Starting phenix.real_space_refine on Wed Mar 4 05:27:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7arm_11887/03_2026/7arm_11887.cif Found real_map, /net/cci-nas-00/data/ceres_data/7arm_11887/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7arm_11887/03_2026/7arm_11887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7arm_11887/03_2026/7arm_11887.map" model { file = "/net/cci-nas-00/data/ceres_data/7arm_11887/03_2026/7arm_11887.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7arm_11887/03_2026/7arm_11887.cif" } 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-5986/lib/python3.9/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: 3 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.57, per 1000 atoms: 0.23 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: 0.89 Conformation dependent library (CDL) restraints added in 531.4 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: 0.26 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: 1.31 Time building geometry restraints manager: 1.18 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: 6149 17.48 - 34.95: 479 34.95 - 52.43: 92 52.43 - 69.91: 19 69.91 - 87.38: 8 Dihedral angle restraints: 6747 sinusoidal: 2653 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 6744 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: 0.610 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.110 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 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 : 13.162 87.384 4109 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 covalent geometry : bond 0.00320 (11159) covalent geometry : angle 0.69827 (15104) hydrogen bonds : bond 0.34501 ( 275) hydrogen bonds : angle 10.63445 ( 786) Misc. bond : bond 0.05176 ( 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 : 0.389 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: 0.1104 time to fit residues: 56.5113 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 : 0.468 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4269 r_free = 0.4269 target = 0.180617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.126479 restraints weight = 19630.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.129824 restraints weight = 10726.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.130407 restraints weight = 6653.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.130598 restraints weight = 6252.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.130818 restraints weight = 5948.087| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3281 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= 0.145 Angle : 0.612 10.437 15104 Z= 0.309 Chirality : 0.044 0.286 1742 Planarity : 0.005 0.054 1950 Dihedral : 5.117 57.537 1579 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.52 % Allowed : 16.68 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.39 (0.17), residues: 1424 helix: -3.33 (0.15), residues: 472 sheet: -2.06 (0.37), residues: 188 loop : -2.89 (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 0.021 0.002 PHE D 68 TRP 0.023 0.002 TRP E 75 HIS 0.008 0.001 HIS D 204 Details of bonding type rmsd covalent geometry : bond 0.00338 (11159) covalent geometry : angle 0.61238 (15104) hydrogen bonds : bond 0.04721 ( 275) hydrogen bonds : angle 5.37677 ( 786) Misc. bond : bond 0.00042 ( 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 310 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 281 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 ARG cc_start: 0.7015 (mmp80) cc_final: 0.5369 (pmt-80) REVERT: C 63 MET cc_start: 0.8485 (tmm) cc_final: 0.8051 (tmm) REVERT: C 212 MET cc_start: 0.5215 (mmm) cc_final: 0.4780 (ttm) REVERT: C 231 LYS cc_start: 0.8520 (mmtt) cc_final: 0.8261 (mttm) REVERT: E 75 TRP cc_start: 0.7235 (m100) cc_final: 0.6966 (m100) REVERT: E 299 SER cc_start: 0.8538 (m) cc_final: 0.8232 (p) REVERT: E 325 LEU cc_start: 0.8996 (mm) cc_final: 0.8757 (mp) REVERT: F 73 MET cc_start: 0.4318 (ppp) cc_final: 0.3968 (ppp) REVERT: F 106 GLU cc_start: 0.7729 (pt0) cc_final: 0.7319 (mt-10) REVERT: F 122 ILE cc_start: 0.8868 (mt) cc_final: 0.8554 (mm) REVERT: F 220 ASP cc_start: 0.7222 (t70) cc_final: 0.6944 (t70) REVERT: D 86 ASN cc_start: 0.7409 (p0) cc_final: 0.6952 (t0) REVERT: D 142 ARG cc_start: 0.8471 (mmt-90) cc_final: 0.8183 (mmt90) REVERT: D 171 GLU cc_start: 0.8000 (tt0) cc_final: 0.7728 (tm-30) outliers start: 29 outliers final: 17 residues