Starting phenix.real_space_refine on Sun Oct 25 06:26:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mx7_48712/10_2026/9mx7_48712.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mx7_48712/10_2026/9mx7_48712.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mx7_48712/10_2026/9mx7_48712.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mx7_48712/10_2026/9mx7_48712.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mx7_48712/10_2026/9mx7_48712.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mx7_48712/10_2026/9mx7_48712.map" } resolution = 3.15 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= 0.003 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 23 5.16 5 C 10079 2.51 5 N 2647 2.21 5 O 3039 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15788 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 499, 3993 Classifications: {'peptide': 499} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 481} Chain breaks: 8 Chain: "B" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3494 Classifications: {'peptide': 435} Link IDs: {'PTRANS': 15, 'TRANS': 419} Chain breaks: 10 Chain: "C" Number of atoms: 3991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 495, 3991 Classifications: {'peptide': 495} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 475} Chain breaks: 10 Chain: "D" Number of atoms: 4310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4310 Classifications: {'peptide': 538} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 516} Chain breaks: 4 Time building chain proxies: 3.63, per 1000 atoms: 0.23 Number of scatterers: 15788 At special positions: 0 Unit cell: (92.88, 126.42, 153.08, 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 23 16.00 O 3039 8.00 N 2647 7.00 C 10079 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=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 723.9 milliseconds 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3740 Finding SS restraints... Secondary structure from input PDB file: 86 helices and 10 sheets defined 42.2% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 104 through 113 removed outlier: 3.667A pdb=" N TYR A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 139 through 144 removed outlier: 3.531A pdb=" N ASN A 144 " --> pdb=" O ASN A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 removed outlier: 3.592A pdb=" N ASP A 170 " --> pdb=" O GLN A 166 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLU A 171 " --> pdb=" O LYS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 215 removed outlier: 3.620A pdb=" N LEU A 214 " --> pdb=" O PRO A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 222 Processing helix chain 'A' and resid 233 through 250 removed outlier: 3.502A pdb=" N HIS A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE A 250 " --> pdb=" O LYS A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 260 removed outlier: 4.131A pdb=" N ILE A 260 " --> pdb=" O LYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 281 removed outlier: 3.650A pdb=" N VAL A 273 " --> pdb=" O ASP A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 342 through 346 removed outlier: 3.854A pdb=" N ASP A 346 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 Processing helix chain 'A' and resid 357 through 367 Processing helix chain 'A' and resid 387 through 412 removed outlier: 3.733A pdb=" N LYS A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LYS A 408 " --> pdb=" O TYR A 404 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 409 " --> pdb=" O HIS A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 431 Processing helix chain 'A' and resid 443 through 454 Processing helix chain 'A' and resid 467 through 471 Processing helix chain 'A' and resid 472 through 477 Processing helix chain 'A' and resid 489 through 500 removed outlier: 3.631A pdb=" N LEU A 499 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 514 removed outlier: 3.778A pdb=" N LEU A 511 " --> pdb=" O THR A 508 " (cutoff:3.500A) Proline residue: A 512 - end of helix Processing helix chain 'A' and resid 547 through 553 Processing helix chain 'A' and resid 560 through 571 Processing helix chain 'B' and resid 107 through 113 removed outlier: 3.626A pdb=" N TYR B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 144 removed outlier: 3.786A pdb=" N PHE B 143 " --> pdb=" O GLY B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 170 Processing helix chain 'B' and resid 211 through 215 removed outlier: 3.989A pdb=" N LEU B 214 " --> pdb=" O PRO B 211 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU B 215 " --> pdb=" O TYR B 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 211 through 215' Processing helix chain 'B' and resid 216 through 224 Processing helix chain 'B' and resid 231 through 249 Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 270 through 282 removed outlier: 4.871A pdb=" N TYR B 276 " --> pdb=" O GLU B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 312 removed outlier: 5.198A pdb=" N HIS B 308 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ARG B 309 " --> pdb=" O ASN B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 342 Processing helix chain 'B' and resid 351 through 355 Processing helix chain 'B' and resid 357 through 367 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 387 through 413 removed outlier: 4.033A pdb=" N CYS B 391 " --> pdb=" O VAL B 387 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 392 " --> pdb=" O LEU B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 432 removed outlier: 4.245A pdb=" N TYR B 431 " --> pdb=" O GLU B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 454 removed outlier: 3.536A pdb=" N LYS B 444 " --> pdb=" O TYR B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 489 through 500 Processing helix chain 'B' and resid 507 through 511 removed outlier: 3.821A pdb=" N LEU B 510 " --> pdb=" O ILE B 507 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 511 " --> pdb=" O THR B 508 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 507 through 511' Processing helix chain 'C' and resid 104 through 113 removed outlier: 3.692A pdb=" N TYR C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 