Starting phenix.real_space_refine on Mon Jul 28 01:53:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7arl_11886/07_2025/7arl_11886.cif Found real_map, /net/cci-nas-00/data/ceres_data/7arl_11886/07_2025/7arl_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7arl_11886/07_2025/7arl_11886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7arl_11886/07_2025/7arl_11886.map" model { file = "/net/cci-nas-00/data/ceres_data/7arl_11886/07_2025/7arl_11886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7arl_11886/07_2025/7arl_11886.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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, 'GLU:plan': 6, 'ARG:plan': 7, '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: {'GLN:plan1': 1, 'ARG:plan': 5, 'ASN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 3} 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 Unresolved non-hydrogen dihedrals: 2 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: 6.23, per 1000 atoms: 0.66 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: 2.31 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.99 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: 2.60 Time building geometry restraints manager: 2.75 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: 5461 21.89 - 43.77: 294 43.77 - 65.66: 30 65.66 - 87.54: 8 87.54 - 109.43: 1 Dihedral angle restraints: 5794 sinusoidal: 2224 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 5791 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 225 or resid 301 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: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.660 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7006 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 : 13.091 109.426 3496 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.27 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.002 0.000 TRP E 321 HIS 0.001 0.000 HIS E 188 PHE 0.011 0.001 PHE F 30 TYR 0.007 0.001 TYR C 199 ARG 0.002 0.000 ARG E 19 Details of bonding type rmsd hydrogen bonds : bond 0.33796 ( 256) hydrogen bonds : angle 11.25393 ( 741) covalent geometry : bond 0.00321 ( 9624) covalent geometry : angle 0.73020 (13059) Misc. bond : bond 0.07005 ( 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 : 0.899 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: 0.7921 (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: 0.2550 time to fit residues: 101.1581 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 : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.0000 chunk 93 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 97 optimal weight: 20.0000 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 6.9990 chunk 72 optimal weight: 0.9990 chunk 112 optimal weight: 0.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4338 r_free = 0.4338 target = 0.208593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.150708 restraints weight = 10820.482| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.97 r_work: 0.3564 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2748 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= 0.121 Angle : 0.591 9.466 13059 Z= 0.277 Chirality : 0.041 0.133 1542 Planarity : 0.004 0.048 1664 Dihedral : 6.045 74.143 1401 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.39 % Allowed : 14.73 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.59 (0.18), residues: 1244 helix: -3.37 (0.15), residues: 468 sheet: -1.97 (0.44), residues: 139 loop : -3.05 (0.19), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 246 HIS 0.005 0.001 HIS F 96 PHE 0.012 0.001 PHE E 319 TYR 0.016 0.001 TYR E 322 ARG 0.004 0.000 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 256) hydrogen bonds : angle 5.58236 ( 741) covalent geometry : bond 0.00266 ( 9624) covalent geometry : angle 0.59058 (13059) Misc. bond : bond 0.00053 ( 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 262 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 239 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 96 ILE cc_start: 0.8615 (tp) cc_final: 0.8344 (tp) REVERT: C 107 ARG cc_start: 0.7490 (mpt-90) cc_final: 0.7203 (mpt-90) REVERT: C 142 TYR cc_start: 0.8208 (m-10) cc_final: 0.7763 (m-10) REVERT: C 175 MET cc_start: 0.2963 (ppp) cc_final: 0.2458 (ppp) REVERT: C 193 ASN cc_start: 0.8828 (t0) cc_final: 0.8500 (t0) REVERT: C 235 LEU cc_start: 0.8294 (mt) cc_final: 0.8017 (mp) REVERT: C 255 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: C 262 MET cc_start: 0.8280 (tmm) cc_final: 0.7958 (ttp) REVERT: E 77 ASN cc_start: 0.8160 (p0) cc_final: 0.7954 (p0) REVERT: E 97 TYR cc_start: 0.8895 (p90) cc_final: 0.8489 (p90) REVERT: E 145 GLU cc_start: 0.6787 (pm20) cc_final: 0.5539 (pm20) REVERT: E 147 GLN cc_start: 0.8486 (mt0) cc_final: 0.8058 (mt0) REVERT: E 210 ASP cc_start: 0.8149 (m-30) cc_final: 0.7400 (t0) REVERT: E 321 TRP cc_start: 0.6648 (m-90) cc_final: 0.6205 (t-100) REVERT: E 374 GLU cc_start: 0.8630 (tt0) cc_final: 0.8315 (tt0) REVERT: F 48 LYS cc_start: 0.7171 (mtmt) cc_final: 0.6963 (mtmm) REVERT: F 73 MET cc_start: 0.8091 (mmm) cc_final: 0.7537 (tpp) REVERT: F 105 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7963 (tt) REVERT: F 116 LYS cc_start: 0.8708 (mtmt) cc_final: 0.8459 (mtmm) REVERT: D 8 CYS cc_start: 0.7689 (m) cc_final: 0.7254 (m) REVERT: D 30 PHE cc_start: 0.8108 (p90) cc_final: 0.7786 (p90) REVERT: D 71 GLN cc_start: 0.7476 (tm-30) cc_final: 0.6769 (tm-30) REVERT: D 121 GLU cc_start: 0.7903 (pm20) cc_final: 0.7548 (pm20) REVERT: D 153 ARG cc_start: 0.8002 (mtp85) cc_final: 0.7388 (ttm110) REVERT: D 165 ARG cc_start: 0.7615 (mmm-85) cc_final: 0.7113 (mmm160) REVERT: D 171 GLU cc_start: 0.8332 (mp0) cc_final: 0.7566 (mp0) REVERT: D 212 MET cc_start: 0.6578 (pmm) cc_final: 0.5263 (ppp) outliers start: 23 outliers final: 14 residues processed: 247 average time/residue: 0.3146 time to fit residues: 105.1630 Evaluate side-chains 222 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 C residue 306 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 148 ILE 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 128 GLU 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 62 optimal weight: 0.1980 chunk 24 optimal weight: 0.4980 chunk 109 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 63 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN C 161 GLN C 281 ASN E 124 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN D 96 HIS D 140 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.191579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.129331 restraints weight = 10888.275| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.94 r_work: 0.3281 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9626 Z= 0.214 Angle : 0.689 10.351 13059 Z= 0.333 Chirality : 0.045 0.152 1542 Planarity : 0.004 0.036 1664 Dihedral : 6.654 55.167 1401 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.11 % Allowed : 17.12 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.47 (0.21), residues: 1244 helix: -2.07 (0.20), residues: 485 sheet: -1.76 (0.43), residues: 144 loop : -2.63 (0.21), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 246 HIS 0.005 0.001 HIS F 96 PHE 0.017 0.002 PHE E 319 TYR 0.019 0.002 TYR E 366 ARG 0.006 0.001 ARG E 12 Details of bonding type rmsd hydrogen bonds : bond 0.04465 ( 256) hydrogen bonds : angle 5.17549 ( 741) covalent geometry : bond 0.00490 ( 9624) covalent geometry : angle 0.68932 (13059) Misc. bond : bond 0.00133 ( 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 256 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 226 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7672 (ttp80) cc_final: 0.6812 (ttp80) REVERT: C 107 ARG cc_start: 0.7613 (mpt-90) cc_final: 0.7372 (mpt-90) REVERT: C 136 ASP cc_start: 0.8737 (m-30) cc_final: 0.8519 (m-30) REVERT: C 142 TYR cc_start: 0.8252 (m-10) cc_final: 0.7861 (m-10) REVERT: C 175 MET cc_start: 0.3209 (ppp) cc_final: 0.2691 (ppp) REVERT: C 212 MET cc_start: 0.4520 (mtp) cc_final: 0.4216 (mtp) REVERT: C 245 LYS cc_start: 0.8750 (ptpt) cc_final: 0.8476 (pttp) REVERT: C 255 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.7975 (mp0) REVERT: C 299 ILE cc_start: 0.8795 (tp) cc_final: 0.8558 (tp) REVERT: C 320 SER cc_start: 0.8836 (OUTLIER) cc_final: 0.8636 (t) REVERT: C 363 LEU cc_start: 0.8822 (tp) cc_final: 0.8526 (tp) REVERT: E 351 TRP cc_start: 0.8077 (t60) cc_final: 0.7467 (t60) REVERT: E 374 GLU cc_start: 0.8686 (tt0) cc_final: 0.8302 (tt0) REVERT: F 23 ASP cc_start: 0.5960 (m-30) cc_final: 0.4636 (t70) REVERT: F 105 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7991 (tt) REVERT: F 116 LYS cc_start: 0.8800 (mtmt) cc_final: 0.8590 (mtmm) REVERT: F 190 GLU cc_start: 0.8228 (tm-30) cc_final: 0.7904 (tm-30) REVERT: D 36 GLU cc_start: 0.6424 (mt-10) cc_final: 0.5929 (mt-10) REVERT: D 121 GLU cc_start: 0.7870 (pm20) cc_final: 0.7411 (pm20) REVERT: D 145 GLU cc_start: 0.7399 (pm20) cc_final: 0.6910 (pm20) REVERT: D 165 ARG cc_start: 0.7881 (mmm-85) cc_final: 0.7272 (mmm160) REVERT: D 171 GLU cc_start: 0.8308 (mp0) cc_final: 0.7651 (mp0) REVERT: D 212 MET cc_start: 0.6131 (pmm) cc_final: 0.5315 (ppp) outliers start: 30 outliers final: 14 residues processed: 