Starting phenix.real_space_refine on Thu Aug 6 20:37:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10nb_75299/08_2026/10nb_75299_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/10nb_75299/08_2026/10nb_75299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10nb_75299/08_2026/10nb_75299_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10nb_75299/08_2026/10nb_75299_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10nb_75299/08_2026/10nb_75299.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10nb_75299/08_2026/10nb_75299.map" } resolution = 3.76 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= -0.000 sd= 0.012 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 84 5.16 5 C 10316 2.51 5 N 3028 2.21 5 O 3112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16540 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2754 Classifications: {'peptide': 350} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 341} Chain: "B" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2758 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 342} Chain: "C" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2758 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 342} Chain: "D" Number of atoms: 2754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2754 Classifications: {'peptide': 350} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 341} Chain: "E" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2758 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 342} Chain: "F" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2758 Classifications: {'peptide': 351} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 342} Time building chain proxies: 4.03, per 1000 atoms: 0.24 Number of scatterers: 16540 At special positions: 0 Unit cell: (143.374, 123.97, 84.084, 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 84 16.00 O 3112 8.00 N 3028 7.00 C 10316 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: 1.50 Conformation dependent library (CDL) restraints added in 661.6 milliseconds 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3936 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 18 sheets defined 47.2% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 1 through 9 removed outlier: 3.589A pdb=" N TYR A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 12 No H-bonds generated for 'chain 'A' and resid 10 through 12' Processing helix chain 'A' and resid 42 through 54 Processing helix chain 'A' and resid 55 through 66 Processing helix chain 'A' and resid 103 through 108 Processing helix chain 'A' and resid 112 through 119 removed outlier: 3.782A pdb=" N LEU A 116 " --> pdb=" O VAL A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 148 removed outlier: 3.778A pdb=" N MET A 138 " --> pdb=" O LYS A 134 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N HIS A 148 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 194 removed outlier: 3.805A pdb=" N ARG A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 194 " --> pdb=" O SER A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 removed outlier: 4.004A pdb=" N GLU A 207 " --> pdb=" O ARG A 204 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N THR A 208 " --> pdb=" O SER A 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 208' Processing helix chain 'A' and resid 209 through 219 Processing helix chain 'A' and resid 233 through 242 Processing helix chain 'A' and resid 246 through 256 Processing helix chain 'A' and resid 285 through 293 Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 314 through 325 removed outlier: 3.681A pdb=" N LEU A 322 " --> pdb=" O ALA A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 348 removed outlier: 4.228A pdb=" N LEU A 345 " --> pdb=" O ASN A 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 14 removed outlier: 3.818A pdb=" N GLN B 5 " --> pdb=" O GLY B 1 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N MET B 10 " --> pdb=" O TYR B 6 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LEU B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N THR B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 54 Processing helix chain 'B' and resid 55 through 66 removed outlier: 3.620A pdb=" N GLU B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 111 through 118 removed outlier: 3.852A pdb=" N ASN B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 148 Processing helix chain 'B' and resid 182 through 194 removed outlier: 3.684A pdb=" N ALA B 186 " --> pdb=" O SER B 182 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LEU B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG B 192 " --> pdb=" O LYS B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 219 removed outlier: 3.575A pdb=" N MET B 209 " --> pdb=" O SER B 205 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR B 218 " --> pdb=" O THR B 214 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY B 219 " --> pdb=" O PHE B 215 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 241 removed outlier: 3.679A pdb=" N LEU B 241 " --> pdb=" O ARG B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 257 Processing helix chain 'B' and resid 285 through 295 Processing helix chain 'B' and resid 296 through 307 Processing helix chain 'B' and resid 314 through 325 Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.512A pdb=" N ALA B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 350 removed outlier: 3.736A pdb=" N LYS B 350 " --> pdb=" O MET B 346 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 42 through 52 Processing helix chain 'C' and resid 55 through 66 Processing helix chain 'C' and resid 111 through 118 removed outlier: 3.584A pdb=" N ASN C 115 " --> pdb=" O GLU C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 149 Processing helix chain 'C' and resid 182 through 192 removed outlier: 3.947A pdb=" N ARG C 192 " --> pdb=" O LYS C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 218 Processing helix chain 'C' and resid 230 through 241 Processing helix chain 'C' and resid 246 through 257 Processing helix chain 'C' and resid 285 through 295 Processing helix chain 'C' and resid 296 through 308 removed outlier: 3.836A pdb=" N LYS C 301 " --> pdb=" O LEU C 297 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA C 302 " --> pdb=" O HIS C 298 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ALA C 305 " --> pdb=" O LYS C 301 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ARG C 306 " --> pdb=" O ALA C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 325 removed outlier: 3.596A pdb=" N ALA C 318 " --> pdb=" O THR C 314 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU C 319 " --> pdb=" O PHE C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 335 removed outlier: 3.831A pdb=" N ALA C 333 " --> pdb=" O SER C 329 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU C 334 " --> pdb=" O GLU C 330 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N HIS C 335 " --> pdb=" O GLN C 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 329 through 335' Processing helix chain 'C' and resid 338 through 350 removed outlier: 3.787A pdb=" N ASP C 342 " --> pdb=" O ASP C 338 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU C 343 " --> pdb=" O SER C 339 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU C 345 " --> pdb=" O ASN C 341 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N MET C 346 " --> pdb=" O ASP C 342 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 347 " --> pdb=" O LEU C 343 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 348 " --> pdb=" O ARG C 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 9 removed outlier: 3.614A pdb=" N TYR D 6 " --> pdb=" O GLU D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 12 No H-bonds generated for 'chain 'D' and resid 10 through 12' Processing helix chain 'D' and resid 42 through 54 Processing helix chain 'D' and resid 55 through 65 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 