119 No H-bonds generated for 'chain 'C' and resid 117 through 119' Processing helix chain 'C' and resid 139 through 145 removed outlier: 3.740A pdb=" N LYS C 145 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 170 removed outlier: 3.751A pdb=" N ASP C 170 " --> pdb=" O GLN C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.631A pdb=" N LEU C 214 " --> pdb=" O PRO C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 232 through 250 removed outlier: 3.657A pdb=" N LYS C 247 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE C 250 " --> pdb=" O LYS C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 282 removed outlier: 3.784A pdb=" N VAL C 273 " --> pdb=" O ASP C 269 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ARG C 280 " --> pdb=" O TYR C 276 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN C 281 " --> pdb=" O ILE C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 312 Processing helix chain 'C' and resid 329 through 341 removed outlier: 3.777A pdb=" N LYS C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE C 340 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N PHE C 341 " --> pdb=" O GLN C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 346 Processing helix chain 'C' and resid 357 through 366 removed outlier: 3.549A pdb=" N ILE C 366 " --> pdb=" O LEU C 362 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 407 Processing helix chain 'C' and resid 428 through 431 Processing helix chain 'C' and resid 440 through 454 Processing helix chain 'C' and resid 467 through 471 Processing helix chain 'C' and resid 472 through 477 Processing helix chain 'C' and resid 489 through 500 removed outlier: 3.541A pdb=" N LEU C 499 " --> pdb=" O TYR C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 507 through 514 removed outlier: 3.753A pdb=" N LEU C 511 " --> pdb=" O THR C 508 " (cutoff:3.500A) Proline residue: C 512 - end of helix Processing helix chain 'C' and resid 547 through 553 Processing helix chain 'C' and resid 560 through 571 Processing helix chain 'D' and resid 25 through 30 Processing helix chain 'D' and resid 104 through 113 removed outlier: 3.639A pdb=" N TYR D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 119 No H-bonds generated for 'chain 'D' and resid 117 through 119' Processing helix chain 'D' and resid 139 through 145 removed outlier: 3.698A pdb=" N LYS D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 170 Processing helix chain 'D' and resid 211 through 215 removed outlier: 3.512A pdb=" N LEU D 214 " --> pdb=" O PRO D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 225 Processing helix chain 'D' and resid 233 through 249 removed outlier: 3.782A pdb=" N VAL D 237 " --> pdb=" O ASN D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 260 removed outlier: 3.544A pdb=" N GLU D 258 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE D 260 " --> pdb=" O LYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 279 removed outlier: 3.548A pdb=" N VAL D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE D 277 " --> pdb=" O VAL D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 312 Processing helix chain 'D' and resid 329 through 341 removed outlier: 3.554A pdb=" N PHE D 341 " --> pdb=" O GLN D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 351 through 354 Processing helix chain 'D' and resid 357 through 366 Processing helix chain 'D' and resid 387 through 407 removed outlier: 3.567A pdb=" N CYS D 391 " --> pdb=" O VAL D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 428 through 431 Processing helix chain 'D' and resid 440 through 458 removed outlier: 5.661A pdb=" N ARG D 455 " --> pdb=" O ALA D 451 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N LYS D 456 " --> pdb=" O LYS D 452 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N TYR D 457 " --> pdb=" O GLU D 453 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 471 Processing helix chain 'D' and resid 472 through 477 Processing helix chain 'D' and resid 489 through 500 Processing helix chain 'D' and resid 507 through 514 removed outlier: 3.822A pdb=" N LEU D 511 " --> pdb=" O THR D 508 " (cutoff:3.500A) Proline residue: D 512 - end of helix Processing helix chain 'D' and resid 549 through 553 Processing helix chain 'D' and resid 560 through 570 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 58 removed outlier: 6.092A pdb=" N LEU A 52 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 80 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N ALA A 54 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N ILE A 78 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N ILE A 56 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 5.679A pdb=" N SER A 76 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN A 58 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 134 through 138 removed outlier: 4.713A pdb=" N SER A 125 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N VAL A 137 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 5.645A pdb=" N THR A 123 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ALA A 148 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE A 185 " --> pdb=" O VAL A 424 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLU A 426 " --> pdb=" O ILE A 185 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N PHE A 187 " --> pdb=" O GLU A 426 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N ILE A 184 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 7.875A pdb=" N LEU A 378 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ILE A 186 " --> pdb=" O LEU A 378 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ASN A 201 " --> pdb=" O ILE A 377 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ASP A 379 " --> pdb=" O ASN A 201 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 203 " --> pdb=" O ASP A 379 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 299 through 300 Processing sheet with id=AA4, first strand: chain 'B' and resid 86 through 88 removed outlier: 6.855A pdb=" N GLU B 74 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N LEU B 53 " --> pdb=" O ILE B 78 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LEU