluded: chain d residue 70 VAL Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 130 ASN Chi-restraints excluded: chain d residue 137 ILE Chi-restraints excluded: chain d residue 139 LEU Chi-restraints excluded: chain e residue 27 LYS Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 27 LYS Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain f residue 130 ASN Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 145 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 194 optimal weight: 3.9990 chunk 61 optimal weight: 0.0170 chunk 230 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 79 optimal weight: 0.0370 chunk 191 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 179 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 212 optimal weight: 7.9990 overall best weight: 1.4102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN e 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.126859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.098780 restraints weight = 28016.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.098015 restraints weight = 23225.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.098396 restraints weight = 21434.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.098670 restraints weight = 18824.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.098833 restraints weight = 17145.342| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19620 Z= 0.134 Angle : 0.647 14.387 26682 Z= 0.307 Chirality : 0.045 0.168 3162 Planarity : 0.004 0.057 3438 Dihedral : 5.112 27.831 2638 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 4.93 % Allowed : 25.25 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.17), residues: 2412 helix: 0.54 (0.23), residues: 522 sheet: -1.08 (0.20), residues: 690 loop : -1.89 (0.16), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 19 TYR 0.019 0.002 TYR e 45 PHE 0.028 0.002 PHE D 262 TRP 0.009 0.001 TRP B 265 HIS 0.002 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00316 (19620) covalent geometry : angle 0.64673 (26682) hydrogen bonds : bond 0.02950 ( 576) hydrogen bonds : angle 4.46610 ( 1719) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 417 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7541 (tmm) cc_final: 0.7096 (tmm) REVERT: A 121 ASN cc_start: 0.7935 (m-40) cc_final: 0.7493 (m-40) REVERT: A 193 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8233 (pp) REVERT: A 268 ASN cc_start: 0.5111 (OUTLIER) cc_final: 0.4794 (p0) REVERT: B 193 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.7517 (pp) REVERT: B 254 TYR cc_start: 0.8284 (m-80) cc_final: 0.7888 (m-80) REVERT: B 268 ASN cc_start: 0.5667 (OUTLIER) cc_final: 0.5373 (p0) REVERT: C 31 ASP cc_start: 0.8150 (t0) cc_final: 0.7745 (t0) REVERT: C 121 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.8191 (m-40) REVERT: C 193 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7241 (pp) REVERT: C 256 LYS cc_start: 0.8670 (mptt) cc_final: 0.8377 (tppt) REVERT: D 105 ASP cc_start: 0.7875 (t0) cc_final: 0.7275 (p0) REVERT: D 193 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8152 (pp) REVERT: D 254 TYR cc_start: 0.8386 (m-80) cc_final: 0.7967 (m-80) REVERT: D 256 LYS cc_start: 0.8751 (mptt) cc_final: 0.8368 (tppt) REVERT: D 268 ASN cc_start: 0.4997 (OUTLIER) cc_final: 0.4694 (p0) REVERT: D 287 LYS cc_start: 0.7400 (pttp) cc_final: 0.7183 (pttp) REVERT: E 105 ASP cc_start: 0.7886 (t0) cc_final: 0.7406 (p0) REVERT: E 193 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.7443 (pp) REVERT: E 230 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7618 (pm20) REVERT: E 254 TYR cc_start: 0.8275 (m-80) cc_final: 0.7880 (m-80) REVERT: E 256 LYS cc_start: 0.8616 (mptt) cc_final: 0.8355 (tppt) REVERT: E 262 PHE cc_start: 0.7094 (p90) cc_final: 0.6836 (p90) REVERT: E 268 ASN cc_start: 0.5666 (OUTLIER) cc_final: 0.5383 (p0) REVERT: F 