Starting phenix.real_space_refine on Wed Sep 17 15:51:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ark_11885/09_2025/7ark_11885.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ark_11885/09_2025/7ark_11885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ark_11885/09_2025/7ark_11885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ark_11885/09_2025/7ark_11885.map" model { file = "/net/cci-nas-00/data/ceres_data/7ark_11885/09_2025/7ark_11885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ark_11885/09_2025/7ark_11885.cif" } resolution = 4.1 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= 0.003 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 51 5.16 5 C 6070 2.51 5 N 1686 2.21 5 O 1755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9570 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 2922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2922 Classifications: {'peptide': 386} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 365} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 3125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3125 Classifications: {'peptide': 405} Link IDs: {'PTRANS': 14, 'TRANS': 390} Chain breaks: 1 Chain: "D" Number of atoms: 1730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1730 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 8, 'TRANS': 217} Chain: "F" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1729 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 8, 'TRANS': 217} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.51, per 1000 atoms: 0.26 Number of scatterers: 9570 At special positions: 0 Unit cell: (126.75, 90.246, 138.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 51 16.00 P 6 15.00 Mg 2 11.99 O 1755 8.00 N 1686 7.00 C 6070 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: 0.96 Conformation dependent library (CDL) restraints added in 411.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2272 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 9 sheets defined 34.0% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.620A pdb=" N ILE C 32 " --> pdb=" O TRP C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 59 removed outlier: 3.695A pdb=" N GLU C 54 " --> pdb=" O GLY C 50 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 55 " --> pdb=" O PHE C 51 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLN C 56 " --> pdb=" O GLU C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 200 removed outlier: 3.979A pdb=" N TYR C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU C 200 " --> pdb=" O VAL C 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 195 through 200' Processing helix chain 'C' and resid 234 through 238 removed outlier: 4.165A pdb=" N GLN C 237 " --> pdb=" O SER C 234 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN C 238 " --> pdb=" O LEU C 235 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 234 through 238' Processing helix chain 'C' and resid 255 through 272 removed outlier: 4.295A pdb=" N GLU C 263 " --> pdb=" O ALA C 259 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LYS C 264 " --> pdb=" O VAL C 260 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN C 265 " --> pdb=" O ARG C 261 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU C 269 " --> pdb=" O ASN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 287 removed outlier: 3.553A pdb=" N ALA C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA C 279 " --> pdb=" O VAL C 275 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N PHE C 280 " --> pdb=" O ALA C 276 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 removed outlier: 3.883A pdb=" N GLU C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 312 No H-bonds generated for 'chain 'C' and resid 310 through 312' Processing helix chain 'C' and resid 313 through 318 removed outlier: 4.008A pdb=" N GLN C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 319 through 338 removed outlier: 3.858A pdb=" N ILE C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA C 326 " --> pdb=" O GLY C 322 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE C 327 " --> pdb=" O ILE C 323 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA C 331 " --> pdb=" O ILE C 327 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 336 " --> pdb=" O LEU C 332 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 379 removed outlier: 4.025A pdb=" N ILE C 366 " --> pdb=" O PRO C 362 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N VAL C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N LEU C 370 " --> pdb=" O ILE C 366 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET C 373 " --> pdb=" O ALA C 369 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ALA C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU C 377 " --> pdb=" O MET C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 385 Processing helix chain 'E' and resid 23 through 34 removed outlier: 3.676A pdb=" N VAL E 28 " --> pdb=" O SER E 24 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE E 29 " --> pdb=" O LEU E 25 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N SER E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ILE E 32 " --> pdb=" O VAL E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 40 removed outlier: 4.020A pdb=" N VAL E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 59 removed outlier: 3.593A pdb=" N SER E 46 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN E 49 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 85 removed outlier: 3.512A pdb=" N LEU E 82 " --> pdb=" O TRP E 78 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP E 83 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N VAL E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 159 removed outlier: 3.941A pdb=" N ALA E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 215 removed outlier: 3.677A pdb=" N GLN E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR E 214 " --> pdb=" O ASP E 210 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU E 215 " --> pdb=" O ALA E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 267 removed outlier: 3.519A pdb=" N ARG E 263 " --> pdb=" O GLY E 259 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP E 264 " --> pdb=" O TYR E 260 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ILE E 265 " --> pdb=" O MET E 261 