112 through 117 removed outlier: 3.975A pdb=" N LEU D 116 " --> pdb=" O VAL D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 133 through 148 removed outlier: 3.714A pdb=" N MET D 138 " --> pdb=" O LYS D 134 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N HIS D 148 " --> pdb=" O TYR D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 193 removed outlier: 3.997A pdb=" N ARG D 192 " --> pdb=" O LYS D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 219 Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 246 through 256 Processing helix chain 'D' and resid 285 through 293 Processing helix chain 'D' and resid 297 through 307 Processing helix chain 'D' and resid 314 through 325 removed outlier: 3.615A pdb=" N LEU D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 348 removed outlier: 4.240A pdb=" N LEU D 345 " --> pdb=" O ASN D 341 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 14 removed outlier: 3.808A pdb=" N GLN E 5 " --> pdb=" O GLY E 1 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET E 10 " --> pdb=" O TYR E 6 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU E 11 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N THR E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 54 Processing helix chain 'E' and resid 55 through 66 removed outlier: 3.857A pdb=" N GLU E 61 " --> pdb=" O ALA E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 111 through 118 removed outlier: 4.043A pdb=" N ASN E 115 " --> pdb=" O GLU E 111 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU E 116 " --> pdb=" O VAL E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 133 through 148 removed outlier: 3.605A pdb=" N THR E 137 " --> pdb=" O GLY E 133 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 194 removed outlier: 3.947A pdb=" N LEU E 191 " --> pdb=" O LEU E 187 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N ARG E 192 " --> pdb=" O LYS E 188 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA E 194 " --> pdb=" O SER E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 219 removed outlier: 4.264A pdb=" N THR E 218 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLY E 219 " --> pdb=" O PHE E 215 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 241 removed outlier: 3.791A pdb=" N LEU E 241 " --> pdb=" O ARG E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 257 Processing helix chain 'E' and resid 285 through 295 Processing helix chain 'E' and resid 296 through 307 Processing helix chain 'E' and resid 314 through 325 Processing helix chain 'E' and resid 329 through 337 removed outlier: 3.573A pdb=" N ALA E 333 " --> pdb=" O SER E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 350 removed outlier: 3.657A pdb=" N LYS E 350 " --> pdb=" O MET E 346 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 13 removed outlier: 3.593A pdb=" N TYR F 6 " --> pdb=" O GLU F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 52 Processing helix chain 'F' and resid 55 through 66 Processing helix chain 'F' and resid 111 through 118 removed outlier: 3.727A pdb=" N ASN F 115 " --> pdb=" O GLU F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 133 through 149 Processing helix chain 'F' and resid 182 through 192 removed outlier: 4.025A pdb=" N ARG F 192 " --> pdb=" O LYS F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 218 Processing helix chain 'F' and resid 230 through 241 Processing helix chain 'F' and resid 246 through 257 Processing helix chain 'F' and resid 285 through 295 Processing helix chain 'F' and resid 296 through 304 removed outlier: 4.069A pdb=" N LYS F 301 " --> pdb=" O LEU F 297 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA F 302 " --> pdb=" O HIS F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 305 through 310 removed outlier: 4.292A pdb=" N GLN F 308 " --> pdb=" O ALA F 305 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU F 309 " --> pdb=" O ARG F 306 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N VAL F 310 " --> pdb=" O SER F 307 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 305 through 310' Processing helix chain 'F' and resid 314 through 325 removed outlier: 3.586A pdb=" N ALA F 318 " --> pdb=" O THR F 314 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU F 319 " --> pdb=" O PHE F 315 " (cutoff:3.500A) Processing helix chain 'F' and resid 329 through 335 removed outlier: 3.790A pdb=" N ALA F 333 " --> pdb=" O SER F 329 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU F 334 " --> pdb=" O GLU F 330 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N HIS F 335 " --> pdb=" O GLN F 331 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 329 through 335' Processing helix chain 'F' and resid 338 through 350 removed outlier: 3.808A pdb=" N ASP F 342 " --> pdb=" O ASP F 338 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU F 343 " --> pdb=" O SER F 339 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 345 " --> pdb=" O ASN F 341 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET F 346 " --> pdb=" O ASP F 342 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU F 347 " --> pdb=" O LEU F 343 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS F 348 " --> pdb=" O ARG F 344 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 36 removed outlier: 5.426A pdb=" N THR A 21 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP A 17 " --> pdb=" O ARG A 29 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 175 removed outlier: 3.719A pdb=" N GLU A 157 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 154 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE A 198 " --> pdb=" O MET A 223 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY A 122 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 9.769A pdb=" N LEU A 226 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL A 126 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 175 removed outlier: 3.719A pdb=" N GLU A 157 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 154 " --> pdb=" O MET A 197 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE A 198 " --> pdb=" O MET A 223 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY A 122 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LEU A 123 " --> pdb=" O GLY A 260 " (cutoff:3.500A) removed outlier: 7.759A pdb=" N ILE A 262 " --> pdb=" O LEU A 123 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 125 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 8.582A pdb=" N GLN A 264 " --> pdb=" O LEU A 125 " (cutoff:3.500A) removed outlier: 8.108A pdb=" N VAL A 127 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 278 " --> pdb=" O GLN A 265 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 34 through 37 removed outlier: 3.768A pdb=" N LEU B 27 " --> pdb=" O TYR B 19 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP B 17 " --> pdb=" O ARG B 29 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 170 through 174 removed outlier: 3.619A pdb=" N THR B 225 " --> pdb=" O ILE B 200 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ALA B 224 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY B 128 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU B 123 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY B 260 " --> pdb=" O LEU B 123 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 33 through 36 removed outlier: 3.813A pdb=" N LEU C 27 " --> pdb=" O TYR C 19 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP C 17 " --> pdb=" O ARG C 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 170 through 171 removed outlier: 7.182A pdb=" N ARG C 174 " --> pdb=" O ILE C 153 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N THR C 155 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 170 through 171 removed outlier: 3.928A pdb=" N THR C 225 " --> pdb=" O ILE C 200 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N GLY C 122 " --> pdb=" O CYS C 222 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N ALA C 224 