31 ASP cc_start: 0.8051 (t0) cc_final: 0.7644 (t0) REVERT: F 50 ASP cc_start: 0.8197 (t70) cc_final: 0.7965 (t0) REVERT: F 105 ASP cc_start: 0.8204 (t0) cc_final: 0.7648 (p0) REVERT: F 121 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8306 (m-40) REVERT: F 193 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.7344 (pp) REVERT: F 230 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7553 (pm20) REVERT: F 256 LYS cc_start: 0.8647 (mptt) cc_final: 0.8255 (tppt) REVERT: a 31 ASN cc_start: 0.8959 (t0) cc_final: 0.8605 (t0) REVERT: a 46 ARG cc_start: 0.7014 (ptt90) cc_final: 0.4821 (ptt90) REVERT: a 85 GLN cc_start: 0.8473 (mt0) cc_final: 0.8216 (mt0) REVERT: a 113 SER cc_start: 0.8933 (t) cc_final: 0.8610 (p) REVERT: a 143 ARG cc_start: 0.8565 (ttt-90) cc_final: 0.7207 (ttt180) REVERT: b 46 ARG cc_start: 0.6798 (ptt90) cc_final: 0.4521 (ptt90) REVERT: b 143 ARG cc_start: 0.8446 (ttt-90) cc_final: 0.7278 (ttt180) REVERT: c 27 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8356 (mtmm) REVERT: c 46 ARG cc_start: 0.6495 (ptt90) cc_final: 0.4493 (ptt90) REVERT: c 82 ASN cc_start: 0.8695 (t0) cc_final: 0.8309 (t0) REVERT: c 140 MET cc_start: 0.8270 (ttt) cc_final: 0.7855 (ttt) REVERT: c 143 ARG cc_start: 0.8478 (ttt-90) cc_final: 0.7411 (ttt180) REVERT: d 31 ASN cc_start: 0.8915 (t0) cc_final: 0.8605 (t0) REVERT: d 46 ARG cc_start: 0.7068 (ptt90) cc_final: 0.4893 (ptt90) REVERT: d 113 SER cc_start: 0.8935 (t) cc_final: 0.8589 (p) REVERT: d 143 ARG cc_start: 0.8585 (ttt-90) cc_final: 0.7269 (ttt180) REVERT: e 46 ARG cc_start: 0.6937 (ptt90) cc_final: 0.4599 (ptt90) REVERT: e 143 ARG cc_start: 0.8619 (ttt-90) cc_final: 0.7373 (ttt180) REVERT: f 46 ARG cc_start: 0.6479 (ptt90) cc_final: 0.4546 (ptt90) REVERT: f 82 ASN cc_start: 0.8713 (t0) cc_final: 0.8406 (t0) REVERT: f 143 ARG cc_start: 0.8409 (ttt-90) cc_final: 0.7209 (ttt180) REVERT: f 146 MET cc_start: 0.7804 (ttm) cc_final: 0.7559 (ttm) outliers start: 108 outliers final: 76 residues processed: 499 average time/residue: 0.1319 time to fit residues: 102.4642 Evaluate side-chains 488 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 397 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 268 ASN Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 230 GLU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 60 GLN Chi-restraints excluded: chain a residue 130 ASN Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain b residue 16 VAL Chi-restraints excluded: chain b residue 27 LYS Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 120 LEU Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 27 LYS Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain c residue 130 ASN Chi-restraints excluded: chain c residue 137 ILE Chi-restraints excluded: chain c residue 145 ILE Chi-restraints excluded: chain d residue 10 VAL Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 137 ILE Chi-restraints excluded: chain d residue 139 LEU Chi-restraints excluded: chain e residue 27 LYS Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 27 LYS Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain f residue 130 ASN Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 145 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 239 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 100 optimal weight: 9.9990 chunk 27 optimal weight: 7.9990 chunk 79 optimal weight: 0.0980 chunk 160 optimal weight: 3.9990 chunk 218 optimal weight: 0.5980 chunk 209 optimal weight: 8.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN D 121 ASN D 260 ASN E 260 ASN d 130 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.126968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.099030 restraints weight = 27914.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.098608 restraints weight = 22020.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.098524 restraints weight = 20542.