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLN E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 274 removed outlier: 3.640A pdb=" N TYR E 273 " --> pdb=" O ALA E 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 284 Processing helix chain 'E' and resid 285 through 294 removed outlier: 3.677A pdb=" N THR E 290 " --> pdb=" O ASN E 286 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU E 291 " --> pdb=" O ILE E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 317 removed outlier: 3.587A pdb=" N ARG E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 318 through 343 removed outlier: 3.750A pdb=" N TYR E 322 " --> pdb=" O ILE E 318 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLY E 323 " --> pdb=" O PHE E 319 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU E 324 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALA E 326 " --> pdb=" O TYR E 322 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N PHE E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL E 335 " --> pdb=" O SER E 331 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ILE E 336 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE E 337 " --> pdb=" O CYS E 333 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL E 339 " --> pdb=" O VAL E 335 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N VAL E 340 " --> pdb=" O ILE E 336 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VAL E 341 " --> pdb=" O ILE E 337 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER E 342 " --> pdb=" O GLY E 338 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU E 343 " --> pdb=" O VAL E 339 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 386 removed outlier: 3.655A pdb=" N THR E 386 " --> pdb=" O TYR E 382 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 395 removed outlier: 3.822A pdb=" N LEU E 393 " --> pdb=" O LEU E 389 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 401 removed outlier: 3.687A pdb=" N ARG E 401 " --> pdb=" O TYR E 397 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 55 removed outlier: 3.554A pdb=" N LEU D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 109 removed outlier: 3.959A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 113 removed outlier: 3.704A pdb=" N LEU D 113 " --> pdb=" O MET D 110 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 110 through 113' Processing helix chain 'D' and resid 118 through 120 No H-bonds generated for 'chain 'D' and resid 118 through 120' Processing helix chain 'D' and resid 121 through 134 removed outlier: 3.766A pdb=" N ALA D 126 " --> pdb=" O ILE D 122 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU D 127 " --> pdb=" O ASN D 123 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N MET D 129 " --> pdb=" O ARG D 125 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LEU D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA D 132 " --> pdb=" O GLU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 157 removed outlier: 3.563A pdb=" N ARG D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ILE D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA D 157 " --> pdb=" O ARG D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 186 removed outlier: 3.632A pdb=" N ASP D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER D 183 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ILE D 184 " --> pdb=" O ASN D 180 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN D 186 " --> pdb=" O ASP D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 195 removed outlier: 3.721A pdb=" N LEU D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN D 192 " --> pdb=" O LEU D 188 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN D 195 " --> pdb=" O LEU D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 212 removed outlier: 3.517A pdb=" N ARG D 211 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 53 removed outlier: 3.539A pdb=" N LEU F 51 " --> pdb=" O GLY F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 77 through 85 removed outlier: 3.776A pdb=" N LYS F 81 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ALA F 82 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU F 83 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU F 84 " --> pdb=" O LYS F 81 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ARG F 85 " --> pdb=" O ALA F 82 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 109 Processing helix chain 'F' and resid 109 through 115 removed outlier: 3.747A pdb=" N ILE F 114 " --> pdb=" O MET F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 134 removed outlier: 3.886A pdb=" N ARG F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ALA F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU F 127 " --> pdb=" O ASN F 123 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU F 128 " --> pdb=" O SER F 124 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET F 129 " --> pdb=" O ARG F 125 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU F 130 " --> pdb=" O ALA F 126 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LYS F 131 " --> pdb=" O LEU F 127 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA F 132 " --> pdb=" O GLU F 128 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL F 133 " --> pdb=" O MET F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 150 through 160 removed outlier: 3.583A pdb=" N ALA F 155 " --> pdb=" O ARG F 151 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ILE F 156 " --> pdb=" O GLN F 152 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ALA F 159 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU F 160 " --> pdb=" O ILE F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 189 removed outlier: 3.726A pdb=" N ASP F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N SER F 183 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN F 186 " --> pdb=" O ASP F 182 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU F 187 " --> pdb=" O SER F 183 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY F 189 " --> pdb=" O PHE F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 212 removed outlier: 3.751A pdb=" N LYS F 210 " --> pdb=" O GLN F 207 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG F 211 " --> pdb=" O LEU F 208 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 94 through 96 removed outlier: 3.502A pdb=" N