Starting phenix.real_space_refine on Thu Jul 2 19:23:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7arl_11886/07_2026/7arl_11886.cif Found real_map, /net/cci-nas-00/data/ceres_data/7arl_11886/07_2026/7arl_11886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7arl_11886/07_2026/7arl_11886.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7arl_11886/07_2026/7arl_11886.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7arl_11886/07_2026/7arl_11886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7arl_11886/07_2026/7arl_11886.map" model { file = "/net/cci-nas-00/data/ceres_data/7arl_11886/07_2026/7arl_11886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7arl_11886/07_2026/7arl_11886.cif" } resolution = 3.2 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 56 atoms to isotropic. 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 4 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 6040 2.51 5 N 1651 2.21 5 O 1722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9467 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2969 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 20, 'TRANS': 371} Chain breaks: 1 Chain: "E" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3159 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 14, 'TRANS': 394} Chain: "F" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1545 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 8, 'TRANS': 214} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 7, 'GLU:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "D" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1609 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 8, 'TRANS': 213} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 5, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "V" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 73 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'Z41': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 17 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.11, per 1000 atoms: 0.22 Number of scatterers: 9467 At special positions: 0 Unit cell: (83.148, 90.246, 148.044, 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 48 16.00 P 4 15.00 Mg 2 11.99 O 1722 8.00 N 1651 7.00 C 6040 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.07 Conformation dependent library (CDL) restraints added in 393.8 milliseconds 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2298 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 13 sheets defined 40.4% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'C' and resid 5 through 10 removed outlier: 3.775A pdb=" N ILE C 9 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 5 through 10' Processing helix chain 'C' and resid 20 through 28 removed outlier: 3.520A pdb=" N ARG C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 26 " --> pdb=" O PHE C 22 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER C 27 " --> pdb=" O GLY C 23 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP C 28 " --> pdb=" O ARG C 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 20 through 28' Processing helix chain 'C' and resid 28 through 59 removed outlier: 3.658A pdb=" N ILE C 32 " --> pdb=" O TRP C 28 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C 37 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR C 43 " --> pdb=" O MET C 39 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VAL C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 155 removed outlier: 3.914A pdb=" N GLN C 153 " --> pdb=" O GLN C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 removed outlier: 3.815A pdb=" N GLY C 198 " --> pdb=" O GLU C 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 195 through 198' Processing helix chain 'C' and resid 248 through 252 removed outlier: 4.096A pdb=" N ASP C 251 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG C 252 " --> pdb=" O TRP C 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 248 through 252' Processing helix chain 'C' and resid 256 through 271 removed outlier: 3.635A pdb=" N VAL C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 293 removed outlier: 3.772A pdb=" N ILE C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 288 " --> pdb=" O THR C 284 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 304 removed outlier: 3.804A pdb=" N ALA C 298 " --> pdb=" O GLN C 294 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE C 299 " --> pdb=" O GLY C 295 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 300 " --> pdb=" O GLU C 296 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 311 removed outlier: 3.732A pdb=" N MET C 311 " --> pdb=" O PRO C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 339 removed outlier: 3.953A pdb=" N VAL C 316 " --> pdb=" O MET C 312 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA C 321 " --> pdb=" O GLN C 317 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 379 removed outlier: 3.744A pdb=" N VAL C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE C 366 " --> pdb=" O PRO C 362 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU C 377 " --> pdb=" O MET C 373 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER C 379 " --> pdb=" O ILE C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 390 removed outlier: 3.758A pdb=" N ALA C 388 " --> pdb=" O SER C 384 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR C 390 " --> pdb=" O ARG C 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 24 removed outlier: 4.338A pdb=" N SER E 24 " --> pdb=" O GLY E 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 21 through 24' Processing helix chain 'E' and resid 25 through 35 removed outlier: 3.676A pdb=" N ILE E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 59 removed outlier: 4.051A pdb=" N MET E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN E 56 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 87 Processing helix chain 'E' and resid 129 through 133 removed outlier: 4.143A pdb=" N PHE E 132 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL E 133 " --> pdb=" O PRO E 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 129 through 133' Processing helix chain 'E' and resid 151 through 159 removed outlier: 3.850A pdb=" N ALA E 155 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 212 removed outlier: 3.728A pdb=" N GLN E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 259 Processing helix chain 'E' and resid 259 through 268 removed outlier: 4.042A pdb=" N ARG E 263 " --> pdb=" O GLY E 259 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE E 268 " --> pdb=" O ASP E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 284 removed outlier: 3.590A pdb=" N LEU E 278 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL E 282 " --> pdb=" O LEU