processed: 296 average time/residue: 0.0903 time to fit residues: 39.0921 Evaluate side-chains 259 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 242 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 306 THR 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: 0.8980 chunk 127 optimal weight: 20.0000 chunk 70 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 22 optimal weight: 0.3980 chunk 4 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 60 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 76 ASN C 309 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.177793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124620 restraints weight = 19572.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.127609 restraints weight = 10484.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.128684 restraints weight = 6817.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.129278 restraints weight = 6441.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.129116 restraints weight = 5325.099| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11161 Z= 0.120 Angle : 0.549 7.999 15104 Z= 0.276 Chirality : 0.043 0.207 1742 Planarity : 0.004 0.047 1950 Dihedral : 4.819 58.711 1579 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.87 % Allowed : 19.29 % Favored : 77.85 % 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: -3.44 (0.19), residues: 1424 helix: -1.88 (0.21), residues: 478 sheet: -1.96 (0.37), residues: 183 loop : -2.68 (0.19), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 151 TYR 0.011 0.001 TYR C 142 PHE 0.025 0.001 PHE D 68 TRP 0.011 0.001 TRP E 321 HIS 0.003 0.000 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00276 (11159) covalent geometry : angle 0.54918 (15104) hydrogen bonds : bond 0.03930 ( 275) hydrogen bonds : angle 4.69155 ( 786) Misc. bond : bond 0.00030 ( 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 287 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 254 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 231 LYS cc_start: 0.8619 (mmtt) cc_final: 0.8365 (mttm) REVERT: E 75 TRP cc_start: 0.7141 (m100) cc_final: 0.6884 (m100) REVERT: E 149 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8570 (mp) REVERT: E 180 MET cc_start: 0.8104 (mtp) cc_final: 0.7894 (mtt) REVERT: E 260 TYR cc_start: 0.8381 (p90) cc_final: 0.8154 (p90) REVERT: E 325 LEU cc_start: 0.8977 (mm) cc_final: 0.8665 (mp) REVERT: F 106 GLU cc_start: 0.7667 (pt0) cc_final: 0.7205 (mt-10) REVERT: F 110 MET cc_start: 0.9039 (tpp) cc_final: 0.8748 (tpp) REVERT: F 190 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7748 (tm-30) REVERT: D 38 MET cc_start: 0.5048 (mmt) cc_final: 0.4812 (mmp) REVERT: D 86 ASN cc_start: 0.7439 (p0) cc_final: 0.6809 (t0) REVERT: D 142 ARG cc_start: 0.8488 (mmt-90) cc_final: 0.8160 (mmt90) REVERT: D 171 GLU cc_start: 0.8179 (tt0) cc_final: 0.7964 (tt0) REVERT: A 51 MET cc_start: 0.6133 (mtt) cc_final: 0.5651 (pmm) outliers start: 33 outliers final: 24 residues processed: 271 average time/residue: 0.0865 time to fit residues: 34.5068 Evaluate side-chains 252 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 227 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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 316 VAL 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 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 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: 6.9990 chunk 54 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 140 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 127 optimal weight: 30.0000 chunk 68 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 GLN E 198 GLN E 359 GLN F 140 ASN D 141 HIS D 152 GLN D 163 ASN A 45 ASN ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.176939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120461 restraints weight = 19532.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.123825 restraints weight = 9308.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.125889 restraints weight = 6081.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.126897 restraints weight = 4918.