Starting phenix.real_space_refine on Wed Mar 4 01:39:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7arl_11886/03_2026/7arl_11886.cif Found real_map, /net/cci-nas-00/data/ceres_data/7arl_11886/03_2026/7arl_11886.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7arl_11886/03_2026/7arl_11886.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7arl_11886/03_2026/7arl_11886.map" model { file = "/net/cci-nas-00/data/ceres_data/7arl_11886/03_2026/7arl_11886.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7arl_11886/03_2026/7arl_11886.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 56 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 6040 2.51 5 N 1651 2.21 5 O 1722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 52 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9467 Number of models: 1 Model: "" Number of chains: 9 Chain: "C" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 2969 Classifications: {'peptide': 392} Link IDs: {'PTRANS': 20, 'TRANS': 371} Chain breaks: 1 Chain: "E" Number of atoms: 3159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 409, 3159 Classifications: {'peptide': 409} Link IDs: {'PTRANS': 14, 'TRANS': 394} Chain: "F" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1545 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 8, 'TRANS': 214} Unresolved non-hydrogen bonds: 162 Unresolved non-hydrogen angles: 198 Unresolved non-hydrogen dihedrals: 126 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 7, 'ARG:plan': 7, 'GLU:plan': 6, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 105 Chain: "D" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1609 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 8, 'TRANS': 213} Unresolved non-hydrogen bonds: 89 Unresolved non-hydrogen angles: 107 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 5, 'GLN:plan1': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 52 Chain: "V" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 73 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'Z41': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 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: 2.21, per 1000 atoms: 0.23 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: 0.91 Conformation dependent library (CDL) restraints added in 529.3 milliseconds 2488 Ramachandran restraints generated. 1244 Oldfield, 0 Emsley, 1244 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2298 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 13 sheets defined 40.4% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'C' and resid 5 through 10 removed outlier: 3.775A pdb=" N ILE C 9 " --> pdb=" O VAL C 5 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLY C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 5 through 10' Processing helix chain 'C' and resid 20 through 28 removed outlier: 3.520A pdb=" N ARG C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL C 26 " --> pdb=" O PHE C 22 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER C 27 " --> pdb=" O GLY C 23 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP C 28 " --> pdb=" O ARG C 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 20 through 28' Processing helix chain 'C' and resid 28 through 59 removed outlier: 3.658A pdb=" N ILE C 32 " --> pdb=" O TRP C 28 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C 37 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N THR C 43 " --> pdb=" O MET C 39 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N VAL C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 155 removed outlier: 3.914A pdb=" N GLN C 153 " --> pdb=" O GLN C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 removed outlier: 3.815A pdb=" N GLY C 198 " --> pdb=" O GLU C 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 195 through 198' Processing helix chain 'C' and resid 248 through 252 removed outlier: 4.096A pdb=" N ASP C 251 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG C 252 " --> pdb=" O TRP C 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 248 through 252' Processing helix chain 'C' and resid 256 through 271 removed outlier: 3.635A pdb=" N VAL C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 293 removed outlier: 3.772A pdb=" N ILE C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ILE C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU C 288 " --> pdb=" O THR C 284 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N MET C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N MET C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLU C 292 " --> pdb=" O LEU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 304 removed outlier: 3.804A pdb=" N ALA C 298 " --> pdb=" O GLN C 294 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ILE C 299 " --> pdb=" O GLY C 295 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 300 " --> pdb=" O GLU C 296 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN C 303 " --> pdb=" O ILE C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 311 removed outlier: 3.732A pdb=" N MET C 311 " --> pdb=" O PRO C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 339 removed outlier: 3.953A pdb=" N VAL C 316 " --> pdb=" O MET C 312 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLN C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ALA C 321 " --> pdb=" O GLN C 317 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLY C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE C 324 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 379 removed outlier: 3.744A pdb=" N VAL C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ILE C 366 " --> pdb=" O PRO C 362 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LEU C 377 " --> pdb=" O MET C 373 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER C 379 " --> pdb=" O ILE C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 390 removed outlier: 3.758A pdb=" N ALA C 388 " --> pdb=" O SER C 384 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR C 390 " --> pdb=" O ARG C 386 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 24 removed outlier: 4.338A pdb=" N SER E 24 " --> pdb=" O GLY E 21 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 21 through 24' Processing helix chain 'E' and resid 25 through 35 removed outlier: 3.676A pdb=" N ILE E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 