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N VAL C 124 " --> pdb=" O ALA C 224 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N LEU C 226 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N VAL C 126 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLY C 260 " --> pdb=" O LEU C 123 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LEU C 125 " --> pdb=" O GLY C 260 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 265 through 268 Processing sheet with id=AB1, first strand: chain 'D' and resid 33 through 36 removed outlier: 5.504A pdb=" N THR D 21 " --> pdb=" O PRO D 25 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASP D 17 " --> pdb=" O ARG D 29 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 170 through 175 removed outlier: 3.729A pdb=" N GLU D 157 " --> pdb=" O ARG D 174 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE D 198 " --> pdb=" O MET D 223 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY D 122 " --> pdb=" O CYS D 222 " (cutoff:3.500A) removed outlier: 9.795A pdb=" N LEU D 226 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N VAL D 126 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 170 through 175 removed outlier: 3.729A pdb=" N GLU D 157 " --> pdb=" O ARG D 174 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE D 198 " --> pdb=" O MET D 223 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY D 122 " --> pdb=" O CYS D 222 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N LEU D 123 " --> pdb=" O GLY D 260 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE D 262 " --> pdb=" O LEU D 123 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N LEU D 125 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N GLN D 264 " --> pdb=" O LEU D 125 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N VAL D 127 " --> pdb=" O GLN D 264 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N VAL D 278 " --> pdb=" O GLN D 265 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 34 through 37 removed outlier: 3.789A pdb=" N LEU E 27 " --> pdb=" O TYR E 19 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP E 17 " --> pdb=" O ARG E 29 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 170 through 174 removed outlier: 3.610A pdb=" N MET E 197 " --> pdb=" O HIS E 152 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR E 225 " --> pdb=" O ILE E 200 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS E 222 " --> pdb=" O GLY E 122 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL E 124 " --> pdb=" O CYS E 222 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ALA E 224 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY E 128 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU E 123 " --> pdb=" O LYS E 259 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N VAL E 261 " --> pdb=" O LEU E 123 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N LEU E 125 " --> pdb=" O VAL E 261 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N ALA E 263 " --> pdb=" O LEU E 125 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL E 127 " --> pdb=" O ALA E 263 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N GLN E 265 " --> pdb=" O VAL E 127 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 33 through 36 removed outlier: 3.795A pdb=" N LEU F 27 " --> pdb=" O TYR F 19 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP F 17 " --> pdb=" O ARG F 29 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 170 through 171 removed outlier: 7.228A pdb=" N ARG F 174 " --> pdb=" O ILE F 153 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N THR F 155 " --> pdb=" O ARG F 174 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 170 through 171 removed outlier: 4.083A pdb=" N THR F 225 " --> pdb=" O ILE F 200 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLY F 260 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU F 125 " --> pdb=" O GLY F 260 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 265 through 268 818 hydrogen bonds defined for protein. 2361 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: 2.83 Time building geometry restraints manager: 1.91 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: 5780 1.34 - 1.46: 2152 1.46 - 1.58: 8674 1.58 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 16762 Sorted by residual: bond pdb=" N TYR D 183 " pdb=" CA TYR D 183 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.33e-02 5.65e+03 5.24e+00 bond pdb=" N TYR A 183 " pdb=" CA TYR A 183 " ideal model delta sigma weight residual 1.456 1.483 -0.027 1.32e-02 5.74e+03 4.29e+00 bond pdb=" CA THR E 225 " pdb=" C THR E 225 " ideal model delta sigma weight residual 1.522 1.499 0.023 1.22e-02 6.72e+03 3.43e+00 bond pdb=" CA THR B 225 " pdb=" C THR B 225 " ideal model delta sigma weight residual 1.522 1.500 0.022 1.20e-02 6.94e+03 3.38e+00 bond pdb=" N ASP F 326 " pdb=" CA ASP F 326 " ideal model delta sigma weight residual 1.457 1.474 -0.017 1.29e-02 6.01e+03 1.66e+00 ... (remaining 16757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 22196 1.46 - 2.93: 327 2.93 - 4.39: 54 4.39 - 5.86: 9 5.86 - 7.32: 6 Bond angle restraints: 22592 Sorted by residual: angle pdb=" CA THR E 225 " pdb=" CB THR E 225 " pdb=" OG1 THR E 225 " ideal model delta sigma weight residual 109.60 102.44 7.16 1.50e+00 4.44e-01 2.28e+01 angle pdb=" CA THR B 225 " pdb=" CB THR B 225 " pdb=" OG1 THR B 225 " ideal model delta sigma weight residual 109.60 102.78 6.82 1.50e+00 4.44e-01 2.07e+01 angle pdb=" CA TYR A 183 " pdb=" CB TYR A 183 " pdb=" CG TYR A 183 " ideal model delta sigma weight residual 113.90 121.09 -7.19 1.80e+00 3.09e-01 1.60e+01 angle pdb=" CA TYR D 183 " pdb=" CB TYR D 183 " pdb=" CG TYR D 183 " ideal model delta sigma weight residual 113.90 120.64 -6.74 1.80e+00 3.09e-01 1.40e+01 angle pdb=" C TYR A 183 " pdb=" CA TYR A 183 " pdb=" CB TYR A 183 " ideal model delta sigma weight residual 110.01 104.26 5.75 1.80e+00 3.09e-01 1.02e+01 ... (remaining 22587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 9124 17.23 - 34.46: 932 34.46 - 51.68: 218 51.68 - 68.91: 24 68.91 - 86.14: 20 Dihedral angle restraints: 10318 sinusoidal: 4242 harmonic: 6076 Sorted by residual: dihedral pdb=" CB GLU D 2 " pdb=" CG GLU D 2 " pdb=" CD GLU D 2 " pdb=" OE1 GLU D 2 " ideal model delta sinusoidal sigma weight residual 0.00 86.14 -86.14 1 3.00e+01 1.11e-03 9.95e+00 dihedral pdb=" CB GLU A 2 " pdb=" CG GLU A 2 " pdb=" CD GLU A 2 " pdb=" OE1 GLU A 2 " ideal model delta sinusoidal sigma weight residual 0.00 85.69 -85.69 1 3.00e+01 1.11e-03 9.87e+00 dihedral pdb=" CG ARG B 145 " pdb=" CD ARG B 145 " pdb=" NE ARG B 145 " pdb=" CZ ARG B 145 " ideal model delta sinusoidal sigma weight residual -90.00 -132.44 42.44 2 1.50e+01 4.44e-03 9.72e+00 ... (remaining 10315 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1804 0.031 - 0.063: 525 0.063 - 0.094: 141 0.094 - 0.126: 128 0.126 - 0.157: 6 Chirality restraints: 2604 Sorted by residual: chirality pdb=" CA ASP A 269 " pdb=" N ASP A 269 " pdb=" C ASP A 269 " pdb=" CB ASP A 269 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA ASP D 269 " pdb=" N ASP D 269 " pdb=" C ASP D 269 " pdb=" CB ASP D 269 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CG LEU E 221 " pdb=" CB LEU E 221 " pdb=" CD1 LEU E 221 " pdb=" CD2 LEU E 221 " both_signs ideal model delta sigma weight residual False -2.59 -2.74 0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 2601 not shown) Planarity restraints: 2962 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR D 183 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C TYR D 183 " -0.034 2.00e-02 2.50e+03 pdb=" O TYR D 183 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU D 184 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 183 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.38e+00 pdb=" C TYR A 183 " -0.027 2.00e-02 2.50e+03 pdb=" O TYR A 183 " 0.010 2.00e-02 2.50e+03 pdb=" N GLU A 184 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 268 