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.127244 restraints weight = 4463.187| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 11161 Z= 0.102 Angle : 0.528 6.960 15104 Z= 0.263 Chirality : 0.043 0.214 1742 Planarity : 0.004 0.046 1950 Dihedral : 4.704 54.653 1579 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.74 % Allowed : 20.16 % 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: -2.78 (0.20), residues: 1424 helix: -1.03 (0.24), residues: 471 sheet: -1.64 (0.38), residues: 176 loop : -2.48 (0.19), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 18 TYR 0.008 0.001 TYR A 104 PHE 0.027 0.001 PHE D 68 TRP 0.012 0.001 TRP E 138 HIS 0.002 0.000 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00241 (11159) covalent geometry : angle 0.52771 (15104) hydrogen bonds : bond 0.03269 ( 275) hydrogen bonds : angle 4.41732 ( 786) Misc. bond : bond 0.00021 ( 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 297 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 254 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 14 MET cc_start: 0.5799 (mmt) cc_final: 0.5196 (mmt) REVERT: C 15 ARG cc_start: 0.6989 (mmp80) cc_final: 0.5521 (ppt170) REVERT: C 299 ILE cc_start: 0.9337 (tp) cc_final: 0.9091 (tp) REVERT: E 325 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8402 (mt) REVERT: E 328 LEU cc_start: 0.9244 (tp) cc_final: 0.9027 (tt) REVERT: F 110 MET cc_start: 0.8866 (tpp) cc_final: 0.8573 (tpp) REVERT: F 186 GLN cc_start: 0.7533 (pp30) cc_final: 0.7306 (pp30) REVERT: F 187 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6804 (mm) REVERT: F 190 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7398 (tm-30) REVERT: D 38 MET cc_start: 0.5325 (mmt) cc_final: 0.5033 (mmp) REVERT: D 86 ASN cc_start: 0.7427 (p0) cc_final: 0.6764 (t0) REVERT: D 171 GLU cc_start: 0.8316 (tt0) cc_final: 0.8087 (tt0) REVERT: A 51 MET cc_start: 0.6037 (mtt) cc_final: 0.5596 (pmm) REVERT: A 153 GLN cc_start: 0.7156 (tm-30) cc_final: 0.6750 (mm-40) outliers start: 43 outliers final: 26 residues processed: 279 average time/residue: 0.0868 time to fit residues: 35.7214 Evaluate side-chains 265 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 237 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 152 SER Chi-restraints excluded: chain C residue 292 GLU 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 186 ARG 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 129 MET 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 A residue 24 VAL Chi-restraints excluded: chain A residue 60 VAL 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: 2.9990 chunk 122 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 84 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 chunk 14 optimal weight: 0.0970 chunk 43 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 140 ASN F 140 ASN D 10 ASN D 27 ASN D 141 HIS D 163 ASN ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.173691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.117204 restraints weight = 19344.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.120466 restraints weight = 10046.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.120913 restraints weight = 6739.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.120912 restraints weight = 6047.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.121288 restraints weight = 6010.418| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4869 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= 0.132 Angle : 0.563 7.158 15104 Z= 0.281 Chirality : 0.045 0.420 1742 Planarity : 0.004 0.050 1950 Dihedral : 4.857 52.405 1579 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 4.00 % Allowed : 20.85 % Favored : 75.15 % 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: -2.37 (0.21), residues: 1424 helix: -0.62 (0.24), residues: 487 sheet: -1.63 (0.37), residues: 185 loop : -2.25 (0.20), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 18 TYR 0.018 0.001 TYR E 260 PHE 0.029 0.001 PHE D 68 TRP 0.022 0.001 TRP E 75 HIS 0.003 0.001 HIS E 84 Details of bonding type rmsd covalent geometry : bond 0.00310 (11159) covalent geometry : angle 0.56322 (15104) hydrogen bonds : bond 0.03336 ( 275) hydrogen bonds : angle 4.38278 ( 786) Misc. bond : bond 0.00042 ( 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 287 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 241 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 165 MET cc_start: 0.7809 (ttp) cc_final: 0.7404 (ttm) REVERT: C 231 LYS cc_start: 0.8658 (mmtt) cc_final: 0.8396 (mttm) REVERT: C 267 MET cc_start: 0.7715 (ttm) cc_final: 0.7306 (ttm) REVERT: C 299 ILE cc_start: 0.9357 (tp) cc_final: 0.9086 (tp) REVERT: E 261 MET cc_start: 0.8809 (tpp) cc_final: 0.8591 (tpp) REVERT: E 325 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8456 (mt) REVERT: F 106 GLU cc_start: 0.7795 (pt0) cc_final: 0.7393 (mp0) REVERT: F 186 GLN cc_start: 0.7753 (pp30) cc_final: 0.7452 (pp30) REVERT: F 187 LEU cc_start: 0.7631 (OUTLIER) cc_final: 0.7273 (mm) REVERT: F 190 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7338 (tm-30) REVERT: D 38 MET cc_start: 0.5231 (mmt) cc_final: 0.4882 (mmp) REVERT: D 86 ASN cc_start: 0.7486 (p0) cc_final: 0.6974 (t0) REVERT: D 171 GLU cc_start: 0.8266 (tt0) cc_final: 0.8039 (tt0) REVERT: A 51 MET cc_start: 0.6062 (mtt) cc_final: 0.5585 (pmm) outliers start: 46 outliers final: 25 residues processed: 262 average time/residue: 0.0877 time to fit residues: 33.9851 Evaluate side-chains 261 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 234 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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 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 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 245 THR 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 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 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: 4.9990 chunk 76 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 130 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 198 GLN E 201 HIS F 140 ASN F 215 GLN D 97 HIS ** 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** A 153 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.166097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.106624 restraints weight = 19302.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.109576 restraints weight = 9588.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.111374 restraints weight = 6483.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.112218 restraints weight = 5320.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.112867 restraints weight = 4869.702| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 11161 Z= 0.263 Angle : 0.733 9.950 15104 Z= 0.369 Chirality : 0.050 0.341 1742 Planarity : 0.005 0.075 1950 Dihedral : 6.144 51.882 1579 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 4.00 % Allowed : 22.59 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.21), residues: 1424 helix: -0.73 (0.23), residues: 506 sheet: -1.70 (0.36), residues: 175 loop : -2.27 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 219 TYR 0.021 0.002 TYR E 260 PHE 0.025 0.002 PHE D 68 TRP 0.028 0.003 TRP E 75 HIS 0.005 0.001 HIS E 358 Details of bonding type rmsd covalent geometry : bond 0.00624 (11159) covalent geometry : angle 0.73311 (15104) hydrogen bonds : bond 0.04534 ( 275) hydrogen bonds : angle 5.05424 ( 786) Misc. bond : bond 0.00080 ( 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 294 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 248 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 165 MET cc_start: 0.7751 (ttp) cc_final: 0.7331 (ttm) REVERT: C 231 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8461 (mttm) REVERT: C 267 MET cc_start: 0.7972 (ttm) cc_final: 0.7586 (ttm) REVERT: E 251 ILE cc_start: 0.8929 (mm) cc_final: 0.8695 (tt) REVERT: E 263 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7603 (ttm170) REVERT: E 325 LEU cc_start: 0.9181 (OUTLIER) cc_final: 0.8655 (mt) REVERT: E 369 ASP cc_start: 0.7546 (t70) cc_final: 0.7188 (t0) REVERT: E 400 ARG cc_start: 0.7539 (OUTLIER) cc_final: 0.7270 (ttt180) REVERT: F 106 GLU cc_start: 0.7781 (pt0) cc_final: 0.7297 (mp0) REVERT: F 187 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.7277 (mm) REVERT: F 190 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7380 (tm-30) REVERT: F 215 GLN cc_start: 0.7638 (OUTLIER) cc_final: 0.7353 (mm110) REVERT: D 38 MET cc_start: 0.5497 (mmt) cc_final: 0.4949 (mmp) REVERT: D 86 ASN cc_start: 0.7637 (p0) cc_final: 0.7061 (t0) REVERT: D 87 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7865 (mm-40) REVERT: D 95 PHE cc_start: 0.6224 (m-10) cc_final: 0.5969 (m-10) REVERT: D 171 GLU cc_start: 0.8215 (tt0) cc_final: 0.7874 (tt0) REVERT: A 153 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.6636 (mt0) outliers start: 46 outliers final: 29 residues processed: 275 average time/residue: 0.0912 time to fit residues: 36.8168 Evaluate side-chains 255 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 220 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 187 ILE 