59 removed outlier: 4.051A pdb=" N MET E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN E 56 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 87 Processing helix chain 'E' and resid 129 through 133 removed outlier: 4.143A pdb=" N PHE E 132 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL E 133 " --> pdb=" O PRO E 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 129 through 133' Processing helix chain 'E' and resid 151 through 159 removed outlier: 3.850A pdb=" N ALA E 155 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 212 removed outlier: 3.728A pdb=" N GLN E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 259 Processing helix chain 'E' and resid 259 through 268 removed outlier: 4.042A pdb=" N ARG E 263 " --> pdb=" O GLY E 259 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN E 266 " --> pdb=" O TYR E 262 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE E 268 " --> pdb=" O ASP E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 271 through 284 removed outlier: 3.590A pdb=" N LEU E 278 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL E 282 " --> pdb=" O LEU E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 290 Processing helix chain 'E' and resid 292 through 297 removed outlier: 3.529A pdb=" N LYS E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 309 removed outlier: 3.710A pdb=" N ILE E 302 " --> pdb=" O LYS E 298 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ALA E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL E 304 " --> pdb=" O GLY E 300 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU E 305 " --> pdb=" O ASP E 301 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU E 308 " --> pdb=" O VAL E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 316 Processing helix chain 'E' and resid 317 through 324 removed outlier: 4.225A pdb=" N TRP E 321 " --> pdb=" O ALA E 317 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 344 removed outlier: 3.760A pdb=" N GLY E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY E 334 " --> pdb=" O GLY E 330 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ILE E 337 " --> pdb=" O CYS E 333 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N VAL E 340 " --> pdb=" O ILE E 336 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL E 341 " --> pdb=" O ILE E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 345 through 353 removed outlier: 3.710A pdb=" N GLU E 350 " --> pdb=" O THR E 346 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TRP E 351 " --> pdb=" O PRO E 347 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE E 352 " --> pdb=" O ILE E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 404 removed outlier: 3.715A pdb=" N PHE E 381 " --> pdb=" O TRP E 377 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL E 385 " --> pdb=" O PHE E 381 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR E 386 " --> pdb=" O TYR E 382 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LEU E 393 " --> pdb=" O LEU E 389 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA E 394 " --> pdb=" O LEU E 390 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N TYR E 397 " --> pdb=" O LEU E 393 " (cutoff:3.500A) Proline residue: E 398 - end of helix removed outlier: 3.722A pdb=" N ARG E 401 " --> pdb=" O TYR E 397 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN E 404 " --> pdb=" O ARG E 400 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 57 Processing helix chain 'F' and resid 77 through 88 removed outlier: 3.932A pdb=" N ALA F 82 " --> pdb=" O SER F 78 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU F 84 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG F 85 " --> pdb=" O LYS F 81 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN F 87 " --> pdb=" O GLU F 83 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS F 88 " --> pdb=" O LEU F 84 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 109 removed outlier: 3.550A pdb=" N ASN F 107 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 115 removed outlier: 3.550A pdb=" N ILE F 114 " --> pdb=" O MET F 110 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY F 115 " --> pdb=" O PRO F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 132 removed outlier: 4.098A pdb=" N ASN F 123 " --> pdb=" O PRO F 119 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N SER F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA F 126 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU F 130 " --> pdb=" O ALA F 126 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS F 131 " --> pdb=" O LEU F 127 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA F 132 " --> pdb=" O GLU F 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 149 through 159 removed outlier: 3.589A pdb=" N ARG F 153 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA F 155 " --> pdb=" O ARG F 151 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA F 159 " --> pdb=" O ALA F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 194 removed outlier: 3.841A pdb=" N ILE F 184 " --> pdb=" O ASN F 180 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N PHE F 185 " --> pdb=" O ALA F 181 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN F 192 " --> pdb=" O LEU F 188 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG F 193 " --> pdb=" O GLY F 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 57 Processing helix chain 'D' and resid 77 through 85 removed outlier: 3.836A pdb=" N ALA D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLU D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG D 85 " --> pdb=" O LYS D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 109 removed outlier: 3.993A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 115 removed outlier: 3.505A pdb=" N ILE D 114 " --> pdb=" O MET D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 134 removed outlier: 3.640A pdb=" N MET D 129 " --> pdb=" O ARG D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 160 removed outlier: 3.899A pdb=" N ALA D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA D 159 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 160 " --> pdb=" O ILE D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 189 removed outlier: 3.520A pdb=" N ILE D 184 " --> pdb=" O ASN D 180 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 93 through 96 