B 80 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA B 51 " --> pdb=" O LEU B 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 375 through 379 removed outlier: 6.810A pdb=" N ILE B 185 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N GLU B 426 " --> pdb=" O ILE B 185 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N PHE B 187 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 19 through 22 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 19 through 22 current: chain 'C' and resid 53 through 60 removed outlier: 7.012A pdb=" N LEU C 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU C 74 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE C 59 " --> pdb=" O MET C 72 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N MET C 72 " --> pdb=" O PHE C 59 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 86 through 88 current: chain 'D' and resid 18 through 23 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 23 current: chain 'D' and resid 50 through 62 removed outlier: 7.044A pdb=" N ALA D 51 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU D 80 " --> pdb=" O ALA D 51 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N LEU D 53 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU D 74 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N PHE D 59 " --> pdb=" O MET D 72 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N MET D 72 " --> pdb=" O PHE D 59 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ILE D 61 " --> pdb=" O LYS D 70 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LYS D 70 " --> pdb=" O ILE D 61 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 134 through 138 removed outlier: 4.587A pdb=" N SER C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL C 137 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N THR C 123 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ALA C 148 " --> pdb=" O ILE C 483 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE C 185 " --> pdb=" O VAL C 424 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N GLU C 426 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N PHE C 187 " --> pdb=" O GLU C 426 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ASN C 201 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ASP C 379 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU C 203 " --> pdb=" O ASP C 379 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 300 through 301 Processing sheet with id=AA9, first strand: chain 'D' and resid 134 through 138 removed outlier: 4.735A pdb=" N SER D 125 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL D 137 " --> pdb=" O THR D 123 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N THR D 123 " --> pdb=" O VAL D 137 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA D 148 " --> pdb=" O ILE D 483 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ILE D 185 " --> pdb=" O VAL D 424 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N GLU D 426 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N PHE D 187 " --> pdb=" O GLU D 426 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE D 184 " --> pdb=" O THR D 376 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N LEU D 378 " --> pdb=" O ILE D 184 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE D 186 " --> pdb=" O LEU D 378 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN D 201 " --> pdb=" O ILE D 377 " (cutoff:3.500A) removed outlier: 7.384A pdb=" N ASP D 379 " --> pdb=" O ASN D 201 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU D 203 " --> pdb=" O ASP D 379 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 298 through 301 571 hydrogen bonds defined for protein. 1545 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.11 Time building geometry restraints manager: 1.65 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: 4944 1.34 - 1.45: 2046 1.45 - 1.57: 9038 1.57 - 1.69: 3 1.69 - 1.81: 35 Bond restraints: 16066 Sorted by residual: bond pdb=" N PRO A 512 " pdb=" CD PRO A 512 " ideal model delta sigma weight residual 1.473 1.404 0.069 1.40e-02 5.10e+03 2.40e+01 bond pdb=" CA PRO A 512 " pdb=" CB PRO A 512 " ideal model delta sigma weight residual 1.533 1.590 -0.057 1.61e-02 3.86e+03 1.24e+01 bond pdb=" CB PRO B 96 " pdb=" CG PRO B 96 " ideal model delta sigma weight residual 1.492 1.321 0.171 5.00e-02 4.00e+02 1.17e+01 bond pdb=" CD2 PHE A 59 " pdb=" CE2 PHE A 59 " ideal model delta sigma weight residual 1.382 1.282 0.100 3.00e-02 1.11e+03 1.11e+01 bond pdb=" CG PRO A 512 " pdb=" CD PRO A 512 " ideal model delta sigma weight residual 1.503 1.611 -0.108 3.40e-02 8.65e+02 1.00e+01 ... (remaining 16061 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 21449 2.40 - 4.80: 195 4.80 - 7.20: 14 7.20 - 9.60: 7 9.60 - 12.00: 2 Bond angle restraints: 21667 Sorted by residual: angle pdb=" N PRO A 512 " pdb=" CD PRO A 512 " pdb=" CG PRO A 512 " ideal model delta sigma weight residual 103.20 110.54 -7.34 1.50e+00 4.44e-01 2.39e+01 angle pdb=" C ARG B 121 " pdb=" N PHE B 122 " pdb=" CA PHE B 122 " ideal model delta sigma weight residual 121.54 130.51 -8.97 1.91e+00 2.74e-01 2.21e+01 angle pdb=" C PHE B 122 " pdb=" N THR B 123 " pdb=" CA THR B 123 " ideal model delta sigma weight residual 121.54 128.98 -7.44 1.91e+00 2.74e-01 1.52e+01 angle pdb=" N PRO A 512 " pdb=" CA PRO A 512 " pdb=" CB PRO A 512 " ideal model delta sigma weight residual 103.41 106.69 -3.28 9.40e-01 1.13e+00 1.22e+01 angle pdb=" CA LEU A 549 " pdb=" CB LEU A 549 " pdb=" CG LEU A 549 " ideal model delta sigma weight residual 116.30 104.30 12.00 3.50e+00 8.16e-02 1.18e+01 ... (remaining 21662 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 8820 16.53 - 33.06: 739 33.06 - 49.59: 144 49.59 - 66.12: 52 66.12 - 82.65: 7 Dihedral angle restraints: 9762 sinusoidal: 4025 harmonic: 5737 Sorted by residual: dihedral pdb=" CA PRO A 96 " pdb=" C PRO A 96 " pdb=" N PRO A 97 " pdb=" CA PRO A 97 " ideal model delta harmonic sigma weight residual 180.00 152.07 27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ASN D 278 " pdb=" C ASN D 278 " pdb=" N ASN D 279 " pdb=" CA ASN D 279 " ideal model delta harmonic sigma weight residual 180.00 152.16 27.84 