238 average time/residue: 0.2411 time to fit residues: 76.7032 Evaluate side-chains 208 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 224 LEU Chi-restraints excluded: chain C residue 255 GLU 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 365 ILE Chi-restraints excluded: chain E residue 368 ILE Chi-restraints excluded: chain F residue 48 LYS 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 18 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 90 optimal weight: 0.9980 chunk 88 optimal weight: 0.0170 chunk 75 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 79 optimal weight: 20.0000 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 ASN C 131 ASN C 281 ASN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 141 HIS F 162 ASN D 96 HIS D 140 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.194496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.132328 restraints weight = 10791.520| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.09 r_work: 0.3315 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4817 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= 0.100 Angle : 0.564 9.388 13059 Z= 0.264 Chirality : 0.041 0.138 1542 Planarity : 0.003 0.026 1664 Dihedral : 6.147 58.354 1401 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.42 % Allowed : 18.36 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.22), residues: 1244 helix: -1.17 (0.23), residues: 486 sheet: -1.51 (0.41), residues: 155 loop : -2.45 (0.22), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP E 138 HIS 0.004 0.001 HIS F 96 PHE 0.010 0.001 PHE E 319 TYR 0.015 0.001 TYR E 258 ARG 0.003 0.000 ARG C 15 Details of bonding type rmsd hydrogen bonds : bond 0.02841 ( 256) hydrogen bonds : angle 4.65445 ( 741) covalent geometry : bond 0.00234 ( 9624) covalent geometry : angle 0.56447 (13059) Misc. bond : bond 0.00048 ( 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: 33 poor density : 212 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7689 (ttp80) cc_final: 0.6812 (ttp80) REVERT: C 107 ARG cc_start: 0.7648 (mpt-90) cc_final: 0.7398 (mpt-90) REVERT: C 142 TYR cc_start: 0.8164 (m-10) cc_final: 0.7775 (m-10) REVERT: C 149 GLN cc_start: 0.8432 (tp40) cc_final: 0.8135 (mt0) REVERT: C 175 MET cc_start: 0.3296 (ppp) cc_final: 0.2820 (ppp) REVERT: C 212 MET cc_start: 0.4471 (mtp) cc_final: 0.4195 (mtp) REVERT: C 245 LYS cc_start: 0.8775 (ptpt) cc_final: 0.8503 (pttp) REVERT: C 255 GLU cc_start: 0.8692 (OUTLIER) cc_final: 0.8041 (mp0) REVERT: C 303 GLN cc_start: 0.8039 (mt0) cc_final: 0.7637 (mt0) REVERT: C 363 LEU cc_start: 0.8682 (tp) cc_final: 0.8413 (tp) REVERT: E 301 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8052 (m-30) REVERT: E 351 TRP cc_start: 0.8053 (t60) cc_final: 0.7374 (t60) REVERT: F 23 ASP cc_start: 0.5997 (m-30) cc_final: 0.4709 (t70) REVERT: F 83 GLU cc_start: 0.8588 (tp30) cc_final: 0.8283 (tp30) REVERT: F 105 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7941 (tt) REVERT: F 190 GLU cc_start: 0.8093 (tm-30) cc_final: 0.7736 (tm-30) REVERT: D 121 GLU cc_start: 0.7822 (pm20) cc_final: 0.7441 (pm20) REVERT: D 145 GLU cc_start: 0.7608 (pm20) cc_final: 0.7129 (pm20) REVERT: D 165 ARG cc_start: 0.7922 (mmm-85) cc_final: 0.7352 (mmm160) REVERT: D 171 GLU cc_start: 0.8285 (mp0) cc_final: 0.7635 (mp0) REVERT: D 212 MET cc_start: 0.5705 (pmm) cc_final: 0.4887 (ppp) outliers start: 33 outliers final: 17 residues processed: 229 average time/residue: 0.2749 time to fit residues: 83.9800 Evaluate side-chains 222 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.967 ------------------------------------------------------------------------------- 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 255 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 195 LEU Chi-restraints excluded: chain E residue 205 MET 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 66 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 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 82 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 89 optimal weight: 0.0000 chunk 105 optimal weight: 8.9990 chunk 78 optimal weight: 0.7980 chunk 118 optimal weight: 0.2980 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 58 ASN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 152 GLN D 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.194304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.129692 restraints weight = 10933.164| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.66 r_work: 0.3352 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9626 Z= 0.093 Angle : 0.544 8.731 13059 