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 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 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 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 129 MET 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 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 122 ILE Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 153 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 112 optimal weight: 6.9990 chunk 101 optimal weight: 0.4980 chunk 45 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 91 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 66 optimal weight: 0.6980 chunk 34 optimal weight: 0.0010 chunk 13 optimal weight: 1.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 161 GLN F 215 GLN D 141 HIS ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4157 r_free = 0.4157 target = 0.171114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.114830 restraints weight = 19133.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.117655 restraints weight = 10399.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.118214 restraints weight = 6826.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.118342 restraints weight = 6242.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.118650 restraints weight = 6056.672| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11161 Z= 0.107 Angle : 0.593 9.209 15104 Z= 0.293 Chirality : 0.045 0.326 1742 Planarity : 0.004 0.062 1950 Dihedral : 5.665 58.468 1579 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.13 % Allowed : 25.72 % Favored : 71.16 % 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: -2.05 (0.22), residues: 1424 helix: -0.12 (0.25), residues: 493 sheet: -1.93 (0.36), residues: 172 loop : -2.12 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 214 TYR 0.016 0.001 TYR E 260 PHE 0.027 0.001 PHE D 68 TRP 0.035 0.001 TRP E 75 HIS 0.001 0.000 HIS D 97 Details of bonding type rmsd covalent geometry : bond 0.00246 (11159) covalent geometry : angle 0.59300 (15104) hydrogen bonds : bond 0.03084 ( 275) hydrogen bonds : angle 4.50017 ( 786) Misc. bond : bond 0.00009 ( 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 283 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 247 time to evaluate : 0.298 Fit side-chains revert: symmetry clash REVERT: C 72 HIS cc_start: 0.7363 (p-80) cc_final: 0.7122 (p-80) REVERT: C 231 LYS cc_start: 0.8705 (mmtt) cc_final: 0.8384 (mttm) REVERT: E 12 ARG cc_start: 0.8116 (mmp80) cc_final: 0.7252 (mmp80) REVERT: E 57 ASN cc_start: 0.8262 (p0) cc_final: 0.8053 (p0) REVERT: E 251 ILE cc_start: 0.8815 (mm) cc_final: 0.8594 (tt) REVERT: E 325 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8506 (mt) REVERT: E 400 ARG cc_start: 0.7386 (mtt180) cc_final: 0.7097 (ttt180) REVERT: F 38 MET cc_start: 0.5922 (tpp) cc_final: 0.5640 (tpp) REVERT: F 102 PHE cc_start: 0.8458 (m-80) cc_final: 0.8078 (m-80) REVERT: F 190 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7328 (tm-30) REVERT: F 215 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7465 (mm110) REVERT: D 38 MET cc_start: 0.5384 (mmt) cc_final: 0.4776 (mmp) REVERT: D 86 ASN cc_start: 0.7781 (p0) cc_final: 0.7259 (t0) REVERT: D 87 GLN cc_start: 0.8292 (mm-40) cc_final: 0.8073 (mm-40) REVERT: D 94 GLN cc_start: 0.7125 (pm20) cc_final: 0.5524 (tm-30) REVERT: D 95 PHE cc_start: 0.6317 (m-10) cc_final: 0.5804 (m-10) REVERT: D 141 HIS cc_start: 0.7694 (OUTLIER) cc_final: 0.6328 (m90) REVERT: D 152 GLN cc_start: 0.9211 (mm-40) cc_final: 0.8943 (mm-40) REVERT: D 212 MET cc_start: 0.6231 (pmm) cc_final: 0.2930 (ptt) REVERT: A 153 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.6632 (mt0) outliers start: 36 outliers final: 17 residues processed: 269 average time/residue: 0.0866 time to fit residues: 34.5718 Evaluate side-chains 253 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 232 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 187 ILE 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 129 LEU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 179 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 F residue 188 LEU Chi-restraints excluded: chain F residue 215 GLN Chi-restraints excluded: chain D residue 141 HIS Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 153 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 11 optimal weight: 5.9990 chunk 12 optimal weight: 0.3980 chunk 0 optimal weight: 9.9990 chunk 89 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 131 optimal weight: 8.9990 chunk 88 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 317 GLN F 140 ASN D 141 HIS ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.170889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.113373 restraints weight = 19253.