0 5.00e+00 4.00e-02 3.10e+01 dihedral pdb=" CA LEU A 95 " pdb=" C LEU A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta harmonic sigma weight residual 180.00 -154.00 -26.00 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 9759 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1926 0.050 - 0.101: 384 0.101 - 0.151: 135 0.151 - 0.202: 6 0.202 - 0.252: 2 Chirality restraints: 2453 Sorted by residual: chirality pdb=" CB THR B 123 " pdb=" CA THR B 123 " pdb=" OG1 THR B 123 " pdb=" CG2 THR B 123 " both_signs ideal model delta sigma weight residual False 2.55 2.30 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" CG LEU A 549 " pdb=" CB LEU A 549 " pdb=" CD1 LEU A 549 " pdb=" CD2 LEU A 549 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" CA LYS A 547 " pdb=" N LYS A 547 " pdb=" C LYS A 547 " pdb=" CB LYS A 547 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.09e-01 ... (remaining 2450 not shown) Planarity restraints: 2770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 121 " 0.418 9.50e-02 1.11e+02 1.87e-01 2.16e+01 pdb=" NE ARG B 121 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG B 121 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 121 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 121 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 96 " 0.066 5.00e-02 4.00e+02 1.01e-01 1.62e+01 pdb=" N PRO A 97 " -0.174 5.00e-02 4.00e+02 pdb=" CA PRO A 97 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 97 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 122 " -0.041 2.00e-02 2.50e+03 2.88e-02 1.45e+01 pdb=" CG PHE B 122 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 PHE B 122 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE B 122 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 122 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 122 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 122 " -0.017 2.00e-02 2.50e+03 ... (remaining 2767 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.41: 30 2.41 - 3.03: 9528 3.03 - 3.66: 21228 3.66 - 4.28: 32612 4.28 - 4.90: 55628 Nonbonded interactions: 119026 Sorted by model distance: nonbonded pdb=" NH1 ARG A 467 " pdb=" O LEU B 500 " model vdw 1.791 3.120 nonbonded pdb=" O PHE A 59 " pdb=" OG SER B 13 " model vdw 1.918 3.040 nonbonded pdb=" OG SER D 294 " pdb=" OD2 ASP D 318 " model vdw 1.980 3.040 nonbonded pdb=" NH2 ARG A 467 " pdb=" OD1 ASN A 489 " model vdw 2.071 3.120 nonbonded pdb=" OG SER A 128 " pdb=" OE2 GLU A 518 " model vdw 2.183 3.040 ... (remaining 119021 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 'A' and (resid 19 through 27 or resid 37 through 44 or resid 52 through 8 \ 4 or resid 95 through 174 or resid 180 through 222 or resid 232 through 251 or r \ esid 258 through 286 or resid 299 through 407 or resid 419 through 500 or resid \ 507 through 539 or resid 548 through 571)) selection = (chain 'C' and (resid 19 through 61 or resid 70 through 84 or resid 95 through 1 \ 74 or resid 180 through 222 or resid 232 through 286 or resid 299 through 301 or \ resid 305 through 432 or resid 442 through 539 or resid 548 through 571)) selection = (chain 'D' and (resid 19 through 27 or resid 37 through 44 or resid 52 through 6 \ 1 or resid 70 through 84 or resid 95 through 222 or resid 232 through 251 or res \ id 258 through 286 or resid 299 through 301 or resid 305 through 407 or resid 41 \ 9 through 432 or resid 442 through 500 or resid 507 through 539 or resid 548 thr \ ough 571)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 13.630 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3222 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 : 0.004 0.171 16066 Z= 0.159 Angle : 0.619 12.002 21667 Z= 0.330 Chirality : 0.046 0.252 2453 Planarity : 0.007 0.187 2770 Dihedral : 13.404 82.652 6022 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.70 % Favored : 94.20 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.19), residues: 1895 helix: 0.76 (0.21), residues: 651 sheet: 0.01 (0.31), residues: 285 loop : -1.32 (0.18), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 467 TYR 0.039 0.001 TYR A 548 PHE 0.061 0.002 PHE B 122 TRP 0.022 0.002 TRP C 568 HIS 0.036 0.001 HIS B 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (16066) covalent geometry : angle 0.61868 / 0.33 (21667) hydrogen bonds : bond 0.21447 / 14.10 ( 571) hydrogen bonds : angle 6.15964 / 4.22 ( 1545) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 495 TYR cc_start: 0.5631 (t80) cc_final: 0.4287 (t80) REVERT: C 246 LYS cc_start: 0.2751 (mmtp) cc_final: 0.2241 (mmtp) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.1258 time to fit residues: 22.1460 Evaluate side-chains 102 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.2980 chunk 124 optimal weight: 0.0870 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN A 159 HIS A 183 HIS ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 HIS A 374 ASN ** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 159 HIS C 180 ASN C 405 HIS C 493 GLN D 159 HIS D 233 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5023 r_free = 0.5023 target = 0.261474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4867 r_free = 0.4867 target = 0.243246 restraints weight = 26918.505| |-----------------------------------------------------------------------------| r_work (start): 0.4866 rms_B_bonded: 2.48 r_work: 0.4783 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4365 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 16066 Z= 0.255 Angle : 0.826 11.857 21667 Z= 0.435 Chirality : 0.054 0.302 2453 Planarity : 0.006 0.103 2770 Dihedral : 5.941 44.278 2074 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.28 % Favored : 94.56 % Rotamer: Outliers : 0.61 % Allowed : 4.63 % Favored : 94.