removed outlier: 3.578A pdb=" N ILE C 96 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLY C 221 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TRP C 222 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ALA C 66 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N SER C 69 " --> pdb=" O LYS C 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 98 through 99 removed outlier: 3.687A pdb=" N MET C 201 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ASN C 204 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ASN C 143 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N SER C 180 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL C 164 " --> pdb=" O ARG C 182 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 91 through 96 removed outlier: 6.714A pdb=" N LYS E 227 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ALA E 94 " --> pdb=" O ALA E 225 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA E 225 " --> pdb=" O ALA E 94 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLU E 67 " --> pdb=" O LYS E 252 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 102 through 103 removed outlier: 3.943A pdb=" N GLY E 102 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE E 113 " --> pdb=" O GLY E 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 115 through 116 removed outlier: 3.574A pdb=" N MET E 205 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE E 149 " --> pdb=" O MET E 205 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 165 through 170 removed outlier: 3.788A pdb=" N VAL E 185 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LYS E 183 " --> pdb=" O ILE E 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 14 through 17 removed outlier: 3.619A pdb=" N VAL F 20 " --> pdb=" O GLU F 17 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 67 through 68 Processing sheet with id=AA9, first strand: chain 'F' and resid 89 through 92 removed outlier: 5.846A pdb=" N GLY F 90 " --> pdb=" O LEU F 168 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ASP F 170 " --> pdb=" O GLY F 90 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE F 92 " --> pdb=" O ASP F 170 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL F 202 " --> pdb=" O ALA F 169 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 218 through 219 Processing sheet with id=AB2, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.597A pdb=" N CYS D 8 " --> pdb=" O PHE D 30 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE D 67 " --> pdb=" O GLN D 7 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 37 through 38 removed outlier: 6.796A pdb=" N PHE D 199 " --> pdb=" O MET D 38 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LEU D 200 " --> pdb=" O VAL D 167 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ALA D 169 " --> pdb=" O LEU D 200 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N GLY D 90 " --> pdb=" O LEU D 168 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 218 through 219 256 hydrogen bonds defined for protein. 741 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.34 Time building geometry restraints manager: 1.20 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 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: 0.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.280 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.920 ------------------------------------------------------------------------------- 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 : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.83 (0.15), residues: 1244 helix: -5.07 (0.05), residues: 413 sheet: -2.45 (0.43), residues: 132 loop : -3.47 (0.16), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 19 TYR 0.007 0.001 TYR C 199 PHE 0.011 0.001 PHE F 30 TRP 0.002 0.000 TRP E 321 HIS 0.001 0.000 HIS E 188 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 9624) covalent geometry : angle 0.73020 (13059) hydrogen bonds : bond 0.33796 ( 256) hydrogen bonds : angle 11.25393 ( 741) 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 : 0.298 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 142 TYR cc_start: 0.8049 (m-10) cc_final: 0.7803 (m-10) REVERT: C 175 MET cc_start: 0.2773 (ppp) cc_final: 0.2452 (ppp) REVERT: C 193 ASN cc_start: 0.8372 (t0) cc_final: 0.8128 (t0) REVERT: C 201 MET cc_start: 0.8586 (ptt) cc_final: 0.8373 (ptm) REVERT: E 77 ASN cc_start: 0.8200 (p0) cc_final: 0.7920 (p0) REVERT: E 98 ILE cc_start: 0.8313 (mt) cc_final: 0.7943 (pt) REVERT: E 145 GLU cc_start: 0.6768 (pm20) cc_final: 0.5617 (pm20) REVERT: E 147 GLN cc_start: 0.8322 (mt0) cc_final: 0.8028 (mt0) REVERT: E 321 TRP cc_start: 0.5316 (m-90) cc_final: 0.4800 (t-100) REVERT: D 8 CYS cc_start: 0.7322 (m) cc_final: 0.7015 (m) REVERT: D 71 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7563 (tm-30) REVERT: D 107 ASN cc_start: 0.8223 (m-40) cc_final: 0.8012 (m110) REVERT: D 110 MET cc_start: 0.8454 (tpp) cc_final: 0.8225 (tpt) REVERT: D 171 GLU cc_start: 0.8187 (mp0) cc_final: 0.7523 (mp0) REVERT: D 192 ASN cc_start: 0.7165 (p0) cc_final: 0.5776 (t0) outliers start: 0 outliers final: 0 residues processed: 298 average time/residue: 0.1127 time to fit residues: 44.8194 Evaluate side-chains 229 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 229 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.0170 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 123 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4366 r_free = 0.4366 target = 0.211473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.152238 restraints weight = 10914.380| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.57 r_work: 0.3655 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3517 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.2530 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= 0.110 Angle : 0.580 9.743 13059 Z= 0.272 Chirality : 0.041 0.139 1542 Planarity : 0.004 0.052 1664 Dihedral : 5.968 77.271 1401 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.28 % Allowed : 14.63 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.58 (0.18), residues: 1244 helix: -3.30 (0.15), residues: 464 sheet: -1.98 (0.44), residues: 139 loop : -3.10 (0.19), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 58 TYR 0.015 0.001 TYR E 322 PHE 0.012 0.001 PHE F 68 TRP 0.012 0.001 TRP C 246 HIS 0.005 