E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 290 Processing helix chain 'E' and resid 292 through 297 removed outlier: 3.529A pdb=" N LYS E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 309 removed outlier: 3.710A pdb=" N ILE E 302 " --> pdb=" O LYS E 298 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL E 304 " --> pdb=" O GLY E 300 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU E 305 " --> pdb=" O ASP E 301 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 308 " --> pdb=" O VAL E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 316 Processing helix chain 'E' and resid 317 through 324 removed outlier: 4.225A pdb=" N TRP E 321 " --> pdb=" O ALA E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 344 removed outlier: 3.760A pdb=" N GLY E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY E 334 " --> pdb=" O GLY E 330 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE E 337 " --> pdb=" O CYS E 333 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL E 340 " --> pdb=" O ILE E 336 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL E 341 " --> pdb=" O ILE E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 353 removed outlier: 3.710A pdb=" N GLU E 350 " --> pdb=" O THR E 346 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP E 351 " --> pdb=" O PRO E 347 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE E 352 " --> pdb=" O ILE E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 404 removed outlier: 3.715A pdb=" N PHE E 381 " --> pdb=" O TRP E 377 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL E 385 " --> pdb=" O PHE E 381 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR E 386 " --> pdb=" O TYR E 382 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU E 393 " --> pdb=" O LEU E 389 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA E 394 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR E 397 " --> pdb=" O LEU E 393 " (cutoff:3.500A) Proline residue: E 398 - end of helix removed outlier: 3.722A pdb=" N ARG E 401 " --> pdb=" O TYR E 397 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN E 404 " --> pdb=" O ARG E 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 57 Processing helix chain 'F' and resid 77 through 88 removed outlier: 3.932A pdb=" N ALA F 82 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 84 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG F 85 " --> pdb=" O LYS F 81 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 109 removed outlier: 3.550A pdb=" N ASN F 107 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 115 removed outlier: 3.550A pdb=" N ILE F 114 " --> pdb=" O MET F 110 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY F 115 " --> pdb=" O PRO F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 132 removed outlier: 4.098A pdb=" N ASN F 123 " --> pdb=" O PRO F 119 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU F 130 " --> pdb=" O ALA F 126 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS F 131 " --> pdb=" O LEU F 127 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA F 132 " --> pdb=" O GLU F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 159 removed outlier: 3.589A pdb=" N ARG F 153 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA F 155 " --> pdb=" O ARG F 151 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA F 159 " --> pdb=" O ALA F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 194 removed outlier: 3.841A pdb=" N ILE F 184 " --> pdb=" O ASN F 180 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE F 185 " --> pdb=" O ALA F 181 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN F 192 " --> pdb=" O LEU F 188 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG F 193 " --> pdb=" O GLY F 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 57 Processing helix chain 'D' and resid 77 through 85 removed outlier: 3.836A pdb=" N ALA D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG D 85 " --> pdb=" O LYS D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 109 removed outlier: 3.993A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 115 removed outlier: 3.505A pdb=" N ILE D 114 " --> pdb=" O MET D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 134 removed outlier: 3.640A pdb=" N MET D 129 " --> pdb=" O ARG D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 160 removed outlier: 3.899A pdb=" N ALA D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 160 " --> pdb=" O ILE D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 189 removed outlier: 3.520A pdb=" N ILE D 184 " --> pdb=" O ASN D 180 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.578A pdb=" N ILE C 96 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY C 221 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP C 222 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA C 66 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 69 " --> pdb=" O LYS C 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 98 through 99 removed outlier: 3.687A pdb=" N MET C 201 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASN C 204 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ASN C 143 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER C 180 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL C 164 " --> pdb=" O ARG C 182 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 91 through 96 removed outlier: 6.714A pdb=" N LYS E 227 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ALA E 94 " --> pdb=" O ALA E 225 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA E 225 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU E 67 " --> pdb=" O LYS E 252 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 102 through 103 removed outlier: 3.943A pdb=" N GLY E 102 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE E 113 " --> pdb=" O GLY E 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 115 through 116 removed outlier: 3.574A pdb=" N MET E 205 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE E 149 " --> pdb=" O MET E 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 165 through 170 removed outlier: 3.788A pdb=" N VAL E 185 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS E 183 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 14 through 17 removed outlier: 3.619A pdb=" N VAL F 20 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 67 through 68 Processing sheet with id=AA9, first strand: chain 'F' and resid 89 through 92 removed outlier: 5.846A pdb=" N GLY F 90 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ASP F 170 " --> pdb=" O GLY F 90 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE F 92 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL F 202 " --> pdb=" O ALA F 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 218 through 219 Processing sheet with id=AB2, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.597A pdb=" N CYS D 8 " --> pdb=" O PHE D 30 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE D 67 " --> pdb=" O GLN D 7 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 37 through 38 removed outlier: 6.796A pdb=" N PHE D 199 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 200 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA D 169 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY D 90 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 218 through 219 256 hydrogen bonds defined for protein. 