Z= 0.252 Chirality : 0.041 0.157 1542 Planarity : 0.003 0.028 1664 Dihedral : 5.935 53.576 1401 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.80 % Allowed : 18.88 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.22), residues: 1244 helix: -0.64 (0.24), residues: 489 sheet: -1.31 (0.43), residues: 149 loop : -2.33 (0.22), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 246 HIS 0.002 0.000 HIS F 137 PHE 0.010 0.001 PHE E 319 TYR 0.014 0.001 TYR E 258 ARG 0.003 0.000 ARG F 151 Details of bonding type rmsd hydrogen bonds : bond 0.02663 ( 256) hydrogen bonds : angle 4.41341 ( 741) covalent geometry : bond 0.00216 ( 9624) covalent geometry : angle 0.54358 (13059) Misc. bond : bond 0.00043 ( 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 243 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 216 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7752 (ttp80) cc_final: 0.6868 (ttp80) REVERT: C 107 ARG cc_start: 0.7689 (mpt-90) cc_final: 0.7475 (mpt-90) REVERT: C 118 ASP cc_start: 0.8268 (t0) cc_final: 0.8023 (t0) REVERT: C 142 TYR cc_start: 0.8214 (m-10) cc_final: 0.7836 (m-10) REVERT: C 175 MET cc_start: 0.3415 (ppp) cc_final: 0.2938 (ppp) REVERT: C 212 MET cc_start: 0.4892 (mtp) cc_final: 0.4532 (mtp) REVERT: C 245 LYS cc_start: 0.8796 (ptpt) cc_final: 0.8500 (pttp) REVERT: C 255 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8205 (mp0) REVERT: C 281 ASN cc_start: 0.8520 (t160) cc_final: 0.8114 (t0) REVERT: C 363 LEU cc_start: 0.8771 (tp) cc_final: 0.8490 (tp) REVERT: E 351 TRP cc_start: 0.8017 (t60) cc_final: 0.7417 (t60) REVERT: F 23 ASP cc_start: 0.6124 (m-30) cc_final: 0.4763 (t70) REVERT: F 83 GLU cc_start: 0.8694 (tp30) cc_final: 0.8463 (tp30) REVERT: F 105 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.8008 (tt) REVERT: F 190 GLU cc_start: 0.8190 (tm-30) cc_final: 0.7796 (tm-30) REVERT: D 121 GLU cc_start: 0.7876 (pm20) cc_final: 0.7481 (pm20) REVERT: D 142 ARG cc_start: 0.7615 (ttm-80) cc_final: 0.7359 (ttm-80) REVERT: D 145 GLU cc_start: 0.7701 (pm20) cc_final: 0.7255 (pm20) REVERT: D 165 ARG cc_start: 0.7899 (mmm-85) cc_final: 0.7304 (mmm160) REVERT: D 171 GLU cc_start: 0.8342 (mp0) cc_final: 0.7706 (mp0) REVERT: D 212 MET cc_start: 0.5713 (pmm) cc_final: 0.5009 (ppp) outliers start: 27 outliers final: 22 residues processed: 229 average time/residue: 0.3212 time to fit residues: 98.7247 Evaluate side-chains 223 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 199 time to evaluate : 1.825 ------------------------------------------------------------------------------- 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 195 GLU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 205 MET 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 46 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 13 optimal weight: 0.0050 chunk 92 optimal weight: 0.0470 chunk 31 optimal weight: 0.9980 chunk 85 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 77 optimal weight: 0.5980 overall best weight: 0.4892 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 134 GLN D 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.194066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.133022 restraints weight = 10942.772| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 3.12 r_work: 0.3321 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.5094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9626 Z= 0.090 Angle : 0.536 9.021 13059 Z= 0.249 Chirality : 0.040 0.134 1542 Planarity : 0.003 0.028 1664 Dihedral : 5.845 49.552 1401 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 3.01 % Allowed : 19.50 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.23), residues: 1244 helix: -0.25 (0.24), residues: 498 sheet: -1.15 (0.43), residues: 149 loop : -2.17 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 246 HIS 0.002 0.000 HIS F 96 PHE 0.010 0.001 PHE E 319 TYR 0.014 0.001 TYR E 258 ARG 0.003 0.000 ARG C 15 Details of bonding type rmsd hydrogen bonds : bond 0.02490 ( 256) hydrogen bonds : angle 4.22191 ( 741) covalent geometry : bond 0.00209 ( 9624) covalent geometry : angle 0.53552 (13059) Misc. bond : bond 0.00041 ( 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 243 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7684 (ttp80) cc_final: 0.6770 (ttp80) REVERT: C 107 ARG cc_start: 0.7646 (mpt-90) cc_final: 0.7427 (mpt-90) REVERT: C 118 ASP cc_start: 0.8247 (t0) cc_final: 0.7986 (t0) REVERT: C 142 TYR cc_start: 0.8169 (m-10) cc_final: 0.7771 (m-10) REVERT: C 175 MET cc_start: 0.3373 (ppp) cc_final: 0.2874 (ppp) REVERT: C 245 LYS cc_start: 0.8815 (ptpt) cc_final: 