ALA C 94 " --> pdb=" O ARG C 223 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ILE C 96 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLY C 221 " --> pdb=" O ILE C 96 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 109 through 113 removed outlier: 3.718A pdb=" N ALA C 110 " --> pdb=" O LEU C 103 " (cutoff:3.500A) removed outlier: 9.772A pdb=" N ASP C 100 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG C 163 " --> pdb=" O GLN C 104 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL C 164 " --> pdb=" O ARG C 182 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ARG C 182 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL C 166 " --> pdb=" O SER C 180 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N SER C 180 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N SER C 168 " --> pdb=" O ILE C 178 " (cutoff:3.500A) removed outlier: 9.341A pdb=" N ILE C 178 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 116 through 117 removed outlier: 6.804A pdb=" N VAL C 203 " --> pdb=" O ILE C 117 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 143 through 146 removed outlier: 3.588A pdb=" N ILE C 187 " --> pdb=" O VAL C 144 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N LEU C 146 " --> pdb=" O ILE C 187 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR C 189 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 66 through 68 removed outlier: 3.532A pdb=" N GLY E 66 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU E 226 " --> pdb=" O GLY E 66 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS E 227 " --> pdb=" O ALA E 93 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA E 93 " --> pdb=" O LYS E 227 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE E 98 " --> pdb=" O GLY E 117 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ALA E 204 " --> pdb=" O GLN E 114 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ILE E 206 " --> pdb=" O LYS E 116 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N PHE E 203 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY E 151 " --> pdb=" O PHE E 203 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ILE E 148 " --> pdb=" O GLY E 191 " (cutoff:3.500A) removed outlier: 8.076A pdb=" N LEU E 193 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE E 150 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS E 183 " --> pdb=" O ILE E 170 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE E 170 " --> pdb=" O LYS E 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 30 through 32 removed outlier: 3.819A pdb=" N PHE D 30 " --> pdb=" O CYS D 8 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS D 8 " --> pdb=" O PHE D 30 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN D 7 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE D 67 " --> pdb=" O GLN D 7 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ASP D 9 " --> pdb=" O ASP D 65 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASP D 65 " --> pdb=" O ASP D 9 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 166 through 170 removed outlier: 6.289A pdb=" N VAL D 167 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N VAL D 202 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ALA D 169 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N MET D 38 " --> pdb=" O VAL D 201 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N THR D 203 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ILE D 40 " --> pdb=" O THR D 203 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ALA D 39 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N MET D 218 " --> pdb=" O ALA D 39 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL D 41 " --> pdb=" O MET D 218 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'F' and resid 6 through 9 removed outlier: 3.914A pdb=" N ASP F 9 " --> pdb=" O ASP F 65 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASP F 65 " --> pdb=" O ASP F 9 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 90 through 91 removed outlier: 3.582A pdb=" N LEU F 168 " --> pdb=" O GLY F 90 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL F 167 " --> pdb=" O ALA F 198 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU F 200 " --> pdb=" O VAL F 167 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL F 202 " --> pdb=" O ALA F 169 " (cutoff:3.500A) 166 hydrogen bonds defined for protein. 474 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: 1.31 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3192 1.35 - 1.46: 1978 1.46 - 1.58: 4456 1.58 - 1.70: 6 1.70 - 1.82: 96 Bond restraints: 9728 Sorted by residual: bond pdb=" O3A ANP F 401 " pdb=" PB ANP F 401 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.23e+01 bond pdb=" O3A ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.03e+01 bond pdb=" C LEU E 129 " pdb=" N PRO E 130 " ideal model delta sigma weight residual 1.334 1.382 -0.049 8.40e-03 1.42e+04 3.38e+01 bond pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 1.795 1.693 0.102 2.00e-02 2.50e+03 2.58e+01 ... (remaining 9723 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.40: 13033 3.40 - 6.80: 124 6.80 - 10.19: 22 10.19 - 13.59: 1 13.59 - 16.99: 2 Bond angle restraints: 13182 Sorted by residual: angle pdb=" PB ANP F 401 " pdb=" N3B ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sigma weight residual 126.95 109.96 16.99 3.00e+00 1.11e-01 3.21e+01 angle pdb=" PB ANP D 401 " pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 126.95 111.05 15.90 3.00e+00 1.11e-01 2.81e+01 angle pdb=" C PRO F 61 " pdb=" N THR F 62 " pdb=" CA THR F 62 " ideal model delta sigma weight residual 121.54 130.43 -8.89 1.91e+00 2.74e-01 2.17e+01 angle pdb=" C LEU E 158 " pdb=" N LYS E 159 " pdb=" CA LYS E 159 " ideal model delta sigma weight residual 121.54 129.23 -7.69 1.91e+00 2.74e-01 1.62e+01 angle pdb=" C ILE E 302 " pdb=" N ALA E 303 " pdb=" CA ALA E 303 " ideal model delta sigma weight residual 120.38 125.74 -5.36 1.37e+00 5.33e-01 1.53e+01 ... (remaining 13177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.75: 5515 21.75 - 43.49: 347 43.49 - 65.24: 32 65.24 - 86.98: 22 86.98 - 108.73: 3 Dihedral angle restraints: 5919 sinusoidal: 2389 harmonic: 3530 Sorted by residual: dihedral pdb=" O1B ANP F 401 " pdb=" N3B ANP F 401 " pdb=" PB ANP F 401 " pdb=" PG ANP F 401 " ideal model delta sinusoidal sigma