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.116675 restraints weight = 9122.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.118692 restraints weight = 6000.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.119588 restraints weight = 4871.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.119938 restraints weight = 4450.366| |-----------------------------------------------------------------------------| r_work (final): 0.3482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.5966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11161 Z= 0.109 Angle : 0.611 14.771 15104 Z= 0.297 Chirality : 0.046 0.342 1742 Planarity : 0.004 0.058 1950 Dihedral : 5.541 59.062 1579 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.35 % Allowed : 26.24 % Favored : 71.42 % 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: -1.83 (0.22), residues: 1424 helix: 0.14 (0.25), residues: 492 sheet: -1.82 (0.37), residues: 178 loop : -2.04 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 15 TYR 0.013 0.001 TYR C 382 PHE 0.027 0.001 PHE A 90 TRP 0.037 0.001 TRP E 75 HIS 0.006 0.001 HIS D 141 Details of bonding type rmsd covalent geometry : bond 0.00254 (11159) covalent geometry : angle 0.61084 (15104) hydrogen bonds : bond 0.03052 ( 275) hydrogen bonds : angle 4.43362 ( 786) Misc. bond : bond 0.00013 ( 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 271 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 244 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 72 HIS cc_start: 0.7302 (p-80) cc_final: 0.7069 (p-80) REVERT: C 87 LEU cc_start: 0.8566 (mp) cc_final: 0.8319 (mt) REVERT: C 212 MET cc_start: 0.4385 (ttm) cc_final: 0.4003 (ttm) REVERT: C 231 LYS cc_start: 0.8697 (mmtt) cc_final: 0.8404 (mttm) REVERT: E 57 ASN cc_start: 0.8244 (p0) cc_final: 0.8030 (p0) REVERT: E 63 VAL cc_start: 0.9472 (t) cc_final: 0.9160 (m) REVERT: E 251 ILE cc_start: 0.8766 (mm) cc_final: 0.8507 (tt) REVERT: E 325 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8496 (mt) REVERT: E 400 ARG cc_start: 0.7408 (mtt180) cc_final: 0.7117 (ttt180) REVERT: F 187 LEU cc_start: 0.7503 (mm) cc_final: 0.7270 (mm) REVERT: F 190 GLU cc_start: 0.7818 (tm-30) cc_final: 0.7250 (tm-30) REVERT: D 38 MET cc_start: 0.5682 (mmt) cc_final: 0.5036 (mmp) REVERT: D 86 ASN cc_start: 0.7674 (p0) cc_final: 0.7076 (t0) REVERT: D 87 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7859 (mm110) REVERT: D 94 GLN cc_start: 0.7110 (pm20) cc_final: 0.5515 (tm-30) REVERT: D 95 PHE cc_start: 0.6306 (m-10) cc_final: 0.5900 (m-10) REVERT: D 117 LYS cc_start: 0.7560 (tppt) cc_final: 0.7030 (tptp) REVERT: A 22 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7254 (pp30) REVERT: A 153 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.6642 (mt0) REVERT: A 178 ASP cc_start: 0.7767 (t0) cc_final: 0.7453 (t0) outliers start: 27 outliers final: 18 residues processed: 259 average time/residue: 0.0899 time to fit residues: 34.2577 Evaluate side-chains 258 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 237 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 187 ILE 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 129 LEU Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 179 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 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 153 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 101 optimal weight: 7.9990 chunk 52 optimal weight: 0.0370 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 79 optimal weight: 0.0370 chunk 76 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 HIS ** 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 = 0.4166 r_free = 0.4166 target = 0.171815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.116874 restraints weight = 19119.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.118969 restraints weight = 10981.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.120616 restraints weight = 6774.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.120784 restraints weight = 6547.