Starting phenix.real_space_refine on Fri Jul 3 00:36:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7arm_11887/07_2026/7arm_11887.cif Found real_map, /net/cci-nas-00/data/ceres_data/7arm_11887/07_2026/7arm_11887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7arm_11887/07_2026/7arm_11887.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7arm_11887/07_2026/7arm_11887.cif" model { file = "/net/cci-nas-00/data/ceres_data/7arm_11887/07_2026/7arm_11887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7arm_11887/07_2026/7arm_11887.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7arm_11887/07_2026/7arm_11887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7arm_11887/07_2026/7arm_11887.map" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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: 4 Type Number sf(0) Gaussians S 53 5.16 5 C 6974 2.51 5 N 1931 2.21 5 O 2013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10971 Number of models: 1 Model: "" Number of chains: 7 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: 1614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1614 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PTRANS': 8, 'TRANS': 212} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 59 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1663 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 215} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 35 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: "A" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1437 Classifications: {'peptide': 182} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 174} Chain: "V" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'PLM': 1, 'Z41': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.37, per 1000 atoms: 0.22 Number of scatterers: 10971 At special positions: 0 Unit cell: (104.442, 161.226, 134.862, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 53 16.00 O 2013 8.00 N 1931 7.00 C 6974 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: 0.59 Conformation dependent library (CDL) restraints added in 378.2 milliseconds 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2638 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 14 sheets defined 37.7% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'C' and resid 5 through 10 removed outlier: 4.033A pdb=" N GLY C 10 " --> pdb=" O ALA C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 26 removed outlier: 3.593A pdb=" N ARG C 24 " --> pdb=" O ASP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 55 removed outlier: 3.574A pdb=" N ILE C 34 " --> pdb=" O SER C 30 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY C 37 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N MET C 39 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU C 45 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL C 47 " --> pdb=" O THR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 137 removed outlier: 3.864A pdb=" N LEU C 137 " --> pdb=" O GLN C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 155 removed outlier: 3.584A pdb=" N GLN C 153 " --> pdb=" O GLN C 149 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LEU C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 198 removed outlier: 3.766A 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: 4.048A pdb=" N ASP C 251 " --> pdb=" O ASP C 248 " (cutoff:3.500A) removed outlier: 3.601A 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 253 through 271 removed outlier: 3.700A pdb=" N PHE C 257 " --> pdb=" O LYS C 253 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA C 259 " --> pdb=" O GLU C 255 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL C 260 " --> pdb=" O LEU C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 293 removed outlier: 3.722A pdb=" N ILE C 282 " --> pdb=" O ALA C 278 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE C 283 " --> pdb=" O ALA C 279 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 288 " --> pdb=" O THR C 284 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET C 289 " --> pdb=" O SER C 285 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N MET C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 302 removed outlier: 3.720A pdb=" N ALA C 298 " --> pdb=" O GLN C 294 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE C 299 " --> pdb=" O GLY C 295 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN C 301 " --> pdb=" O VAL C 297 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N THR C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 337 removed outlier: 4.013A pdb=" N MET C 312 " --> pdb=" O ARG C 308 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE C 314 " --> pdb=" O ILE C 310 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN C 317 " --> pdb=" O VAL C 313 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY C 318 " --> pdb=" O PHE C 314 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ALA C 321 " --> pdb=" O GLN C 317 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY C 322 " --> pdb=" O GLY C 318 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA C 337 " --> pdb=" O GLY C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 348 removed outlier: 4.071A pdb=" N ILE C 347 " --> pdb=" O MET C 344 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLY C 348 " --> pdb=" O PRO C 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 344 through 348' Processing helix chain 'C' and resid 361 through 379 removed outlier: 3.569A pdb=" N VAL C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE C 366 " --> pdb=" O PRO C 362 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ALA C 376 " --> pdb=" O ALA C 372 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU C 377 " --> pdb=" O MET C 373 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 389 removed outlier: 3.722A pdb=" N ARG C 386 " --> pdb=" O TYR C 382 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 387 " --> pdb=" O PRO C 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 11 removed outlier: 4.060A pdb=" N LEU E 11 " --> pdb=" O LEU E 7 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 59 removed outlier: 3.919A pdb=" N ILE E 26 " --> pdb=" O MET E 22 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 28 " --> pdb=" O SER E 24 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLY E 37 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL E 38 " --> pdb=" O ILE E 34 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N VAL E 43 " --> pdb=" O ALA E 39 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA E 47 " --> pdb=" O VAL E 43 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN E 56 " --> pdb=" O GLU E 52 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASN E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 85 removed outlier: 4.014A pdb=" N ASP E 83 " --> pdb=" O GLN E 79 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 126 removed outlier: 3.599A pdb=" N ARG E 125 " --> pdb=" O GLN E 122 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU E 126 " --> pdb=" O GLU E 123 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 122 through 126' Processing helix chain 'E' and resid 129 through 133 removed outlier: 3.713A pdb=" N PHE E 132 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 3.927A 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 152 through 159 removed outlier: 3.647A pdb=" N ASP E 156 " --> pdb=" O LYS E 152 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA E 157 " --> pdb=" O GLY E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.689A pdb=" N GLN E 212 " --> pdb=" O LEU E 208 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 208 through 212' Processing helix chain 'E' and resid 235 through 244 removed outlier: 