0.8564 (pttp) REVERT: C 255 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.8112 (mp0) REVERT: C 281 ASN cc_start: 0.8348 (t160) cc_final: 0.8131 (t0) REVERT: C 363 LEU cc_start: 0.8626 (tp) cc_final: 0.8327 (tp) REVERT: E 77 ASN cc_start: 0.8281 (p0) cc_final: 0.8044 (p0) REVERT: E 301 ASP cc_start: 0.8620 (OUTLIER) cc_final: 0.8025 (m-30) REVERT: E 351 TRP cc_start: 0.8071 (t60) cc_final: 0.7460 (t60) REVERT: F 23 ASP cc_start: 0.6261 (m-30) cc_final: 0.4770 (t70) REVERT: F 83 GLU cc_start: 0.8758 (tp30) cc_final: 0.8452 (tp30) REVERT: F 92 ILE cc_start: 0.8668 (mt) cc_final: 0.8453 (mt) REVERT: F 105 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7856 (tt) REVERT: F 138 ARG cc_start: 0.8297 (ptp-170) cc_final: 0.7803 (ptp-170) REVERT: F 145 GLU cc_start: 0.7206 (pp20) cc_final: 0.6910 (pp20) REVERT: F 190 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7795 (tm-30) REVERT: D 107 ASN cc_start: 0.8015 (m-40) cc_final: 0.7757 (m110) REVERT: D 121 GLU cc_start: 0.7844 (pm20) cc_final: 0.7444 (pm20) REVERT: D 142 ARG cc_start: 0.7456 (ttm-80) cc_final: 0.7211 (ttm-80) REVERT: D 145 GLU cc_start: 0.7719 (pm20) cc_final: 0.7277 (pm20) REVERT: D 165 ARG cc_start: 0.7929 (mmm-85) cc_final: 0.7337 (mmm160) REVERT: D 171 GLU cc_start: 0.8249 (mp0) cc_final: 0.7480 (mp0) REVERT: D 212 MET cc_start: 0.5409 (pmm) cc_final: 0.4817 (ppp) outliers start: 29 outliers final: 22 residues processed: 230 average time/residue: 0.3168 time to fit residues: 98.2518 Evaluate side-chains 235 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 210 time to evaluate : 1.252 ------------------------------------------------------------------------------- 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 195 GLU Chi-restraints excluded: chain C residue 224 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 316 VAL Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 129 LEU 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 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 51 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 69 optimal weight: 0.8980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 GLN ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN D 140 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.185812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120122 restraints weight = 11037.482| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.64 r_work: 0.3237 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9626 Z= 0.189 Angle : 0.642 9.695 13059 Z= 0.305 Chirality : 0.044 0.141 1542 Planarity : 0.003 0.038 1664 Dihedral : 6.357 53.505 1401 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 3.84 % Allowed : 20.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.23), residues: 1244 helix: -0.31 (0.24), residues: 502 sheet: -0.95 (0.43), residues: 156 loop : -2.19 (0.24), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 138 HIS 0.003 0.001 HIS F 137 PHE 0.013 0.002 PHE E 319 TYR 0.014 0.002 TYR E 262 ARG 0.005 0.000 ARG E 139 Details of bonding type rmsd hydrogen bonds : bond 0.03654 ( 256) hydrogen bonds : angle 4.52381 ( 741) covalent geometry : bond 0.00462 ( 9624) covalent geometry : angle 0.64163 (13059) Misc. bond : bond 0.00118 ( 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 240 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7539 (ttp80) cc_final: 0.6659 (ttp80) REVERT: C 107 ARG cc_start: 0.7789 (mpt-90) cc_final: 0.7566 (mpt-90) REVERT: C 212 MET cc_start: 0.5263 (mtp) cc_final: 0.4720 (mtp) REVERT: C 230 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8350 (mm) REVERT: C 245 LYS cc_start: 0.8785 (ptpt) cc_final: 0.8504 (pttp) REVERT: C 255 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8306 (mp0) REVERT: C 281 ASN cc_start: 0.8621 (t160) cc_final: 0.8316 (t0) REVERT: C 363 LEU cc_start: 0.8829 (tp) cc_final: 0.8538 (tp) REVERT: E 97 TYR cc_start: 0.9027 (p90) cc_final: 0.8723 (p90) REVERT: E 146 GLN cc_start: 0.8062 (pm20) cc_final: 0.7439 (pt0) REVERT: E 301 ASP cc_start: 0.8809 (OUTLIER) cc_final: 0.8166 (m-30) REVERT: E 351 TRP cc_start: 0.8320 (t60) cc_final: 0.7697 (t60) REVERT: E 353 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8182 (mt-10) REVERT: F 23 ASP cc_start: 0.6265 (m-30) cc_final: 0.4774 (t70) REVERT: F 190 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7909 (tm-30) REVERT: D 51 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8371 (pp) REVERT: D 121 GLU cc_start: 0.7973 (pm20) cc_final: 0.7626 (pm20) REVERT: D 165 ARG cc_start: 0.8164 (mmm-85) cc_final: 0.7612 (mmm160) REVERT: D 171 GLU cc_start: 0.8246 (mp0) cc_final: 0.7487 (mp0) REVERT: D 212 MET cc_start: 0.5411 (pmm) cc_final: 0.4958 (ppp) outliers start: 37 outliers final: 26 residues processed: 221 average time/residue: 0.2591 time to fit residues: 75.9014 Evaluate side-chains 237 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 195 GLU 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 316 VAL Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 129 LEU 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 97 HIS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 1.9990 chunk 118 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 67 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 111 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 131 ASN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.187570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.124935 restraints weight = 11061.949| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 3.05 r_work: 0.3241 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.5906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9626 Z= 0.129 Angle : 0.599 9.230 13059 Z= 0.280 Chirality : 0.043 0.172 1542 Planarity : 0.003 0.036 1664 Dihedral : 6.137 52.870 1401 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.84 % Allowed : 20.54 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.23), residues: 1244 helix: -0.02 (0.24), residues: 504 sheet: -1.07 (0.43), residues: 155 loop : -2.19 (0.23), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 246 HIS 0.002 0.000 HIS E 65 PHE 0.015 0.001 PHE E 319 TYR 0.014 0.001 TYR E 258 ARG 0.008 0.000 ARG F 211 Details of bonding type rmsd hydrogen bonds : bond 0.02926 ( 256) hydrogen bonds : angle 4.35318 ( 741) covalent geometry : bond 0.00312 ( 9624) covalent geometry : angle 0.59943 (13059) Misc. bond : bond 0.00071 ( 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 244 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 207 time to evaluate : 1.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7476 (ttp80) cc_final: 0.6612 (ttp80) REVERT: C 107 ARG cc_start: 0.7627 (mpt-90) cc_final: 0.7407 (mpt-90) REVERT: C 118 ASP cc_start: 0.8494 (t0) cc_final: 0.8246 (t0) REVERT: C 141 LYS cc_start: 0.8293 (mtpp) cc_final: 0.7975 (mtmm) REVERT: C 201 MET cc_start: 0.9093 (ptp) cc_final: 0.8813 (ptm) REVERT: C 212 MET cc_start: 0.5006 (mtp) cc_final: 0.4514 (mtp) REVERT: C 230 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8295 (mm) REVERT: C 245 LYS cc_start: 0.8785 (ptpt) cc_final: 0.8544 (pttp) REVERT: C 255 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8048 (mp0) REVERT: C 281 ASN cc_start: 0.8418 (t160) cc_final: 0.8205 (t0) REVERT: C 346 ILE cc_start: 0.3269 (OUTLIER) cc_final: 0.3027 (mt) REVERT: C 363 LEU cc_start: 0.8724 (tp) cc_final: 0.8421 (tp) REVERT: E 77 ASN cc_start: 0.8139 (p0) cc_final: 0.7910 (p0) REVERT: E 97 TYR cc_start: 0.8919 (p90) cc_final: 0.8621 (p90) REVERT: E 145 GLU cc_start: 0.6955 (pm20) cc_final: 0.6689 (pm20) REVERT: E 301 ASP cc_start: 0.8604 (OUTLIER) cc_final: 0.7872 (m-30) REVERT: E 351 TRP cc_start: 0.8298 (t60) cc_final: 0.7671 (t60) REVERT: E 353 GLU cc_start: 0.8244 (mt-10) cc_final: 0.7998 (mt-10) REVERT: F 23 ASP cc_start: 0.6366 (m-30) cc_final: 0.4708 (t70) REVERT: F 83 GLU cc_start: 0.8671 (tp30) cc_final: 0.8434 (tp30) REVERT: F 145 GLU cc_start: 0.7348 (pp20) cc_final: 0.6971 (pp20) REVERT: F 190 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7914 (tm-30) REVERT: D 51 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8334 (pp) REVERT: D 73 MET cc_start: 0.8042 (tpp) cc_final: 0.7323 (mmm) REVERT: D 121 GLU cc_start: 0.7913 (pm20) cc_final: 0.7600 (pm20) REVERT: D 165 ARG cc_start: 0.8135 (mmm-85) cc_final: 0.7591 (mmm160) REVERT: D 171 GLU cc_start: 0.8230 (mp0) cc_final: 0.7433 (mp0) outliers start: 37 outliers final: 25 residues processed: 225 average time/residue: 0.2710 time to fit residues: 80.6288 Evaluate side-chains 234 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 195 GLU 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 346 ILE Chi-restraints excluded: chain C residue 386 ARG Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 85 VAL Chi-restraints excluded: chain E residue 129 LEU 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 245 THR 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 97 HIS Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 54 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 106 optimal weight: 1.9990 chunk 83 optimal weight: 0.1980 chunk 29 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.0010 chunk 85 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 74 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 overall best weight: 0.