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.18), residues: 1895 helix: 0.21 (0.19), residues: 681 sheet: -0.04 (0.31), residues: 286 loop : -1.58 (0.18), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 344 TYR 0.035 0.003 TYR B 425 PHE 0.034 0.004 PHE A 311 TRP 0.017 0.003 TRP C 568 HIS 0.014 0.002 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.26 (16066) covalent geometry : angle 0.82637 / 0.44 (21667) hydrogen bonds : bond 0.05625 / 3.83 ( 571) hydrogen bonds : angle 5.54053 / 3.81 ( 1545) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.519 Fit side-chains revert: symmetry clash REVERT: A 344 ARG cc_start: 0.6029 (mtp85) cc_final: 0.5550 (ttt180) REVERT: A 345 LEU cc_start: 0.5881 (mp) cc_final: 0.5200 (tt) REVERT: A 477 SER cc_start: 0.8014 (p) cc_final: 0.7813 (t) REVERT: B 72 MET cc_start: 0.5749 (tmm) cc_final: 0.3737 (tmm) REVERT: B 485 MET cc_start: 0.2569 (mmt) cc_final: 0.0513 (mmt) REVERT: C 179 LEU cc_start: 0.8010 (mm) cc_final: 0.7768 (mt) REVERT: D 499 LEU cc_start: 0.8286 (mt) cc_final: 0.8082 (mp) outliers start: 11 outliers final: 6 residues processed: 146 average time/residue: 0.1450 time to fit residues: 30.5580 Evaluate side-chains 125 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 119 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 78 ILE Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 392 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [185, 91, 53, 139, 33, 59, 147, 15, 175, 165, 56] chunk 185 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 175 optimal weight: 0.7980 chunk 165 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 GLN ** A 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 281 ASN A 374 ASN ** B 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 249 HIS C 245 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5027 r_free = 0.5027 target = 0.261381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4863 r_free = 0.4863 target = 0.242467 restraints weight = 26493.571| |-----------------------------------------------------------------------------| r_work (start): 0.4865 rms_B_bonded: 2.79 r_work: 0.4775 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.4775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4417 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16066 Z= 0.133 Angle : 0.550 9.093 21667 Z= 0.295 Chirality : 0.045 0.253 2453 Planarity : 0.005 0.101 2770 Dihedral : 5.054 58.072 2074 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.64 % Favored : 95.25 % Rotamer: Outliers : 1.00 % Allowed : 7.08 % Favored : 91.92 % 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: -0.47 (0.19), residues: 1895 helix: 0.80 (0.20), residues: 693 sheet: 0.23 (0.32), residues: 289 loop : -1.39 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 344 TYR 0.018 0.002 TYR C 425 PHE 0.022 0.002 PHE B 347 TRP 0.018 0.002 TRP C 213 HIS 0.029 0.002 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (16066) covalent geometry : angle 0.55000 / 0.30 (21667) hydrogen bonds : bond 0.04048 / 2.76 ( 571) hydrogen bonds : angle 4.72044 / 3.25 ( 1545) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.536 Fit side-chains revert: symmetry clash REVERT: A 344 ARG cc_start: 0.5892 (mtp85) cc_final: 0.5487 (ttt180) REVERT: B 72 MET cc_start: 0.5684 (tmm) cc_final: 0.3411 (tmm) REVERT: C 213 TRP cc_start: 0.4312 (p-90) cc_final: 0.3677 (p-90) REVERT: D 80 LEU cc_start: 0.1310 (OUTLIER) cc_final: 0.0152 (tp) REVERT: D 164 ILE cc_start: 0.4745 (OUTLIER) cc_final: 0.4307 (mt) REVERT: D 499 LEU cc_start: 0.8363 (mt) cc_final: 0.8101 (mp) REVERT: D 533 LYS cc_start: 0.6325 (tmtt) cc_final: 0.6107 (tmtt) outliers start: 18 outliers final: 6 residues processed: 139 average time/residue: 0.1292 time to fit residues: 26.8010 Evaluate side-chains 126 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 HIS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 164 ILE Chi-restraints excluded: chain D residue 383 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [187, 54, 18, 129, 167, 124, 82, 116, 37, 34, 26] chunk 187 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 129 optimal weight: 5.9990 chunk 167 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 116 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 HIS ** A 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 144 ASN C 146 HIS ** C 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 299 ASN ** D 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4924 r_free = 0.4924 target = 0.248636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.228831 restraints weight = 24945.435| |-----------------------------------------------------------------------------| r_work (start): 0.4743 rms_B_bonded: 2.45 r_work: 0.4652 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4982 moved from start: 0.7632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 16066 Z= 0.375 Angle : 0.947 13.891 21667 Z= 0.510 Chirality : 0.058 0.302 2453 Planarity : 0.007 0.089 2770 Dihedral : 7.075 79.974 2074 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.23 % Favored : 92.61 % Rotamer: Outliers : 2.23 % Allowed : 9.75 % Favored : 88.02 % 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: -2.06 (0.18), residues: 1895 helix: -0.87 (0.18), residues: 694 sheet: -0.70 (0.32), residues: 274 loop : -1.94 (0.18), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 344 TYR 0.040 0.003 TYR B 425 PHE 0.051 0.004 PHE A 358 TRP 0.032 0.004 TRP C 213 HIS 0.010 0.002 HIS A 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00824 / 0.38 (16066) covalent geometry : angle 0.94677 / 0.51 (21667) hydrogen bonds : bond 0.07341 / 5.02 ( 571) hydrogen bonds : angle 6.50939 / 4.52 ( 1545) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 142 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 ARG cc_start: 0.6509 (mtp85) cc_final: 0.5444 (ttt180) REVERT: B 60 SER cc_start: 0.4684 (p) cc_final: 0.4275 (p) REVERT: B 72 MET cc_start: 0.5649 (tmm) cc_final: 0.4921 (tmm) REVERT: B 264 SER cc_start: 0.7892 (m) cc_final: 0.7613 (p) REVERT: C 179 LEU cc_start: 0.8163 (mm) cc_final: 0.7831 (mt) REVERT: C 379 ASP cc_start: 0.7052 (t0) cc_final: 0.6742 (t0) REVERT: D 246 LYS cc_start: 0.3651 (OUTLIER) cc_final: 0.1535 (mtpp) REVERT: D 279 ASN cc_start: 0.3914 (OUTLIER) cc_final: 0.3614 (m-40) outliers start: 40 outliers final: 26 residues processed: 170 average time/residue: 0.1263 time to fit residues: 32.3176 Evaluate side-chains 155 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 127 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain A residue 