3.759A pdb=" N ARG E 239 " --> pdb=" O ASN E 235 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP E 240 " --> pdb=" O LYS E 236 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA E 241 " --> pdb=" O LEU E 237 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU E 243 " --> pdb=" O ARG E 239 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL E 244 " --> pdb=" O ASP E 240 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 263 removed outlier: 3.702A pdb=" N TYR E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 284 removed outlier: 4.294A pdb=" N TYR E 273 " --> pdb=" O ARG E 269 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU E 274 " --> pdb=" O ALA E 270 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU E 278 " --> pdb=" O LEU E 274 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N VAL E 279 " --> pdb=" O ALA E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 298 removed outlier: 3.731A pdb=" N MET E 293 " --> pdb=" O SER E 289 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA E 294 " --> pdb=" O THR E 290 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS E 296 " --> pdb=" O VAL E 292 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS E 298 " --> pdb=" O ALA E 294 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 308 removed outlier: 3.505A pdb=" N ILE E 302 " --> pdb=" O LYS E 298 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU E 305 " --> pdb=" O ASP E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 336 removed outlier: 3.622A pdb=" N ILE E 315 " --> pdb=" O LYS E 311 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE E 319 " --> pdb=" O ILE E 315 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP E 321 " --> pdb=" O ALA E 317 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA E 326 " --> pdb=" O TYR E 322 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLY E 330 " --> pdb=" O ALA E 326 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS E 333 " --> pdb=" O PHE E 329 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 345 through 353 removed outlier: 3.820A pdb=" N GLU E 350 " --> pdb=" O THR E 346 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP E 351 " --> pdb=" O PRO E 347 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE E 352 " --> pdb=" O ILE E 348 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 402 removed outlier: 3.904A pdb=" N VAL E 380 " --> pdb=" O HIS E 376 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N PHE E 381 " --> pdb=" O TRP E 377 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL E 383 " --> pdb=" O ASP E 379 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER E 391 " --> pdb=" O ALA E 387 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N TYR E 397 " --> pdb=" O LEU E 393 " (cutoff:3.500A) Proline residue: E 398 - end of helix removed outlier: 3.501A pdb=" N ARG E 401 " --> pdb=" O TYR E 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 55 removed outlier: 3.790A pdb=" N HIS F 53 " --> pdb=" O SER F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 4.047A pdb=" N VAL F 108 " --> pdb=" O ALA F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 115 removed outlier: 3.651A pdb=" N ILE F 114 " --> pdb=" O MET F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 129 removed outlier: 3.722A pdb=" N ASN F 123 " --> pdb=" O PRO F 119 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N SER F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU F 127 " --> pdb=" O ASN F 123 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU F 128 " --> pdb=" O SER F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 129 through 134 Processing helix chain 'F' and resid 147 through 160 removed outlier: 3.565A pdb=" N GLN F 152 " --> pdb=" O GLY F 148 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG F 153 " --> pdb=" O GLY F 149 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL F 154 " --> pdb=" O GLU F 150 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA F 155 " --> pdb=" O ARG F 151 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ILE F 156 " --> pdb=" O GLN F 152 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA F 159 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU F 160 " --> pdb=" O ILE F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 191 removed outlier: 4.664A pdb=" N ASP F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER F 183 " --> pdb=" O ARG F 179 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE F 184 " --> pdb=" O ASN F 180 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE F 185 " --> pdb=" O ALA F 181 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 55 removed outlier: 3.825A pdb=" N LEU D 54 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 50 through 55' Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.983A pdb=" N VAL D 108 " --> pdb=" O ALA D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 115 removed outlier: 3.517A pdb=" N GLY D 115 " --> pdb=" O PRO D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 122 removed outlier: 4.095A pdb=" N ILE D 122 " --> pdb=" O PRO D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 132 removed outlier: 3.607A pdb=" N LEU D 130 " --> pdb=" O ALA D 126 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA D 132 " --> pdb=" O GLU D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.615A pdb=" N GLU D 145 " --> pdb=" O ARG D 142 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 146 " --> pdb=" O PRO D 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 142 through 146' Processing helix chain 'D' and resid 147 through 158 removed outlier: 3.611A pdb=" N GLN D 152 " --> pdb=" O GLY D 148 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG D 153 " --> pdb=" O GLY D 149 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ALA D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 190 removed outlier: 3.674A pdb=" N ALA D 181 " --> pdb=" O ASP D 177 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASP D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER D 183 " --> pdb=" O ARG D 179 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU D 187 " --> pdb=" O SER D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 193 No H-bonds generated for 'chain 'D' and resid 191 through 193' Processing helix chain 'D' and resid 205 through 209 removed outlier: 3.926A pdb=" N LEU D 208 " --> pdb=" O ASP D 205 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA D 209 " --> pdb=" O LEU D 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 205 through 209' Processing helix chain 'A' and resid 1 through 5 removed outlier: 4.311A pdb=" N SER A 4 " --> pdb=" O ASP A 1 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ASP A 5 " --> pdb=" O ALA A 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1 through 5' Processing helix chain 'A' and resid 88 through 96 removed outlier: 4.101A pdb=" N LEU A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ILE A 93 " --> pdb=" O PRO A 89 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA A 94 " --> pdb=" O PHE A 90 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASN A 96 " --> pdb=" O LEU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 Processing sheet with id=AA1, first strand: chain 'C' and resid 67 through 69 Processing sheet with id=AA2, first strand: chain 'C' and resid 90 through 96 removed outlier: 4.705A pdb=" N ARG C 92 " --> pdb=" O TRP C 225 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N TRP C 225 " --> pdb=" O ARG C 92 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY C 221 " --> pdb=" O ILE C 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 98 through 104 removed outlier: 3.670A pdb=" N GLY C 99 " --> pdb=" O MET C 114 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N