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.098960 restraints weight = 19335.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.099069 restraints weight = 16520.069| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19620 Z= 0.119 Angle : 0.640 14.503 26682 Z= 0.302 Chirality : 0.044 0.165 3162 Planarity : 0.004 0.055 3438 Dihedral : 4.981 28.332 2636 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 5.02 % Allowed : 25.16 % Favored : 69.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.58 (0.17), residues: 2412 helix: 0.67 (0.23), residues: 522 sheet: -1.03 (0.20), residues: 684 loop : -1.84 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 19 TYR 0.019 0.002 TYR D 83 PHE 0.028 0.002 PHE C 262 TRP 0.010 0.001 TRP f 110 HIS 0.001 0.001 HIS E 200 Details of bonding type rmsd covalent geometry : bond 0.00279 (19620) covalent geometry : angle 0.64005 (26682) hydrogen bonds : bond 0.02863 ( 576) hydrogen bonds : angle 4.43463 ( 1719) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 428 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 MET cc_start: 0.7487 (tmm) cc_final: 0.7017 (tmm) REVERT: A 121 ASN cc_start: 0.7930 (m-40) cc_final: 0.7521 (m-40) REVERT: A 193 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8233 (pp) REVERT: A 268 ASN cc_start: 0.5035 (OUTLIER) cc_final: 0.4715 (p0) REVERT: B 193 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7481 (pp) REVERT: B 230 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7684 (pm20) REVERT: B 254 TYR cc_start: 0.8278 (m-80) cc_final: 0.7870 (m-80) REVERT: B 268 ASN cc_start: 0.5653 (OUTLIER) cc_final: 0.5366 (p0) REVERT: C 31 ASP cc_start: 0.8144 (t0) cc_final: 0.7885 (t0) REVERT: C 121 ASN cc_start: 0.8604 (OUTLIER) cc_final: 0.8172 (m-40) REVERT: C 193 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7223 (pp) REVERT: C 256 LYS cc_start: 0.8681 (mptt) cc_final: 0.8372 (tppt) REVERT: D 105 ASP cc_start: 0.7904 (t0) cc_final: 0.7328 (p0) REVERT: D 193 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8164 (pp) REVERT: D 254 TYR cc_start: 0.8375 (m-80) cc_final: 0.7976 (m-80) REVERT: D 256 LYS cc_start: 0.8761 (mptt) cc_final: 0.8388 (tppt) REVERT: D 268 ASN cc_start: 0.4993 (OUTLIER) cc_final: 0.4758 (p0) REVERT: D 287 LYS cc_start: 0.7385 (pttp) cc_final: 0.7160 (pttp) REVERT: E 152 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8870 (pp) REVERT: E 193 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7427 (pp) REVERT: E 230 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7653 (pm20) REVERT: E 254 TYR cc_start: 0.8280 (m-80) cc_final: 0.7867 (m-80) REVERT: E 256 LYS cc_start: 0.8612 (mptt) cc_final: 0.8347 (tppt) REVERT: E 262 PHE cc_start: 0.7145 (p90) cc_final: 0.6930 (p90) REVERT: E 268 ASN cc_start: 0.5660 (OUTLIER) cc_final: 0.5361 (p0) REVERT: F 31 ASP cc_start: 0.8035 (t0) cc_final: 0.7606 (t0) REVERT: F 50 ASP cc_start: 0.8152 (t70) cc_final: 0.7948 (t0) REVERT: F 105 ASP cc_start: 0.8210 (t0) cc_final: 0.7653 (p0) REVERT: F 121 ASN cc_start: 0.8629 (OUTLIER) cc_final: 0.8294 (m-40) REVERT: F 193 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7316 (pp) REVERT: F 256 LYS cc_start: 0.8705 (mptt) cc_final: 0.8281 (tppt) REVERT: a 31 ASN cc_start: 0.8971 (t0) cc_final: 0.8624 (t0) REVERT: a 46 ARG cc_start: 0.6905 (ptt90) cc_final: 0.4678 (ptt90) REVERT: a 85 GLN cc_start: 0.8536 (mt0) cc_final: 0.8259 (mt0) REVERT: a 111 ASN cc_start: 0.9077 (p0) cc_final: 0.8767 (p0) REVERT: a 113 SER cc_start: 0.8925 (t) cc_final: 0.8575 (p) REVERT: a 143 ARG cc_start: 0.8553 (ttt-90) cc_final: 0.7268 (ttt180) REVERT: b 46 ARG cc_start: 0.6900 (ptt90) cc_final: 0.4651 (ptt90) REVERT: b 143 ARG cc_start: 0.8619 (ttt-90) cc_final: 0.7325 (ttt180) REVERT: c 46 ARG cc_start: 0.6453 (ptt90) cc_final: 0.4502 (ptt90) REVERT: c 82 ASN cc_start: 0.8670 (t0) cc_final: 0.8317 (t0) REVERT: c 140 MET cc_start: 0.8271 (ttt) cc_final: 0.7858 (ttt) REVERT: c 143 ARG cc_start: 0.8444 (ttt-90) cc_final: 0.7321 (ttt180) REVERT: d 31 ASN cc_start: 0.8913 (t0) cc_final: 0.8618 (t0) REVERT: d 46 ARG cc_start: 0.6969 (ptt90) cc_final: 0.4795 (ptt90) REVERT: d 85 GLN cc_start: 0.8466 (mt0) cc_final: 0.8209 (mt0) REVERT: d 111 ASN cc_start: 0.8999 (p0) cc_final: 0.8724 (p0) REVERT: d 113 SER cc_start: 0.8921 (t) cc_final: 0.8553 (p) REVERT: d 143 ARG cc_start: 0.8562 (ttt-90) cc_final: 0.7310 (ttt180) REVERT: e 46 ARG cc_start: 0.6856 (ptt90) cc_final: 0.4588 (mtp85) REVERT: e 143 ARG cc_start: 0.8612 (ttt-90) cc_final: 0.7366 (ttt180) REVERT: f 46 ARG cc_start: 0.6460 (ptt90) cc_final: 0.4540 (ptt90) REVERT: f 82 ASN cc_start: 0.8707 (t0) cc_final: 0.8391 (t0) REVERT: f 143 ARG cc_start: 0.8400 (ttt-90) cc_final: 0.7177 (ttt180) outliers start: 110 outliers final: 84 residues processed: 510 average time/residue: 0.1300 time to fit residues: 104.1298 Evaluate side-chains 504 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 405 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 268 ASN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain F residue 250 THR Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 60 GLN Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 130 ASN Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain b residue 10 VAL Chi-restraints excluded: chain b residue 16 VAL Chi-restraints excluded: chain b residue 27 LYS Chi-restraints excluded: chain b residue 28 ILE Chi-restraints excluded: chain b residue 60 GLN Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 120 LEU Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain c residue 130 ASN Chi-restraints excluded: chain c residue 137 ILE Chi-restraints excluded: chain c residue 145 ILE Chi-restraints excluded: chain d residue 10 VAL Chi-restraints excluded: chain d residue 70 VAL Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 130 ASN Chi-restraints excluded: chain d residue 137 ILE Chi-restraints excluded: chain d residue 139 LEU Chi-restraints excluded: chain e residue 27 LYS Chi-restraints excluded: chain e residue 28 ILE Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 27 LYS Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain f residue 130 ASN Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 145 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 160 optimal weight: 9.9990 chunk 142 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 116 optimal weight: 0.9990 chunk 104 optimal weight: 2.9990 chunk 141 optimal weight: 7.9990 chunk 233 optimal weight: 0.8980 chunk 70 optimal weight: 0.0040 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 260 ASN D 121 ASN D 260 ASN d 130 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.128218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.102893 restraints weight = 27841.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.100000 restraints weight = 32456.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.100757 restraints weight = 32827.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.100946 restraints weight = 26579.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.101155 restraints weight = 22841.862| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19620 Z= 0.154 Angle : 0.659 14.511 26682 Z= 0.314 Chirality : 0.045 0.169 3162 Planarity : 0.004 0.054 3438 Dihedral : 5.076 27.806 2636 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 5.21 % Allowed : 25.53 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.51 (0.17), residues: 2412 helix: 0.75 (0.23), residues: 522 sheet: -1.02 (0.20), residues: 684 loop : -1.79 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 19 TYR 0.019 0.002 TYR D 132 PHE 0.029 0.002 PHE F 262 TRP 0.010 0.001 TRP c 110 HIS 0.002 0.001 HIS F 200 Details of bonding type rmsd