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9624) covalent geometry : angle 0.58027 (13059) hydrogen bonds : bond 0.03901 ( 256) hydrogen bonds : angle 5.63283 ( 741) Misc. bond : bond 0.00048 ( 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 260 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 238 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 96 ILE cc_start: 0.8660 (tp) cc_final: 0.8375 (tp) REVERT: C 107 ARG cc_start: 0.7575 (mpt-90) cc_final: 0.7258 (mpt-90) REVERT: C 142 TYR cc_start: 0.8264 (m-10) cc_final: 0.7788 (m-80) REVERT: C 175 MET cc_start: 0.2962 (ppp) cc_final: 0.2496 (ppp) REVERT: C 193 ASN cc_start: 0.8802 (t0) cc_final: 0.8457 (t0) REVERT: C 235 LEU cc_start: 0.8246 (mt) cc_final: 0.7926 (mp) REVERT: C 255 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.7988 (mp0) REVERT: C 262 MET cc_start: 0.8440 (tmm) cc_final: 0.8098 (ttp) REVERT: C 386 ARG cc_start: 0.8382 (mmm160) cc_final: 0.8181 (mmp-170) REVERT: E 77 ASN cc_start: 0.8169 (p0) cc_final: 0.7960 (p0) REVERT: E 145 GLU cc_start: 0.6784 (pm20) cc_final: 0.5499 (pm20) REVERT: E 147 GLN cc_start: 0.8524 (mt0) cc_final: 0.8109 (mt0) REVERT: E 210 ASP cc_start: 0.8150 (m-30) cc_final: 0.7430 (t0) REVERT: E 321 TRP cc_start: 0.6700 (m-90) cc_final: 0.6140 (t-100) REVERT: E 332 LEU cc_start: 0.8610 (mp) cc_final: 0.8404 (mt) REVERT: E 374 GLU cc_start: 0.8680 (tt0) cc_final: 0.8381 (tt0) REVERT: F 48 LYS cc_start: 0.7094 (mtmt) cc_final: 0.6886 (mtmm) REVERT: F 73 MET cc_start: 0.8121 (mmm) cc_final: 0.7616 (tpp) REVERT: F 105 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.8021 (tt) REVERT: F 116 LYS cc_start: 0.8684 (mtmt) cc_final: 0.8439 (mtmm) REVERT: D 8 CYS cc_start: 0.7727 (m) cc_final: 0.7240 (m) REVERT: D 71 GLN cc_start: 0.7499 (tm-30) cc_final: 0.6772 (tm-30) REVERT: D 121 GLU cc_start: 0.7928 (pm20) cc_final: 0.7605 (pm20) REVERT: D 151 ARG cc_start: 0.7650 (mtm-85) cc_final: 0.5942 (ttp80) REVERT: D 153 ARG cc_start: 0.7991 (mtp85) cc_final: 0.7382 (ttm110) REVERT: D 165 ARG cc_start: 0.7603 (mmm-85) cc_final: 0.7114 (mmm160) REVERT: D 171 GLU cc_start: 0.8345 (mp0) cc_final: 0.7623 (mp0) REVERT: D 212 MET cc_start: 0.6665 (pmm) cc_final: 0.5338 (ppp) outliers start: 22 outliers final: 12 residues processed: 247 average time/residue: 0.1032 time to fit residues: 34.2842 Evaluate side-chains 234 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 220 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain E residue 346 THR Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 103 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 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 66 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 11 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 96 optimal weight: 0.0050 chunk 76 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 96 HIS 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 = 0.4297 r_free = 0.4297 target = 0.204715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.151523 restraints weight = 10901.019| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.68 r_work: 0.3497 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9626 Z= 0.103 Angle : 0.550 10.449 13059 Z= 0.257 Chirality : 0.041 0.144 1542 Planarity : 0.003 0.033 1664 Dihedral : 5.704 55.235 1401 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.39 % Allowed : 16.29 % Favored : 81.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.37 (0.21), residues: 1244 helix: -1.89 (0.21), residues: 474 sheet: -1.83 (0.45), residues: 130 loop : -2.62 (0.20), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 15 TYR 0.012 0.001 TYR E 97 PHE 0.013 0.001 PHE E 319 TRP 0.014 0.001 TRP C 246 HIS 0.003 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 9624) covalent geometry : angle 0.55010 (13059) hydrogen bonds : bond 0.03366 ( 256) hydrogen bonds : angle 4.75921 ( 741) Misc. bond : bond 0.00081 ( 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 253 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 58 ASN cc_start: 0.8548 (t0) cc_final: 0.7948 (t0) REVERT: C 107 ARG cc_start: 0.7553 (mpt-90) cc_final: 0.7213 (mpt-90) REVERT: C 142 TYR cc_start: 0.8215 (m-10) cc_final: 0.7933 (m-10) REVERT: C 175 MET cc_start: 0.3131 (ppp) cc_final: 0.2659 (ppp) REVERT: C 193 ASN cc_start: 0.8843 (t0) cc_final: 0.8642 (t0) REVERT: C 212 MET cc_start: 0.4826 (mtp) cc_final: 0.4443 (mtp) REVERT: C 235 LEU cc_start: 0.8372 (mt) cc_final: 0.8135 (mp) REVERT: C 255 GLU cc_start: 0.8605 (mp0) cc_final: 0.8010 (mp0) REVERT: C 262 MET cc_start: 0.8188 (tmm) cc_final: 0.7963 (ttp) REVERT: C 386 ARG cc_start: 0.8293 (mmm160) cc_final: 0.8083 (mmp-170) REVERT: E 97 TYR cc_start: 0.8696 (p90) cc_final: 0.8314 (p90) REVERT: E 145 GLU cc_start: 0.6909 (pm20) cc_final: 0.5663 (pm20) REVERT: E 147 GLN cc_start: 0.8501 (mt0) cc_final: 0.7940 (mt0) REVERT: E 321 TRP cc_start: 0.6864 (m-90) cc_final: 0.6575 (m-90) REVERT: E 374 GLU cc_start: 0.8584 (tt0) cc_final: 0.8231 (tt0) REVERT: F 96 HIS cc_start: 0.4850 (OUTLIER) cc_final: 0.4584 (t-170) REVERT: F 105 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7937 (tt) REVERT: F 116 LYS cc_start: 0.8745 (mtmt) cc_final: 0.8500 (mtmm) REVERT: F 190 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7808 (tm-30) REVERT: D 36 GLU cc_start: 0.5630 (mt-10) cc_final: 0.5107 (mt-10) REVERT: D 71 GLN cc_start: 0.7557 (tm-30) cc_final: 0.6883 (tm-30) REVERT: D 121 GLU cc_start: 0.7836 (pm20) cc_final: 0.7223 (pm20) REVERT: D 142 ARG cc_start: 0.7342 (mtt90) cc_final: 0.7139 (ttm110) REVERT: D 165 ARG cc_start: 0.7750 (mmm-85) cc_final: 0.7258 (mmm160) REVERT: D 171 GLU cc_start: 0.8395 (mp0) cc_final: 0.7706 (mp0) REVERT: D 212 MET cc_start: 0.5750 (pmm) cc_final: 0.4819 (ppp) outliers start: 23 outliers final: 13 residues processed: 236 average time/residue: 0.1031 time to fit residues: 32.9350 Evaluate side-chains 216 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 201 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 68 ILE Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain F residue 96 HIS Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 42 optimal weight: 0.0270 chunk 117 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 116 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 101 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 99 optimal