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.19e+00 pdb=" C ARG D 268 " 0.026 2.00e-02 2.50e+03 pdb=" O ARG D 268 " -0.010 2.00e-02 2.50e+03 pdb=" N ASP D 269 " -0.009 2.00e-02 2.50e+03 ... (remaining 2959 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1499 2.75 - 3.29: 16228 3.29 - 3.82: 27197 3.82 - 4.36: 31154 4.36 - 4.90: 53507 Nonbonded interactions: 129585 Sorted by model distance: nonbonded pdb=" ND2 ASN A 229 " pdb=" OE1 GLN F 249 " model vdw 2.209 3.120 nonbonded pdb=" OG SER D 205 " pdb=" OE1 GLU D 207 " model vdw 2.209 3.040 nonbonded pdb=" O GLU C 236 " pdb=" ND1 HIS C 240 " model vdw 2.246 3.120 nonbonded pdb=" O PHE C 279 " pdb=" NE2 GLN C 313 " model vdw 2.264 3.120 nonbonded pdb=" OE1 GLN C 249 " pdb=" ND2 ASN D 229 " model vdw 2.280 3.120 ... (remaining 129580 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 350) selection = (chain 'C' and resid 1 through 350) selection = chain 'D' selection = (chain 'E' and resid 1 through 350) selection = (chain 'F' and resid 1 through 350) } 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.460 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: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 16.010 Find NCS groups from input model: 0.390 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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 : 0.002 0.031 16762 Z= 0.094 Angle : 0.462 7.320 22592 Z= 0.250 Chirality : 0.039 0.157 2604 Planarity : 0.003 0.037 2962 Dihedral : 14.651 86.140 6382 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.18), residues: 2092 helix: 0.73 (0.18), residues: 904 sheet: 0.81 (0.24), residues: 484 loop : -1.40 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 294 TYR 0.021 0.001 TYR A 183 PHE 0.013 0.001 PHE D 215 HIS 0.009 0.000 HIS A 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00176 / 0.09 (16762) covalent geometry : angle 0.46207 / 0.25 (22592) hydrogen bonds : bond 0.20191 / 13.66 ( 801) hydrogen bonds : angle 6.75952 / 4.67 ( 2361) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 250 PHE cc_start: 0.9049 (t80) cc_final: 0.8662 (t80) REVERT: A 320 TYR cc_start: 0.9188 (t80) cc_final: 0.8883 (t80) REVERT: A 322 LEU cc_start: 0.9360 (mp) cc_final: 0.9086 (mp) REVERT: A 328 ILE cc_start: 0.8489 (mm) cc_final: 0.7999 (mm) REVERT: B 215 PHE cc_start: 0.8557 (m-80) cc_final: 0.8237 (m-80) REVERT: B 312 MET cc_start: 0.7902 (mmp) cc_final: 0.7584 (mmp) REVERT: B 335 HIS cc_start: 0.9562 (m90) cc_final: 0.9308 (m-70) REVERT: C 31 ASP cc_start: 0.7900 (t0) cc_final: 0.7621 (t0) REVERT: C 53 MET cc_start: 0.8633 (ppp) cc_final: 0.8412 (ppp) REVERT: C 54 MET cc_start: 0.7443 (ptp) cc_final: 0.7163 (ptt) REVERT: D 250 PHE cc_start: 0.9215 (t80) cc_final: 0.8823 (t80) REVERT: D 278 VAL cc_start: 0.8695 (t) cc_final: 0.8300 (t) REVERT: D 320 TYR cc_start: 0.9245 (t80) cc_final: 0.9022 (t80) REVERT: D 322 LEU cc_start: 0.9099 (mp) cc_final: 0.8858 (mp) REVERT: D 328 ILE cc_start: 0.8525 (mm) cc_final: 0.8237 (mm) REVERT: E 215 PHE cc_start: 0.8457 (m-80) cc_final: 0.8134 (m-80) REVERT: E 312 MET cc_start: 0.7427 (mmp) cc_final: 0.7216 (mmp) REVERT: E 320 TYR cc_start: 0.9289 (t80) cc_final: 0.8972 (t80) REVERT: F 31 ASP cc_start: 0.7765 (t0) cc_final: 0.7481 (t0) REVERT: F 53 MET cc_start: 0.8712 (ppp) cc_final: 0.8404 (ppp) REVERT: F 54 MET cc_start: 0.7227 (ptp) cc_final: 0.6940 (ptt) REVERT: F 141 MET cc_start: 0.8917 (ppp) cc_final: 0.8536 (ppp) REVERT: F 335 HIS cc_start: 0.8677 (m-70) cc_final: 0.8380 (m-70) outliers start: 0 outliers final: 0 residues processed: 195 average time/residue: 0.1286 time to fit residues: 38.5216 Evaluate side-chains 158 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 59 GLN B 173 GLN C 229 ASN C 313 GLN C 317 GLN D 51 HIS E 59 GLN ** F 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.083860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.064175 restraints weight = 84944.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.065768 restraints weight = 50446.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.066738 restraints weight = 36461.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.067574 restraints weight = 29897.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.067981 restraints weight = 25720.664| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 16762 Z= 0.299 Angle : 0.705 7.438 22592 Z= 0.368 Chirality : 0.044 0.163 2604 Planarity : 0.005 0.046 2962 Dihedral : 4.355 19.085 2308 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 1.02 % Allowed : 11.96 % Favored : 87.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.18), residues: 2092 helix: 0.57 (0.17), residues: 926 sheet: 0.65 (0.24), residues: 488 loop : -1.59 (0.22), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 66 TYR 0.027 0.003 TYR E 19 PHE 0.015 0.002 PHE E 250 HIS 0.012 0.002 HIS D 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.30 (16762) covalent geometry : angle 0.70450 / 0.37 (22592) hydrogen bonds : bond 0.04111 / 2.75 ( 801) hydrogen bonds : angle 5.16254 / 3.52 ( 2361) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.8269 (ptp) cc_final: 0.8054 (ptp) REVERT: A 207 GLU cc_start: 0.8388 (tt0) cc_final: 0.7493 (tm-30) REVERT: A 250 PHE cc_start: 0.9353 (t80) cc_final: 0.8890 (t80) REVERT: A 320 TYR cc_start: 0.9382 (t80) cc_final: 0.8942 (t80) REVERT: B 197 MET cc_start: 0.8672 (tmm) cc_final: 0.7796 (tmm) REVERT: B 312 MET cc_start: 0.8549 (mmp) cc_final: 0.7444 (mmp) REVERT: B 335 HIS cc_start: 0.9578 (m90) cc_final: 0.9358 (m90) REVERT: C 31 ASP cc_start: 0.7763 (t0) cc_final: 0.7505 (t0) REVERT: C 54 MET cc_start: 0.7922 (ptp) cc_final: 0.7713 (ptt) REVERT: C 319 LEU cc_start: 0.9839 (mt) cc_final: 0.9548 (pp) REVERT: D 10 MET cc_start: 0.9057 (tpt) cc_final: 0.8807 (tpt) REVERT: D 250 PHE cc_start: 0.9384 (t80) cc_final: 0.8998 (t80) REVERT: D 304 MET cc_start: 0.7957 (tpt) cc_final: 0.6546 (tpp) REVERT: D 312 MET cc_start: 0.4021 (mmm) cc_final: 0.3502 (mmp) REVERT: D 320 TYR cc_start: 0.9389 (t80) cc_final: 0.9034 (t80) REVERT: D 328 ILE cc_start: 0.8830 (mm) cc_final: 0.8530 (mm) REVERT: E 138 MET cc_start: 0.9037 (mmm) cc_final: 0.8749 (mmm) REVERT: E 213 MET cc_start: 0.8945 (tpp) cc_final: 0.8642 (tpp) REVERT: E 250 PHE cc_start: 0.8850 (t80) cc_final: 0.8649 (t80) REVERT: E 304 MET cc_start: 0.8399 (mmm) cc_final: 0.7978 (mmm) REVERT: E 312 MET cc_start: 0.8160 (mmp) cc_final: 0.7221 (mmp) REVERT: E 320 TYR cc_start: 0.9153 (t80) cc_final: 0.8788 (t80) REVERT: F 54 MET cc_start: 0.7813 (ptp) cc_final: 0.7571 (ptt) REVERT: F 197 MET cc_start: 0.8571 (tmm) cc_final: 0.7887 (tmm) outliers start: 18 outliers final: 6 residues processed: 164 average time/residue: 0.1299 time to fit residues: 32.5758 Evaluate side-chains 137 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 131 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 317 GLN Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 183 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 12 optimal weight: 0.6980 chunk 184 optimal weight: 2.9990 chunk 141 optimal weight: 0.9990 chunk 166 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 164 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 178 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 HIS ** F 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 313 GLN F 317 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.087646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.067824 restraints weight = 85134.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.069564 restraints weight = 46092.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.070702 restraints weight = 31709.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.071538 restraints weight = 25083.