weight residual 35.15 -73.58 108.73 1 3.00e+01 1.11e-03 1.41e+01 dihedral pdb=" O1A ANP D 401 " pdb=" O3A ANP D 401 " pdb=" PA ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sinusoidal sigma weight residual 83.11 -168.48 -108.41 1 3.00e+01 1.11e-03 1.40e+01 dihedral pdb=" CA GLY D 47 " pdb=" C GLY D 47 " pdb=" N LYS D 48 " pdb=" CA LYS D 48 " ideal model delta harmonic sigma weight residual 180.00 -162.75 -17.25 0 5.00e+00 4.00e-02 1.19e+01 ... (remaining 5916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1216 0.055 - 0.110: 268 0.110 - 0.165: 45 0.165 - 0.220: 5 0.220 - 0.275: 2 Chirality restraints: 1536 Sorted by residual: chirality pdb=" C3' ANP F 401 " pdb=" C2' ANP F 401 " pdb=" C4' ANP F 401 " pdb=" O3' ANP F 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' ANP D 401 " pdb=" C2' ANP D 401 " pdb=" C4' ANP D 401 " pdb=" O3' ANP D 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA THR F 62 " pdb=" N THR F 62 " pdb=" C THR F 62 " pdb=" CB THR F 62 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.40e-01 ... (remaining 1533 not shown) Planarity restraints: 1682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 382 " 0.032 5.00e-02 4.00e+02 4.79e-02 3.68e+00 pdb=" N PRO C 383 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO C 383 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 383 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 397 " -0.031 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO E 398 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO E 398 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO E 398 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE E 206 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO E 207 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 207 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 207 " -0.025 5.00e-02 4.00e+02 ... (remaining 1679 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 476 2.73 - 3.27: 8374 3.27 - 3.82: 14687 3.82 - 4.36: 17119 4.36 - 4.90: 28338 Nonbonded interactions: 68994 Sorted by model distance: nonbonded pdb=" O1G ANP D 401 " pdb="MG MG D 402 " model vdw 2.191 2.170 nonbonded pdb=" OD1 ASP F 170 " pdb="MG MG F 402 " model vdw 2.205 2.170 nonbonded pdb=" NE2 GLN D 94 " pdb="MG MG D 402 " model vdw 2.258 2.250 nonbonded pdb=" O ILE C 96 " pdb=" OG1 THR C 220 " model vdw 2.326 3.040 nonbonded pdb=" OE2 GLU D 36 " pdb=" OG SER D 213 " model vdw 2.327 3.040 ... (remaining 68989 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and ((resid 3 and (name CA or name C or name O or name CB or name CG \ or name CD or name CE or name NZ )) or resid 4 through 402)) selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.530 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5542 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 : 0.004 0.145 9728 Z= 0.228 Angle : 0.850 16.989 13182 Z= 0.404 Chirality : 0.049 0.275 1536 Planarity : 0.005 0.048 1682 Dihedral : 14.620 108.725 3647 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.10 % Allowed : 9.70 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.58 (0.16), residues: 1229 helix: -5.05 (0.08), residues: 333 sheet: -2.38 (0.44), residues: 119 loop : -3.49 (0.16), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 85 TYR 0.015 0.001 TYR E 248 PHE 0.011 0.001 PHE F 199 TRP 0.009 0.001 TRP C 249 HIS 0.002 0.001 HIS E 376 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 9728) covalent geometry : angle 0.85048 (13182) hydrogen bonds : bond 0.34684 ( 166) hydrogen bonds : angle 11.84143 ( 474) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 303 time to evaluate : 0.317 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: C 29 LEU cc_start: 0.8346 (tp) cc_final: 0.7530 (tp) REVERT: C 184 PHE cc_start: 0.7113 (m-80) cc_final: 0.6834 (m-80) REVERT: C 315 MET cc_start: 0.7886 (ppp) cc_final: 0.7583 (tmm) REVERT: E 237 LEU cc_start: 0.5024 (tt) cc_final: 0.3413 (mm) REVERT: E 285 PHE cc_start: 0.3833 (m-80) cc_final: 0.2993 (m-80) REVERT: D 37 MET cc_start: 0.6105 (mpp) cc_final: 0.5823 (mpp) REVERT: F 24 VAL cc_start: 0.7397 (m) cc_final: 0.7066 (p) REVERT: F 25 LEU cc_start: 0.6648 (tp) cc_final: 0.6359 (tt) REVERT: F 99 LEU cc_start: 0.6611 (mp) cc_final: 0.5718 (mt) outliers start: 1 outliers final: 0 residues processed: 303 average time/residue: 0.1151 time to fit residues: 46.8075 Evaluate side-chains 212 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.0000 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 GLN E 86 GLN E 146 GLN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 286 ASN D 7 GLN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 215 GLN F 96 HIS F 107 ASN F 204 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.223358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.190753 restraints weight = 21740.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.193971 restraints weight = 14709.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.196374 restraints weight = 10904.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.197926 restraints weight = 8704.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.198825 restraints weight = 7373.407| |-----------------------------------------------------------------------------| r_work (final): 0.4543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5933 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9728 Z= 0.144 Angle : 0.621 9.505 13182 Z= 0.306 Chirality : 0.043 0.139 1536 Planarity : 0.005 0.048 1682 Dihedral : 8.944 115.616 1391 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 0.20 % Allowed : 6.17 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.63 (0.18), residues: 1229 helix: -3.65 (0.17), residues: 380 sheet: -1.42 (0.49), residues: 115 loop : -3.17 (0.18), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 17 TYR 0.015 0.001 TYR C 128 PHE 0.015 0.002 PHE F 95 TRP 0.018 0.001 TRP E 165 HIS 0.007 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 9728) covalent geometry : angle 0.62106 (13182) hydrogen bonds : bond 0.03652 ( 166) hydrogen bonds : angle 6.00282 ( 474) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 248 time to evaluate : 0.347 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: C 28 TRP cc_start: 0.5376 (m-90) cc_final: 0.4998 (m-90) REVERT: C 88 ASP cc_start: 0.3490 (p0) cc_final: 0.3109 (p0) REVERT: C 164 VAL cc_start: 0.8852 (t) cc_final: 0.8518 (t) REVERT: C 184 PHE cc_start: 0.7164 (m-80) cc_final: 0.6647 (m-80) REVERT: C 253 LYS cc_start: 0.6806 (mmmt) cc_final: 0.6160 (pttm) REVERT: C 289 MET cc_start: 0.7894 (mmp) cc_final: 0.7455 (mmp) REVERT: E 228 MET cc_start: 0.1717 (ptt) cc_final: 0.1235 (ptt) REVERT: E 276 MET cc_start: 0.5932 (mmp) cc_final: 0.5098 (mmp) REVERT: D 23 ASP cc_start: 0.5869 (m-30) cc_final: 0.5665 (m-30) REVERT: D 190 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7570 (mt-10) REVERT: D 195 GLN cc_start: 0.6306 (pm20) cc_final: 0.6031 (pm20) REVERT: F 38 MET cc_start: 0.7521 (ptp) cc_final: 0.7214 (ptp) outliers start: 2 outliers final: 1 residues processed: 250 average time/residue: 0.1110 time to fit residues: 37.6757 Evaluate side-chains 202 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 201 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 67 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 108 optimal weight: 0.3980 chunk 92 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 ASN E 266 GLN ** D 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 ASN F 94 GLN F 97 HIS F 107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.221306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.188895 restraints weight = 21449.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.192119 restraints weight = 15579.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.193266 restraints weight = 11680.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.194762 restraints weight = 9642.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.195490 restraints weight = 8350.001| |-----------------------------------------------------------------------------| r_work (final): 0.4502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 9728 Z= 0.106 Angle : 0.562 7.336 13182 Z= 0.273 Chirality : 0.041 0.128 1536 Planarity : 0.004 0.033 1682 Dihedral : 8.621 120.407 1391 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.89 (0.20), residues: 1229 helix: -2.71 (0.23), residues: 378 sheet: -1.23 (0.50), residues: 115 loop : -2.86 (0.19), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 165 TYR 0.010 0.001 TYR F 93 PHE 0.029 0.002 PHE C 257 TRP 0.018 0.001 TRP E 377 HIS 0.006 0.001 HIS F 204 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9728) covalent geometry : angle 0.56169 (13182) hydrogen bonds : bond 0.02895 ( 166) hydrogen bonds : angle 5.29385 ( 474) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 242 time to evaluate : 0.364 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: C 28 TRP cc_start: 0.5212 (m-90) cc_final: 0.4872 (m-90) REVERT: C 88 ASP cc_start: 0.3068 (p0) cc_final: 0.2678 (p0) REVERT: C 184 PHE cc_start: 0.7025 (m-80) cc_final: 0.6594 (m-80) REVERT: C 253 LYS cc_start: 0.6622 (mmmt) cc_final: 0.6091 (pttm) REVERT: C 264 LYS cc_start: 0.7281 (tttt) cc_final: 0.6468 (ttpp) REVERT: C 289 MET cc_start: 0.7897 (mmp) cc_final: 0.7384 (mmp) REVERT: E 228 MET cc_start: 0.1676 (ptt) cc_final: 0.1406 (ptp) REVERT: E 272 MET cc_start: 0.6043 (mmt) cc_final: 0.5518 (mmp) REVERT: E 276 MET cc_start: 0.6354 (mmp) cc_final: 0.5477 (mmp) REVERT: E 285 PHE cc_start: 0.4908 (m-80) cc_final: 0.3458 (m-80) REVERT: E 298 LYS cc_start: 0.2626 (mmmt) cc_final: 0.2112 (mmmt) REVERT: D 23 ASP cc_start: 0.6008 (m-30) cc_final: 0.5795 (m-30) REVERT: D 103 THR cc_start: 0.7583 (m) cc_final: 0.6934 (m) REVERT: D 171 GLU cc_start: 0.7960 (tp30) cc_final: 0.7100 (tp30) outliers start: 0 outliers final: 0 residues processed: 242 average time/residue: 0.1102 time to fit residues: 36.4558 Evaluate side-chains 196 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 59 optimal weight: 20.0000 chunk 109 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 21 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 GLN E 212 GLN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 HIS D 215 GLN ** F 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 94 GLN ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4700 r_free = 0.4700 target = 0.213172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.178887 restraints weight = 22040.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.181926 restraints weight = 15151.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.184090 restraints weight = 11456.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.185570 restraints weight = 9333.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.186320 restraints weight = 8033.927| |-----------------------------------------------------------------------------| r_work (final): 0.4405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6270 moved from start: 0.4469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9728 Z= 0.127 Angle : 0.598 6.407 13182 Z= 0.291 Chirality : 0.042 0.164 1536 Planarity : 0.004 0.030 1682 Dihedral : 8.788 137.765 1391 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.54 (0.21), residues: 1229 helix: -2.39 (0.24), residues: 379 sheet: -1.06 (0.52), residues: 110 loop : -2.64 (0.20), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 269 TYR 0.015 0.001 TYR F 93 PHE 0.029 0.002 PHE D 185 TRP 0.016 0.001 TRP E 321 HIS 0.007 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 9728) covalent geometry : angle 0.59803 (13182) hydrogen bonds : bond 0.02819 ( 166) hydrogen bonds : angle 5.10249 ( 474) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.379 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: C 28 TRP cc_start: 0.5460 (m-90) cc_final: 0.5067 (m-90) REVERT: C 88 ASP cc_start: 0.3266 (p0) cc_final: 0.2840 (p0) REVERT: C 164 VAL cc_start: 0.8901 (t) cc_final: 0.8469 (t) REVERT: C 184 PHE cc_start: 0.7410 (m-80) cc_final: 0.6682 (m-80) REVERT: C 253 LYS cc_start: 0.7055 (mmmt) cc_final: 0.6698 (tppt) REVERT: C 289 MET cc_start: 0.8418 (mmp) cc_final: 0.7818 (mmp) REVERT: C 380 THR cc_start: 0.6627 (m) cc_final: 0.6427 (m) REVERT: E 228 MET cc_start: 0.1908 (ptt) cc_final: 0.1537 (ptp) REVERT: E 285 PHE cc_start: 0.5231 (m-80) cc_final: 0.4105 (m-80) REVERT: E 298 LYS cc_start: 0.3160 (mmmt) cc_final: 0.2266 (mmmt) REVERT: E 337 ILE cc_start: 0.8964 (pt) cc_final: 0.8407 (mp) REVERT: E 397 TYR cc_start: 0.7120 (t80) cc_final: 0.6919 (t80) REVERT: D 171 GLU cc_start: 0.8048 (tp30) cc_final: 0.7224 (tp30) REVERT: F 81 LYS cc_start: 0.8774 (pttt) cc_final: 0.8517 (pttm) REVERT: F 190 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7445 (tm-30) REVERT: F 191 LEU cc_start: 0.8130 (mt) cc_final: 0.7898 (mm) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.1177 time to fit residues: 37.6300 Evaluate side-chains 188 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 65 optimal weight: 0.0670 chunk 77 optimal weight: 0.0970 chunk 117 optimal weight: 0.0670 chunk 121 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 97 optimal weight: 7.9990 chunk 81 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN E 266 GLN D 21 GLN ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 ASN F 94 GLN F 107 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4719 r_free = 0.4719 target = 0.214921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.180517 restraints weight = 21780.