weight: 9.9990 overall best weight: 1.0640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 281 ASN ** C 303 GLN ** 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 = 0.4223 r_free = 0.4223 target = 0.197151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.132772 restraints weight = 10943.951| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.66 r_work: 0.3400 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 9626 Z= 0.137 Angle : 0.578 9.170 13059 Z= 0.274 Chirality : 0.042 0.136 1542 Planarity : 0.003 0.030 1664 Dihedral : 6.023 59.845 1401 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 3.22 % Allowed : 17.53 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.21), residues: 1244 helix: -1.21 (0.23), residues: 470 sheet: -1.38 (0.44), residues: 143 loop : -2.42 (0.21), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 15 TYR 0.012 0.001 TYR E 366 PHE 0.030 0.002 PHE F 95 TRP 0.015 0.001 TRP E 138 HIS 0.016 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 9624) covalent geometry : angle 0.57783 (13059) hydrogen bonds : bond 0.03222 ( 256) hydrogen bonds : angle 4.57364 ( 741) Misc. bond : bond 0.00082 ( 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 244 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 213 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 175 MET cc_start: 0.3304 (ppp) cc_final: 0.2849 (ppp) REVERT: C 231 LYS cc_start: 0.9010 (ptpt) cc_final: 0.8809 (ptpp) REVERT: C 255 GLU cc_start: 0.8929 (mp0) cc_final: 0.8290 (mp0) REVERT: C 281 ASN cc_start: 0.8658 (t160) cc_final: 0.8369 (t0) REVERT: C 386 ARG cc_start: 0.8415 (mmm160) cc_final: 0.8077 (mmp-170) REVERT: E 321 TRP cc_start: 0.7320 (m-90) cc_final: 0.7072 (m-90) REVERT: E 401 ARG cc_start: 0.8295 (ttt-90) cc_final: 0.8067 (ttm170) REVERT: F 105 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7958 (tt) REVERT: F 190 GLU cc_start: 0.8305 (tm-30) cc_final: 0.7914 (tm-30) REVERT: D 165 ARG cc_start: 0.7949 (mmm-85) cc_final: 0.7373 (mmm160) REVERT: D 171 GLU cc_start: 0.8385 (mp0) cc_final: 0.7723 (mp0) REVERT: D 212 MET cc_start: 0.5864 (pmm) cc_final: 0.5002 (ppp) outliers start: 31 outliers final: 21 residues processed: 223 average time/residue: 0.1053 time to fit residues: 31.7257 Evaluate side-chains 223 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 201 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 75 TRP Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 195 LEU Chi-restraints excluded: chain E residue 226 LEU Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 48 LYS Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 85 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 94 optimal weight: 0.2980 chunk 3 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 152 GLN 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 = 0.4177 r_free = 0.4177 target = 0.192682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.131121 restraints weight = 10904.979| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 3.10 r_work: 0.3293 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9626 Z= 0.145 Angle : 0.593 8.308 13059 Z= 0.282 Chirality : 0.042 0.153 1542 Planarity : 0.003 0.036 1664 Dihedral : 6.104 52.958 1401 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 3.53 % Allowed : 18.78 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.41 (0.22), residues: 1244 helix: -0.75 (0.24), residues: 482 sheet: -1.42 (0.42), residues: 148 loop : -2.36 (0.22), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 15 TYR 0.012 0.002 TYR E 366 PHE 0.016 0.001 PHE E 319 TRP 0.016 0.001 TRP E 138 HIS 0.004 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 9624) covalent geometry : angle 0.59347 (13059) hydrogen bonds : bond 0.03237 ( 256) hydrogen bonds : angle 4.55599 ( 741) Misc. bond : bond 0.00081 ( 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: 34 poor density : 209 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 ARG cc_start: 0.7695 (mpt-90) cc_final: 0.7432 (mpt-90) REVERT: C 118 ASP cc_start: 0.8245 (t0) cc_final: 0.8023 (t0) REVERT: C 175 MET cc_start: 0.3231 (ppp) cc_final: 0.2740 (ppp) REVERT: C 182 ARG cc_start: 0.7935 (tpp80) cc_final: 0.7404 (tpt90) REVERT: C 230 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8138 (mm) REVERT: C 255 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8111 (mp0) REVERT: C 281 ASN cc_start: 0.8441 (t160) cc_final: 0.8153 (t0) REVERT: C 315 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8347 (tpp) REVERT: C 386 ARG cc_start: 0.8287 (mmm160) cc_final: 0.7969 (mmp-170) REVERT: E 351 TRP cc_start: 0.8052 (t60) cc_final: 0.7412 (t60) REVERT: E 401 ARG cc_start: 0.8303 (ttt-90) cc_final: 0.8036 (ttm170) REVERT: F 23 ASP cc_start: 0.6000 (m-30) cc_final: 0.4667 (t70) REVERT: F 83 GLU cc_start: 0.8671 (tp30) cc_final: 0.8412 (tp30) REVERT: F 105 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7922 (tt) REVERT: F 135 LEU cc_start: 0.7733 (mm) cc_final: 0.7307 (mm) REVERT: F 190 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7936 (tm-30) REVERT: D 121 GLU cc_start: 0.7941 (pm20) cc_final: 0.7192 (pm20) REVERT: D 142 ARG cc_start: 0.7388 (ttm-80) cc_final: 0.7072 (ttm-80) REVERT: D 165 ARG cc_start: 0.8035 (mmm-85) cc_final: 0.7452 (mmm160) REVERT: D 171 GLU cc_start: 0.8277 (mp0) cc_final: 0.7624 (mp0) REVERT: D 212 MET cc_start: 0.5715 (pmm) cc_final: 0.5214 (ppp) outliers start: 34 outliers final: 20 residues processed: 227 average time/residue: 0.1111 time to fit residues: 33.6541 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 : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 315 MET Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain E residue 75 TRP 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 364 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 48 LYS Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 127 LEU Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 153 ARG Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 1 optimal weight: 0.0970 chunk 99 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 chunk 68 optimal weight: 0.2980 chunk 80 optimal weight: 7.9990 chunk 122 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 162 ASN D 140 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.193916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.131149 restraints weight = 