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.072089 restraints weight = 21471.914| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16762 Z= 0.154 Angle : 0.544 8.075 22592 Z= 0.285 Chirality : 0.042 0.162 2604 Planarity : 0.003 0.054 2962 Dihedral : 4.028 17.319 2308 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.30 % Allowed : 14.97 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.18), residues: 2092 helix: 0.79 (0.17), residues: 930 sheet: 0.47 (0.24), residues: 474 loop : -1.65 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 344 TYR 0.014 0.002 TYR D 6 PHE 0.010 0.001 PHE A 62 HIS 0.010 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (16762) covalent geometry : angle 0.54370 / 0.28 (22592) hydrogen bonds : bond 0.03479 / 2.34 ( 801) hydrogen bonds : angle 4.76226 / 3.26 ( 2361) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.9293 (m-80) cc_final: 0.8943 (m-80) REVERT: A 10 MET cc_start: 0.9123 (tpt) cc_final: 0.8780 (tpt) REVERT: A 54 MET cc_start: 0.7993 (ptp) cc_final: 0.7669 (ptt) REVERT: A 207 GLU cc_start: 0.8577 (tt0) cc_final: 0.7380 (tm-30) REVERT: A 250 PHE cc_start: 0.9433 (t80) cc_final: 0.8949 (t80) REVERT: A 304 MET cc_start: 0.8114 (tpt) cc_final: 0.6846 (tpp) REVERT: A 320 TYR cc_start: 0.9417 (t80) cc_final: 0.9167 (t80) REVERT: B 197 MET cc_start: 0.8801 (tmm) cc_final: 0.7628 (tmm) REVERT: B 304 MET cc_start: 0.8722 (mmm) cc_final: 0.8129 (mmm) REVERT: B 312 MET cc_start: 0.8708 (mmp) cc_final: 0.7397 (mmt) REVERT: B 335 HIS cc_start: 0.9636 (m90) cc_final: 0.9381 (m-70) REVERT: C 31 ASP cc_start: 0.8052 (t0) cc_final: 0.7661 (t0) REVERT: C 54 MET cc_start: 0.8183 (ptp) cc_final: 0.7954 (ptt) REVERT: D 6 TYR cc_start: 0.9085 (m-80) cc_final: 0.8736 (m-80) REVERT: D 250 PHE cc_start: 0.9463 (t80) cc_final: 0.8991 (t80) REVERT: D 320 TYR cc_start: 0.9442 (t80) cc_final: 0.9175 (t80) REVERT: D 328 ILE cc_start: 0.8857 (mm) cc_final: 0.8586 (mm) REVERT: E 198 ILE cc_start: 0.9250 (mp) cc_final: 0.8874 (tp) REVERT: E 209 MET cc_start: 0.8913 (tmm) cc_final: 0.8426 (tmm) REVERT: E 213 MET cc_start: 0.9189 (tpp) cc_final: 0.8815 (tpp) REVERT: E 304 MET cc_start: 0.8590 (mmm) cc_final: 0.8043 (mmm) REVERT: E 312 MET cc_start: 0.8480 (mmp) cc_final: 0.7254 (mmt) REVERT: E 320 TYR cc_start: 0.9335 (t80) cc_final: 0.8889 (t80) REVERT: F 11 LEU cc_start: 0.9232 (tp) cc_final: 0.8968 (tt) REVERT: F 31 ASP cc_start: 0.7584 (t0) cc_final: 0.7317 (t0) REVERT: F 54 MET cc_start: 0.8089 (ptp) cc_final: 0.7784 (ptt) REVERT: F 335 HIS cc_start: 0.8852 (m-70) cc_final: 0.8450 (m90) outliers start: 23 outliers final: 10 residues processed: 160 average time/residue: 0.1080 time to fit residues: 26.7705 Evaluate side-chains 143 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain B residue 10 MET Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 183 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 152 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 207 optimal weight: 0.1980 chunk 3 optimal weight: 0.1980 chunk 124 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 159 optimal weight: 0.9980 chunk 161 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 317 GLN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN E 193 GLN E 232 ASN ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.084996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.065120 restraints weight = 84856.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.066812 restraints weight = 49216.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.067909 restraints weight = 35062.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.068759 restraints weight = 28284.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.069273 restraints weight = 24362.082| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16762 Z= 0.109 Angle : 0.521 9.557 22592 Z= 0.269 Chirality : 0.041 0.158 2604 Planarity : 0.003 0.034 2962 Dihedral : 3.902 16.202 2308 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.93 % Allowed : 15.42 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.18), residues: 2092 helix: 0.91 (0.17), residues: 930 sheet: 0.37 (0.24), residues: 474 loop : -1.63 (0.21), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 344 TYR 0.008 0.001 TYR C 144 PHE 0.022 0.001 PHE E 250 HIS 0.009 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (16762) covalent geometry : angle 0.52143 / 0.27 (22592) hydrogen bonds : bond 0.03091 / 2.10 ( 801) hydrogen bonds : angle 4.57586 / 3.12 ( 2361) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.9113 (m-80) cc_final: 0.8834 (m-80) REVERT: A 207 GLU cc_start: 0.8277 (tt0) cc_final: 0.7119 (tm-30) REVERT: A 250 PHE cc_start: 0.9314 (t80) cc_final: 0.8828 (t80) REVERT: A 320 TYR cc_start: 0.9398 (t80) cc_final: 0.9159 (t80) REVERT: B 197 MET cc_start: 0.8607 (tmm) cc_final: 0.7714 (tmm) REVERT: B 304 MET cc_start: 0.8544 (mmm) cc_final: 0.8003 (mmm) REVERT: B 312 MET cc_start: 0.8814 (mmp) cc_final: 0.7441 (mmp) REVERT: C 31 ASP cc_start: 0.7773 (t0) cc_final: 0.7535 (t0) REVERT: C 209 MET cc_start: 0.8697 (mtt) cc_final: 0.8495 (ptp) REVERT: C 258 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8376 (tp) REVERT: D 6 TYR cc_start: 0.8819 (m-80) cc_final: 0.8515 (m-80) REVERT: D 250 PHE cc_start: 0.9365 (t80) cc_final: 0.8914 (t80) REVERT: D 320 TYR cc_start: 0.9408 (t80) cc_final: 0.9178 (t80) REVERT: D 328 ILE cc_start: 0.8826 (mm) cc_final: 0.8559 (mm) REVERT: E 198 ILE cc_start: 0.9186 (mp) cc_final: 0.8909 (tp) REVERT: E 209 MET cc_start: 0.8724 (tmm) cc_final: 0.8497 (tmm) REVERT: E 213 MET cc_start: 0.8995 (tpp) cc_final: 0.8679 (tpp) REVERT: E 304 MET cc_start: 0.8537 (mmm) cc_final: 0.7946 (mmm) REVERT: E 312 MET cc_start: 0.8733 (mmp) cc_final: 0.7376 (mmt) REVERT: F 11 LEU cc_start: 0.9088 (tp) cc_final: 0.8866 (tt) REVERT: F 31 ASP cc_start: 0.7359 (t0) cc_final: 0.7003 (t0) REVERT: F 54 MET cc_start: 0.7893 (ptp) cc_final: 0.7627 (ptt) REVERT: F 258 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8478 (tp) REVERT: F 312 MET cc_start: 0.5967 (tmm) cc_final: 0.5551 (tmm) REVERT: F 335 HIS cc_start: 0.8609 (m-70) cc_final: 0.8303 (m90) outliers start: 34 outliers final: 17 residues processed: 171 average time/residue: 0.1166 time to fit residues: 30.3122 Evaluate side-chains 149 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 130 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain B residue 10 MET Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 298 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 33 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 49 optimal weight: 0.7980 chunk 147 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 152 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 51 HIS A 164 HIS A 233 GLN B 173 GLN B 264 GLN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 GLN D 317 GLN ** F 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.085435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.064190 restraints weight = 85948.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.065862 restraints weight = 48342.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.066914 restraints weight = 34336.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.067687 restraints weight = 27785.