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 309 GLN E 201 HIS ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.190032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.127083 restraints weight = 10869.426| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.95 r_work: 0.3292 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.5917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9626 Z= 0.098 Angle : 0.587 11.373 13059 Z= 0.272 Chirality : 0.041 0.159 1542 Planarity : 0.003 0.035 1664 Dihedral : 5.797 45.113 1401 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.11 % Allowed : 21.27 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.24), residues: 1244 helix: 0.33 (0.25), residues: 500 sheet: -0.99 (0.43), residues: 155 loop : -2.13 (0.23), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 246 HIS 0.002 0.000 HIS E 188 PHE 0.011 0.001 PHE D 30 TYR 0.015 0.001 TYR E 258 ARG 0.007 0.000 ARG F 211 Details of bonding type rmsd hydrogen bonds : bond 0.02460 ( 256) hydrogen bonds : angle 4.21330 ( 741) covalent geometry : bond 0.00224 ( 9624) covalent geometry : angle 0.58674 (13059) Misc. bond : bond 0.00047 ( 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 235 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 205 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7489 (ttp80) cc_final: 0.6561 (ttp80) REVERT: C 107 ARG cc_start: 0.7685 (mpt-90) cc_final: 0.7463 (mpt-90) REVERT: C 118 ASP cc_start: 0.8498 (t0) cc_final: 0.8220 (t0) REVERT: C 201 MET cc_start: 0.9193 (ptp) cc_final: 0.8926 (ptm) REVERT: C 245 LYS cc_start: 0.8737 (ptpt) cc_final: 0.8487 (pttm) REVERT: C 255 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8287 (mp0) REVERT: C 281 ASN cc_start: 0.8477 (t160) cc_final: 0.8059 (t0) REVERT: C 296 GLU cc_start: 0.8311 (mp0) cc_final: 0.8083 (mp0) REVERT: C 363 LEU cc_start: 0.8726 (tp) cc_final: 0.8434 (tp) REVERT: E 77 ASN cc_start: 0.8290 (p0) cc_final: 0.8030 (p0) REVERT: E 83 ASP cc_start: 0.7924 (p0) cc_final: 0.7543 (m-30) REVERT: E 145 GLU cc_start: 0.6936 (pm20) cc_final: 0.6579 (pm20) REVERT: E 301 ASP cc_start: 0.8676 (OUTLIER) cc_final: 0.7966 (m-30) REVERT: E 351 TRP cc_start: 0.8214 (t60) cc_final: 0.7563 (t60) REVERT: E 353 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8062 (mt-10) REVERT: F 23 ASP cc_start: 0.6357 (m-30) cc_final: 0.4708 (t70) REVERT: F 83 GLU cc_start: 0.8769 (tp30) cc_final: 0.8542 (tp30) REVERT: F 92 ILE cc_start: 0.8918 (mm) cc_final: 0.8700 (mm) REVERT: F 138 ARG cc_start: 0.7846 (ptp-170) cc_final: 0.7468 (ptp-170) REVERT: F 145 GLU cc_start: 0.7384 (pp20) cc_final: 0.6973 (pp20) REVERT: F 190 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7980 (tm-30) REVERT: D 37 MET cc_start: 0.4508 (OUTLIER) cc_final: 0.3793 (pmm) REVERT: D 51 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8280 (pp) REVERT: D 73 MET cc_start: 0.8093 (tpp) cc_final: 0.7776 (mmm) REVERT: D 121 GLU cc_start: 0.7943 (pm20) cc_final: 0.7641 (pm20) REVERT: D 165 ARG cc_start: 0.8119 (mmm-85) cc_final: 0.7530 (mmm160) REVERT: D 171 GLU cc_start: 0.8279 (mp0) cc_final: 0.7472 (mp0) outliers start: 30 outliers final: 22 residues processed: 220 average time/residue: 0.3173 time to fit residues: 93.2179 Evaluate side-chains 224 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 198 time to evaluate : 1.099 ------------------------------------------------------------------------------- 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 195 GLU Chi-restraints excluded: chain C residue 224 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 68 ILE Chi-restraints excluded: chain E residue 85 VAL 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 F residue 168 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 54 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 84 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 85 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 52 optimal weight: 0.0970 chunk 18 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 46 optimal weight: 5.