covalent geometry : bond 0.00366 (19620) covalent geometry : angle 0.65932 (26682) hydrogen bonds : bond 0.02981 ( 576) hydrogen bonds : angle 4.46045 ( 1719) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 516 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 402 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 43 MET cc_start: 0.7419 (ttm) cc_final: 0.7144 (ttm) REVERT: A 193 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8238 (pp) REVERT: A 268 ASN cc_start: 0.5130 (OUTLIER) cc_final: 0.4791 (p0) REVERT: B 193 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7452 (pp) REVERT: B 230 GLU cc_start: 0.8045 (OUTLIER) cc_final: 0.7823 (pm20) REVERT: B 254 TYR cc_start: 0.8272 (m-80) cc_final: 0.7910 (m-80) REVERT: B 268 ASN cc_start: 0.5710 (OUTLIER) cc_final: 0.5377 (p0) REVERT: C 31 ASP cc_start: 0.8111 (t0) cc_final: 0.7882 (t0) REVERT: C 121 ASN cc_start: 0.8533 (OUTLIER) cc_final: 0.8141 (m-40) REVERT: C 193 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7249 (pp) REVERT: C 256 LYS cc_start: 0.8632 (mptt) cc_final: 0.8402 (tppt) REVERT: D 105 ASP cc_start: 0.7855 (t0) cc_final: 0.7270 (p0) REVERT: D 193 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8190 (pp) REVERT: D 254 TYR cc_start: 0.8346 (m-80) cc_final: 0.7998 (m-80) REVERT: D 256 LYS cc_start: 0.8746 (mptt) cc_final: 0.8427 (tppt) REVERT: D 268 ASN cc_start: 0.5084 (OUTLIER) cc_final: 0.4745 (p0) REVERT: D 287 LYS cc_start: 0.7234 (pttp) cc_final: 0.6995 (pttp) REVERT: E 193 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.7436 (pp) REVERT: E 230 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7749 (pm20) REVERT: E 254 TYR cc_start: 0.8259 (m-80) cc_final: 0.7910 (m-80) REVERT: E 256 LYS cc_start: 0.8638 (mptt) cc_final: 0.8359 (tppt) REVERT: E 268 ASN cc_start: 0.5749 (OUTLIER) cc_final: 0.5420 (p0) REVERT: F 31 ASP cc_start: 0.8011 (t0) cc_final: 0.7781 (t0) REVERT: F 105 ASP cc_start: 0.8179 (t0) cc_final: 0.7598 (p0) REVERT: F 121 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8282 (m-40) REVERT: F 193 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7264 (pp) REVERT: F 256 LYS cc_start: 0.8626 (mptt) cc_final: 0.8334 (tppt) REVERT: a 46 ARG cc_start: 0.7006 (ptt90) cc_final: 0.4805 (ptt90) REVERT: a 85 GLN cc_start: 0.8545 (mt0) cc_final: 0.8224 (mt0) REVERT: a 113 SER cc_start: 0.8914 (t) cc_final: 0.8588 (p) REVERT: a 143 ARG cc_start: 0.8560 (ttt-90) cc_final: 0.7299 (ttt180) REVERT: b 46 ARG cc_start: 0.7044 (ptt90) cc_final: 0.4720 (ptt90) REVERT: b 143 ARG cc_start: 0.8623 (ttt-90) cc_final: 0.7358 (ttt180) REVERT: c 46 ARG cc_start: 0.6561 (ptt90) cc_final: 0.4603 (ptt90) REVERT: c 82 ASN cc_start: 0.8661 (t0) cc_final: 0.8312 (t0) REVERT: c 140 MET cc_start: 0.8268 (ttt) cc_final: 0.7820 (ttt) REVERT: c 143 ARG cc_start: 0.8493 (ttt-90) cc_final: 0.7422 (ttt180) REVERT: d 46 ARG cc_start: 0.7082 (ptt90) cc_final: 0.4883 (ptt90) REVERT: d 85 GLN cc_start: 0.8503 (mt0) cc_final: 0.8216 (mt0) REVERT: d 113 SER cc_start: 0.8904 (t) cc_final: 0.8551 (p) REVERT: d 143 ARG cc_start: 0.8503 (ttt-90) cc_final: 0.7164 (ttt180) REVERT: e 46 ARG cc_start: 0.6997 (ptt90) cc_final: 0.4102 (mtm110) REVERT: e 143 ARG cc_start: 0.8600 (ttt-90) cc_final: 0.7390 (ttt180) REVERT: f 46 ARG cc_start: 0.6386 (ptt90) cc_final: 0.4406 (ptt90) REVERT: f 82 ASN cc_start: 0.8704 (t0) cc_final: 0.8384 (t0) REVERT: f 143 ARG cc_start: 0.8407 (ttt-90) cc_final: 0.7167 (ttt180) outliers start: 114 outliers final: 86 residues processed: 484 average time/residue: 0.1325 time to fit residues: 100.4471 Evaluate side-chains 490 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 390 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 287 LYS Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 53 GLU Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 268 ASN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 