MET C 201 " --> pdb=" O VAL C 111 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C 113 " --> pdb=" O MET C 201 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL C 203 " --> pdb=" O VAL C 113 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N LEU C 115 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N ASN C 204 " --> pdb=" O ASN C 143 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ASN C 143 " --> pdb=" O ASN C 204 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER C 180 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET C 165 " --> pdb=" O VAL C 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 67 through 69 removed outlier: 3.694A pdb=" N GLU E 67 " --> pdb=" O LYS E 252 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 91 through 96 removed outlier: 4.087A pdb=" N ALA E 93 " --> pdb=" O LYS E 227 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 98 through 104 removed outlier: 3.624A pdb=" N GLY E 102 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ARG E 111 " --> pdb=" O VAL E 104 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N ALA E 204 " --> pdb=" O ALA E 112 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N GLN E 114 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N ILE E 206 " --> pdb=" O GLN E 114 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LYS E 116 " --> pdb=" O ILE E 206 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET E 205 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE E 149 " --> pdb=" O MET E 205 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N GLN E 147 " --> pdb=" O PRO E 207 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE E 150 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE E 192 " --> pdb=" O ILE E 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 14 through 16 Processing sheet with id=AA8, first strand: chain 'F' and resid 38 through 41 removed outlier: 6.309A pdb=" N MET F 38 " --> pdb=" O VAL F 201 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N THR F 203 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE F 40 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ILE F 92 " --> pdb=" O ASP F 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 12 through 13 Processing sheet with id=AB1, first strand: chain 'D' and resid 90 through 91 removed outlier: 5.707A pdb=" N GLY D 90 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL D 167 " --> pdb=" O LEU D 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.932A pdb=" N ALA A 18 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 31 through 35 removed outlier: 5.238A pdb=" N GLN A 33 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N VAL A 24 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER A 150 " --> pdb=" O ALA A 142 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ALA A 142 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLN A 126 " --> pdb=" O VAL A 143 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 66 through 70 Processing sheet with id=AB5, first strand: chain 'A' and resid 130 through 131 removed outlier: 6.274A pdb=" N ASN A 130 " --> pdb=" O HIS A 138 " (cutoff:3.500A) 275 hydrogen bonds defined for protein. 786 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: 1.48 Time building geometry restraints manager: 0.80 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: 3604 1.34 - 1.46: 1430 1.46 - 1.57: 6026 1.57 - 1.69: 0 1.69 - 1.81: 99 Bond restraints: 11159 Sorted by residual: bond pdb=" C16 Z41 V 101 " pdb=" O2 Z41 V 101 " ideal model delta sigma weight residual 1.332 1.454 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" C19 Z41 V 101 " pdb=" O3 Z41 V 101 " ideal model delta sigma weight residual 1.333 1.455 -0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" C ARG A 43 " pdb=" N PRO A 44 " ideal model delta sigma weight residual 1.334 1.387 -0.054 2.34e-02 1.83e+03 5.24e+00 bond pdb=" C GLN A 53 " pdb=" N PRO A 54 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.95e+00 bond pdb=" CA THR F 62 " pdb=" CB THR F 62 " ideal model delta sigma weight residual 1.530 1.552 -0.022 1.69e-02 3.50e+03 1.70e+00 ... (remaining 11154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 14836 2.39 - 4.78: 216 4.78 - 7.16: 44 7.16 - 9.55: 6 9.55 - 11.94: 2 Bond angle restraints: 15104 Sorted by residual: angle pdb=" N ILE E 356 " pdb=" CA ILE E 356 " pdb=" C ILE E 356 " ideal model delta sigma weight residual 113.47 108.97 4.50 1.01e+00 9.80e-01 1.98e+01 angle pdb=" C PRO F 61 " pdb=" N THR F 62 " pdb=" CA THR F 62 " ideal model delta sigma weight residual 121.54 130.03 -8.49 1.91e+00 2.74e-01 1.98e+01 angle pdb=" C GLN A 103 " pdb=" N TYR A 104 " pdb=" CA TYR A 104 " ideal model delta sigma weight residual 122.82 128.64 -5.82 1.42e+00 4.96e-01 1.68e+01 angle pdb=" C GLY F 115 " pdb=" N LYS F 116 " pdb=" CA LYS F 116 " ideal model delta sigma weight residual 122.82 127.92 -5.10 1.42e+00 4.96e-01 1.29e+01 angle pdb=" CA LEU D 160 " pdb=" CB LEU D 160 " pdb=" CG LEU D 160 " ideal model delta sigma weight residual 116.30 128.24 -11.94 3.50e+00 8.16e-02 1.16e+01 ... (remaining 15099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.48: 6143 17.48 - 34.95: 479 34.95 - 52.43: 92 52.43 - 69.91: 19 69.91 - 87.38: 8 Dihedral angle restraints: 6741 sinusoidal: 2647 harmonic: 4094 Sorted by residual: dihedral pdb=" CA PRO E 74 " pdb=" C PRO E 74 " pdb=" N TRP E 75 " pdb=" CA TRP E 75 " ideal model delta harmonic sigma weight residual 180.00 160.10 19.90 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA ARG A 43 " pdb=" C ARG A 43 " pdb=" N PRO A 44 " pdb=" CA PRO A 44 " ideal model delta harmonic sigma weight residual -180.00 -160.66 -19.34 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA MET C 63 " pdb=" C MET C 63 " pdb=" N PRO C 64 " pdb=" CA PRO C 64 " ideal model delta harmonic sigma weight residual 180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 6738 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1207 0.042 - 0.083: 378 0.083 - 0.125: 130 0.125 - 0.166: 23 0.166 - 0.208: 4 Chirality restraints: 1742 Sorted by residual: chirality pdb=" CB ILE E 149 " pdb=" CA ILE E 149 " pdb=" CG1 ILE E 149 " pdb=" CG2 ILE E 149 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB ILE C 178 " pdb=" CA ILE C 178 " pdb=" CG1 ILE C 178 " pdb=" CG2 ILE C 178 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CB ILE D 4 " pdb=" CA ILE D 4 " pdb=" CG1 ILE D 4 " pdb=" CG2 ILE D 4 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.41e-01 ... (remaining 1739 not shown) Planarity restraints: 1950 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE C 178 " 0.041 5.00e-02 4.00e+02 6.29e-02 6.33e+00 pdb=" N PRO C 179 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO C 179 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 179 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET D 110 " 0.037 5.00e-02 4.00e+02 5.45e-02 4.76e+00 pdb=" N PRO D 111 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 111 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 111 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 346 " 0.036 5.00e-02 4.00e+02 5.35e-02 4.57e+00 pdb=" N PRO E 347 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 347 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 347 " 0.030 5.00e-02 4.00e+02 ... (remaining 1947 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 3502 2.84 - 3.36: 8703 3.36 - 3.87: 16984 3.87 - 4.39: 19180 4.39 - 4.90: 32738 Nonbonded interactions: 81107 Sorted by model distance: nonbonded pdb=" O PRO E 74 " pdb=" OG SER E 220 " model vdw 2.328 3.040 nonbonded pdb=" O LEU F 6 " pdb=" OG SER F 31 " model vdw 2.350 3.040 nonbonded pdb=" O SER E 342 " pdb=" OG SER E 373 " model vdw 2.350 3.040 