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.183924 restraints weight = 14840.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.186236 restraints weight = 10975.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.187910 restraints weight = 8754.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.188925 restraints weight = 7429.400| |-----------------------------------------------------------------------------| r_work (final): 0.4437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6191 moved from start: 0.4725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9728 Z= 0.094 Angle : 0.561 7.534 13182 Z= 0.267 Chirality : 0.041 0.131 1536 Planarity : 0.003 0.035 1682 Dihedral : 8.690 139.700 1391 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.20 (0.22), residues: 1229 helix: -1.99 (0.26), residues: 366 sheet: -0.94 (0.53), residues: 110 loop : -2.49 (0.20), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 211 TYR 0.008 0.001 TYR F 93 PHE 0.020 0.001 PHE D 185 TRP 0.012 0.001 TRP E 377 HIS 0.004 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 9728) covalent geometry : angle 0.56075 (13182) hydrogen bonds : bond 0.02370 ( 166) hydrogen bonds : angle 4.80362 ( 474) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.432 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: C 28 TRP cc_start: 0.5385 (m-90) cc_final: 0.5156 (m-90) REVERT: C 88 ASP cc_start: 0.3699 (p0) cc_final: 0.3306 (p0) REVERT: C 164 VAL cc_start: 0.8789 (t) cc_final: 0.8322 (t) REVERT: C 184 PHE cc_start: 0.7312 (m-80) cc_final: 0.6638 (m-80) REVERT: C 253 LYS cc_start: 0.6932 (mmmt) cc_final: 0.6625 (tppt) REVERT: C 289 MET cc_start: 0.8399 (mmp) cc_final: 0.7795 (mmp) REVERT: E 228 MET cc_start: 0.1871 (ptt) cc_final: 0.1545 (ptp) REVERT: E 285 PHE cc_start: 0.4913 (m-10) cc_final: 0.3796 (m-80) REVERT: E 298 LYS cc_start: 0.2888 (mmmt) cc_final: 0.2014 (mmmt) REVERT: E 337 ILE cc_start: 0.8852 (pt) cc_final: 0.8334 (mp) REVERT: D 195 GLN cc_start: 0.6340 (pm20) cc_final: 0.6039 (pm20) REVERT: F 81 LYS cc_start: 0.8681 (pttt) cc_final: 0.8393 (pttm) REVERT: F 190 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7428 (tm-30) REVERT: F 191 LEU cc_start: 0.8012 (mt) cc_final: 0.7718 (mm) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.1067 time to fit residues: 33.9252 Evaluate side-chains 195 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 7 optimal weight: 0.7980 chunk 53 optimal weight: 9.9990 chunk 90 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 100 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 chunk 113 optimal weight: 0.3980 chunk 56 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 120 optimal weight: 0.0370 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 69 ASN F 94 GLN F 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.214182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.179927 restraints weight = 21499.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.183029 restraints weight = 14463.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.185397 restraints weight = 10869.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.187090 restraints weight = 8722.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.187934 restraints weight = 7377.693| |-----------------------------------------------------------------------------| r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9728 Z= 0.092 Angle : 0.570 7.559 13182 Z= 0.271 Chirality : 0.041 0.125 1536 Planarity : 0.004 0.073 1682 Dihedral : 8.647 138.395 1391 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.04 (0.22), residues: 1229 helix: -1.83 (0.26), residues: 374 sheet: -1.02 (0.51), residues: 114 loop : -2.39 (0.20), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 252 TYR 0.009 0.001 TYR F 93 PHE 0.022 0.001 PHE D 185 TRP 0.012 0.001 TRP E 377 HIS 0.004 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 9728) covalent geometry : angle 0.56977 (13182) hydrogen bonds : bond 0.02296 ( 166) hydrogen bonds : angle 4.72386 ( 474) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.3797 (p0) cc_final: 0.3409 (p0) REVERT: C 164 VAL cc_start: 0.8754 (t) cc_final: 0.8297 (t) REVERT: C 184 PHE cc_start: 0.7288 (m-80) cc_final: 0.6609 (m-80) REVERT: C 253 LYS cc_start: 0.7040 (mmmt) cc_final: 0.6455 (pttm) REVERT: C 289 MET cc_start: 0.8520 (mmp) cc_final: 0.7908 (mmp) REVERT: E 228 MET cc_start: 0.2367 (ptt) cc_final: 0.2057 (ptp) REVERT: E 298 LYS cc_start: 0.2655 (mmmt) cc_final: 0.1843 (mmmt) REVERT: E 337 ILE cc_start: 0.8853 (pt) cc_final: 0.8345 (mp) REVERT: D 122 ILE cc_start: 0.7954 (mm) cc_final: 0.7715 (mm) REVERT: D 127 LEU cc_start: 0.8433 (tp) cc_final: 0.7439 (tp) REVERT: D 195 GLN cc_start: 0.6365 (pm20) cc_final: 0.6134 (pm20) REVERT: F 190 GLU cc_start: 0.8023 (tm-30) cc_final: 0.7531 (tm-30) REVERT: F 191 LEU cc_start: 0.8031 (mt) cc_final: 0.7740 (mm) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1006 time to fit residues: 31.8265 Evaluate side-chains 192 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 192 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 119 optimal weight: 0.5980 chunk 66 optimal weight: 5.9990 chunk 59 optimal weight: 8.9990 chunk 107 optimal weight: 0.0870 chunk 18 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 34 optimal weight: 20.0000 chunk 22 optimal weight: 0.3980 chunk 19 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 109 ASN ** E 266 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 ASN F 97 HIS ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4631 r_free = 0.4631 target = 0.205442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.169069 restraints weight = 21742.