43 MET Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 128 ILE Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 60 GLN Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 130 ASN Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain b residue 16 VAL Chi-restraints excluded: chain b residue 27 LYS Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 120 LEU Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain c residue 130 ASN Chi-restraints excluded: chain c residue 137 ILE Chi-restraints excluded: chain c residue 145 ILE Chi-restraints excluded: chain d residue 10 VAL Chi-restraints excluded: chain d residue 27 LYS Chi-restraints excluded: chain d residue 70 VAL Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 130 ASN Chi-restraints excluded: chain d residue 137 ILE Chi-restraints excluded: chain d residue 139 LEU Chi-restraints excluded: chain e residue 27 LYS Chi-restraints excluded: chain e residue 60 GLN Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 106 LEU Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 27 LYS Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain f residue 130 ASN Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 145 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 125 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 152 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 216 optimal weight: 0.9990 chunk 103 optimal weight: 20.0000 chunk 30 optimal weight: 0.3980 chunk 163 optimal weight: 1.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN D 260 ASN E 260 ASN d 130 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.126644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.098376 restraints weight = 28035.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.097877 restraints weight = 21355.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.098091 restraints weight = 21961.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.098637 restraints weight = 17472.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.098791 restraints weight = 16212.022| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19620 Z= 0.137 Angle : 0.663 14.622 26682 Z= 0.313 Chirality : 0.045 0.175 3162 Planarity : 0.004 0.054 3438 Dihedral : 5.049 28.009 2636 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Rotamer: Outliers : 5.02 % Allowed : 25.94 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.17), residues: 2412 helix: 0.85 (0.23), residues: 522 sheet: -0.99 (0.20), residues: 684 loop : -1.77 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 19 TYR 0.019 0.002 TYR D 132 PHE 0.028 0.002 PHE C 262 TRP 0.011 0.001 TRP c 110 HIS 0.002 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00325 (19620) covalent geometry : angle 0.66279 (26682) hydrogen bonds : bond 0.02929 ( 576) hydrogen bonds : angle 4.46658 ( 1719) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4824 Ramachandran restraints generated. 2412 Oldfield, 0 Emsley, 2412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 411 time to evaluate : 0.519 Fit side-chains REVERT: A 38 MET cc_start: 0.7340 (tmm) cc_final: 0.6653 (tmm) REVERT: A 43 MET cc_start: 0.7491 (ttm) cc_final: 0.7234 (ttm) REVERT: A 121 ASN cc_start: 0.8004 (m-40) cc_final: 0.7632 (m-40) REVERT: A 268 ASN cc_start: 0.5283 (OUTLIER) cc_final: 0.4974 (p0) REVERT: B 193 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.7491 (pp) REVERT: B 230 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7522 (pm20) REVERT: B 254 TYR cc_start: 0.8262 (m-80) cc_final: 0.7830 (m-80) REVERT: B 268 ASN cc_start: 0.5661 (OUTLIER) cc_final: 0.5353 (p0) REVERT: C 31 ASP cc_start: 0.8128 (t0) cc_final: 0.7846 (t0) REVERT: C 121 ASN cc_start: 0.8634 (OUTLIER) cc_final: 0.8248 (m-40) REVERT: C 193 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7251 (pp) REVERT: C 256 LYS cc_start: 0.8679 (mptt) cc_final: 0.8349 (tppt) REVERT: D 105 ASP cc_start: 0.7912 (t0) cc_final: 0.7339 (p0) REVERT: D 193 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8213 (pp) REVERT: D 254 TYR cc_start: 0.8397 (m-80) cc_final: 0.8014 (m-80) REVERT: D 256 LYS cc_start: 0.8775 (mptt) cc_final: 0.8373 (tppt) REVERT: D 268 ASN cc_start: 0.5189 (OUTLIER) cc_final: 0.4849 (p0) REVERT: E 230 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7436 (pm20) REVERT: E 254 TYR cc_start: 0.8306 (m-80) cc_final: 0.7925 (m-80) REVERT: E 256 LYS cc_start: 0.8643 (mptt) cc_final: 0.8269 (tppt) REVERT: E 268 ASN cc_start: 0.5677 (OUTLIER) cc_final: 0.5356 (p0) REVERT: F 31 ASP cc_start: 0.8025 (t0) cc_final: 0.7769 (t0) REVERT: F 105 ASP cc_start: 0.8242 (t0) cc_final: 0.7651 (p0) REVERT: F 121 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8339 (m-40) REVERT: F 193 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7278 (pp) REVERT: F 256 LYS cc_start: 0.8677 (mptt) cc_final: 0.8303 (tppt) REVERT: a 46 ARG cc_start: 0.6909 (ptt90) cc_final: 0.4645 (ptt90) REVERT: a 85 GLN cc_start: 0.8596 (mt0) cc_final: 0.8233 (mt0) REVERT: a 113 SER cc_start: 0.8933 (t) cc_final: 0.8619 (p) REVERT: a 143 ARG cc_start: 0.8575 (ttt-90) cc_final: 0.7275 (ttt180) REVERT: b 45 TYR cc_start: 0.9070 (t80) cc_final: 0.8837 (t80) REVERT: b 46 ARG cc_start: 0.7005 (ptt90) cc_final: 0.4620 (ptt90) REVERT: b 143 ARG cc_start: 0.8611 (ttt-90) cc_final: 0.7341 (ttt180) REVERT: c 46 ARG cc_start: 0.6464 (ptt90) cc_final: 0.4489 (ptt90) REVERT: c 82 ASN cc_start: 0.8695 (t0) cc_final: 0.8344 (t0) REVERT: c 140 MET cc_start: 0.8281 (ttt) cc_final: 0.7818 (ttt) REVERT: c 143 ARG cc_start: 0.8487 (ttt-90) cc_final: 0.7322 (ttt180) REVERT: d 31 ASN cc_start: 0.8893 (t0) cc_final: 0.8590 (t0) REVERT: d 46 ARG cc_start: 0.6940 (ptt90) cc_final: 0.4720 (ptt90) REVERT: d 85 GLN cc_start: 0.8580 (mt0) cc_final: 0.8234 (mt0) REVERT: d 113 SER cc_start: 0.8961 (t) cc_final: 0.8602 (p) REVERT: d 143 ARG cc_start: 0.8520 (ttt-90) cc_final: 0.7218 (ttt180) REVERT: e 31 ASN cc_start: 0.8942 (t0) cc_final: 0.8658 (t0) REVERT: e 46 ARG cc_start: 0.6989 (ptt90) cc_final: 0.4095 (mtm110) REVERT: e 143 ARG cc_start: 0.8613 (ttt-90) cc_final: 0.7382 (ttt180) REVERT: f 46 ARG cc_start: 0.6239 (ptt90) cc_final: 0.4220 (ptt90) REVERT: f 82 ASN cc_start: 0.8743 (t0) cc_final: 0.8436 (t0) REVERT: f 87 ASN cc_start: 0.8506 (p0) cc_final: 0.8287 (p0) REVERT: f 143 ARG cc_start: 0.8421 (ttt-90) cc_final: 0.7145 (ttt180) outliers start: 110 outliers final: 83 residues processed: 491 average time/residue: 0.1287 time to fit residues: 99.0290 Evaluate side-chains 494 residues out of total 2190 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 399 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 186 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 268 ASN Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 186 THR Chi-restraints excluded: chain B residue 193 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 230 GLU Chi-restraints excluded: chain B residue 231 THR Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 170 LEU Chi-restraints excluded: chain C residue 178 THR Chi-restraints excluded: chain C residue 185 SER Chi-restraints excluded: chain C residue 193 LEU Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain D residue 79 ILE Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 121 ASN Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 178 THR Chi-restraints excluded: chain D residue 186 THR Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 268 ASN Chi-restraints excluded: chain E residue 79 ILE Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 186 THR Chi-restraints excluded: chain E residue 228 VAL Chi-restraints excluded: chain E residue 230 GLU Chi-restraints excluded: chain E residue 231 THR Chi-restraints excluded: chain E residue 