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.120699 restraints weight = 5569.485| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5993 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= 0.102 Angle : 0.617 12.954 15104 Z= 0.298 Chirality : 0.045 0.354 1742 Planarity : 0.004 0.055 1950 Dihedral : 5.467 58.926 1579 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.27 % Favored : 94.73 % Rotamer: Outliers : 2.35 % Allowed : 27.02 % Favored : 70.63 % 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: -1.65 (0.22), residues: 1424 helix: 0.39 (0.25), residues: 487 sheet: -1.76 (0.38), residues: 173 loop : -1.99 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 15 TYR 0.008 0.001 TYR A 104 PHE 0.028 0.001 PHE D 68 TRP 0.039 0.001 TRP E 75 HIS 0.001 0.000 HIS D 137 Details of bonding type rmsd covalent geometry : bond 0.00235 (11159) covalent geometry : angle 0.61716 (15104) hydrogen bonds : bond 0.02883 ( 275) hydrogen bonds : angle 4.34834 ( 786) Misc. bond : bond 0.00002 ( 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 279 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 252 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 15 ARG cc_start: 0.7658 (mmp80) cc_final: 0.5799 (ppt170) REVERT: C 72 HIS cc_start: 0.7365 (p-80) cc_final: 0.7132 (p-80) REVERT: C 87 LEU cc_start: 0.8587 (mp) cc_final: 0.8340 (mt) REVERT: C 212 MET cc_start: 0.4455 (ttm) cc_final: 0.4066 (ttm) REVERT: C 231 LYS cc_start: 0.8690 (mmtt) cc_final: 0.8405 (mttm) REVERT: E 63 VAL cc_start: 0.9460 (t) cc_final: 0.9158 (m) REVERT: E 251 ILE cc_start: 0.8800 (mm) cc_final: 0.8530 (tt) REVERT: E 306 ARG cc_start: 0.9239 (mmm160) cc_final: 0.9023 (mmt180) REVERT: E 325 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8489 (mt) REVERT: F 38 MET cc_start: 0.6132 (tpp) cc_final: 0.5650 (tpp) REVERT: F 190 GLU cc_start: 0.7819 (tm-30) cc_final: 0.7247 (tm-30) REVERT: D 38 MET cc_start: 0.5601 (mmt) cc_final: 0.4899 (mmp) REVERT: D 86 ASN cc_start: 0.7658 (p0) cc_final: 0.7163 (t0) REVERT: D 87 GLN cc_start: 0.8152 (mm-40) cc_final: 0.7875 (mm-40) REVERT: D 94 GLN cc_start: 0.7084 (pm20) cc_final: 0.5299 (tm-30) REVERT: D 95 PHE cc_start: 0.6366 (m-10) cc_final: 0.5936 (m-10) REVERT: D 152 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8923 (mm-40) REVERT: A 153 GLN cc_start: 0.7438 (OUTLIER) cc_final: 0.6645 (mt0) REVERT: A 178 ASP cc_start: 0.7722 (t0) cc_final: 0.7353 (t0) outliers start: 27 outliers final: 22 residues processed: 267 average time/residue: 0.0859 time to fit residues: 34.1425 Evaluate side-chains 268 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 244 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 187 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 266 MET 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 129 LEU Chi-restraints excluded: chain E residue 134 GLN Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 179 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 49 SER Chi-restraints excluded: chain F residue 137 HIS Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 153 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 107 optimal weight: 40.0000 chunk 131 optimal weight: 10.0000 chunk 33 optimal weight: 0.0000 chunk 78 optimal weight: 0.8980 chunk 98 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 102 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 97 optimal weight: 9.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 141 HIS ** 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 = 0.4152 r_free = 0.4152 target = 0.170618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.114482 restraints weight = 19387.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.117538 restraints weight = 10214.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.118092 restraints weight = 6765.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.118214 restraints weight = 6366.