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.172101 restraints weight = 15281.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.174089 restraints weight = 11671.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.175442 restraints weight = 9607.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.176498 restraints weight = 8416.656| |-----------------------------------------------------------------------------| r_work (final): 0.4313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6475 moved from start: 0.5857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9728 Z= 0.144 Angle : 0.672 7.989 13182 Z= 0.325 Chirality : 0.044 0.162 1536 Planarity : 0.004 0.066 1682 Dihedral : 9.086 145.651 1391 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.10 (0.22), residues: 1229 helix: -2.02 (0.24), residues: 401 sheet: -1.10 (0.52), residues: 108 loop : -2.30 (0.21), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 18 TYR 0.020 0.001 TYR F 93 PHE 0.041 0.002 PHE E 285 TRP 0.035 0.002 TRP C 28 HIS 0.011 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9728) covalent geometry : angle 0.67178 (13182) hydrogen bonds : bond 0.03011 ( 166) hydrogen bonds : angle 5.00145 ( 474) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.363 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: C 88 ASP cc_start: 0.3681 (p0) cc_final: 0.3284 (p0) REVERT: C 164 VAL cc_start: 0.8794 (t) cc_final: 0.8375 (t) REVERT: C 184 PHE cc_start: 0.7344 (m-80) cc_final: 0.6531 (m-80) REVERT: C 366 ILE cc_start: 0.7908 (tt) cc_final: 0.7287 (mm) REVERT: E 228 MET cc_start: 0.3086 (ptt) cc_final: 0.2690 (ptp) REVERT: E 296 LYS cc_start: 0.7591 (ttpp) cc_final: 0.7373 (tttm) REVERT: E 298 LYS cc_start: 0.2933 (mmmt) cc_final: 0.1890 (mmmt) REVERT: E 319 PHE cc_start: 0.7069 (m-10) cc_final: 0.6628 (m-10) REVERT: E 337 ILE cc_start: 0.8894 (pt) cc_final: 0.8454 (mp) REVERT: D 216 LEU cc_start: 0.8715 (mp) cc_final: 0.8474 (mp) REVERT: F 81 LYS cc_start: 0.8725 (pttt) cc_final: 0.8432 (pttm) REVERT: F 102 PHE cc_start: 0.7864 (m-10) cc_final: 0.7621 (m-10) REVERT: F 190 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7685 (tm-30) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.0993 time to fit residues: 33.5492 Evaluate side-chains 197 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 87 optimal weight: 1.9990 chunk 114 optimal weight: 0.7980 chunk 13 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 97 optimal weight: 0.3980 chunk 98 optimal weight: 0.3980 chunk 2 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 109 ASN E 266 GLN F 69 ASN ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4648 r_free = 0.4648 target = 0.207374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.173602 restraints weight = 21320.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.176529 restraints weight = 14653.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.178594 restraints weight = 11057.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.180052 restraints weight = 9040.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.180805 restraints weight = 7779.139| |-----------------------------------------------------------------------------| r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.6085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9728 Z= 0.109 Angle : 0.632 8.973 13182 Z= 0.299 Chirality : 0.043 0.146 1536 Planarity : 0.003 0.054 1682 Dihedral : 8.830 146.053 1391 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.90 (0.22), residues: 1229 helix: -1.78 (0.25), residues: 405 sheet: -1.17 (0.50), residues: 112 loop : -2.19 (0.21), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 142 TYR 0.014 0.001 TYR F 93 PHE 0.025 0.001 PHE E 285 TRP 0.028 0.002 TRP C 28 HIS 0.006 0.001 HIS E 376 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9728) covalent geometry : angle 0.63173 (13182) hydrogen bonds : bond 0.02450 ( 166) hydrogen bonds : angle 4.74257 ( 474) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.406 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: C 88 ASP cc_start: 0.3777 (p0) cc_final: 0.3348 (p0) REVERT: C 264 LYS cc_start: 0.7831 (tttt) cc_final: 0.7351 (ttmm) REVERT: C 292 GLU cc_start: 0.7445 (pt0) cc_final: 0.7104 (pt0) REVERT: C 311 MET cc_start: 0.6451 (ppp) cc_final: 0.5918 (pmm) REVERT: C 363 LEU cc_start: 0.7752 (mp) cc_final: 0.7502 (mt) REVERT: C 366 ILE cc_start: 0.7820 (tt) cc_final: 0.7177 (mm) REVERT: E 228 MET cc_start: 0.3187 (ptt) cc_final: 0.2868 (ptp) REVERT: E 298 LYS cc_start: 0.2748 (mmmt) cc_final: 0.1897 (mmmt) REVERT: E 319 PHE cc_start: 0.7099 (m-10) cc_final: 0.6727 (m-10) REVERT: E 337 ILE cc_start: 0.8857 (pt) cc_final: 0.8417 (mp) REVERT: D 68 PHE cc_start: 0.7013 (t80) cc_final: 0.6781 (t80) REVERT: D 217 GLU cc_start: 0.7391 (tm-30) cc_final: 0.6946 (tm-30) REVERT: F 102 PHE cc_start: 0.7984 (m-10) cc_final: 0.7752 (m-10) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.0966 time to fit residues: 32.0518 Evaluate side-chains 202 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 111 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 64 optimal weight: 0.0570 chunk 0 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.5504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 HIS E 109 ASN D 53 HIS ** F 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 69 ASN ** F 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.203477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.168833 restraints weight = 21663.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.171569 restraints weight = 15329.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.173486 restraints weight = 11863.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.174764 restraints weight = 9837.