520 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 274 ILE Chi-restraints excluded: chain B residue 475 ILE Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 213 TRP Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 483 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 111 ILE Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 279 ASN Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 392 VAL Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 548 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [82, 169, 67, 131, 31, 139, 143, 164, 84, 15, 14] chunk 82 optimal weight: 5.9990 chunk 169 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 131 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 143 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 84 optimal weight: 0.3980 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 183 HIS ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 286 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 HIS C 271 ASN C 374 ASN C 493 GLN D 286 ASN D 308 HIS D 466 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4967 r_free = 0.4967 target = 0.253134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4796 r_free = 0.4796 target = 0.234085 restraints weight = 25375.997| |-----------------------------------------------------------------------------| r_work (start): 0.4798 rms_B_bonded: 2.44 r_work: 0.4713 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4772 moved from start: 0.7496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16066 Z= 0.125 Angle : 0.583 11.201 21667 Z= 0.308 Chirality : 0.045 0.212 2453 Planarity : 0.005 0.097 2770 Dihedral : 5.644 87.543 2074 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.49 % Favored : 95.41 % Rotamer: Outliers : 1.28 % Allowed : 12.60 % Favored : 86.12 % 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: -1.17 (0.19), residues: 1895 helix: 0.23 (0.20), residues: 673 sheet: -0.42 (0.33), residues: 275 loop : -1.65 (0.19), residues: 947 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 486 TYR 0.019 0.001 TYR C 425 PHE 0.032 0.002 PHE C 142 TRP 0.017 0.002 TRP C 213 HIS 0.008 0.001 HIS A 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (16066) covalent geometry : angle 0.58334 / 0.31 (21667) hydrogen bonds : bond 0.03976 / 2.68 ( 571) hydrogen bonds : angle 5.21175 / 3.63 ( 1545) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 ARG cc_start: 0.6332 (mtp85) cc_final: 0.5104 (ttt180) REVERT: B 124 PHE cc_start: 0.6776 (t80) cc_final: 0.6450 (t80) REVERT: C 379 ASP cc_start: 0.6758 (t0) cc_final: 0.6454 (t0) REVERT: D 499 LEU cc_start: 0.8527 (mt) cc_final: 0.8281 (mp) outliers start: 23 outliers final: 17 residues processed: 145 average time/residue: 0.1240 time to fit residues: 27.3267 Evaluate side-chains 145 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 128 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 308 HIS Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 213 TRP Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 466 GLN Chi-restraints excluded: chain D residue 548 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [123, 192, 43, 23, 126, 141, 19, 178, 92, 22, 183] chunk 123 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 19 optimal weight: 0.3980 chunk 178 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 22 optimal weight: 0.8980 chunk 183 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 HIS D 282 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4973 r_free = 0.4973 target = 0.253383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4800 r_free = 0.4800 target = 0.234545 restraints weight = 25448.096| |-----------------------------------------------------------------------------| r_work (start): 0.4804 rms_B_bonded: 2.62 r_work: 0.4716 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.4716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4766 moved from start: 0.7643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16066 Z= 0.112 Angle : 0.532 8.734 21667 Z= 0.280 Chirality : 0.044 0.213 2453 Planarity : 0.005 0.097 2770 Dihedral : 5.090 86.379 2074 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.80 % Favored : 95.09 % Rotamer: Outliers : 1.51 % Allowed : 13.15 % Favored : 85.34 % 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: -0.72 (0.19), residues: 1895 helix: 0.66 (0.20), residues: 677 sheet: -0.17 (0.33), residues: 274 loop : -1.44 (0.19), residues: 944 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 486 TYR 0.018 0.001 TYR C 425 PHE 0.027 0.002 PHE C 142 TRP 0.016 0.001 TRP C 213 HIS 0.008 0.001 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 (16066) covalent geometry : angle 0.53206 / 0.28 (21667) hydrogen bonds : bond 0.03536 / 2.41 ( 571) hydrogen bonds : angle 4.84788 / 3.37 ( 1545) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 ARG cc_start: 0.6290 (mtp85) cc_final: 0.5252 (ttt180) REVERT: B 72 MET cc_start: 0.5480 (tmm) cc_final: 0.4795 (tmm) REVERT: B 123 THR cc_start: 0.6558 (OUTLIER) cc_final: 0.6331 (m) REVERT: B 124 PHE cc_start: 0.6766 (t80) cc_final: 0.6454 (t80) REVERT: C 379 ASP cc_start: 0.6643 (t0) cc_final: 0.6367 (t0) REVERT: D 499 LEU cc_start: 0.8506 (mt) cc_final: 0.8287 (mp) outliers start: 27 outliers final: 16 residues processed: 150 average time/residue: 0.1251 time to fit residues: 28.5589 Evaluate side-chains 144 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 127 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 251 GLN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 548 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [163, 94, 43, 44, 148, 32, 74, 15, 28, 120, 70] chunk 163 optimal weight: 2.9990 chunk 94 optimal weight: 0.0670 chunk 43 optimal weight: 2.9990 chunk 44 optimal weight: 0.0670 chunk 148 optimal weight: 0.6980 chunk 32 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 15 optimal weight: 0.0470 chunk 28 optimal weight: 0.9990 chunk 120 optimal weight: 0.0980 chunk 70 optimal weight: 6.9990 overall best weight: 0.1954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5009 r_free = 0.5009 target = 0.256856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4844 