741 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: 1.40 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3066 1.34 - 1.46: 1148 1.46 - 1.57: 5315 1.57 - 1.69: 6 1.69 - 1.81: 89 Bond restraints: 9624 Sorted by residual: bond pdb=" C19 Z41 C 401 " pdb=" O3 Z41 C 401 " ideal model delta sigma weight residual 1.333 1.457 -0.124 2.00e-02 2.50e+03 3.85e+01 bond pdb=" C16 Z41 C 401 " pdb=" O2 Z41 C 401 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" C LEU E 129 " pdb=" N PRO E 130 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.91e+00 bond pdb=" C1 PLM V 201 " pdb=" C2 PLM V 201 " ideal model delta sigma weight residual 1.542 1.511 0.031 2.00e-02 2.50e+03 2.45e+00 bond pdb=" N GLN E 146 " pdb=" CA GLN E 146 " ideal model delta sigma weight residual 1.460 1.482 -0.022 1.42e-02 4.96e+03 2.44e+00 ... (remaining 9619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.06: 12916 3.06 - 6.12: 128 6.12 - 9.18: 13 9.18 - 12.24: 1 12.24 - 15.29: 1 Bond angle restraints: 13059 Sorted by residual: angle pdb=" CA LEU D 51 " pdb=" CB LEU D 51 " pdb=" CG LEU D 51 " ideal model delta sigma weight residual 116.30 131.59 -15.29 3.50e+00 8.16e-02 1.91e+01 angle pdb=" C PHE D 68 " pdb=" N ASN D 69 " pdb=" CA ASN D 69 " ideal model delta sigma weight residual 121.54 128.86 -7.32 1.91e+00 2.74e-01 1.47e+01 angle pdb=" C GLU E 145 " pdb=" N GLN E 146 " pdb=" CA GLN E 146 " ideal model delta sigma weight residual 122.82 127.89 -5.07 1.42e+00 4.96e-01 1.27e+01 angle pdb=" C ASP F 170 " pdb=" N GLU F 171 " pdb=" CA GLU F 171 " ideal model delta sigma weight residual 121.80 130.32 -8.52 2.44e+00 1.68e-01 1.22e+01 angle pdb=" N ARG D 211 " pdb=" CA ARG D 211 " pdb=" C ARG D 211 " ideal model delta sigma weight residual 114.31 109.90 4.41 1.29e+00 6.01e-01 1.17e+01 ... (remaining 13054 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.89: 5455 21.89 - 43.77: 294 43.77 - 65.66: 30 65.66 - 87.54: 8 87.54 - 109.43: 1 Dihedral angle restraints: 5788 sinusoidal: 2218 harmonic: 3570 Sorted by residual: dihedral pdb=" O1B ADP D 301 " pdb=" O3A ADP D 301 " pdb=" PB ADP D 301 " pdb=" PA ADP D 301 " ideal model delta sinusoidal sigma weight residual -60.00 -169.43 109.43 1 2.00e+01 2.50e-03 3.20e+01 dihedral pdb=" CA ASP C 160 " pdb=" CB ASP C 160 " pdb=" CG ASP C 160 " pdb=" OD1 ASP C 160 " ideal model delta sinusoidal sigma weight residual -30.00 -82.10 52.10 1 2.00e+01 2.50e-03 9.26e+00 dihedral pdb=" CB MET D 129 " pdb=" CG MET D 129 " pdb=" SD MET D 129 " pdb=" CE MET D 129 " ideal model delta sinusoidal sigma weight residual 60.00 113.02 -53.02 3 1.50e+01 4.44e-03 9.17e+00 ... (remaining 5785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 970 0.035 - 0.071: 386 0.071 - 0.106: 136 0.106 - 0.141: 40 0.141 - 0.176: 10 Chirality restraints: 1542 Sorted by residual: chirality pdb=" CB VAL C 130 " pdb=" CA VAL C 130 " pdb=" CG1 VAL C 130 " pdb=" CG2 VAL C 130 " both_signs ideal model delta sigma weight residual False -2.63 -2.81 0.18 2.00e-01 2.50e+01 7.78e-01 chirality pdb=" CB ILE D 67 " pdb=" CA ILE D 67 " pdb=" CG1 ILE D 67 " pdb=" CG2 ILE D 67 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" CB ILE E 148 " pdb=" CA ILE E 148 " pdb=" CG1 ILE E 148 " pdb=" CG2 ILE E 148 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.51e-01 ... (remaining 1539 not shown) Planarity restraints: 1664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 346 " 0.037 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO E 347 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO E 347 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 347 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 110 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.13e+00 pdb=" N PRO D 111 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO D 111 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 111 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET F 110 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO F 111 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO F 111 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 111 " -0.027 5.00e-02 4.00e+02 ... (remaining 1661 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 3289 2.88 - 3.39: 8008 3.39 - 3.89: 14425 3.89 - 4.40: 16261 4.40 - 4.90: 28320 Nonbonded interactions: 70303 Sorted by model distance: nonbonded pdb=" OG SER C 170 " pdb=" O ILE C 178 " model vdw 2.378 3.040 nonbonded pdb=" O GLU E 105 " pdb=" OG SER E 167 " model vdw 2.383 3.040 nonbonded pdb=" OH TYR E 248 " pdb=" O LEU V 10 " model vdw 2.397 3.040 nonbonded pdb=" OG SER C 74 " pdb=" O ILE C 219 " model vdw 2.413 3.040 nonbonded pdb=" O SER E 342 " pdb=" OG SER E 373 " model vdw 2.424 3.040 ... (remaining 70298 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 4 through 6 or (resid 7 and (name N or name CA or name C o \ r name O or name CB )) or resid 8 through 16 or (resid 17 and (name N or name CA \ or name C or name O or name CB )) or (resid 18 through 21 and (name N or name C \ A or name C or name O or name CB )) or resid 22 through 26 or (resid 27 and (nam \ e N or name CA or name C or name O or name CB )) or resid 28 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 64 or (resid 65 and (name N or name CA or name C or name O or name CB )) or re \ sid 66 through 105 or (resid 106 and (name N or name CA or name C or name O or n \ ame CB )) or resid 107 through 116 or (resid 117 through 118 and (name N or name \ CA or name C or name O or name CB )) or resid 119 through 120 or (resid 121 and \ (name N or name CA or name C or name O or name CB )) or resid 122 through 127 o \ r (resid 128 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 29 through 141 or (resid 142 and (name N or name CA or name C or name O or name \ CB )) or resid 143 through 152 or (resid 153 and (name N or name CA or name C or \ name O or name CB )) or resid 154 through 185 or (resid 186 through 187 and (na \ me N or name CA or name C or name O or name CB )) or resid 188 through 191 or (r \ esid 192 through 195 and (name N or name CA or name C or name O or name CB )) or \ resid 196 or (resid 197 through 198 and (name N or name CA or name C or name O \ or name