nonbonded pdb=" O ALA E 61 " pdb=" OG SER E 127 " model vdw 2.351 3.040 nonbonded pdb=" O CYS D 8 " pdb=" OG SER D 29 " model vdw 2.371 3.040 ... (remaining 81102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'D' and (resid 3 through 12 or (resid 13 through 14 and (name N or name C \ A or name C or name O or name CB )) or resid 15 or (resid 16 through 17 and (nam \ e N or name CA or name C or name O or name CB )) or resid 18 through 19 or (resi \ d 20 and (name N or name CA or name C or name O or name CB )) or resid 21 throug \ h 27 or (resid 28 and (name N or name CA or name C or name O or name CB )) or re \ sid 29 through 35 or (resid 36 and (name N or name CA or name C or name O or nam \ e CB )) or resid 37 through 47 or (resid 48 and (name N or name CA or name C or \ name O or name CB )) or resid 49 through 54 or (resid 55 and (name N or name CA \ or name C or name O or name CB )) or resid 56 through 59 or (resid 60 and (name \ N or name CA or name C or name O or name CB )) or resid 61 through 64 or (resid \ 65 and (name N or name CA or name C or name O or name CB )) or resid 66 through \ 75 or (resid 76 and (name N or name CA or name C or name O or name CB )) or resi \ d 77 through 132 or (resid 133 and (name N or name CA or name C or name O or nam \ e CB )) or resid 134 or (resid 135 and (name N or name CA or name C or name O or \ name CB )) or resid 136 through 170 or (resid 171 and (name N or name CA or nam \ e C or name O or name CB )) or resid 172 through 175 or (resid 176 through 178 a \ nd (name N or name CA or name C or name O or name CB )) or resid 179 through 211 \ or (resid 212 and (name N or name CA or name C or name O or name CB )) or resid \ 213 through 215 or (resid 216 through 217 and (name N or name CA or name C or n \ ame O or name CB )) or resid 218 through 222 or (resid 223 and (name N or name C \ A or name C or name O or name CB )))) selection = (chain 'F' and (resid 3 through 164 or (resid 165 through 166 and (name N or nam \ e CA or name C or name O or name CB )) or resid 167 through 172 or (resid 173 an \ d (name N or name CA or name C or name O or name CB )) or resid 174 through 181 \ or (resid 182 and (name N or name CA or name C or name O or name CB )) or resid \ 183 through 186 or (resid 187 and (name N or name CA or name C or name O or name \ CB )) or resid 188 through 200 or (resid 201 and (name N or name CA or name C o \ r name O or name CB )) or resid 202 through 214 or (resid 215 through 217 and (n \ ame N or name CA or name C or name O or name CB )) or resid 218 through 221 or ( \ resid 222 through 223 and (name N or name CA or name C or name O or name CB )))) \ } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 9.840 Find NCS groups from input model: 0.080 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:0.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 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 0.122 11161 Z= 0.178 Angle : 0.698 11.942 15104 Z= 0.355 Chirality : 0.047 0.208 1742 Planarity : 0.005 0.063 1950 Dihedral : 13.167 87.384 4103 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.17 % Allowed : 6.69 % Favored : 93.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.79 (0.14), residues: 1424 helix: -5.09 (0.05), residues: 449 sheet: -2.44 (0.36), residues: 155 loop : -3.50 (0.15), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 219 TYR 0.010 0.001 TYR A 104 PHE 0.030 0.001 PHE D 30 TRP 0.006 0.001 TRP A 101 HIS 0.003 0.000 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.16 (11159) covalent geometry : angle 0.69827 / 0.35 (15104) hydrogen bonds : bond 0.34501 / 22.30 ( 275) hydrogen bonds : angle 10.63445 / 7.35 ( 786) Misc. bond : bond 0.05176 / 2.72 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 371 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 48 MET cc_start: 0.7930 (mtp) cc_final: 0.7641 (mtp) REVERT: E 12 ARG cc_start: 0.4395 (mmp80) cc_final: 0.3684 (mmt180) REVERT: E 136 ASP cc_start: 0.7304 (t0) cc_final: 0.7097 (t0) REVERT: E 382 TYR cc_start: 0.7600 (m-10) cc_final: 0.7394 (m-10) REVERT: F 106 GLU cc_start: 0.6841 (pt0) cc_final: 0.6434 (mt-10) REVERT: F 129 MET cc_start: 0.7170 (mmm) cc_final: 0.6812 (tpp) REVERT: F 191 LEU cc_start: 0.8227 (mp) cc_final: 0.7716 (mp) REVERT: D 86 ASN cc_start: 0.6854 (p0) cc_final: 0.6267 (t0) REVERT: V 10 LEU cc_start: 0.4279 (mt) cc_final: 0.3179 (mt) REVERT: A 112 ASP cc_start: 0.5680 (m-30) cc_final: 0.4766 (t0) outliers start: 2 outliers final: 0 residues processed: 372 average time/residue: 0.1159 time to fit residues: 59.6264 Evaluate side-chains 254 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 ASN C 281 ASN C 317 GLN C 339 GLN C 391 GLN E 56 ASN E 73 GLN E 140 ASN E 286 ASN E 404 ASN F 137 HIS D 69 ASN D 141 HIS D 152 GLN D 204 HIS ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 157 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.180773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.127796 restraints weight = 19641.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130756 restraints weight = 11118.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.131272 restraints weight = 7442.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.132219 restraints weight = 6849.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.131956 restraints weight = 6059.899| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11161 Z= 0.145 Angle : 0.606 10.473 15104 Z= 0.307 Chirality : 0.044 0.246 1742 Planarity : 0.005 0.053 1950 Dihedral : 4.871 55.567 1573 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.35 % Allowed : 17.03 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.39 (0.17), residues: 1424 helix: -3.32 (0.15), residues: 472 sheet: -2.05 (0.37), residues: 188 loop : -2.90 (0.18), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 18 TYR 0.010 0.001 TYR E 260 PHE 0.020 0.002 PHE D 68 TRP 0.023 0.002 TRP E 75 HIS 0.009 0.001 HIS D 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (11159) covalent geometry : angle 0.60602 / 0.31 (15104) hydrogen bonds : bond 0.04776 / 3.04 ( 275) hydrogen bonds : angle 5.39994 / 3.76 ( 786) Misc. bond : bond 0.00025 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 278 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 ARG cc_start: 0.7004 (mmp80) cc_final: 0.5391 (pmt-80) REVERT: C 63 MET cc_start: 0.8470 (tmm) cc_final: 0.8044 (tmm) REVERT: C 231 LYS cc_start: 0.8493 (mmtt) cc_final: 0.8237 (mttm) REVERT: E 75 TRP cc_start: 0.7130 (m100) cc_final: 0.6871 (m100) REVERT: E 299 SER cc_start: 0.8561 (m) cc_final: 0.8235 (p) REVERT: E 325 LEU cc_start: 0.8998 (mm) cc_final: 0.8756 (mp) REVERT: F 73 MET cc_start: 0.4308 (ppp) cc_final: 0.3960 (ppp) REVERT: F 106 GLU cc_start: 0.7702 (pt0) cc_final: 0.7285 (mt-10) REVERT: F 121 GLU cc_start: 0.8340 (tp30) cc_final: 0.8080 (tm-30) REVERT: F 122 ILE cc_start: 0.8848 (mt) cc_final: 0.8541 (mm) REVERT: D 51 LEU cc_start: 0.8702 (mt) cc_final: 0.8446 (mt) REVERT: D 86 ASN cc_start: 0.7378 (p0) cc_final: 0.6904 (t0) REVERT: D 142 ARG cc_start: 0.8444 (mmt-90) cc_final: 0.8172 (mmt90) outliers start: 27 outliers final: 16 residues processed: 292 average time/residue: 0.0993 time to fit residues: 42.2025 Evaluate side-chains 252 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 236 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 157 ASN Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain E residue 101 THR Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 358 HIS Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 152 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 104 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 chunk 27 optimal weight: 0.7980 chunk 60 optimal weight: 7.9990 chunk 136 optimal weight: 6.