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.188724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124745 restraints weight = 10952.106| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.61 r_work: 0.3288 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.6056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9626 Z= 0.107 Angle : 0.593 11.230 13059 Z= 0.275 Chirality : 0.042 0.152 1542 Planarity : 0.003 0.037 1664 Dihedral : 5.753 43.261 1401 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.01 % Allowed : 21.58 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.24), residues: 1244 helix: 0.50 (0.25), residues: 496 sheet: -0.79 (0.43), residues: 157 loop : -2.10 (0.23), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 246 HIS 0.002 0.000 HIS E 188 PHE 0.013 0.001 PHE E 319 TYR 0.014 0.001 TYR E 258 ARG 0.009 0.000 ARG F 211 Details of bonding type rmsd hydrogen bonds : bond 0.02659 ( 256) hydrogen bonds : angle 4.20401 ( 741) covalent geometry : bond 0.00254 ( 9624) covalent geometry : angle 0.59269 (13059) Misc. bond : bond 0.00060 ( 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: 29 poor density : 207 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7505 (ttp80) cc_final: 0.6580 (ttp80) REVERT: C 107 ARG cc_start: 0.7727 (mpt-90) cc_final: 0.7493 (mpt-90) REVERT: C 118 ASP cc_start: 0.8516 (t0) cc_final: 0.8284 (t0) REVERT: C 141 LYS cc_start: 0.8427 (mtpp) cc_final: 0.7987 (mtmm) REVERT: C 181 GLN cc_start: 0.8910 (pt0) cc_final: 0.8612 (pt0) REVERT: C 201 MET cc_start: 0.9168 (ptp) cc_final: 0.8903 (ptm) REVERT: C 245 LYS cc_start: 0.8742 (ptpt) cc_final: 0.8501 (pttm) REVERT: C 255 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8277 (mp0) REVERT: C 281 ASN cc_start: 0.8524 (t160) cc_final: 0.8185 (t0) REVERT: C 363 LEU cc_start: 0.8740 (tp) cc_final: 0.8437 (tp) REVERT: E 77 ASN cc_start: 0.8307 (p0) cc_final: 0.8024 (p0) REVERT: E 83 ASP cc_start: 0.7969 (p0) cc_final: 0.7559 (m-30) REVERT: E 97 TYR cc_start: 0.8953 (p90) cc_final: 0.8635 (p90) REVERT: E 301 ASP cc_start: 0.8677 (OUTLIER) cc_final: 0.7960 (m-30) REVERT: E 351 TRP cc_start: 0.8226 (t60) cc_final: 0.7571 (t60) REVERT: E 353 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8021 (mt-10) REVERT: F 83 GLU cc_start: 0.8747 (tp30) cc_final: 0.8529 (tp30) REVERT: F 92 ILE cc_start: 0.8975 (mm) cc_final: 0.8758 (mm) REVERT: F 145 GLU cc_start: 0.7393 (pp20) cc_final: 0.6946 (pp20) REVERT: F 190 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7995 (tm-30) REVERT: D 37 MET cc_start: 0.4788 (OUTLIER) cc_final: 0.4216 (pmm) REVERT: D 51 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8305 (pp) REVERT: D 73 MET cc_start: 0.8128 (tpp) cc_final: 0.7577 (mmm) REVERT: D 121 GLU cc_start: 0.7956 (pm20) cc_final: 0.7650 (pm20) REVERT: D 165 ARG cc_start: 0.8115 (mmm-85) cc_final: 0.7552 (mmm160) REVERT: D 171 GLU cc_start: 0.8335 (mp0) cc_final: 0.7505 (mp0) outliers start: 29 outliers final: 23 residues processed: 221 average time/residue: 0.2441 time to fit residues: 71.6464 Evaluate side-chains 231 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 204 time to evaluate : 0.990 ------------------------------------------------------------------------------- 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 195 GLU Chi-restraints excluded: chain C residue 224 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 68 ILE Chi-restraints excluded: chain E residue 85 VAL 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 97 HIS Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 168 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 54 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 34 optimal weight: 0.0870 chunk 41 optimal weight: 0.6980 chunk 56 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 101 optimal weight: 9.9990 chunk 42 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 131 ASN ** C 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.188963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.125287 restraints weight = 10939.900| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 2.60 r_work: 0.3296 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9626 Z= 0.108 Angle : 0.603 11.612 13059 Z= 0.279 Chirality : 0.042 0.153 1542 Planarity : 0.003 0.037 1664 Dihedral : 5.703 43.698 1401 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.11 % Allowed : 21.58 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.24), residues: 1244 helix: 0.61 (0.25), residues: 496 sheet: -0.73 (0.43), residues: 157 loop : -2.07 (0.23), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 246 HIS 0.006 0.001 HIS F 97 PHE 0.012 0.001 PHE E 319 TYR 0.015 0.001 TYR E 258 ARG 0.008 0.000 ARG F 211 Details of bonding type rmsd hydrogen bonds : bond 0.02614 ( 256) hydrogen bonds : angle 4.20095 ( 741) covalent geometry : bond 0.00259 ( 9624) covalent geometry : angle 0.60270 (13059) Misc. bond : bond 0.00057 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6105.93 seconds wall clock time: 108 minutes 5.69 seconds (6485.69 seconds total)