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.068117 restraints weight = 24221.904| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16762 Z= 0.228 Angle : 0.639 11.117 22592 Z= 0.328 Chirality : 0.043 0.182 2604 Planarity : 0.004 0.033 2962 Dihedral : 4.255 17.745 2308 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 2.04 % Allowed : 17.06 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.18), residues: 2092 helix: 0.60 (0.17), residues: 944 sheet: 0.23 (0.24), residues: 472 loop : -1.85 (0.21), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 168 TYR 0.018 0.002 TYR F 28 PHE 0.010 0.002 PHE A 62 HIS 0.007 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.23 (16762) covalent geometry : angle 0.63909 / 0.33 (22592) hydrogen bonds : bond 0.03520 / 2.37 ( 801) hydrogen bonds : angle 4.91759 / 3.35 ( 2361) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.9377 (m-80) cc_final: 0.8933 (m-80) REVERT: A 207 GLU cc_start: 0.8665 (tt0) cc_final: 0.7636 (tm-30) REVERT: A 215 PHE cc_start: 0.9344 (m-80) cc_final: 0.9008 (m-10) REVERT: A 250 PHE cc_start: 0.9507 (t80) cc_final: 0.9042 (t80) REVERT: A 304 MET cc_start: 0.8247 (tpt) cc_final: 0.7222 (tpp) REVERT: A 312 MET cc_start: 0.5648 (mmp) cc_final: 0.5358 (mmm) REVERT: A 320 TYR cc_start: 0.9469 (t80) cc_final: 0.9191 (t80) REVERT: B 197 MET cc_start: 0.8777 (tmm) cc_final: 0.7927 (tmm) REVERT: B 304 MET cc_start: 0.8839 (mmm) cc_final: 0.8179 (tpp) REVERT: B 312 MET cc_start: 0.8819 (mmp) cc_final: 0.7418 (mmp) REVERT: B 320 TYR cc_start: 0.9240 (t80) cc_final: 0.8849 (t80) REVERT: C 31 ASP cc_start: 0.8131 (t0) cc_final: 0.7804 (t0) REVERT: C 213 MET cc_start: 0.8968 (mpp) cc_final: 0.8766 (mpp) REVERT: C 266 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8857 (mt) REVERT: D 6 TYR cc_start: 0.9117 (m-80) cc_final: 0.8703 (m-80) REVERT: D 250 PHE cc_start: 0.9509 (t80) cc_final: 0.9030 (t80) REVERT: D 304 MET cc_start: 0.8076 (tpt) cc_final: 0.7005 (tpp) REVERT: D 312 MET cc_start: 0.5550 (mmp) cc_final: 0.5225 (mmm) REVERT: D 320 TYR cc_start: 0.9469 (t80) cc_final: 0.9225 (t80) REVERT: D 328 ILE cc_start: 0.8810 (mm) cc_final: 0.8592 (mm) REVERT: E 85 PHE cc_start: 0.9164 (OUTLIER) cc_final: 0.8892 (m-10) REVERT: E 209 MET cc_start: 0.8949 (tmm) cc_final: 0.8426 (tmm) REVERT: E 213 MET cc_start: 0.9228 (tpp) cc_final: 0.8837 (tpp) REVERT: E 304 MET cc_start: 0.8817 (mmm) cc_final: 0.8095 (tpp) REVERT: E 312 MET cc_start: 0.8734 (mmp) cc_final: 0.7364 (mmp) REVERT: F 31 ASP cc_start: 0.7807 (t0) cc_final: 0.7498 (t0) REVERT: F 54 MET cc_start: 0.8424 (ptp) cc_final: 0.8109 (ptt) REVERT: F 213 MET cc_start: 0.8996 (mpp) cc_final: 0.8782 (mpp) REVERT: F 266 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.8964 (mt) outliers start: 36 outliers final: 22 residues processed: 171 average time/residue: 0.1037 time to fit residues: 27.4649 Evaluate side-chains 161 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 197 MET Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 308 GLN Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 148 HIS Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 197 MET Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 85 PHE Chi-restraints excluded: chain E residue 124 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 298 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 74 optimal weight: 3.9990 chunk 179 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 72 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 193 optimal weight: 2.9990 chunk 116 optimal weight: 0.2980 chunk 177 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 98 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 173 GLN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.086988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.067443 restraints weight = 84055.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.069128 restraints weight = 44733.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.070318 restraints weight = 30856.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.071018 restraints weight = 24340.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.071566 restraints weight = 20986.157| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.3807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 16762 Z= 0.114 Angle : 0.567 9.950 22592 Z= 0.284 Chirality : 0.042 0.186 2604 Planarity : 0.003 0.043 2962 Dihedral : 4.024 17.688 2308 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.93 % Allowed : 17.18 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.18), residues: 2092 helix: 0.72 (0.17), residues: 944 sheet: 0.48 (0.24), residues: 450 loop : -1.80 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 294 TYR 0.009 0.001 TYR B 28 PHE 0.023 0.001 PHE E 250 HIS 0.007 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (16762) covalent geometry : angle 0.56679 / 0.28 (22592) hydrogen bonds : bond 0.03022 / 2.04 ( 801) hydrogen bonds : angle 4.62197 / 3.16 ( 2361) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 140 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.9307 (m-80) cc_final: 0.8878 (m-80) REVERT: A 207 GLU cc_start: 0.8524 (tt0) cc_final: 0.7347 (tm-30) REVERT: A 215 PHE cc_start: 0.9282 (m-80) cc_final: 0.8917 (m-10) REVERT: A 250 PHE cc_start: 0.9424 (t80) cc_final: 0.8954 (t80) REVERT: A 304 MET cc_start: 0.8148 (tpt) cc_final: 0.7189 (tpp) REVERT: A 312 MET cc_start: 0.5962 (mmp) cc_final: 0.5697 (mmm) REVERT: A 320 TYR cc_start: 0.9422 (t80) cc_final: 0.9170 (t80) REVERT: B 138 MET cc_start: 0.9364 (tpp) cc_final: 0.9139 (tpp) REVERT: B 197 MET cc_start: 0.8784 (tmm) cc_final: 0.7918 (tmm) REVERT: B 304 MET cc_start: 0.8696 (mmm) cc_final: 0.7945 (tpp) REVERT: B 312 MET cc_start: 0.8862 (mmp) cc_final: 0.7478 (mmp) REVERT: C 31 ASP cc_start: 0.8039 (t0) cc_final: 0.7714 (t0) REVERT: C 209 MET cc_start: 0.9058 (mtt) cc_final: 0.8804 (ptp) REVERT: C 266 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8828 (mt) REVERT: D 6 TYR cc_start: 0.8969 (m-80) cc_final: 0.8624 (m-80) REVERT: D 250 PHE cc_start: 0.9416 (t80) cc_final: 0.8977 (t80) REVERT: D 320 TYR cc_start: 0.9436 (t80) cc_final: 0.9176 (t80) REVERT: D 328 ILE cc_start: 0.8849 (mm) cc_final: 0.8555 (mm) REVERT: E 209 MET cc_start: 0.8860 (tmm) cc_final: 0.8459 (tmm) REVERT: E 211 TYR cc_start: 0.9439 (m-80) cc_final: 0.9147 (m-80) REVERT: E 213 MET cc_start: 0.9225 (tpp) cc_final: 0.8807 (tpp) REVERT: E 304 MET cc_start: 0.8701 (mmm) cc_final: 0.7987 (tpp) REVERT: E 312 MET cc_start: 0.8980 (mmp) cc_final: 0.7598 (mmp) REVERT: F 31 ASP cc_start: 0.7780 (t0) cc_final: 0.7420 (t0) REVERT: F 54 MET cc_start: 0.8386 (ptp) cc_final: 0.8050 (ptt) REVERT: F 209 MET cc_start: 0.9179 (ptp) cc_final: 0.8939 (ptp) REVERT: F 258 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8532 (mt) REVERT: F 266 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8941 (mt) REVERT: F 335 HIS cc_start: 0.8857 (m-70) cc_final: 0.8454 (m90) outliers start: 34 outliers final: 20 residues processed: 169 average time/residue: 0.1056 time to fit residues: 27.6322 Evaluate side-chains 157 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain F residue 258 LEU Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 298 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 153 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 200 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 120 optimal weight: 0.0870 chunk 81 optimal weight: 0.2980 chunk 204 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 173 GLN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 313 GLN ** F 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.088009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.068493 restraints weight = 84467.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.070214 restraints weight = 45198.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.071298 restraints weight = 31103.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.072116 restraints weight = 24576.