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 76 ASN C 317 GLN F 140 ASN D 141 HIS ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.178083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.124513 restraints weight = 19617.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.127447 restraints weight = 10003.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.130778 restraints weight = 6211.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.130339 restraints weight = 5814.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.129834 restraints weight = 4853.625| |-----------------------------------------------------------------------------| r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11161 Z= 0.117 Angle : 0.548 7.734 15104 Z= 0.277 Chirality : 0.043 0.211 1742 Planarity : 0.004 0.045 1950 Dihedral : 4.468 52.921 1573 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.04 % Allowed : 19.03 % Favored : 77.93 % 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: -3.45 (0.19), residues: 1424 helix: -1.90 (0.21), residues: 478 sheet: -1.98 (0.37), residues: 183 loop : -2.67 (0.19), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 151 TYR 0.021 0.001 TYR E 260 PHE 0.024 0.001 PHE D 68 TRP 0.010 0.001 TRP E 321 HIS 0.003 0.001 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 (11159) covalent geometry : angle 0.54808 / 0.28 (15104) hydrogen bonds : bond 0.03949 / 2.53 ( 275) hydrogen bonds : angle 4.69550 / 3.23 ( 786) Misc. bond : bond 0.00026 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 260 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 212 MET cc_start: 0.4765 (mtp) cc_final: 0.4458 (ttm) REVERT: C 231 LYS cc_start: 0.8605 (mmtt) cc_final: 0.8355 (mttm) REVERT: E 75 TRP cc_start: 0.7148 (m100) cc_final: 0.6874 (m100) REVERT: E 149 ILE cc_start: 0.8799 (OUTLIER) cc_final: 0.8549 (mp) REVERT: E 260 TYR cc_start: 0.8389 (p90) cc_final: 0.8166 (p90) REVERT: E 299 SER cc_start: 0.8635 (m) cc_final: 0.8430 (p) REVERT: E 325 LEU cc_start: 0.8977 (mm) cc_final: 0.8657 (mp) REVERT: F 106 GLU cc_start: 0.7725 (pt0) cc_final: 0.7273 (mt-10) REVERT: F 110 MET cc_start: 0.9055 (tpp) cc_final: 0.8792 (tpp) REVERT: F 128 GLU cc_start: 0.7769 (pp20) cc_final: 0.7414 (pp20) REVERT: F 190 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7740 (tm-30) REVERT: D 38 MET cc_start: 0.5018 (mmt) cc_final: 0.4788 (mmp) REVERT: D 86 ASN cc_start: 0.7439 (p0) cc_final: 0.6810 (t0) REVERT: D 142 ARG cc_start: 0.8483 (mmt-90) cc_final: 0.8158 (mmt90) REVERT: A 51 MET cc_start: 0.6118 (mtt) cc_final: 0.5607 (pmm) outliers start: 35 outliers final: 25 residues processed: 280 average time/residue: 0.0983 time to fit residues: 40.2245 Evaluate side-chains 251 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 225 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 PHE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 152 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 158 LEU Chi-restraints excluded: chain E residue 186 ARG Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 272 MET Chi-restraints excluded: chain E residue 321 TRP Chi-restraints excluded: chain E residue 358 HIS Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 108 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 132 optimal weight: 4.9990 chunk 54 optimal weight: 0.1980 chunk 75 optimal weight: 2.9990 chunk 140 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 127 optimal weight: 8.9990 chunk 68 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 317 GLN E 198 GLN E 359 GLN F 140 ASN D 141 HIS D 152 GLN A 45 ASN ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.175543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.121285 restraints weight = 19464.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.123397 restraints weight = 10793.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.126890 restraints weight = 6603.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.126054 restraints weight = 5973.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.125822 restraints weight = 5440.029| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11161 Z= 0.114 Angle : 0.543 6.996 15104 Z= 0.272 Chirality : 0.044 0.417 1742 Planarity : 0.004 0.048 1950 Dihedral : 4.442 44.883 1573 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 4.08 % Allowed : 19.81 % Favored : 76.11 % 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: -2.85 (0.20), residues: 1424 helix: -1.17 (0.23), residues: 483 sheet: -1.76 (0.37), residues: 182 loop : -2.46 (0.19), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 139 TYR 0.016 0.001 TYR E 260 PHE 0.029 0.001 PHE D 68 TRP 0.011 0.001 TRP E 138 HIS 0.002 0.000 HIS D 96 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.11 (11159) covalent geometry : angle 0.54300 / 0.27 (15104) hydrogen bonds : bond 0.03417 / 2.21 ( 275) hydrogen bonds : angle 4.47903 / 3.10 ( 786) Misc. bond : bond 0.00032 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 245 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 212 MET cc_start: 0.4735 (mtp) cc_final: 0.4422 (ttm) REVERT: C 299 ILE cc_start: 0.9335 (tp) cc_final: 0.9114 (tp) REVERT: E 75 TRP cc_start: 0.7279 (m100) cc_final: 0.6958 (m100) REVERT: E 325 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8435 (mt) REVERT: F 186 GLN cc_start: 0.7794 (pp30) cc_final: 0.7540 (pp30) REVERT: F 187 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7033 (mm) REVERT: F 190 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7404 (tm-30) REVERT: F 220 ASP cc_start: 0.7064 (t70) cc_final: 0.6774 (t0) REVERT: D 38 MET cc_start: 0.5236 (mmt) cc_final: 0.4933 (mmp) REVERT: D 86 ASN cc_start: 0.7483 (p0) cc_final: 0.6901 (t0) REVERT: D 142 ARG cc_start: 0.8491 (mmt-90) cc_final: 0.8231 (mmt90) REVERT: D 171 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7699 (tm-30) REVERT: A 51 MET cc_start: 0.6136 (mtt) cc_final: 0.5607 (pmm) outliers start: 47 outliers final: 24 residues processed: 269 average time/residue: 0.0943 time to fit residues: 37.2498 Evaluate side-chains 259 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 232 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 358 HIS Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 187 LEU Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 152 GLN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain A residue 88 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 13 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 127 optimal weight: 7.9990 chunk 111 optimal weight: 7.9990 chunk 63 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 102 optimal weight: 0.0770 chunk 121 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 overall best weight: 3.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 140 ASN F 215 GLN D 27 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.167085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.108822 restraints weight = 19268.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.112505 restraints weight = 10245.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.114012 restraints weight = 6152.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.114126 restraints weight = 6604.