10976.171| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 2.94 r_work: 0.3330 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9626 Z= 0.099 Angle : 0.553 8.454 13059 Z= 0.258 Chirality : 0.041 0.139 1542 Planarity : 0.003 0.026 1664 Dihedral : 6.019 56.933 1401 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.01 % Allowed : 19.29 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.23), residues: 1244 helix: -0.33 (0.24), residues: 488 sheet: -1.24 (0.43), residues: 148 loop : -2.23 (0.23), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 211 TYR 0.013 0.001 TYR E 258 PHE 0.011 0.001 PHE E 319 TRP 0.012 0.001 TRP C 246 HIS 0.003 0.000 HIS E 84 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 9624) covalent geometry : angle 0.55271 (13059) hydrogen bonds : bond 0.02709 ( 256) hydrogen bonds : angle 4.33271 ( 741) Misc. bond : bond 0.00045 ( 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 233 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 ARG cc_start: 0.7679 (mpt-90) cc_final: 0.7430 (mpt-90) REVERT: C 175 MET cc_start: 0.3385 (ppp) cc_final: 0.2856 (ppp) REVERT: C 182 ARG cc_start: 0.7857 (tpp80) cc_final: 0.7431 (tpt90) REVERT: C 212 MET cc_start: 0.4756 (mtp) cc_final: 0.4356 (mtp) REVERT: C 255 GLU cc_start: 0.8783 (mp0) cc_final: 0.8103 (mp0) REVERT: C 281 ASN cc_start: 0.8372 (t160) cc_final: 0.8073 (t0) REVERT: C 386 ARG cc_start: 0.8266 (mmm160) cc_final: 0.7974 (mmp-170) REVERT: E 77 ASN cc_start: 0.8229 (p0) cc_final: 0.8001 (p0) REVERT: E 145 GLU cc_start: 0.6905 (pm20) cc_final: 0.6239 (pm20) REVERT: E 351 TRP cc_start: 0.8105 (t60) cc_final: 0.7449 (t60) REVERT: E 401 ARG cc_start: 0.8254 (ttt-90) cc_final: 0.8023 (ttm170) REVERT: F 23 ASP cc_start: 0.6120 (m-30) cc_final: 0.4742 (t70) REVERT: F 83 GLU cc_start: 0.8664 (tp30) cc_final: 0.8378 (tp30) REVERT: F 105 LEU cc_start: 0.8149 (OUTLIER) cc_final: 0.7929 (tt) REVERT: F 190 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8037 (tm-30) REVERT: D 121 GLU cc_start: 0.8048 (pm20) cc_final: 0.7772 (pm20) REVERT: D 142 ARG cc_start: 0.7349 (ttm-80) cc_final: 0.7042 (ttm-80) REVERT: D 165 ARG cc_start: 0.7971 (mmm-85) cc_final: 0.7415 (mmm160) REVERT: D 171 GLU cc_start: 0.8270 (mp0) cc_final: 0.7628 (mp0) outliers start: 29 outliers final: 22 residues processed: 219 average time/residue: 0.1095 time to fit residues: 32.0293 Evaluate side-chains 227 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 204 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 100 ASP Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 75 TRP 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 364 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 48 LYS 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 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 0.9990 chunk 64 optimal weight: 0.5980 chunk 87 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 0.2980 chunk 27 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 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 = 0.4176 r_free = 0.4176 target = 0.192872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.129286 restraints weight = 10952.043| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.65 r_work: 0.3345 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3194 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.5213 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= 0.099 Angle : 0.552 7.991 13059 Z= 0.257 Chirality : 0.041 0.143 1542 Planarity : 0.003 0.029 1664 Dihedral : 5.753 48.821 1401 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.22 % Allowed : 18.98 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.23), residues: 1244 helix: -0.02 (0.25), residues: 494 sheet: -1.16 (0.46), residues: 138 loop : -2.11 (0.23), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 211 TYR 0.014 0.001 TYR E 258 PHE 0.011 0.001 PHE E 319 TRP 0.012 0.001 TRP C 246 HIS 0.001 0.000 HIS E 65 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 9624) covalent geometry : angle 0.55214 (13059) hydrogen bonds : bond 0.02635 ( 256) hydrogen bonds : angle 4.21965 ( 741) Misc. bond : bond 0.00045 ( 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 255 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 224 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 107 ARG cc_start: 0.7750 (mpt-90) cc_final: 0.7489 (mpt-90) REVERT: C 118 ASP cc_start: 0.8325 (t0) cc_final: 0.8075 (t0) REVERT: C 141 LYS cc_start: 0.8349 (mtpp) cc_final: 0.7994 (mtmm) REVERT: C 175 MET cc_start: 0.3503 (ppp) cc_final: 0.3023 (ppp) REVERT: C 212 MET cc_start: 0.5128 (mtp) cc_final: 0.4703 (mtp) REVERT: C 230 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8206 (mm) REVERT: C 255 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8335 (mp0) REVERT: C 281 ASN cc_start: 0.8504 (t160) cc_final: 0.8089 (t0) REVERT: C 386 ARG cc_start: 0.8313 (mmm160) cc_final: 0.8064 (mmp-170) REVERT: E 77 ASN cc_start: 0.8275 (p0) cc_final: 0.8054 (p0) REVERT: E 145 GLU cc_start: 0.6959 (pm20) cc_final: 0.6298 (pm20) REVERT: E 351 TRP cc_start: 0.8122 (t60) cc_final: 0.7504 (t60) REVERT: E 401 ARG cc_start: 0.8378 (ttt-90) cc_final: 0.8102 (ttm170) REVERT: F 23 ASP cc_start: 0.6254 (m-30) cc_final: 0.4773 (t70) REVERT: F 83 GLU cc_start: 0.8718 (tp30) cc_final: 0.8408 (tp30) REVERT: F 105 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7953 (tt) REVERT: F 190 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8097 (tm-30) REVERT: D 73 MET cc_start: 0.7984 (tpp) cc_final: 0.7349 (mmm) REVERT: D 121 GLU cc_start: 0.8018 (pm20) cc_final: 0.7647 (pm20) REVERT: D 142 ARG cc_start: 0.7337 (ttm-80) cc_final: 0.7054 (ttm-80) REVERT: D 165 ARG cc_start: 0.8067 (mmm-85) cc_final: 0.7505 (mmm160) REVERT: D 171 GLU cc_start: 0.8295 (mp0) cc_final: 0.7545 (mp0) REVERT: D 212 MET cc_start: 0.6318 (pmm) cc_final: 0.4753 (ppp) outliers start: 31 outliers final: 23 residues processed: 238 average time/residue: 0.1127 time to fit residues: 36.0528 Evaluate side-chains 237 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 211 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 100 ASP 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 306 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 75 TRP 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 336 ILE Chi-restraints excluded: chain E residue 364 ASP Chi-restraints excluded: chain F residue 24 VAL Chi-restraints excluded: chain F residue 48 LYS 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 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 14 optimal weight: 0.0000 chunk 82 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 16 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 57 optimal weight: 9.9990 chunk 111 optimal weight: 0.0670 chunk 58 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 113 optimal weight: 4.9990 overall best weight: 0.