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.072561 restraints weight = 21093.605| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16762 Z= 0.114 Angle : 0.582 13.136 22592 Z= 0.289 Chirality : 0.042 0.180 2604 Planarity : 0.003 0.034 2962 Dihedral : 3.954 17.337 2308 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.10 % Allowed : 17.40 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.18), residues: 2092 helix: 0.76 (0.17), residues: 942 sheet: 0.48 (0.24), residues: 450 loop : -1.80 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 294 TYR 0.013 0.001 TYR B 320 PHE 0.021 0.001 PHE E 250 HIS 0.012 0.001 HIS A 276 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (16762) covalent geometry : angle 0.58211 / 0.29 (22592) hydrogen bonds : bond 0.03000 / 2.03 ( 801) hydrogen bonds : angle 4.61159 / 3.15 ( 2361) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.7759 (ptp) cc_final: 0.7129 (ptp) REVERT: A 250 PHE cc_start: 0.9417 (t80) cc_final: 0.8967 (t80) REVERT: A 304 MET cc_start: 0.8137 (tpt) cc_final: 0.7118 (tpp) REVERT: A 312 MET cc_start: 0.6030 (mmp) cc_final: 0.5774 (mmm) REVERT: A 320 TYR cc_start: 0.9422 (t80) cc_final: 0.9217 (t80) REVERT: B 197 MET cc_start: 0.8767 (tmm) cc_final: 0.7897 (tmm) REVERT: B 213 MET cc_start: 0.9024 (tpt) cc_final: 0.8796 (tpp) REVERT: B 304 MET cc_start: 0.8738 (mmm) cc_final: 0.7984 (tpp) REVERT: B 312 MET cc_start: 0.8840 (mmp) cc_final: 0.7494 (mmp) REVERT: C 31 ASP cc_start: 0.8026 (t0) cc_final: 0.7702 (t0) REVERT: C 266 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8811 (mt) REVERT: D 6 TYR cc_start: 0.8948 (m-80) cc_final: 0.8616 (m-80) REVERT: D 53 MET cc_start: 0.8469 (ttp) cc_final: 0.8199 (tmm) REVERT: D 250 PHE cc_start: 0.9407 (t80) cc_final: 0.8939 (t80) REVERT: D 320 TYR cc_start: 0.9430 (t80) cc_final: 0.9199 (t80) REVERT: E 209 MET cc_start: 0.8863 (tmm) cc_final: 0.8492 (tmm) REVERT: E 211 TYR cc_start: 0.9437 (m-80) cc_final: 0.9151 (m-80) REVERT: E 213 MET cc_start: 0.9235 (tpp) cc_final: 0.8855 (tpp) REVERT: E 304 MET cc_start: 0.8745 (mmm) cc_final: 0.8045 (mmm) REVERT: E 312 MET cc_start: 0.8977 (mmp) cc_final: 0.7616 (mmp) REVERT: F 31 ASP cc_start: 0.7767 (t0) cc_final: 0.7399 (t0) REVERT: F 54 MET cc_start: 0.8487 (ptp) cc_final: 0.8120 (ptt) REVERT: F 209 MET cc_start: 0.9184 (OUTLIER) cc_final: 0.8975 (ptp) REVERT: F 266 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8920 (mt) REVERT: F 335 HIS cc_start: 0.8857 (m-70) cc_final: 0.8493 (m90) outliers start: 37 outliers final: 25 residues processed: 173 average time/residue: 0.1129 time to fit residues: 29.5812 Evaluate side-chains 163 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 306 ARG Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain F residue 209 MET Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 279 PHE Chi-restraints excluded: chain F residue 298 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 201 optimal weight: 6.9990 chunk 206 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 176 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 141 optimal weight: 0.0970 chunk 134 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 208 optimal weight: 9.9990 chunk 77 optimal weight: 0.5980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 37 GLN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.086399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.066972 restraints weight = 85761.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.068643 restraints weight = 45845.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.069710 restraints weight = 31614.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.070482 restraints weight = 25141.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.071000 restraints weight = 21591.485| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16762 Z= 0.202 Angle : 0.647 11.247 22592 Z= 0.327 Chirality : 0.043 0.259 2604 Planarity : 0.003 0.033 2962 Dihedral : 4.184 17.311 2308 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.21 % Allowed : 17.40 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.18), residues: 2092 helix: 0.59 (0.17), residues: 944 sheet: 0.13 (0.24), residues: 476 loop : -1.76 (0.22), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 168 TYR 0.013 0.002 TYR F 28 PHE 0.021 0.001 PHE B 250 HIS 0.010 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (16762) covalent geometry : angle 0.64734 / 0.33 (22592) hydrogen bonds : bond 0.03292 / 2.23 ( 801) hydrogen bonds : angle 4.86857 / 3.33 ( 2361) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.9311 (m-10) cc_final: 0.8869 (m-80) REVERT: A 215 PHE cc_start: 0.9350 (m-80) cc_final: 0.8936 (m-10) REVERT: A 235 LEU cc_start: 0.9767 (tp) cc_final: 0.9548 (mp) REVERT: A 250 PHE cc_start: 0.9438 (t80) cc_final: 0.8962 (t80) REVERT: A 258 LEU cc_start: 0.9479 (tt) cc_final: 0.9259 (mp) REVERT: A 304 MET cc_start: 0.8272 (tpt) cc_final: 0.7476 (tpp) REVERT: A 312 MET cc_start: 0.6689 (mmp) cc_final: 0.6389 (mmm) REVERT: A 320 TYR cc_start: 0.9431 (t80) cc_final: 0.9222 (t80) REVERT: B 85 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8875 (m-10) REVERT: B 197 MET cc_start: 0.8788 (tmm) cc_final: 0.7974 (tmm) REVERT: B 213 MET cc_start: 0.9037 (tpt) cc_final: 0.8803 (tpp) REVERT: B 304 MET cc_start: 0.8789 (mmm) cc_final: 0.8024 (tpp) REVERT: B 312 MET cc_start: 0.8911 (mmp) cc_final: 0.7594 (mmp) REVERT: C 31 ASP cc_start: 0.8082 (t0) cc_final: 0.7759 (t0) REVERT: C 258 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8386 (mt) REVERT: C 266 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8823 (mt) REVERT: D 6 TYR cc_start: 0.9030 (m-80) cc_final: 0.8606 (m-80) REVERT: D 250 PHE cc_start: 0.9461 (t80) cc_final: 0.9028 (t80) REVERT: D 304 MET cc_start: 0.8182 (tpt) cc_final: 0.7150 (tpp) REVERT: D 312 MET cc_start: 0.5893 (mmp) cc_final: 0.5569 (mmp) REVERT: D 320 TYR cc_start: 0.9420 (t80) cc_final: 0.9199 (t80) REVERT: E 209 MET cc_start: 0.8808 (tmm) cc_final: 0.8483 (tmm) REVERT: E 213 MET cc_start: 0.9223 (tpp) cc_final: 0.8812 (tpp) REVERT: E 304 MET cc_start: 0.8838 (mmm) cc_final: 0.8130 (tpp) REVERT: E 312 MET cc_start: 0.9021 (mmp) cc_final: 0.7633 (mmp) REVERT: F 31 ASP cc_start: 0.7760 (t0) cc_final: 0.7424 (t0) REVERT: F 54 MET cc_start: 0.8642 (ptp) cc_final: 0.8345 (ptt) REVERT: F 207 GLU cc_start: 0.9583 (OUTLIER) cc_final: 0.9349 (pm20) REVERT: F 258 LEU cc_start: 0.8592 (tp) cc_final: 0.8294 (mp) REVERT: F 266 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8918 (mt) REVERT: F 306 ARG cc_start: 0.9225 (ptp-170) cc_final: 0.8963 (ptp-170) outliers start: 39 outliers final: 25 residues processed: 171 average time/residue: 0.1110 time to fit residues: 29.6073 Evaluate side-chains 157 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 127 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 85 PHE Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 148 HIS Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 279 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 130 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 199 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 165 optimal weight: 0.5980 chunk 196 optimal weight: 0.7980 chunk 206 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 118 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 193 GLN ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 313 GLN ** F 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.070107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.049867 restraints weight = 86350.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.051565 restraints weight = 45693.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.052697 restraints weight = 31519.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.053410 restraints weight = 25012.