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.113978 restraints weight = 5512.895| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11161 Z= 0.251 Angle : 0.705 7.699 15104 Z= 0.358 Chirality : 0.049 0.318 1742 Planarity : 0.005 0.075 1950 Dihedral : 5.735 55.647 1573 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 4.43 % Allowed : 21.98 % Favored : 73.59 % 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: -2.71 (0.20), residues: 1424 helix: -1.09 (0.22), residues: 499 sheet: -1.83 (0.36), residues: 177 loop : -2.32 (0.20), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 158 TYR 0.017 0.002 TYR E 322 PHE 0.029 0.002 PHE D 68 TRP 0.020 0.002 TRP C 28 HIS 0.005 0.001 HIS E 358 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.25 (11159) covalent geometry : angle 0.70531 / 0.36 (15104) hydrogen bonds : bond 0.04463 / 2.86 ( 275) hydrogen bonds : angle 5.00879 / 3.51 ( 786) Misc. bond : bond 0.00072 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 249 time to evaluate : 0.447 Fit side-chains revert: symmetry clash REVERT: C 8 PHE cc_start: 0.8422 (OUTLIER) cc_final: 0.8211 (m-80) REVERT: C 165 MET cc_start: 0.7649 (ttp) cc_final: 0.7209 (ttm) REVERT: C 231 LYS cc_start: 0.8796 (mmtt) cc_final: 0.8528 (mttm) REVERT: E 75 TRP cc_start: 0.7395 (m100) cc_final: 0.6948 (m100) REVERT: E 263 ARG cc_start: 0.7900 (OUTLIER) cc_final: 0.7672 (ttm170) REVERT: E 321 TRP cc_start: 0.7810 (OUTLIER) cc_final: 0.6873 (m-90) REVERT: E 322 TYR cc_start: 0.9155 (t80) cc_final: 0.8943 (t80) REVERT: E 325 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8647 (mt) REVERT: E 369 ASP cc_start: 0.7558 (t70) cc_final: 0.7237 (t0) REVERT: E 400 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.7232 (ttt180) REVERT: F 106 GLU cc_start: 0.7826 (pt0) cc_final: 0.7265 (mp0) REVERT: F 190 GLU cc_start: 0.7885 (tm-30) cc_final: 0.7430 (tm-30) REVERT: F 208 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7263 (pt) REVERT: F 215 GLN cc_start: 0.7654 (OUTLIER) cc_final: 0.7315 (mm110) REVERT: F 218 MET cc_start: 0.6718 (tpt) cc_final: 0.6334 (tpt) REVERT: D 38 MET cc_start: 0.5199 (mmt) cc_final: 0.4758 (mmp) REVERT: D 86 ASN cc_start: 0.7649 (p0) cc_final: 0.7118 (t0) REVERT: D 117 LYS cc_start: 0.7842 (tppt) cc_final: 0.7160 (tptp) REVERT: D 142 ARG cc_start: 0.8563 (mmt-90) cc_final: 0.8243 (mmt90) REVERT: D 160 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8060 (pp) REVERT: D 171 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7733 (tm-30) outliers start: 51 outliers final: 29 residues processed: 277 average time/residue: 0.0892 time to fit residues: 36.6391 Evaluate side-chains 255 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 217 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 PHE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 263 ARG Chi-restraints excluded: chain E residue 321 TRP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 358 HIS Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 400 ARG Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 154 VAL Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 208 LEU Chi-restraints excluded: chain F residue 215 GLN Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 140 ASN Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain A residue 88 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 120 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 118 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 135 optimal weight: 20.0000 chunk 59 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 GLN E 201 HIS F 215 GLN D 10 ASN D 186 GLN ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.169763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.111199 restraints weight = 19205.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.114426 restraints weight = 9348.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.116437 restraints weight = 6198.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.117378 restraints weight = 5022.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.118023 restraints weight = 4601.528| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11161 Z= 0.135 Angle : 0.606 11.932 15104 Z= 0.298 Chirality : 0.046 0.318 1742 Planarity : 0.004 0.065 1950 Dihedral : 5.422 58.419 1573 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.48 % Allowed : 24.33 % Favored : 72.20 % 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: -2.30 (0.21), residues: 1424 helix: -0.52 (0.24), residues: 498 sheet: -1.78 (0.35), residues: 189 loop : -2.21 (0.21), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 214 TYR 0.013 0.001 TYR E 260 PHE 0.025 0.001 PHE D 68 TRP 0.013 0.001 TRP E 138 HIS 0.002 0.000 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 (11159) covalent geometry : angle 0.60591 / 0.30 (15104) hydrogen bonds : bond 0.03421 / 2.21 ( 275) hydrogen bonds : angle 4.62987 / 3.20 ( 786) Misc. bond : bond 0.00037 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 236 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: C 8 PHE cc_start: 0.8339 (OUTLIER) cc_final: 0.8103 (m-80) REVERT: C 165 MET cc_start: 0.7789 (ttp) cc_final: 0.7376 (ttm) REVERT: C 212 MET cc_start: 0.4969 (ttm) cc_final: 0.4611 (ttm) REVERT: C 231 LYS cc_start: 0.8723 (mmtt) cc_final: 0.8410 (mttm) REVERT: E 12 ARG cc_start: 0.8024 (mmp80) cc_final: 0.7108 (mmp80) REVERT: E 75 TRP cc_start: 0.7077 (m100) cc_final: 0.6672 (m100) REVERT: E 308 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9122 (mp) REVERT: E 325 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8580 (mt) REVERT: E 369 ASP cc_start: 0.7491 (t70) cc_final: 0.7116 (t0) REVERT: E 400 ARG cc_start: 0.7426 (mtt180) cc_final: 0.7134 (ttt180) REVERT: F 121 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8331 (tm-30) REVERT: F 187 LEU cc_start: 0.7429 (mm) cc_final: 0.7109 (mm) REVERT: F 190 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7270 (tm-30) REVERT: F 215 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7261 (mm110) REVERT: D 38 MET cc_start: 0.5622 (mmt) cc_final: 0.5054 (mmp) REVERT: D 86 ASN cc_start: 0.7668 (p0) cc_final: 0.7077 (t0) REVERT: D 87 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7854 (mm-40) REVERT: D 142 ARG cc_start: 0.8407 (mmt-90) cc_final: 0.8083 (mmt180) REVERT: D 171 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.7749 (tm-30) REVERT: A 51 MET cc_start: 0.6038 (mtt) cc_final: 0.5453 (ttt) outliers start: 40 outliers final: 23 residues processed: 262 average time/residue: 0.0886 time to fit residues: 34.4065 Evaluate side-chains 255 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 227 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 8 PHE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 308 LEU Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 215 GLN Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain A residue 88 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 112 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 57 optimal weight: 8.9990 chunk 117 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 201 HIS F 140 ASN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 HIS D 186 GLN ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.167001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.108808 restraints weight = 19122.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.111800 restraints weight = 10160.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.112386 restraints weight = 6769.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112380 restraints weight = 6293.