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.118523 restraints weight = 6075.777| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.6090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11161 Z= 0.121 Angle : 0.630 9.335 15104 Z= 0.310 Chirality : 0.046 0.345 1742 Planarity : 0.004 0.056 1950 Dihedral : 5.457 59.137 1579 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.52 % Allowed : 27.02 % Favored : 70.46 % 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: -1.54 (0.22), residues: 1424 helix: 0.43 (0.25), residues: 496 sheet: -1.68 (0.39), residues: 171 loop : -1.91 (0.21), residues: 757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 158 TYR 0.016 0.001 TYR A 152 PHE 0.034 0.001 PHE D 68 TRP 0.031 0.001 TRP E 75 HIS 0.002 0.001 HIS D 137 Details of bonding type rmsd covalent geometry : bond 0.00288 (11159) covalent geometry : angle 0.62990 (15104) hydrogen bonds : bond 0.03123 ( 275) hydrogen bonds : angle 4.35159 ( 786) Misc. bond : bond 0.00026 ( 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 272 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 243 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 72 HIS cc_start: 0.7450 (p-80) cc_final: 0.7211 (p-80) REVERT: C 87 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8347 (mt) REVERT: C 212 MET cc_start: 0.4533 (ttm) cc_final: 0.4086 (ttm) REVERT: C 231 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8438 (mttm) REVERT: C 299 ILE cc_start: 0.9305 (tp) cc_final: 0.9085 (tp) REVERT: E 63 VAL cc_start: 0.9470 (t) cc_final: 0.9164 (m) REVERT: E 251 ILE cc_start: 0.8864 (mm) cc_final: 0.8612 (tt) REVERT: E 306 ARG cc_start: 0.9236 (mmm160) cc_final: 0.9035 (mmt180) REVERT: E 325 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8507 (mt) REVERT: F 129 MET cc_start: 0.8048 (tpp) cc_final: 0.7782 (tpp) REVERT: F 190 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7296 (tm-30) REVERT: D 38 MET cc_start: 0.5541 (mmt) cc_final: 0.4897 (mmp) REVERT: D 86 ASN cc_start: 0.7766 (p0) cc_final: 0.7184 (t0) REVERT: D 94 GLN cc_start: 0.6885 (pm20) cc_final: 0.4894 (tm-30) REVERT: D 95 PHE cc_start: 0.6333 (m-10) cc_final: 0.6089 (m-10) REVERT: D 117 LYS cc_start: 0.7684 (tppt) cc_final: 0.7055 (tptp) REVERT: D 171 GLU cc_start: 0.8222 (tt0) cc_final: 0.7922 (tm-30) REVERT: A 143 VAL cc_start: 0.5229 (OUTLIER) cc_final: 0.4910 (p) REVERT: A 153 GLN cc_start: 0.7361 (OUTLIER) cc_final: 0.6693 (mt0) REVERT: A 178 ASP cc_start: 0.7710 (t0) cc_final: 0.7401 (t0) outliers start: 29 outliers final: 23 residues processed: 256 average time/residue: 0.0879 time to fit residues: 33.5099 Evaluate side-chains 266 residues out of total 1191 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 239 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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 87 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 187 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 266 MET 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 101 THR 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 179 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 F residue 137 HIS Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 153 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 51 optimal weight: 0.2980 chunk 11 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 128 optimal weight: 0.4980 chunk 140 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 141 HIS A 50 HIS ** 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 = 0.4165 r_free = 0.4165 target = 0.171724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.115908 restraints weight = 19241.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.118959 restraints weight = 10304.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.119437 restraints weight = 6904.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.119504 restraints weight = 6143.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.119759 restraints weight = 6105.632| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.6097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11161 Z= 0.106 Angle : 0.623 13.343 15104 Z= 0.301 Chirality : 0.045 0.351 1742 Planarity : 0.004 0.054 1950 Dihedral : 5.316 58.252 1579 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.35 % Allowed : 27.11 % Favored : 70.55 % 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: -1.38 (0.22), residues: 1424 helix: 0.65 (0.26), residues: 484 sheet: -1.60 (0.39), residues: 173 loop : -1.85 (0.21), residues: 767 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 15 TYR 0.012 0.001 TYR A 152 PHE 0.034 0.001 PHE D 68 TRP 0.036 0.001 TRP E 75 HIS 0.001 0.000 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00245 (11159) covalent geometry : angle 0.62338 (15104) hydrogen bonds : bond 0.02882 ( 275) hydrogen bonds : angle 4.28587 ( 786) Misc. bond : bond 0.00008 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2431.98 seconds wall clock time: 42 minutes 15.88 seconds (2535.88 seconds total)