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.053796 restraints weight = 21752.085| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16762 Z= 0.169 Angle : 0.639 11.625 22592 Z= 0.318 Chirality : 0.043 0.242 2604 Planarity : 0.003 0.033 2962 Dihedral : 4.186 17.929 2308 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 1.81 % Allowed : 18.48 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.18), residues: 2092 helix: 0.59 (0.17), residues: 944 sheet: 0.29 (0.25), residues: 448 loop : -1.79 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 168 TYR 0.012 0.002 TYR E 28 PHE 0.017 0.001 PHE E 250 HIS 0.011 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (16762) covalent geometry : angle 0.63856 / 0.32 (22592) hydrogen bonds : bond 0.03162 / 2.13 ( 801) hydrogen bonds : angle 4.79808 / 3.28 ( 2361) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.9297 (m-10) cc_final: 0.8874 (m-80) REVERT: A 250 PHE cc_start: 0.9461 (t80) cc_final: 0.8996 (t80) REVERT: A 258 LEU cc_start: 0.9457 (tt) cc_final: 0.9151 (pp) REVERT: A 304 MET cc_start: 0.8373 (tpt) cc_final: 0.7569 (tpp) REVERT: A 312 MET cc_start: 0.6567 (mmp) cc_final: 0.6315 (mmm) REVERT: A 320 TYR cc_start: 0.9469 (t80) cc_final: 0.9261 (t80) REVERT: B 197 MET cc_start: 0.8730 (tmm) cc_final: 0.7854 (tmm) REVERT: B 304 MET cc_start: 0.8809 (mmm) cc_final: 0.8160 (tpp) REVERT: B 312 MET cc_start: 0.8975 (mmp) cc_final: 0.7717 (mmp) REVERT: C 31 ASP cc_start: 0.8074 (t0) cc_final: 0.7737 (t0) REVERT: C 258 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8400 (mt) REVERT: C 266 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8747 (mt) REVERT: D 6 TYR cc_start: 0.9045 (m-80) cc_final: 0.8605 (m-80) REVERT: D 250 PHE cc_start: 0.9446 (t80) cc_final: 0.9003 (t80) REVERT: D 304 MET cc_start: 0.8230 (tpt) cc_final: 0.7152 (tpp) REVERT: D 320 TYR cc_start: 0.9436 (t80) cc_final: 0.9213 (t80) REVERT: E 213 MET cc_start: 0.9202 (tpp) cc_final: 0.8804 (tpp) REVERT: E 304 MET cc_start: 0.8823 (mmm) cc_final: 0.8157 (tpp) REVERT: E 312 MET cc_start: 0.9054 (mmp) cc_final: 0.7724 (mmp) REVERT: F 31 ASP cc_start: 0.7785 (t0) cc_final: 0.7425 (t0) REVERT: F 54 MET cc_start: 0.8682 (ptp) cc_final: 0.8350 (ptt) REVERT: F 207 GLU cc_start: 0.9614 (OUTLIER) cc_final: 0.9372 (pm20) REVERT: F 266 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8871 (mt) REVERT: F 335 HIS cc_start: 0.8954 (m-70) cc_final: 0.8523 (m-70) outliers start: 32 outliers final: 25 residues processed: 164 average time/residue: 0.1158 time to fit residues: 28.8948 Evaluate side-chains 159 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 130 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 148 HIS Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain A residue 310 VAL Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 281 VAL Chi-restraints excluded: chain D residue 306 ARG Chi-restraints excluded: chain E residue 125 LEU Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 279 PHE Chi-restraints excluded: chain F residue 298 HIS Chi-restraints excluded: chain F residue 310 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 21 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 177 optimal weight: 0.0000 chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 24 optimal weight: 0.0980 chunk 92 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 95 optimal weight: 5.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.088120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.066233 restraints weight = 84940.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.067997 restraints weight = 48102.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.069066 restraints weight = 34311.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.069850 restraints weight = 27828.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.070311 restraints weight = 24359.921| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16762 Z= 0.112 Angle : 0.627 12.044 22592 Z= 0.308 Chirality : 0.043 0.229 2604 Planarity : 0.003 0.033 2962 Dihedral : 4.063 18.992 2308 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.53 % Allowed : 18.71 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.18), residues: 2092 helix: 0.67 (0.17), residues: 936 sheet: 0.34 (0.24), residues: 446 loop : -1.78 (0.21), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 74 TYR 0.008 0.001 TYR C 320 PHE 0.017 0.001 PHE E 250 HIS 0.011 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (16762) covalent geometry : angle 0.62685 / 0.31 (22592) hydrogen bonds : bond 0.02934 / 1.99 ( 801) hydrogen bonds : angle 4.67442 / 3.20 ( 2361) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4184 Ramachandran restraints generated. 2092 Oldfield, 0 Emsley, 2092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 TYR cc_start: 0.9302 (m-10) cc_final: 0.8836 (m-80) REVERT: A 250 PHE cc_start: 0.9461 (t80) cc_final: 0.8994 (t80) REVERT: A 258 LEU cc_start: 0.9455 (tt) cc_final: 0.9121 (pp) REVERT: A 304 MET cc_start: 0.8379 (tpt) cc_final: 0.7559 (tpp) REVERT: A 312 MET cc_start: 0.6134 (mmp) cc_final: 0.5872 (mmm) REVERT: A 320 TYR cc_start: 0.9507 (t80) cc_final: 0.9293 (t80) REVERT: B 197 MET cc_start: 0.8730 (tmm) cc_final: 0.7963 (tmm) REVERT: B 304 MET cc_start: 0.8819 (mmm) cc_final: 0.8183 (mmm) REVERT: B 312 MET cc_start: 0.8783 (mmp) cc_final: 0.7508 (mmp) REVERT: C 31 ASP cc_start: 0.8158 (t0) cc_final: 0.7817 (t0) REVERT: C 266 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8736 (mt) REVERT: D 6 TYR cc_start: 0.9043 (m-80) cc_final: 0.8597 (m-80) REVERT: D 250 PHE cc_start: 0.9454 (t80) cc_final: 0.9001 (t80) REVERT: D 304 MET cc_start: 0.8220 (tpt) cc_final: 0.7216 (tpp) REVERT: D 320 TYR cc_start: 0.9477 (t80) cc_final: 0.9272 (t80) REVERT: E 211 TYR cc_start: 0.9420 (m-80) cc_final: 0.9178 (m-80) REVERT: E 213 MET cc_start: 0.9247 (tpp) cc_final: 0.8803 (tpp) REVERT: E 304 MET cc_start: 0.8891 (mmm) cc_final: 0.8224 (mmm) REVERT: E 312 MET cc_start: 0.9009 (mmp) cc_final: 0.7834 (mmp) REVERT: F 31 ASP cc_start: 0.7849 (t0) cc_final: 0.7461 (t0) REVERT: F 54 MET cc_start: 0.8706 (ptp) cc_final: 0.8376 (ptt) REVERT: F 207 GLU cc_start: 0.9604 (OUTLIER) cc_final: 0.9345 (pm20) REVERT: F 266 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8866 (mt) REVERT: F 306 ARG cc_start: 0.9294 (ptp-170) cc_final: 0.9034 (ptp-170) outliers start: 27 outliers final: 21 residues processed: 161 average time/residue: 0.1074 time to fit residues: 26.5994 Evaluate side-chains 154 residues out of total 1764 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 HIS Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 183 TYR Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 306 ARG Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 279 PHE Chi-restraints excluded: chain D residue 13 HIS Chi-restraints excluded: chain D residue 26 ILE Chi-restraints excluded: chain D residue 72 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 183 TYR Chi-restraints excluded: chain D residue 306 ARG Chi-restraints excluded: chain E residue 300 LEU Chi-restraints excluded: chain F residue 207 GLU Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain F residue 279 PHE Chi-restraints excluded: chain F residue 298 HIS Chi-restraints excluded: chain F residue 310 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 88 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 11 optimal weight: 0.0670 chunk 124 optimal weight: 0.5980 chunk 52 optimal weight: 3.9990 chunk 209 optimal weight: 0.7980 chunk 189 optimal weight: 3.9990 chunk 117 optimal weight: 0.4980 chunk 92 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 157 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.083334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.063752 restraints weight = 85154.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.065465 restraints weight = 46809.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.066664 restraints weight = 32777.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.067362 restraints weight = 26085.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.067807 restraints weight = 22562.880| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16762 Z= 0.115 Angle : 0.663 13.320 22592 Z= 0.322 Chirality : 0.043 0.314 2604 Planarity : 0.003 0.033 2962 Dihedral : 4.021 18.906 2308 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 1.53 % Allowed : 19.05 % Favored : 79.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.18), residues: 2092 helix: 0.61 (0.17), residues: 936 sheet: 0.38 (0.24), residues: 448 loop : -1.75 (0.21), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 206 TYR 0.007 0.001 TYR C 320 PHE 0.018 0.001 PHE E 250 HIS 0.011 0.001 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (16762) covalent geometry : angle 0.66262 / 0.32 (22592) hydrogen bonds : bond 0.02930 / 1.97 ( 801) hydrogen bonds : angle 4.67785 / 3.21 ( 2361) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2404.57 seconds wall clock time: 42 minutes 29.14 seconds (2549.14 seconds total)