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.112691 restraints weight = 6178.911| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 11161 Z= 0.201 Angle : 0.670 10.534 15104 Z= 0.334 Chirality : 0.048 0.305 1742 Planarity : 0.004 0.068 1950 Dihedral : 5.570 58.974 1573 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.91 % Allowed : 25.37 % Favored : 70.72 % 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: -2.22 (0.21), residues: 1424 helix: -0.40 (0.24), residues: 500 sheet: -1.89 (0.35), residues: 181 loop : -2.15 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 158 TYR 0.017 0.001 TYR E 322 PHE 0.025 0.002 PHE D 68 TRP 0.026 0.002 TRP E 138 HIS 0.005 0.001 HIS E 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.20 (11159) covalent geometry : angle 0.66991 / 0.33 (15104) hydrogen bonds : bond 0.03970 / 2.55 ( 275) hydrogen bonds : angle 4.86707 / 3.37 ( 786) Misc. bond : bond 0.00057 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 231 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: C 165 MET cc_start: 0.7776 (ttp) cc_final: 0.7379 (ttm) REVERT: C 212 MET cc_start: 0.4849 (ttm) cc_final: 0.4523 (ttm) REVERT: C 231 LYS cc_start: 0.8762 (mmtt) cc_final: 0.8440 (mttm) REVERT: E 12 ARG cc_start: 0.8164 (mmp80) cc_final: 0.6462 (mpt180) REVERT: E 75 TRP cc_start: 0.7340 (m100) cc_final: 0.6845 (m100) REVERT: E 251 ILE cc_start: 0.8969 (mm) cc_final: 0.8761 (tt) REVERT: E 263 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7610 (ttm170) REVERT: E 321 TRP cc_start: 0.7798 (OUTLIER) cc_final: 0.7161 (m-90) REVERT: E 325 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8615 (mt) REVERT: E 369 ASP cc_start: 0.7523 (t70) cc_final: 0.7135 (t0) REVERT: E 400 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.7229 (ttt180) REVERT: F 121 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8173 (tm-30) REVERT: F 125 ARG cc_start: 0.9084 (ttm170) cc_final: 0.8711 (ttm170) REVERT: F 186 GLN cc_start: 0.7247 (pp30) cc_final: 0.6980 (pp30) REVERT: F 190 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7296 (tm-30) REVERT: F 205 ASP cc_start: 0.7765 (p0) cc_final: 0.7561 (p0) REVERT: D 38 MET cc_start: 0.5419 (mmt) cc_final: 0.4896 (mmp) REVERT: D 86 ASN cc_start: 0.7742 (p0) cc_final: 0.7213 (t0) REVERT: D 87 GLN cc_start: 0.8315 (mm-40) cc_final: 0.7946 (mm-40) REVERT: D 142 ARG cc_start: 0.8571 (mmt-90) cc_final: 0.7907 (mtt-85) REVERT: D 171 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7750 (tm-30) REVERT: A 51 MET cc_start: 0.5865 (mtt) cc_final: 0.5271 (ttt) outliers start: 45 outliers final: 31 residues processed: 260 average time/residue: 0.0887 time to fit residues: 34.0370 Evaluate side-chains 254 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 218 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 196 VAL Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain C residue 340 LEU Chi-restraints excluded: chain E residue 23 VAL Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 140 ASN Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 263 ARG Chi-restraints excluded: chain E residue 321 TRP Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain E residue 358 HIS Chi-restraints excluded: chain E residue 371 LEU Chi-restraints excluded: chain E residue 400 ARG Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain D residue 190 GLU Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 141 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 11 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 89 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 131 optimal weight: 9.9990 chunk 88 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 186 GLN ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.169341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.111327 restraints weight = 19127.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.114593 restraints weight = 9168.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.116503 restraints weight = 6054.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.117619 restraints weight = 4937.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.117880 restraints weight = 4482.647| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11161 Z= 0.117 Angle : 0.614 14.518 15104 Z= 0.299 Chirality : 0.046 0.440 1742 Planarity : 0.004 0.060 1950 Dihedral : 5.331 57.309 1573 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 3.30 % Allowed : 26.41 % Favored : 70.29 % 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: -1.97 (0.22), residues: 1424 helix: -0.09 (0.24), residues: 503 sheet: -1.86 (0.35), residues: 178 loop : -2.07 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 18 TYR 0.018 0.001 TYR E 322 PHE 0.027 0.001 PHE D 68 TRP 0.024 0.001 TRP E 138 HIS 0.002 0.000 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (11159) covalent geometry : angle 0.61413 / 0.30 (15104) hydrogen bonds : bond 0.03248 / 2.10 ( 275) hydrogen bonds : angle 4.62098 / 3.19 ( 786) Misc. bond : bond 0.00015 / 0.01 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 245 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: C 212 MET cc_start: 0.4702 (ttm) cc_final: 0.4394 (ttm) REVERT: C 231 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8408 (mttm) REVERT: E 12 ARG cc_start: 0.8095 (mmp80) cc_final: 0.7443 (mmp80) REVERT: E 251 ILE cc_start: 0.8820 (mm) cc_final: 0.8608 (tt) REVERT: E 325 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8544 (mt) REVERT: E 400 ARG cc_start: 0.7421 (mtt180) cc_final: 0.7141 (ttt180) REVERT: F 121 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8106 (tp30) REVERT: F 190 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7281 (tm-30) REVERT: F 205 ASP cc_start: 0.7909 (p0) cc_final: 0.7629 (p0) REVERT: D 38 MET cc_start: 0.5707 (mmt) cc_final: 0.5055 (mmp) REVERT: D 86 ASN cc_start: 0.7729 (p0) cc_final: 0.7003 (t0) REVERT: D 87 GLN cc_start: 0.8118 (mm-40) cc_final: 0.7743 (mm-40) REVERT: D 142 ARG cc_start: 0.8412 (mmt-90) cc_final: 0.7808 (mtt-85) REVERT: D 171 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7801 (tm-30) REVERT: A 51 MET cc_start: 0.5839 (mtt) cc_final: 0.5303 (ttt) REVERT: A 178 ASP cc_start: 0.7803 (t0) cc_final: 0.7509 (t0) outliers start: 38 outliers final: 21 residues processed: 266 average time/residue: 0.0903 time to fit residues: 35.0483 Evaluate side-chains 257 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 234 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain E residue 129 LEU Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 141 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 101 optimal weight: 20.0000 chunk 52 optimal weight: 0.0670 chunk 42 optimal weight: 0.7980 chunk 16 optimal weight: 10.0000 chunk 79 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 123 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 chunk 82 optimal weight: 20.0000 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 161 GLN C 238 GLN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN A 22 GLN ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.170729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.113738 restraints weight = 19046.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.116997 restraints weight = 8968.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.118808 restraints weight = 5899.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 71)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.120004 restraints weight = 4816.