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.175488 restraints weight = 8603.454| |-----------------------------------------------------------------------------| r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6523 moved from start: 0.6631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9728 Z= 0.140 Angle : 0.694 14.824 13182 Z= 0.327 Chirality : 0.044 0.154 1536 Planarity : 0.004 0.053 1682 Dihedral : 8.961 146.164 1391 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.88 (0.22), residues: 1229 helix: -1.89 (0.24), residues: 395 sheet: -1.29 (0.50), residues: 112 loop : -2.08 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 142 TYR 0.015 0.001 TYR D 15 PHE 0.023 0.002 PHE E 285 TRP 0.031 0.002 TRP C 28 HIS 0.012 0.002 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9728) covalent geometry : angle 0.69370 (13182) hydrogen bonds : bond 0.03029 ( 166) hydrogen bonds : angle 5.13793 ( 474) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 231 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.4064 (p0) cc_final: 0.3696 (p0) REVERT: C 289 MET cc_start: 0.8797 (mmp) cc_final: 0.8535 (mmp) REVERT: C 292 GLU cc_start: 0.7339 (pt0) cc_final: 0.6983 (pt0) REVERT: C 363 LEU cc_start: 0.7883 (mp) cc_final: 0.7646 (mt) REVERT: C 366 ILE cc_start: 0.7978 (tt) cc_final: 0.7307 (mm) REVERT: E 228 MET cc_start: 0.3620 (ptt) cc_final: 0.3317 (ptp) REVERT: E 298 LYS cc_start: 0.3009 (mmmt) cc_final: 0.1949 (mmmt) REVERT: E 319 PHE cc_start: 0.7216 (m-10) cc_final: 0.6936 (m-10) REVERT: E 337 ILE cc_start: 0.8885 (pt) cc_final: 0.8491 (mp) REVERT: D 127 LEU cc_start: 0.8632 (tp) cc_final: 0.8210 (tp) REVERT: D 131 LYS cc_start: 0.7872 (mtmm) cc_final: 0.7650 (mtmm) REVERT: D 145 GLU cc_start: 0.6968 (pt0) cc_final: 0.6393 (pt0) REVERT: D 205 ASP cc_start: 0.5418 (p0) cc_final: 0.4905 (p0) outliers start: 0 outliers final: 0 residues processed: 231 average time/residue: 0.0946 time to fit residues: 31.1968 Evaluate side-chains 197 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 38 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 26 optimal weight: 0.0770 chunk 116 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 63 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 GLN D 141 HIS F 21 GLN F 53 HIS ** F 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 215 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.206223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.170841 restraints weight = 21879.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.173726 restraints weight = 15326.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.175768 restraints weight = 11734.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.177195 restraints weight = 9616.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.177909 restraints weight = 8340.474| |-----------------------------------------------------------------------------| r_work (final): 0.4332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6435 moved from start: 0.6644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9728 Z= 0.102 Angle : 0.642 15.899 13182 Z= 0.299 Chirality : 0.043 0.140 1536 Planarity : 0.004 0.061 1682 Dihedral : 8.707 142.663 1391 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.66 (0.23), residues: 1229 helix: -1.69 (0.25), residues: 399 sheet: -1.04 (0.51), residues: 111 loop : -1.97 (0.22), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 142 TYR 0.005 0.001 TYR D 15 PHE 0.021 0.001 PHE D 185 TRP 0.026 0.001 TRP C 28 HIS 0.007 0.001 HIS E 376 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 9728) covalent geometry : angle 0.64181 (13182) hydrogen bonds : bond 0.02431 ( 166) hydrogen bonds : angle 4.91772 ( 474) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2458 Ramachandran restraints generated. 1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 237 time to evaluate : 0.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 88 ASP cc_start: 0.4098 (p0) cc_final: 0.3682 (p0) REVERT: C 264 LYS cc_start: 0.7800 (tttt) cc_final: 0.7340 (ttmm) REVERT: C 363 LEU cc_start: 0.7903 (mp) cc_final: 0.7613 (mt) REVERT: C 366 ILE cc_start: 0.7827 (tt) cc_final: 0.7140 (mm) REVERT: E 169 MET cc_start: 0.2910 (ppp) cc_final: 0.0969 (pmm) REVERT: E 228 MET cc_start: 0.3584 (ptt) cc_final: 0.3312 (ptp) REVERT: E 261 MET cc_start: 0.7599 (pmm) cc_final: 0.7366 (pmm) REVERT: E 298 LYS cc_start: 0.2836 (mmmt) cc_final: 0.1951 (mmmt) REVERT: E 337 ILE cc_start: 0.8865 (pt) cc_final: 0.8459 (mp) REVERT: D 127 LEU cc_start: 0.8563 (tp) cc_final: 0.8142 (tp) REVERT: D 131 LYS cc_start: 0.7840 (mtmm) cc_final: 0.7574 (mtmm) REVERT: D 145 GLU cc_start: 0.6736 (pt0) cc_final: 0.6195 (pt0) REVERT: D 205 ASP cc_start: 0.5362 (p0) cc_final: 0.4816 (p0) outliers start: 0 outliers final: 0 residues processed: 237 average time/residue: 0.0961 time to fit residues: 32.3156 Evaluate side-chains 197 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 19 optimal weight: 20.0000 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 24 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 15 optimal weight: 0.0980 chunk 110 optimal weight: 0.5980 chunk 88 optimal weight: 0.2980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 107 ASN F 215 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.206958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.172675 restraints weight = 21499.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.176013 restraints weight = 14316.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.178128 restraints weight = 10516.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.179815 restraints weight = 8451.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.180720 restraints weight = 7167.634| |-----------------------------------------------------------------------------| r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.6777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9728 Z= 0.100 Angle : 0.645 12.322 13182 Z= 0.301 Chirality : 0.043 0.138 1536 Planarity : 0.004 0.056 1682 Dihedral : 8.547 136.993 1391 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.23), residues: 1229 helix: -1.46 (0.25), residues: 411 sheet: -0.91 (0.53), residues: 111 loop : -1.98 (0.22), residues: 707 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 142 TYR 0.007 0.001 TYR D 15 PHE 0.023 0.002 PHE D 185 TRP 0.023 0.001 TRP C 28 HIS 0.007 0.001 HIS E 376 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9728) covalent geometry : angle 0.64494 (13182) hydrogen bonds : bond 0.02267 ( 166) hydrogen bonds : angle 4.69909 ( 474) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1944.78 seconds wall clock time: 34 minutes 13.53 seconds (2053.53 seconds total)