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 309 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 = 0.4192 r_free = 0.4192 target = 0.194146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.134182 restraints weight = 10887.142| |-----------------------------------------------------------------------------| r_work (start): 0.3533 rms_B_bonded: 3.05 r_work: 0.3333 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.5319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9626 Z= 0.091 Angle : 0.546 8.046 13059 Z= 0.254 Chirality : 0.041 0.160 1542 Planarity : 0.003 0.040 1664 Dihedral : 5.580 51.786 1401 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.80 % Allowed : 19.40 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.24), residues: 1244 helix: 0.30 (0.25), residues: 490 sheet: -1.01 (0.46), residues: 138 loop : -2.12 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 211 TYR 0.014 0.001 TYR E 258 PHE 0.008 0.001 PHE E 319 TRP 0.012 0.001 TRP C 246 HIS 0.005 0.000 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00210 ( 9624) covalent geometry : angle 0.54556 (13059) hydrogen bonds : bond 0.02437 ( 256) hydrogen bonds : angle 4.12247 ( 741) Misc. bond : bond 0.00031 ( 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 236 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 0.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 107 ARG cc_start: 0.7640 (mpt-90) cc_final: 0.7370 (mpt-90) REVERT: C 175 MET cc_start: 0.3407 (ppp) cc_final: 0.2908 (ppp) REVERT: C 182 ARG cc_start: 0.7803 (tpp80) cc_final: 0.7399 (tpt90) REVERT: C 212 MET cc_start: 0.4919 (mtp) cc_final: 0.4467 (mtp) REVERT: C 230 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8160 (mm) REVERT: C 255 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8086 (mp0) REVERT: C 281 ASN cc_start: 0.8431 (t160) cc_final: 0.8124 (t0) REVERT: C 296 GLU cc_start: 0.8171 (mp0) cc_final: 0.7898 (mp0) REVERT: E 77 ASN cc_start: 0.8231 (p0) cc_final: 0.8002 (p0) REVERT: E 145 GLU cc_start: 0.6965 (pm20) cc_final: 0.6756 (pm20) REVERT: E 351 TRP cc_start: 0.8131 (t60) cc_final: 0.7526 (t60) REVERT: E 401 ARG cc_start: 0.8232 (ttt-90) cc_final: 0.8007 (ttm170) REVERT: F 23 ASP cc_start: 0.6452 (m-30) cc_final: 0.4822 (t70) REVERT: F 83 GLU cc_start: 0.8697 (tp30) cc_final: 0.8359 (tp30) REVERT: F 105 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7862 (tt) REVERT: F 190 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7993 (tm-30) REVERT: D 73 MET cc_start: 0.7942 (tpp) cc_final: 0.7269 (mmm) REVERT: D 107 ASN cc_start: 0.8115 (m-40) cc_final: 0.7871 (m110) REVERT: D 121 GLU cc_start: 0.7931 (pm20) cc_final: 0.7710 (pm20) REVERT: D 142 ARG cc_start: 0.7232 (ttm-80) cc_final: 0.6949 (ttm-80) REVERT: D 163 ASN cc_start: 0.8701 (p0) cc_final: 0.8388 (p0) REVERT: D 165 ARG cc_start: 0.8084 (mmm-85) cc_final: 0.7494 (mmm160) REVERT: D 171 GLU cc_start: 0.8226 (mp0) cc_final: 0.7462 (mp0) REVERT: D 212 MET cc_start: 0.6178 (pmm) cc_final: 0.4651 (ppp) outliers start: 27 outliers final: 19 residues processed: 223 average time/residue: 0.1107 time to fit residues: 33.2476 Evaluate side-chains 234 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 212 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain E residue 8 LEU 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 48 LYS 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 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 92 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 80 optimal weight: 0.0980 chunk 120 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 73 optimal weight: 0.8980 chunk 5 optimal weight: 0.4980 chunk 91 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.192684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.131870 restraints weight = 11011.726| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.02 r_work: 0.3311 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.5474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9626 Z= 0.100 Angle : 0.568 10.389 13059 Z= 0.263 Chirality : 0.042 0.149 1542 Planarity : 0.003 0.037 1664 Dihedral : 5.575 48.900 1401 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.59 % Allowed : 19.71 % Favored : 77.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.24), residues: 1244 helix: 0.47 (0.25), residues: 491 sheet: -0.95 (0.46), residues: 138 loop : -2.09 (0.23), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 211 TYR 0.013 0.001 TYR E 258 PHE 0.011 0.001 PHE D 30 TRP 0.011 0.001 TRP C 246 HIS 0.001 0.000 HIS C 72 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9624) covalent geometry : angle 0.56817 (13059) hydrogen bonds : bond 0.02561 ( 256) hydrogen bonds : angle 4.17431 ( 741) Misc. bond : bond 0.00041 ( 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 236 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 211 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7699 (ttp80) cc_final: 0.6854 (ttp80) REVERT: C 107 ARG cc_start: 0.7630 (mpt-90) cc_final: 0.7342 (mpt-90) REVERT: C 118 ASP cc_start: 0.8275 (t0) cc_final: 0.8001 (t0) REVERT: C 175 MET cc_start: 0.3096 (ppp) cc_final: 0.2602 (ppp) REVERT: C 181 GLN cc_start: 0.8844 (pt0) cc_final: 0.8553 (pt0) REVERT: C 182 ARG cc_start: 0.7747 (tpp80) cc_final: 0.7338 (tpt90) REVERT: C 212 MET cc_start: 0.4964 (mtp) cc_final: 0.4486 (mtp) REVERT: C 230 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8148 (mm) REVERT: C 255 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8109 (mp0) REVERT: C 281 ASN cc_start: 0.8377 (t160) cc_final: 0.8093 (t0) REVERT: C 296 GLU cc_start: 0.8181 (mp0) cc_final: 0.7916 (mp0) REVERT: E 77 ASN cc_start: 0.8223 (p0) cc_final: 0.7983 (p0) REVERT: E 145 GLU cc_start: 0.7089 (pm20) cc_final: 0.6889 (pm20) REVERT: E 351 TRP cc_start: 0.8108 (t60) cc_final: 0.7514 (t60) REVERT: E 