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.120362 restraints weight = 4377.242| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.6171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11161 Z= 0.110 Angle : 0.620 9.335 15104 Z= 0.303 Chirality : 0.045 0.303 1742 Planarity : 0.004 0.055 1950 Dihedral : 5.081 57.828 1573 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.35 % Allowed : 27.37 % Favored : 70.29 % 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: -1.75 (0.22), residues: 1424 helix: 0.20 (0.25), residues: 497 sheet: -1.78 (0.36), residues: 185 loop : -1.99 (0.21), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 15 TYR 0.017 0.001 TYR E 322 PHE 0.029 0.002 PHE A 90 TRP 0.029 0.001 TRP E 138 HIS 0.002 0.000 HIS E 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (11159) covalent geometry : angle 0.61960 / 0.30 (15104) hydrogen bonds : bond 0.03045 / 1.96 ( 275) hydrogen bonds : angle 4.51270 / 3.11 ( 786) Misc. bond : bond 0.00002 / 0.00 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 254 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 212 MET cc_start: 0.4743 (ttm) cc_final: 0.4384 (ttm) REVERT: C 231 LYS cc_start: 0.8701 (mmtt) cc_final: 0.8395 (mttm) REVERT: E 251 ILE cc_start: 0.8782 (mm) cc_final: 0.8518 (tt) REVERT: E 325 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8467 (mt) REVERT: F 38 MET cc_start: 0.5945 (tpp) cc_final: 0.5507 (tpp) REVERT: F 121 GLU cc_start: 0.8701 (tm-30) cc_final: 0.7954 (tp30) REVERT: F 190 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7184 (tm-30) REVERT: F 205 ASP cc_start: 0.7950 (p0) cc_final: 0.7693 (p0) REVERT: D 38 MET cc_start: 0.5792 (mmt) cc_final: 0.5070 (mmp) REVERT: D 86 ASN cc_start: 0.7658 (p0) cc_final: 0.6986 (t0) REVERT: D 87 GLN cc_start: 0.8012 (mm-40) cc_final: 0.7735 (mm110) REVERT: D 142 ARG cc_start: 0.8426 (mmt-90) cc_final: 0.7797 (mtt-85) REVERT: D 171 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7776 (tm-30) REVERT: D 210 LYS cc_start: 0.8448 (pttm) cc_final: 0.8205 (ptpp) REVERT: A 22 GLN cc_start: 0.7430 (OUTLIER) cc_final: 0.7192 (pp30) REVERT: A 51 MET cc_start: 0.5898 (mtt) cc_final: 0.5294 (ttt) REVERT: A 143 VAL cc_start: 0.5315 (OUTLIER) cc_final: 0.4980 (p) REVERT: A 178 ASP cc_start: 0.7908 (t0) cc_final: 0.7584 (t0) outliers start: 27 outliers final: 21 residues processed: 270 average time/residue: 0.0940 time to fit residues: 36.8216 Evaluate side-chains 264 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 239 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 316 VAL Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain D residue 108 VAL Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain A residue 22 GLN Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 143 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 107 optimal weight: 0.4980 chunk 131 optimal weight: 0.0470 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 5.9990 chunk 98 optimal weight: 0.0670 chunk 32 optimal weight: 2.9990 chunk 112 optimal weight: 0.0970 chunk 21 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 overall best weight: 0.2814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 HIS ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.172042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.117511 restraints weight = 19242.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.120000 restraints weight = 10659.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.120146 restraints weight = 6381.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.120434 restraints weight = 6752.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.120716 restraints weight = 6092.934| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.6150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11161 Z= 0.107 Angle : 0.643 10.511 15104 Z= 0.312 Chirality : 0.045 0.335 1742 Planarity : 0.004 0.055 1950 Dihedral : 4.732 56.785 1573 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.82 % Allowed : 28.32 % Favored : 69.85 % 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: -1.55 (0.22), residues: 1424 helix: 0.42 (0.25), residues: 493 sheet: -1.61 (0.38), residues: 179 loop : -1.92 (0.21), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 125 TYR 0.018 0.001 TYR E 322 PHE 0.029 0.001 PHE D 68 TRP 0.030 0.001 TRP E 138 HIS 0.001 0.000 HIS A 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.11 (11159) covalent geometry : angle 0.64318 / 0.31 (15104) hydrogen bonds : bond 0.02897 / 1.89 ( 275) hydrogen bonds : angle 4.43482 / 3.06 ( 786) Misc. bond : bond 0.00006 / 0.00 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2848 Ramachandran restraints generated. 1424 Oldfield, 0 Emsley, 1424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 252 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 15 ARG cc_start: 0.7610 (mmp80) cc_final: 0.5761 (ppt170) REVERT: C 212 MET cc_start: 0.4646 (ttm) cc_final: 0.4255 (ttm) REVERT: C 231 LYS cc_start: 0.8676 (mmtt) cc_final: 0.8386 (mttm) REVERT: E 180 MET cc_start: 0.7373 (mtt) cc_final: 0.7027 (mtt) REVERT: E 251 ILE cc_start: 0.8832 (mm) cc_final: 0.8558 (tt) REVERT: E 325 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8440 (mt) REVERT: F 38 MET cc_start: 0.5779 (tpp) cc_final: 0.5324 (tpp) REVERT: F 121 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8310 (tm-30) REVERT: F 190 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7301 (tm-30) REVERT: F 205 ASP cc_start: 0.7829 (p0) cc_final: 0.7588 (p0) REVERT: D 38 MET cc_start: 0.5642 (mmt) cc_final: 0.4874 (mmp) REVERT: D 86 ASN cc_start: 0.7744 (p0) cc_final: 0.7132 (t0) REVERT: D 142 ARG cc_start: 0.8505 (mmt-90) cc_final: 0.7914 (mtt-85) REVERT: D 171 GLU cc_start: 0.8217 (OUTLIER) cc_final: 0.7760 (tm-30) REVERT: D 210 LYS cc_start: 0.8565 (pttm) cc_final: 0.8317 (pttm) REVERT: D 212 MET cc_start: 0.6418 (pmm) cc_final: 0.3189 (ptt) REVERT: A 51 MET cc_start: 0.5989 (mtt) cc_final: 0.5299 (ttt) REVERT: A 143 VAL cc_start: 0.5226 (OUTLIER) cc_final: 0.4905 (p) REVERT: A 178 ASP cc_start: 0.7759 (t0) cc_final: 0.7430 (t0) outliers start: 21 outliers final: 15 residues processed: 263 average time/residue: 0.0895 time to fit residues: 34.9596 Evaluate side-chains 261 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 243 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 39 MET Chi-restraints excluded: chain C residue 67 ILE Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 292 GLU Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 335 LEU Chi-restraints excluded: chain E residue 188 HIS Chi-restraints excluded: chain E residue 201 HIS Chi-restraints excluded: chain E residue 325 LEU Chi-restraints excluded: chain F residue 12 CYS Chi-restraints excluded: chain F residue 49 SER Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 186 GLN Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 143 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 54 optimal weight: 0.0270 chunk 36 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 128 optimal weight: 7.9990 chunk 140 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 140 ASN ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN A 22 GLN ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.169966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.112275 restraints weight = 19216.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.115504 restraints weight = 9237.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.117518 restraints weight = 6031.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.118333 restraints weight = 4908.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.118893 restraints weight = 4496.559| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.6285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11161 Z= 0.133 Angle : 0.653 11.437 15104 Z= 0.320 Chirality : 0.046 0.347 1742 Planarity : 0.004 0.056 1950 Dihedral : 4.838 52.519 1573 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.35 % Allowed : 28.15 % Favored : 69.50 % 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: -1.47 (0.22), residues: 1424 helix: 0.40 (0.25), residues: 499 sheet: -1.54 (0.38), residues: 178 loop : -1.84 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 125 TYR 0.017 0.001 TYR E 322 PHE 0.035 0.002 PHE D 68 TRP 0.029 0.001 TRP E 138 HIS 0.005 0.001 HIS E 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.13 (11159) covalent geometry : angle 0.65336 / 0.32 (15104) hydrogen bonds : bond 0.03270 / 2.11 ( 275) hydrogen bonds : angle 4.52921 / 3.14 ( 786) Misc. bond : bond 0.00028 / 0.01 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2512.24 seconds wall clock time: 43 minutes 46.89 seconds (2626.89 seconds total)