CB )) or resid 199 through 206 or (resid 207 through 212 and (name N or \ name CA or name C or name O or name CB )) or resid 213 through 214 or (resid 215 \ and (name N or name CA or name C or name O or name CB )) or resid 216 through 2 \ 18 or (resid 219 through 220 and (name N or name CA or name C or name O or name \ CB )) or (resid 221 through 225 and (name N or name CA or name C or name O or na \ me CB )) or resid 301 through 302)) selection = (chain 'F' and (resid 4 through 8 or (resid 9 through 10 and (name N or name CA \ or name C or name O or name CB )) or resid 11 through 33 or (resid 34 and (name \ N or name CA or name C or name O or name CB )) or resid 35 through 37 or (resid \ 38 through 39 and (name N or name CA or name C or name O or name CB )) or resid \ 40 through 45 or (resid 46 and (name N or name CA or name C or name O or name CB \ )) or resid 47 or (resid 48 and (name N or name CA or name C or name O or name \ CB )) or resid 49 through 73 or (resid 74 and (name N or name CA or name C or na \ me O or name CB )) or resid 75 through 179 or (resid 180 through 182 and (name N \ or name CA or name C or name O or name CB )) or resid 183 through 210 or (resid \ 211 through 212 and (name N or name CA or name C or name O or name CB )) or res \ id 213 through 302)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.510 Find NCS groups from input model: 0.110 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7256 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 : 0.003 0.124 9626 Z= 0.195 Angle : 0.730 15.294 13059 Z= 0.356 Chirality : 0.046 0.176 1542 Planarity : 0.005 0.055 1664 Dihedral : 13.092 109.426 3490 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.83 (0.15), residues: 1244 helix: -5.07 (0.05), residues: 413 sheet: -2.45 (0.43), residues: 132 loop : -3.47 (0.16), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 19 TYR 0.007 0.001 TYR C 199 PHE 0.011 0.001 PHE F 30 TRP 0.002 0.000 TRP E 321 HIS 0.001 0.000 HIS E 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.17 ( 9624) covalent geometry : angle 0.73020 / 0.36 (13059) hydrogen bonds : bond 0.33796 / 21.06 ( 256) hydrogen bonds : angle 11.25393 / 7.60 ( 741) Misc. bond : bond 0.07005 / 3.69 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 298 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 142 TYR cc_start: 0.8049 (m-10) cc_final: 0.7803 (m-10) REVERT: C 175 MET cc_start: 0.2773 (ppp) cc_final: 0.2452 (ppp) REVERT: C 193 ASN cc_start: 0.8372 (t0) cc_final: 0.8128 (t0) REVERT: C 201 MET cc_start: 0.8586 (ptt) cc_final: 0.8373 (ptm) REVERT: E 77 ASN cc_start: 0.8200 (p0) cc_final: 0.7920 (p0) REVERT: E 98 ILE cc_start: 0.8313 (mt) cc_final: 0.7943 (pt) REVERT: E 145 GLU cc_start: 0.6768 (pm20) cc_final: 0.5617 (pm20) REVERT: E 147 GLN cc_start: 0.8322 (mt0) cc_final: 0.8028 (mt0) REVERT: E 321 TRP cc_start: 0.5316 (m-90) cc_final: 0.4800 (t-100) REVERT: D 8 CYS cc_start: 0.7322 (m) cc_final: 0.7015 (m) REVERT: D 71 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7563 (tm-30) REVERT: D 107 ASN cc_start: 0.8223 (m-40) cc_final: 0.8012 (m110) REVERT: D 110 MET cc_start: 0.8454 (tpp) cc_final: 0.8225 (tpt) REVERT: D 171 GLU cc_start: 0.8187 (mp0) cc_final: 0.7523 (mp0) REVERT: D 192 ASN cc_start: 0.7165 (p0) cc_final: 0.5776 (t0) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.1063 time to fit residues: 42.6755 Evaluate side-chains 229 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.0170 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 56 GLN C 79 GLN C 121 GLN C 153 GLN E 56 ASN E 134 GLN E 213 GLN F 71 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 HIS F 162 ASN D 140 ASN V 4 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.211392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.154381 restraints weight = 10946.177| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.91 r_work: 0.3610 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9626 Z= 0.107 Angle : 0.577 9.616 13059 Z= 0.270 Chirality : 0.041 0.132 1542 Planarity : 0.004 0.045 1664 Dihedral : 5.734 75.369 1395 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.28 % Allowed : 14.21 % Favored : 83.51 % 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 are not related in a simple way. whole: -4.61 (0.18), residues: 1244 helix: -3.36 (0.15), residues: 464 sheet: -1.99 (0.44), residues: 139 loop : -3.09 (0.19), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 58 TYR 0.014 0.001 TYR E 322 PHE 0.013 0.001 PHE F 68 TRP 0.013 0.001 TRP C 246 HIS 0.007 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 9624) covalent geometry : angle 0.57697 / 0.27 (13059) hydrogen bonds : bond 0.03843 / 2.47 ( 256) hydrogen bonds : angle 5.62910 / 3.82 ( 741) Misc. bond : bond 0.00028 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 239 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 96 ILE cc_start: 0.8630 (tp) cc_final: 0.8352 (tp) REVERT: C 107 ARG cc_start: 0.7466 (mpt-90) cc_final: 0.7175 (mpt-90) REVERT: C 142 TYR cc_start: 0.8202 (m-10) cc_final: 0.7722 (m-80) REVERT: C 175 MET cc_start: 0.2940 (ppp) cc_final: 0.2477 (ppp) REVERT: C 193 ASN cc_start: 0.8770 (t0) cc_final: 0.8429 (t0) REVERT: C 235 LEU cc_start: 0.8216 (mt) cc_final: 0.7966 (mp) REVERT: C 255 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7845 (mp0) REVERT: C 262 MET cc_start: 0.8319 (tmm) cc_final: 0.7975 (ttp) REVERT: E 77 ASN cc_start: 0.8137 (p0) cc_final: 0.7932 (p0) REVERT: E 97 TYR cc_start: 0.8893 (p90) cc_final: 0.8454 (p90) REVERT: E 145 GLU cc_start: 0.6706 (pm20) cc_final: 0.5412 (pm20) REVERT: E 147 GLN cc_start: 0.8486 (mt0) cc_final: 0.8081 (mt0) REVERT: E 210 ASP cc_start: 0.8127 (m-30) cc_final: 0.7421 (t0) REVERT: E 321 TRP cc_start: 0.6530 (m-90) cc_final: 0.6087 (t-100) REVERT: E 374 GLU cc_start: 0.8540 (tt0) cc_final: 0.8244 (tt0) REVERT: F 48 LYS cc_start: 0.7128 (mtmt) cc_final: 0.6917 (mtmm) REVERT: F 73 MET cc_start: 0.8082 (mmm) cc_final: 0.7538 (tpp) REVERT: F 105 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7899 (tt) REVERT: F 116 LYS cc_start: 0.8685 (mtmt) cc_final: 0.8437 (mtmm) REVERT: D 8 CYS cc_start: 0.7698 (m) cc_final: 0.7237 (m) REVERT: D 71 GLN cc_start: 0.7478 (tm-30) cc_final: 0.6792 (tm-30) REVERT: D 121 GLU cc_start: 0.7895 (pm20) cc_final: 0.7552 (pm20) REVERT: D 153 ARG cc_start: 0.7972 (mtp85) cc_final: 0.7356 (ttm110) REVERT: D 165 ARG cc_start: 0.7614 (mmm-85) cc_final: 0.7109 (mmm160) REVERT: D 171 GLU cc_start: 0.8313 (mp0) cc_final: 0.7564 (mp0) REVERT: D 212 MET cc_start: 0.6579 (pmm) cc_final: 0.5186 (ppp) outliers start: 22 outliers final: 11 residues processed: 248 average time/residue: 0.1047 time to fit residues: 35.0448 Evaluate side-chains 230 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 217 