r_free = 0.4844 target = 0.238468 restraints weight = 26217.607| |-----------------------------------------------------------------------------| r_work (start): 0.4843 rms_B_bonded: 2.69 r_work: 0.4755 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4636 moved from start: 0.7611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16066 Z= 0.085 Angle : 0.482 9.126 21667 Z= 0.250 Chirality : 0.043 0.276 2453 Planarity : 0.004 0.093 2770 Dihedral : 4.534 80.859 2074 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.85 % Favored : 96.04 % Rotamer: Outliers : 0.84 % Allowed : 14.33 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.39 % 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: -0.25 (0.20), residues: 1895 helix: 1.14 (0.21), residues: 680 sheet: 0.20 (0.33), residues: 281 loop : -1.30 (0.20), residues: 934 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 43 TYR 0.011 0.001 TYR C 425 PHE 0.029 0.001 PHE B 86 TRP 0.008 0.001 TRP D 293 HIS 0.004 0.001 HIS A 405 Details of bonding type rmsd/Z covalent geometry : bond 0.00182 / 0.09 (16066) covalent geometry : angle 0.48217 / 0.25 (21667) hydrogen bonds : bond 0.02677 / 1.81 ( 571) hydrogen bonds : angle 4.46882 / 3.11 ( 1545) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 ARG cc_start: 0.6109 (mtp85) cc_final: 0.5180 (ttt180) REVERT: B 72 MET cc_start: 0.5206 (tmm) cc_final: 0.4898 (tmm) REVERT: C 379 ASP cc_start: 0.6406 (t0) cc_final: 0.6143 (t0) REVERT: C 457 TYR cc_start: 0.5394 (m-80) cc_final: 0.5129 (m-80) REVERT: D 246 LYS cc_start: 0.3180 (OUTLIER) cc_final: 0.1662 (ptpt) REVERT: D 499 LEU cc_start: 0.8384 (mt) cc_final: 0.8177 (mp) REVERT: D 553 ARG cc_start: 0.5701 (mtm110) cc_final: 0.5481 (mtm-85) outliers start: 15 outliers final: 8 residues processed: 135 average time/residue: 0.1305 time to fit residues: 26.4145 Evaluate side-chains 130 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 121 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 52 LEU Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 548 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [122, 109, 66, 98, 27, 170, 110, 148, 179, 174, 185] chunk 122 optimal weight: 1.9990 chunk 109 optimal weight: 1.9990 chunk 66 optimal weight: 8.9990 chunk 98 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 chunk 170 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 148 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 174 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 overall best weight: 1.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 166 GLN ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN C 493 GLN D 159 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.251121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4791 r_free = 0.4791 target = 0.232296 restraints weight = 25704.970| |-----------------------------------------------------------------------------| r_work (start): 0.4789 rms_B_bonded: 2.36 r_work: 0.4707 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.4707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4844 moved from start: 0.8136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16066 Z= 0.161 Angle : 0.587 8.021 21667 Z= 0.310 Chirality : 0.046 0.184 2453 Planarity : 0.005 0.098 2770 Dihedral : 5.195 85.977 2074 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.75 % Favored : 94.14 % Rotamer: Outliers : 1.34 % Allowed : 13.88 % Favored : 84.78 % 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: -0.66 (0.19), residues: 1895 helix: 0.69 (0.20), residues: 674 sheet: -0.00 (0.33), residues: 268 loop : -1.42 (0.19), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 280 TYR 0.020 0.002 TYR B 425 PHE 0.029 0.002 PHE D 561 TRP 0.013 0.002 TRP A 213 HIS 0.008 0.001 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (16066) covalent geometry : angle 0.58679 / 0.31 (21667) hydrogen bonds : bond 0.04266 / 2.90 ( 571) hydrogen bonds : angle 4.99477 / 3.50 ( 1545) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 ARG cc_start: 0.6509 (mtp85) cc_final: 0.5605 (ttt180) REVERT: B 72 MET cc_start: 0.5416 (tmm) cc_final: 0.5153 (tmm) REVERT: C 379 ASP cc_start: 0.6703 (t0) cc_final: 0.6427 (t0) REVERT: C 457 TYR cc_start: 0.5640 (m-80) cc_final: 0.5307 (m-80) REVERT: D 246 LYS cc_start: 0.3699 (OUTLIER) cc_final: 0.1707 (ptpt) REVERT: D 492 ASP cc_start: 0.6995 (m-30) cc_final: 0.6387 (m-30) REVERT: D 499 LEU cc_start: 0.8490 (mt) cc_final: 0.8272 (mp) REVERT: D 533 LYS cc_start: 0.6728 (tmtt) cc_final: 0.6280 (tmtt) REVERT: D 553 ARG cc_start: 0.6234 (mtm110) cc_final: 0.5732 (ptm-80) outliers start: 24 outliers final: 18 residues processed: 149 average time/residue: 0.1290 time to fit residues: 28.8476 Evaluate side-chains 144 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 548 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [155, 43, 62, 188, 42, 2, 31, 96, 111, 59, 175] chunk 155 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 188 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 190 HIS B 140 ASN ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN D 282 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4960 r_free = 0.4960 target = 0.250735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.231136 restraints weight = 25595.644| |-----------------------------------------------------------------------------| r_work (start): 0.4777 rms_B_bonded: 2.77 r_work: 0.4684 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.4684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4900 moved from start: 0.8461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16066 Z= 0.148 Angle : 0.570 7.873 21667 Z= 0.302 Chirality : 0.045 0.176 2453 Planarity : 0.005 0.092 2770 Dihedral : 5.229 87.341 2074 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.33 % Favored : 95.57 % Rotamer: Outliers : 1.51 % Allowed : 13.94 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.19), residues: 1895 helix: 0.59 (0.20), residues: 672 sheet: -0.04 (0.36), residues: 244 loop : -1.47 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 280 TYR 0.020 0.002 TYR C 425 PHE 0.032 0.002 PHE C 142 TRP 0.010 0.002 TRP D 552 HIS 0.006 0.001 