401 ARG cc_start: 0.8228 (ttt-90) cc_final: 0.8007 (ttm170) REVERT: F 23 ASP cc_start: 0.6379 (m-30) cc_final: 0.4767 (t70) REVERT: F 105 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7858 (tt) REVERT: F 190 GLU cc_start: 0.8403 (tm-30) cc_final: 0.8020 (tm-30) REVERT: D 73 MET cc_start: 0.7951 (tpp) cc_final: 0.7313 (mmm) REVERT: D 142 ARG cc_start: 0.7275 (ttm-80) cc_final: 0.7013 (ttm-80) REVERT: D 163 ASN cc_start: 0.8705 (p0) cc_final: 0.8400 (p0) REVERT: D 165 ARG cc_start: 0.8141 (mmm-85) cc_final: 0.7559 (mmm160) REVERT: D 171 GLU cc_start: 0.8209 (mp0) cc_final: 0.7436 (mp0) REVERT: D 212 MET cc_start: 0.6134 (pmm) cc_final: 0.4364 (ppp) outliers start: 25 outliers final: 21 residues processed: 223 average time/residue: 0.1084 time to fit residues: 32.5339 Evaluate side-chains 224 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 200 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain E residue 8 LEU 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 274 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 48 LYS Chi-restraints excluded: chain F residue 76 LEU Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 28 VAL Chi-restraints excluded: chain D residue 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 13 optimal weight: 0.0070 chunk 38 optimal weight: 0.0050 chunk 93 optimal weight: 3.9990 chunk 116 optimal weight: 0.3980 chunk 110 optimal weight: 5.9990 overall best weight: 0.3612 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.194203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.134391 restraints weight = 10852.303| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 3.04 r_work: 0.3343 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 9626 Z= 0.091 Angle : 0.567 10.797 13059 Z= 0.261 Chirality : 0.041 0.148 1542 Planarity : 0.003 0.036 1664 Dihedral : 5.461 54.915 1401 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.39 % Allowed : 20.12 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.24), residues: 1244 helix: 0.65 (0.25), residues: 492 sheet: -0.89 (0.44), residues: 148 loop : -2.05 (0.23), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 211 TYR 0.014 0.001 TYR E 258 PHE 0.007 0.001 PHE E 13 TRP 0.012 0.001 TRP C 246 HIS 0.001 0.000 HIS F 137 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 9624) covalent geometry : angle 0.56675 (13059) hydrogen bonds : bond 0.02358 ( 256) hydrogen bonds : angle 4.07651 ( 741) Misc. bond : bond 0.00027 ( 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 231 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 24 ARG cc_start: 0.7678 (ttp80) cc_final: 0.6832 (ttp80) REVERT: C 107 ARG cc_start: 0.7637 (mpt-90) cc_final: 0.7359 (mpt-90) REVERT: C 161 GLN cc_start: 0.8773 (tt0) cc_final: 0.8525 (tt0) REVERT: C 175 MET cc_start: 0.3204 (ppp) cc_final: 0.2662 (ppp) REVERT: C 182 ARG cc_start: 0.7744 (tpp80) cc_final: 0.7356 (tpt90) REVERT: C 212 MET cc_start: 0.4805 (mtp) cc_final: 0.4381 (mtp) REVERT: C 230 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8151 (mm) REVERT: C 255 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8146 (mp0) REVERT: C 281 ASN cc_start: 0.8397 (t160) cc_final: 0.8111 (t0) REVERT: E 77 ASN cc_start: 0.8225 (p0) cc_final: 0.7974 (p0) REVERT: E 145 GLU cc_start: 0.6939 (pm20) cc_final: 0.6722 (pm20) REVERT: E 293 MET cc_start: 0.8163 (tpp) cc_final: 0.7874 (mmm) REVERT: E 351 TRP cc_start: 0.8175 (t60) cc_final: 0.7575 (t60) REVERT: E 401 ARG cc_start: 0.8249 (ttt-90) cc_final: 0.8033 (ttm170) REVERT: F 23 ASP cc_start: 0.6380 (m-30) cc_final: 0.4709 (t70) REVERT: F 83 GLU cc_start: 0.8657 (tp30) cc_final: 0.8446 (tp30) REVERT: F 105 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7811 (tt) REVERT: F 138 ARG cc_start: 0.7708 (ptp-170) cc_final: 0.7388 (ptp-170) REVERT: F 190 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8046 (tm-30) REVERT: D 11 LEU cc_start: 0.8409 (mm) cc_final: 0.8206 (mm) REVERT: D 73 MET cc_start: 0.7942 (tpp) cc_final: 0.7339 (mmm) REVERT: D 163 ASN cc_start: 0.8668 (p0) cc_final: 0.8377 (p0) REVERT: D 165 ARG cc_start: 0.8108 (mmm-85) cc_final: 0.7526 (mmm160) REVERT: D 171 GLU cc_start: 0.8215 (mp0) cc_final: 0.7423 (mp0) REVERT: D 212 MET cc_start: 0.6208 (pmm) cc_final: 0.4592 (ppp) outliers start: 23 outliers final: 18 residues processed: 219 average time/residue: 0.1130 time to fit residues: 33.1058 Evaluate side-chains 223 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 255 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 195 LEU 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 48 LYS 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 128 GLU Chi-restraints excluded: chain D residue 137 HIS Chi-restraints excluded: chain D residue 194 LEU Chi-restraints excluded: chain D residue 204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 88 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 96 optimal weight: 9.9990 chunk 94 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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** C 309 GLN F 152 GLN D 96 HIS D 140 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.185189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.123674 restraints weight = 10948.843| |-----------------------------------------------------------------------------| r_work (start): 0.3406 rms_B_bonded: 3.11 r_work: 0.3212 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.6122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9626 Z= 0.200 Angle : 0.684 10.800 13059 Z= 0.323 Chirality : 0.046 0.159 1542 Planarity : 0.003 0.034 1664 Dihedral : 6.196 50.880 1401 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.22 % Allowed : 20.02 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.42 (0.24), residues: 1244 helix: 0.27 (0.24), residues: 498 sheet: -0.61 (0.42), residues: 167 loop : -2.18 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 211 TYR 0.014 0.002 TYR E 258 PHE 0.014 0.002 PHE E 13 TRP 0.012 0.002 TRP E 321 HIS 0.006 0.001 HIS E 201 Details of bonding type rmsd covalent geometry : bond 0.00492 ( 9624) covalent geometry : angle 0.68378 (13059) hydrogen bonds : bond 0.03728 ( 256) hydrogen bonds : angle 4.55408 ( 741) Misc. bond : bond 0.00132 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2642.17 seconds wall clock time: 45 minutes 41.88 seconds (2741.88 seconds total)