245 SER Chi-restraints excluded: chain E residue 268 ASN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 43 MET Chi-restraints excluded: chain F residue 51 ILE Chi-restraints excluded: chain F residue 79 ILE Chi-restraints excluded: chain F residue 115 VAL Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 170 LEU Chi-restraints excluded: chain F residue 178 THR Chi-restraints excluded: chain F residue 193 LEU Chi-restraints excluded: chain F residue 231 THR Chi-restraints excluded: chain a residue 10 VAL Chi-restraints excluded: chain a residue 27 LYS Chi-restraints excluded: chain a residue 60 GLN Chi-restraints excluded: chain a residue 89 VAL Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 120 LEU Chi-restraints excluded: chain a residue 130 ASN Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 139 LEU Chi-restraints excluded: chain b residue 27 LYS Chi-restraints excluded: chain b residue 60 GLN Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 106 LEU Chi-restraints excluded: chain b residue 120 LEU Chi-restraints excluded: chain c residue 10 VAL Chi-restraints excluded: chain c residue 89 VAL Chi-restraints excluded: chain c residue 120 LEU Chi-restraints excluded: chain c residue 130 ASN Chi-restraints excluded: chain c residue 137 ILE Chi-restraints excluded: chain c residue 145 ILE Chi-restraints excluded: chain d residue 10 VAL Chi-restraints excluded: chain d residue 27 LYS Chi-restraints excluded: chain d residue 70 VAL Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 137 ILE Chi-restraints excluded: chain d residue 139 LEU Chi-restraints excluded: chain e residue 27 LYS Chi-restraints excluded: chain e residue 89 VAL Chi-restraints excluded: chain e residue 106 LEU Chi-restraints excluded: chain e residue 120 LEU Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 16 VAL Chi-restraints excluded: chain f residue 27 LYS Chi-restraints excluded: chain f residue 70 VAL Chi-restraints excluded: chain f residue 89 VAL Chi-restraints excluded: chain f residue 120 LEU Chi-restraints excluded: chain f residue 130 ASN Chi-restraints excluded: chain f residue 137 ILE Chi-restraints excluded: chain f residue 145 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 246 random chunks: chunk 182 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 181 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 132 optimal weight: 5.9990 chunk 163 optimal weight: 3.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN D 260 ASN E 260 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.102081 restraints weight = 27997.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.101221 restraints weight = 23500.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.101631 restraints weight = 20895.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.101821 restraints weight = 19613.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.101969 restraints weight = 17655.810| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19620 Z= 0.181 Angle : 0.697 14.627 26682 Z= 0.331 Chirality : 0.046 0.178 3162 Planarity : 0.004 0.053 3438 Dihedral : 5.199 27.360 2634 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 4.61 % Allowed : 26.16 % Favored : 69.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.47 (0.17), residues: 2412 helix: 0.71 (0.23), residues: 534 sheet: -1.05 (0.20), residues: 684 loop : -1.71 (0.17), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 123 TYR 0.024 0.002 TYR e 45 PHE 0.028 0.002 PHE F 262 TRP 0.009 0.001 TRP c 110 HIS 0.002 0.001 HIS D 52 Details of bonding type rmsd covalent geometry : bond 0.00434 (19620) covalent geometry : angle 0.69696 (26682) hydrogen bonds : bond 0.03122 ( 576) hydrogen bonds : angle 4.55840 ( 1719) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3185.87 seconds wall clock time: 55 minutes 53.40 seconds (3353.40 seconds total)