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 66 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 118 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 96 HIS F 152 GLN F 162 ASN D 140 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.201329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.138026 restraints weight = 10909.694| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 2.64 r_work: 0.3461 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9626 Z= 0.120 Angle : 0.573 10.615 13059 Z= 0.269 Chirality : 0.041 0.146 1542 Planarity : 0.003 0.033 1664 Dihedral : 5.501 59.092 1395 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.49 % Allowed : 16.80 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.32 (0.21), residues: 1244 helix: -1.85 (0.21), residues: 466 sheet: -1.74 (0.43), residues: 143 loop : -2.60 (0.21), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 151 TYR 0.011 0.001 TYR E 273 PHE 0.015 0.001 PHE E 319 TRP 0.014 0.001 TRP C 246 HIS 0.005 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.12 ( 9624) covalent geometry : angle 0.57292 / 0.27 (13059) hydrogen bonds : bond 0.03599 / 2.36 ( 256) hydrogen bonds : angle 4.80783 / 3.27 ( 741) Misc. bond : bond 0.00115 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 226 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 58 ASN cc_start: 0.8781 (t0) cc_final: 0.8124 (t0) REVERT: C 107 ARG cc_start: 0.7638 (mpt-90) cc_final: 0.7310 (mpt-90) REVERT: C 118 ASP cc_start: 0.7975 (t0) cc_final: 0.7728 (t0) REVERT: C 142 TYR cc_start: 0.8213 (m-10) cc_final: 0.7803 (m-10) REVERT: C 175 MET cc_start: 0.3255 (ppp) cc_final: 0.2795 (ppp) REVERT: C 212 MET cc_start: 0.5126 (mtp) cc_final: 0.4673 (mtp) REVERT: C 235 LEU cc_start: 0.8425 (mt) cc_final: 0.8115 (mp) REVERT: C 255 GLU cc_start: 0.8861 (mp0) cc_final: 0.8246 (mp0) REVERT: C 262 MET cc_start: 0.8381 (tmm) cc_final: 0.8155 (ttp) REVERT: C 303 GLN cc_start: 0.7919 (mt0) cc_final: 0.7625 (mt0) REVERT: C 320 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8824 (t) REVERT: E 145 GLU cc_start: 0.6934 (pm20) cc_final: 0.5672 (pm20) REVERT: E 147 GLN cc_start: 0.8518 (mt0) cc_final: 0.7913 (mt0) REVERT: E 321 TRP cc_start: 0.7052 (m-90) cc_final: 0.6685 (m-90) REVERT: F 96 HIS cc_start: 0.4915 (OUTLIER) cc_final: 0.4144 (t70) REVERT: F 105 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7951 (tt) REVERT: F 116 LYS cc_start: 0.8723 (mtmt) cc_final: 0.8468 (mtmm) REVERT: F 190 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7919 (tm-30) REVERT: D 36 GLU cc_start: 0.5681 (mt-10) cc_final: 0.5117 (mt-10) REVERT: D 121 GLU cc_start: 0.7891 (pm20) cc_final: 0.7315 (pm20) REVERT: D 142 ARG cc_start: 0.7362 (mtt90) cc_final: 0.7128 (ttm110) REVERT: D 165 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.7260 (mmm160) REVERT: D 171 GLU cc_start: 0.8440 (mp0) cc_final: 0.7772 (mp0) REVERT: D 212 MET cc_start: 0.5866 (pmm) cc_final: 0.4939 (ppp) outliers start: 24 outliers final: 14 residues processed: 235 average time/residue: 0.1067 time to fit residues: 34.2274 Evaluate side-chains 219 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 320 SER Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain F residue 96 HIS Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 42 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 116 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 chunk 20 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 118 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 58 ASN C 161 GLN C 281 ASN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN F 162 ASN D 140 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.192017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.130621 restraints weight = 10967.412| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.01 r_work: 0.3293 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9626 Z= 0.180 Angle : 0.638 8.729 13059 Z= 0.306 Chirality : 0.044 0.216 1542 Planarity : 0.003 0.038 1664 Dihedral : 5.801 50.253 1395 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.53 % Allowed : 17.53 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.90 (0.22), residues: 1244 helix: -1.33 (0.22), residues: 483 sheet: -1.53 (0.40), residues: 159 loop : -2.54 (0.22), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 12 TYR 0.016 0.001 TYR E 366 PHE 0.029 0.002 PHE F 95 TRP 0.014 0.002 TRP C 246 HIS 0.021 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.18 ( 9624) covalent geometry : angle 0.63791 / 0.31 (13059) hydrogen bonds : bond 0.03562 / 2.30 ( 256) hydrogen bonds : angle 4.73708 / 3.19 ( 741) Misc. bond : bond 0.00092 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 58 ASN cc_start: 0.8595 (OUTLIER) cc_final: 0.8389 (t0) REVERT: C 107 ARG cc_start: 0.7677 (mpt-90) cc_final: 0.7421 (mpt-90) REVERT: C 142 TYR cc_start: 0.8206 (m-10) cc_final: 0.7860 (m-10) REVERT: C 175 MET cc_start: 0.3270 (ppp) cc_final: 0.2740 (ppp) REVERT: C 255 GLU cc_start: 0.8847 (mp0) cc_final: 0.8140 (mp0) REVERT: E 351 TRP cc_start: 0.8023 (t60) cc_final: 0.7422 (t60) REVERT: E 401 ARG cc_start: 0.8310 (ttt-90) cc_final: 0.8051 (ttm170) REVERT: F 23 ASP cc_start: 0.5978 (m-30) cc_final: 0.4594 (t70) REVERT: F 83 GLU cc_start: 0.8576 (tp30) cc_final: 0.8264 (tp30) REVERT: F 105 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7960 (tt) REVERT: F 145 GLU cc_start: 0.7170 (pp20) cc_final: 0.6926 (pp20) REVERT: F 190 GLU cc_start: 0.8311 (tm-30) cc_final: 0.7878 (tm-30) REVERT: D 36 GLU cc_start: 0.6163 (mt-10) cc_final: 0.5723 (mm-30) REVERT: D 145 GLU cc_start: 0.7387 (pm20) cc_final: 0.6974 (pm20) REVERT: D 165 ARG cc_start: 0.7928 (mmm-85) cc_final: 0.7364 (mmm160) REVERT: D 171 GLU cc_start: 0.8252 (mp0) cc_final: 0.7609 (mp0) REVERT: D 212 MET cc_start: 0.5864 (pmm) cc_final: 0.5232 (ppp) outliers start: 34 outliers final: 21 residues processed: 227 average time/residue: 0.1005 time to fit residues: 30.9400 Evaluate side-chains 220 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 48 LYS Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 29 optimal weight: 0.0370 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 41 optimal weight: 0.9990 chunk 94 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 281 ASN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN F 152 GLN F 162 ASN D 140 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.193267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.131909 restraints weight = 10939.391| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 3.15 r_work: 0.3310 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9626 Z= 0.108 Angle : 0.562 8.800 13059 Z= 0.263 Chirality : 0.041 0.155 1542 Planarity : 0.003 0.028 1664 Dihedral : 5.592 53.861 1395 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.63 % Allowed : 19.19 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.42 (0.22), residues: 1244 helix: -0.75 (0.23), residues: 483 sheet: -1.23 (0.41), residues: 153 loop : -2.45 (0.22), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 210 TYR 0.010 0.001 TYR E 322 PHE 0.010 0.001 PHE E 319 TRP 0.013 0.001 TRP C 246 HIS 0.005 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 ( 9624) covalent geometry : angle 0.56195 / 0.26 (13059) hydrogen bonds : bond 0.02918 / 1.89 ( 256) hydrogen bonds : angle 4.54444 / 3.06 ( 741) Misc. bond : bond 0.00047 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7725 (ttp80) cc_final: 0.6868 (ttp80) REVERT: C 107 ARG cc_start: 0.7669 (mpt-90) cc_final: 0.7433 (mpt-90) REVERT: C 142 TYR cc_start: 0.8195 (m-10) cc_final: 0.7857 (m-10) REVERT: C 175 MET cc_start: 0.3266 (ppp) cc_final: 0.2784 (ppp) REVERT: C 230 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8105 (mm) REVERT: C 255 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8120 (mp0) REVERT: E 351 TRP cc_start: 0.8062 (t60) cc_final: 0.7399 (t60) REVERT: E 401 ARG cc_start: 0.8304 (ttt-90) cc_final: 0.8048 (ttm170) REVERT: F 23 ASP cc_start: 0.6023 (m-30) cc_final: 0.4681 (t70) REVERT: F 83 GLU cc_start: 0.8703 (tp30) cc_final: 0.8376 (tp30) REVERT: F 105 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7948 (tt) REVERT: F 145 GLU cc_start: 0.7280 (pp20) cc_final: 0.7028 (pp20) REVERT: F 151 ARG cc_start: 0.8268 (tpp80) cc_final: 0.7637 (ttm170) REVERT: F 190 GLU cc_start: 0.8383 (tm-30) cc_final: 0.7956 (tm-30) REVERT: D 121 GLU cc_start: 0.7984 (pm20) cc_final: 0.7741 (pm20) REVERT: D 145 GLU cc_start: 0.7398 (pm20) cc_final: 0.6875 (pm20) REVERT: D 165 ARG cc_start: 0.7965 (mmm-85) cc_final: 0.7395 (mmm160) REVERT: D 171 GLU cc_start: 0.8244 (mp0) cc_final: 0.7623 (mp0) REVERT: D 212 MET cc_start: 0.5683 (pmm) cc_final: 0.5227 (ppp) outliers start: 35 outliers final: 23 residues processed: 230 average time/residue: 0.1078 time to fit residues: 33.4352 Evaluate side-chains 222 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 124 GLN Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 1 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 122 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 58 ASN C 281 ASN F 152 GLN F 162 ASN D 140 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.191534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.126792 restraints weight = 10962.233| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 2.65 r_work: 0.3319 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9626 Z= 0.123 Angle : 0.579 8.060 13059 Z= 0.272 Chirality : 0.042 0.166 1542 Planarity : 0.003 0.029 1664 Dihedral : 5.629 57.161 1395 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.84 % Allowed : 19.19 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.23), residues: 1244 helix: -0.30 (0.24), residues: 487 sheet: -1.19 (0.43), residues: 149 loop : -2.27 (0.22), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 125 TYR 0.014 0.001 TYR E 258 PHE 0.012 0.001 PHE E 319 TRP 0.012 0.001 TRP C 246 HIS 0.003 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.12 ( 9624) covalent geometry : angle 0.57856 / 0.27 (13059) hydrogen bonds : bond 0.02932 / 1.89 ( 256) hydrogen bonds : angle 4.41234 / 2.97 ( 741) Misc. bond : bond 0.00055 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 213 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7777 (ttp80) cc_final: 0.6909 (ttp80) REVERT: C 58 ASN cc_start: 0.8645 (t0) cc_final: 0.8334 (t0) REVERT: C 107 ARG cc_start: 0.7783 (mpt-90) cc_final: 0.7543 (mpt-90) REVERT: C 142 TYR cc_start: 0.8247 (m-10) cc_final: 0.7884 (m-10) REVERT: C 175 MET cc_start: 0.3290 (ppp) cc_final: 0.2799 (ppp) REVERT: C 230 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8211 (mm) REVERT: C 255 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8347 (mp0) REVERT: C 281 ASN cc_start: 0.8724 (OUTLIER) cc_final: 0.8483 (t0) REVERT: C 315 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8484 (tpp) REVERT: E 77 ASN cc_start: 0.8285 (p0) cc_final: 0.8056 (p0) REVERT: E 145 GLU cc_start: 0.6847 (pm20) cc_final: 0.6612 (pm20) REVERT: E 351 TRP cc_start: 0.8112 (t60) cc_final: 0.7501 (t60) REVERT: E 401 ARG cc_start: 0.8376 (ttt-90) cc_final: 0.8114 (ttm170) REVERT: F 23 ASP cc_start: 0.6135 (m-30) cc_final: 0.4755 (t70) REVERT: F 105 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.8009 (tt) REVERT: F 145 GLU cc_start: 0.7428 (pp20) cc_final: 0.7158 (pp20) REVERT: F 190 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8022 (tm-30) REVERT: D 121 GLU cc_start: 0.7922 (pm20) cc_final: 0.7668 (pm20) REVERT: D 145 GLU cc_start: 0.7556 (pm20) cc_final: 0.7161 (pm20) REVERT: D 165 ARG cc_start: 0.8063 (mmm-85) cc_final: 0.7507 (mmm160) REVERT: D 171 GLU cc_start: 0.8282 (mp0) cc_final: 0.7680 (mp0) REVERT: D 212 MET cc_start: 0.5080 (pmm) cc_final: 0.4839 (ppp) outliers start: 37 outliers final: 23 residues processed: 231 average time/residue: 0.1106 time to fit residues: 34.0303 Evaluate side-chains 239 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 211 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 281 ASN Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 336 ILE Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 15 optimal weight: 0.0670 chunk 45 optimal weight: 0.8980 chunk 108 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 281 ASN C 309 GLN E 134 GLN F 152 GLN D 140 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.192206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.131255 restraints weight = 10941.549| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.98 r_work: 0.3305 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.5305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 9626 Z= 0.103 Angle : 0.568 8.735 13059 Z= 0.267 Chirality : 0.041 0.176 1542 Planarity : 0.003 0.030 1664 Dihedral : 5.346 45.864 1395 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.53 % Allowed : 19.92 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.23), residues: 1244 helix: 0.03 (0.25), residues: 485 sheet: -1.03 (0.41), residues: 159 loop : -2.18 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 211 TYR 0.014 0.001 TYR E 258 PHE 0.011 0.001 PHE D 30 TRP 0.012 0.001 TRP C 246 HIS 0.001 0.000 HIS E 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.10 ( 9624) covalent geometry : angle 0.56771 / 0.27 (13059) hydrogen bonds : bond 0.02658 / 1.72 ( 256) hydrogen bonds : angle 4.32230 / 2.92 ( 741) Misc. bond : bond 0.00038 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 220 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7658 (ttp80) cc_final: 0.6843 (ttp80) REVERT: C 58 ASN cc_start: 0.8520 (t0) cc_final: 0.8188 (t0) REVERT: C 107 ARG cc_start: 0.7606 (mpt-90) cc_final: 0.7363 (mpt-90) REVERT: C 118 ASP cc_start: 0.8300 (t0) cc_final: 0.8042 (t0) REVERT: C 230 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8151 (mm) REVERT: C 255 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: E 77 ASN cc_start: 0.8226 (p0) cc_final: 0.7981 (p0) REVERT: E 145 GLU cc_start: 0.6841 (pm20) cc_final: 0.6605 (pm20) REVERT: E 351 TRP cc_start: 0.8161 (t60) cc_final: 0.7565 (t60) REVERT: E 401 ARG cc_start: 0.8224 (ttt-90) cc_final: 0.8007 (ttm170) REVERT: F 23 ASP cc_start: 0.6311 (m-30) cc_final: 0.4749 (t70) REVERT: F 83 GLU cc_start: 0.8697 (tp30) cc_final: 0.8432 (tp30) REVERT: F 92 ILE cc_start: 0.8767 (mt) cc_final: 0.8564 (mt) REVERT: F 105 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7902 (tt) REVERT: F 145 GLU cc_start: 0.7346 (pp20) cc_final: 0.7058 (pp20) REVERT: F 190 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8050 (tm-30) REVERT: D 51 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8248 (pp) REVERT: D 121 GLU cc_start: 0.7864 (pm20) cc_final: 0.7630 (pm20) REVERT: D 138 ARG cc_start: 0.7205 (mmm-85) cc_final: 0.6938 (mtm-85) REVERT: D 165 ARG cc_start: 0.8032 (mmm-85) cc_final: 0.7438 (mmm160) REVERT: D 171 GLU cc_start: 0.8258 (mp0) cc_final: 0.7497 (mp0) outliers start: 34 outliers final: 24 residues processed: 236 average time/residue: 0.1022 time to fit residues: 32.5547 Evaluate side-chains 237 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 209 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 336 ILE Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 14 optimal weight: 0.8980 chunk 82 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 111 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 281 ASN F 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.189000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.124714 restraints weight = 10864.389| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.58 r_work: 0.3294 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.5700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9626 Z= 0.138 Angle : 0.599 8.103 13059 Z= 0.284 Chirality : 0.042 0.164 1542 Planarity : 0.003 0.041 1664 Dihedral : 5.422 40.439 1395 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.53 % Allowed : 20.33 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.24), residues: 1244 helix: 0.11 (0.25), residues: 494 sheet: -0.85 (0.40), residues: 167 loop : -2.18 (0.23), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 211 TYR 0.014 0.001 TYR E 258 PHE 0.012 0.001 PHE E 319 TRP 0.010 0.001 TRP C 246 HIS 0.002 0.001 HIS E 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 ( 9624) covalent geometry : angle 0.59871 / 0.28 (13059) hydrogen bonds : bond 0.03072 / 1.97 ( 256) hydrogen bonds : angle 4.36890 / 2.96 ( 741) Misc. bond : bond 0.00064 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7541 (ttp80) cc_final: 0.6668 (ttp80) REVERT: C 91 ASN cc_start: 0.7845 (p0) cc_final: 0.7640 (p0) REVERT: C 107 ARG cc_start: 0.7683 (mpt-90) cc_final: 0.7419 (mpt-90) REVERT: C 142 TYR cc_start: 0.8523 (m-10) cc_final: 0.8311 (m-80) REVERT: C 212 MET cc_start: 0.5126 (mtp) cc_final: 0.4673 (mtp) REVERT: C 230 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8228 (mm) REVERT: C 255 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8268 (mp0) REVERT: E 77 ASN cc_start: 0.8299 (p0) cc_final: 0.8054 (p0) REVERT: E 145 GLU cc_start: 0.6903 (pm20) cc_final: 0.6589 (pm20) REVERT: E 146 GLN cc_start: 0.8107 (pm20) cc_final: 0.7528 (pt0) REVERT: E 351 TRP cc_start: 0.8251 (t60) cc_final: 0.7640 (t60) REVERT: E 401 ARG cc_start: 0.8386 (ttt-90) cc_final: 0.8064 (ttm170) REVERT: F 23 ASP cc_start: 0.6230 (m-30) cc_final: 0.4704 (t70) REVERT: F 83 GLU cc_start: 0.8705 (tp30) cc_final: 0.8397 (tp30) REVERT: F 145 GLU cc_start: 0.7549 (pp20) cc_final: 0.7288 (pp20) REVERT: F 190 GLU cc_start: 0.8504 (tm-30) cc_final: 0.8135 (tm-30) REVERT: D 51 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8296 (pp) REVERT: D 73 MET cc_start: 0.8057 (tpp) cc_final: 0.7410 (mmm) REVERT: D 121 GLU cc_start: 0.7858 (pm20) cc_final: 0.7617 (pm20) REVERT: D 138 ARG cc_start: 0.7264 (mmm-85) cc_final: 0.6989 (mtm-85) REVERT: D 142 ARG cc_start: 0.7582 (mtm-85) cc_final: 0.7199 (mtt-85) REVERT: D 165 ARG cc_start: 0.8082 (mmm-85) cc_final: 0.7510 (mmm160) REVERT: D 171 GLU cc_start: 0.8284 (mp0) cc_final: 0.7519 (mp0) REVERT: D 212 MET cc_start: 0.5838 (pmm) cc_final: 0.4219 (ppp) outliers start: 34 outliers final: 23 residues processed: 224 average time/residue: 0.1049 time to fit residues: 31.4679 Evaluate side-chains 237 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 120 optimal weight: 0.3980 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 91 optimal weight: 0.7980 chunk 111 optimal weight: 0.4980 chunk 98 optimal weight: 9.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 281 ASN ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 HIS ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.190726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.126944 restraints weight = 10946.099| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 2.59 r_work: 0.3318 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3168 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.5766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9626 Z= 0.106 Angle : 0.584 11.554 13059 Z= 0.272 Chirality : 0.041 0.157 1542 Planarity : 0.003 0.035 1664 Dihedral : 5.276 42.460 1395 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.70 % Allowed : 20.85 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.24), residues: 1244 helix: 0.38 (0.25), residues: 492 sheet: -0.95 (0.40), residues: 165 loop : -2.14 (0.23), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 211 TYR 0.014 0.001 TYR E 258 PHE 0.011 0.001 PHE D 30 TRP 0.012 0.001 TRP C 246 HIS 0.007 0.001 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 9624) covalent geometry : angle 0.58358 / 0.27 (13059) hydrogen bonds : bond 0.02676 / 1.73 ( 256) hydrogen bonds : angle 4.27130 / 2.89 ( 741) Misc. bond : bond 0.00038 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 212 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7509 (ttp80) cc_final: 0.6655 (ttp80) REVERT: C 91 ASN cc_start: 0.7806 (p0) cc_final: 0.7599 (p0) REVERT: C 107 ARG cc_start: 0.7690 (mpt-90) cc_final: 0.7421 (mpt-90) REVERT: C 118 ASP cc_start: 0.8476 (t0) cc_final: 0.8269 (t0) REVERT: C 212 MET cc_start: 0.5210 (mtp) cc_final: 0.4888 (mtp) REVERT: C 230 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8189 (mm) REVERT: C 255 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8258 (mp0) REVERT: E 77 ASN cc_start: 0.8272 (p0) cc_final: 0.8008 (p0) REVERT: E 145 GLU cc_start: 0.6879 (pm20) cc_final: 0.6544 (pm20) REVERT: E 146 GLN cc_start: 0.8091 (pm20) cc_final: 0.7494 (pt0) REVERT: E 301 ASP cc_start: 0.8642 (t0) cc_final: 0.7922 (m-30) REVERT: E 351 TRP cc_start: 0.8100 (t60) cc_final: 0.7479 (t60) REVERT: E 401 ARG cc_start: 0.8312 (ttt-90) cc_final: 0.7987 (ttm170) REVERT: F 23 ASP cc_start: 0.6298 (m-30) cc_final: 0.4704 (t70) REVERT: F 83 GLU cc_start: 0.8752 (tp30) cc_final: 0.8439 (tp30) REVERT: F 145 GLU cc_start: 0.7430 (pp20) cc_final: 0.7095 (pp20) REVERT: F 190 GLU cc_start: 0.8492 (tm-30) cc_final: 0.8107 (tm-30) REVERT: D 11 LEU cc_start: 0.8515 (mm) cc_final: 0.8293 (mm) REVERT: D 51 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8372 (pp) REVERT: D 73 MET cc_start: 0.8010 (tpp) cc_final: 0.7432 (mmm) REVERT: D 121 GLU cc_start: 0.7900 (pm20) cc_final: 0.7646 (pm20) REVERT: D 138 ARG cc_start: 0.7207 (mmm-85) cc_final: 0.6998 (mtm-85) REVERT: D 142 ARG cc_start: 0.7549 (mtm-85) cc_final: 0.7153 (mtt-85) REVERT: D 165 ARG cc_start: 0.8100 (mmm-85) cc_final: 0.7498 (mmm160) REVERT: D 171 GLU cc_start: 0.8300 (mp0) cc_final: 0.7501 (mp0) REVERT: D 212 MET cc_start: 0.5637 (pmm) cc_final: 0.3937 (ppp) outliers start: 26 outliers final: 18 residues processed: 225 average time/residue: 0.0944 time to fit residues: 28.4522 Evaluate side-chains 222 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 86 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 93 optimal weight: 0.2980 chunk 116 optimal weight: 3.9990 chunk 110 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 58 ASN C 281 ASN ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.190489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.126366 restraints weight = 10821.474| |-----------------------------------------------------------------------------| r_work (start): 0.3440 rms_B_bonded: 2.62 r_work: 0.3315 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.5896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9626 Z= 0.106 Angle : 0.576 10.955 13059 Z= 0.269 Chirality : 0.041 0.148 1542 Planarity : 0.003 0.036 1664 Dihedral : 5.174 42.469 1395 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 2.70 % Allowed : 20.75 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.24), residues: 1244 helix: 0.54 (0.25), residues: 490 sheet: -0.91 (0.41), residues: 166 loop : -2.08 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 211 TYR 0.014 0.001 TYR E 258 PHE 0.011 0.001 PHE E 319 TRP 0.011 0.001 TRP C 246 HIS 0.003 0.000 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 ( 9624) covalent geometry : angle 0.57582 / 0.27 (13059) hydrogen bonds : bond 0.02687 / 1.74 ( 256) hydrogen bonds : angle 4.22084 / 2.87 ( 741) Misc. bond : bond 0.00039 / 0.02 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 210 time to evaluate : 0.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7492 (ttp80) cc_final: 0.6629 (ttp80) REVERT: C 91 ASN cc_start: 0.7790 (p0) cc_final: 0.7577 (p0) REVERT: C 107 ARG cc_start: 0.7635 (mpt-90) cc_final: 0.7358 (mpt-90) REVERT: C 118 ASP cc_start: 0.8513 (t0) cc_final: 0.8285 (t0) REVERT: C 212 MET cc_start: 0.5164 (mtp) cc_final: 0.4914 (mtp) REVERT: C 230 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8207 (mm) REVERT: C 245 LYS cc_start: 0.8762 (ptpt) cc_final: 0.8487 (pttm) REVERT: C 255 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8269 (mp0) REVERT: E 77 ASN cc_start: 0.8273 (p0) cc_final: 0.7991 (p0) REVERT: E 97 TYR cc_start: 0.8913 (p90) cc_final: 0.8559 (p90) REVERT: E 145 GLU cc_start: 0.6927 (pm20) cc_final: 0.6595 (pm20) REVERT: E 146 GLN cc_start: 0.8088 (pm20) cc_final: 0.7520 (pt0) REVERT: E 301 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.7969 (m-30) REVERT: E 351 TRP cc_start: 0.8139 (t60) cc_final: 0.7528 (t60) REVERT: E 401 ARG cc_start: 0.8314 (ttt-90) cc_final: 0.7997 (ttm170) REVERT: F 23 ASP cc_start: 0.6343 (m-30) cc_final: 0.4694 (t70) REVERT: F 145 GLU cc_start: 0.7539 (pp20) cc_final: 0.7106 (pp20) REVERT: F 151 ARG cc_start: 0.8266 (tpp80) cc_final: 0.7792 (ttm170) REVERT: F 190 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8062 (tm-30) REVERT: D 11 LEU cc_start: 0.8541 (mm) cc_final: 0.8324 (mm) REVERT: D 51 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8394 (pp) REVERT: D 73 MET cc_start: 0.8021 (tpp) cc_final: 0.7465 (mmm) REVERT: D 121 GLU cc_start: 0.7899 (pm20) cc_final: 0.7675 (pm20) REVERT: D 142 ARG cc_start: 0.7516 (mtm-85) cc_final: 0.7095 (mtt-85) REVERT: D 152 GLN cc_start: 0.8316 (tp40) cc_final: 0.7977 (mm-40) REVERT: D 165 ARG cc_start: 0.8099 (mmm-85) cc_final: 0.7517 (mmm160) REVERT: D 171 GLU cc_start: 0.8296 (mp0) cc_final: 0.7472 (mp0) REVERT: D 212 MET cc_start: 0.5330 (pmm) cc_final: 0.2538 (tpt) outliers start: 26 outliers final: 19 residues processed: 223 average time/residue: 0.0991 time to fit residues: 29.6381 Evaluate side-chains 229 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 206 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 138 TRP Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 205 MET Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 301 ASP Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 194 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 88 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 106 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 96 optimal weight: 0.4980 chunk 94 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 101 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 86 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 281 ASN ** C 317 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.189997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.127733 restraints weight = 10754.111| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.92 r_work: 0.3295 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.6000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9626 Z= 0.109 Angle : 0.583 11.252 13059 Z= 0.272 Chirality : 0.042 0.148 1542 Planarity : 0.003 0.036 1664 Dihedral : 5.172 42.118 1395 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.59 % Allowed : 21.16 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.24), residues: 1244 helix: 0.58 (0.25), residues: 494 sheet: -0.80 (0.41), residues: 165 loop : -2.02 (0.24), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 211 TYR 0.014 0.001 TYR E 258 PHE 0.012 0.001 PHE E 319 TRP 0.011 0.001 TRP C 246 HIS 0.002 0.000 HIS F 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 ( 9624) covalent geometry : angle 0.58270 / 0.27 (13059) hydrogen bonds : bond 0.02692 / 1.74 ( 256) hydrogen bonds : angle 4.24694 / 2.89 ( 741) Misc. bond : bond 0.00042 / 0.02 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2543.06 seconds wall clock time: 44 minutes 2.86 seconds (2642.86 seconds total)