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 (16066) covalent geometry : angle 0.57000 / 0.30 (21667) hydrogen bonds : bond 0.03975 / 2.67 ( 571) hydrogen bonds : angle 5.04660 / 3.54 ( 1545) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 ARG cc_start: 0.6510 (mtp85) cc_final: 0.5461 (ttt180) REVERT: B 72 MET cc_start: 0.5560 (tmm) cc_final: 0.4982 (tmm) REVERT: C 379 ASP cc_start: 0.6720 (t0) cc_final: 0.6458 (t0) REVERT: C 457 TYR cc_start: 0.5542 (m-80) cc_final: 0.5212 (m-80) REVERT: D 246 LYS cc_start: 0.3785 (OUTLIER) cc_final: 0.1675 (ptpt) REVERT: D 499 LEU cc_start: 0.8525 (mt) cc_final: 0.8309 (mp) REVERT: D 533 LYS cc_start: 0.6840 (tmtt) cc_final: 0.6342 (tmtt) REVERT: D 553 ARG cc_start: 0.6318 (mtm110) cc_final: 0.5842 (ptm-80) outliers start: 27 outliers final: 21 residues processed: 150 average time/residue: 0.1297 time to fit residues: 28.9497 Evaluate side-chains 146 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain B residue 528 ILE Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 71 TYR Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 487 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [85, 108, 146, 127, 177, 187, 92, 65, 78, 114, 122] chunk 85 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 146 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 177 optimal weight: 3.9990 chunk 187 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 78 optimal weight: 0.0870 chunk 114 optimal weight: 0.4980 chunk 122 optimal weight: 1.9990 overall best weight: 1.1162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 509 ASN ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 180 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4959 r_free = 0.4959 target = 0.250732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.231327 restraints weight = 25429.975| |-----------------------------------------------------------------------------| r_work (start): 0.4777 rms_B_bonded: 2.77 r_work: 0.4682 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4911 moved from start: 0.8669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16066 Z= 0.140 Angle : 0.563 10.563 21667 Z= 0.297 Chirality : 0.045 0.172 2453 Planarity : 0.005 0.096 2770 Dihedral : 5.148 86.675 2074 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.70 % Favored : 94.20 % Rotamer: Outliers : 1.34 % Allowed : 14.16 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.79 (0.19), residues: 1895 helix: 0.58 (0.20), residues: 676 sheet: -0.00 (0.35), residues: 249 loop : -1.49 (0.19), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 280 TYR 0.019 0.001 TYR C 425 PHE 0.040 0.002 PHE B 124 TRP 0.011 0.002 TRP A 213 HIS 0.007 0.001 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (16066) covalent geometry : angle 0.56264 / 0.30 (21667) hydrogen bonds : bond 0.03913 / 2.65 ( 571) hydrogen bonds : angle 5.02965 / 3.53 ( 1545) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3790 Ramachandran restraints generated. 1895 Oldfield, 0 Emsley, 1895 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 344 ARG cc_start: 0.6496 (mtp85) cc_final: 0.5388 (ttt180) REVERT: C 379 ASP cc_start: 0.6734 (t0) cc_final: 0.6476 (t0) REVERT: C 457 TYR cc_start: 0.5487 (m-80) cc_final: 0.5174 (m-80) REVERT: D 246 LYS cc_start: 0.3741 (OUTLIER) cc_final: 0.1683 (ptpt) REVERT: D 499 LEU cc_start: 0.8515 (mt) cc_final: 0.8302 (mp) REVERT: D 533 LYS cc_start: 0.6907 (tmtt) cc_final: 0.6391 (tmtt) REVERT: D 553 ARG cc_start: 0.6408 (mtm110) cc_final: 0.5999 (ptm-80) outliers start: 24 outliers final: 21 residues processed: 145 average time/residue: 0.1276 time to fit residues: 27.4544 Evaluate side-chains 149 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 251 GLN Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 546 ILE Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 181 ASN Chi-restraints excluded: chain B residue 230 ASN Chi-restraints excluded: chain B residue 522 MET Chi-restraints excluded: chain C residue 180 ASN Chi-restraints excluded: chain C residue 423 ILE Chi-restraints excluded: chain C residue 481 THR Chi-restraints excluded: chain D residue 56 ILE Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 150 VAL Chi-restraints excluded: chain D residue 184 ILE Chi-restraints excluded: chain D residue 246 LYS Chi-restraints excluded: chain D residue 356 VAL Chi-restraints excluded: chain D residue 419 ILE Chi-restraints excluded: chain D residue 423 ILE Chi-restraints excluded: chain D residue 487 LEU Chi-restraints excluded: chain D residue 548 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: [33, 34, 58, 67, 115, 104, 100, 82, 167, 0, 3] chunk 33 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 104 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 167 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 47 ASN ** B 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.250112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.230726 restraints weight = 25337.713| |-----------------------------------------------------------------------------| r_work (start): 0.4778 rms_B_bonded: 2.73 r_work: 0.4685 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4898 moved from start: 0.8833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16066 Z= 0.127 Angle : 0.545 8.832 21667 Z= 0.288 Chirality : 0.044 0.172 2453 Planarity : 0.005 0.092 2770 Dihedral : 5.041 86.115 2074 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.22 % Favored : 95.67 % Rotamer: Outliers : 1.62 % Allowed : 13.94 % Favored : 84.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.19), residues: 1895 helix: 0.62 (0.20), residues: 680 sheet: -0.13 (0.36), residues: 237 loop : -1.40 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 280 TYR 0.018 0.001 TYR C 425 PHE 0.038 0.002 PHE B 124 TRP 0.010 0.001 TRP A 213 HIS 0.007 0.001 HIS D 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (16066) covalent geometry : angle 0.54482 / 0.29 (21667) hydrogen bonds : bond 0.03680 / 2.47 ( 571) hydrogen bonds : angle 4.93315 / 3.46 ( 1545) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3284.58 seconds wall clock time: 57 minutes 13.52 seconds (3433.52 seconds total)