Starting phenix.real_space_refine on Thu Feb 13 21:41:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6x3e_22020/02_2025/6x3e_22020.cif Found real_map, /net/cci-nas-00/data/ceres_data/6x3e_22020/02_2025/6x3e_22020.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6x3e_22020/02_2025/6x3e_22020.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6x3e_22020/02_2025/6x3e_22020.map" model { file = "/net/cci-nas-00/data/ceres_data/6x3e_22020/02_2025/6x3e_22020.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6x3e_22020/02_2025/6x3e_22020.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 69 5.16 5 Na 3 4.78 5 C 6200 2.51 5 N 1505 2.21 5 O 1692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9469 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3193 Number of conformers: 1 Conformer: "" Number of residues, atoms: 419, 3193 Classifications: {'peptide': 419} Link IDs: {'PTRANS': 11, 'TRANS': 407} Chain breaks: 2 Chain: "B" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3132 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 11, 'TRANS': 399} Chain breaks: 2 Chain: "C" Number of atoms: 3132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3132 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 11, 'TRANS': 399} Chain breaks: 2 Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' NA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.21, per 1000 atoms: 0.66 Number of scatterers: 9469 At special positions: 0 Unit cell: (112.32, 108.16, 86.528, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 69 16.00 Na 3 11.00 O 1692 8.00 N 1505 7.00 C 6200 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: 2.47 Conformation dependent library (CDL) restraints added in 1.2 seconds 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2296 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 5 sheets defined 80.8% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 18 through 42 removed outlier: 3.767A pdb=" N LEU A 22 " --> pdb=" O ASN A 18 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR A 24 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 37 " --> pdb=" O THR A 33 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ARG A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 Processing helix chain 'A' and resid 53 through 81 removed outlier: 3.541A pdb=" N LEU A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE A 66 " --> pdb=" O MET A 62 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N LEU A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix removed outlier: 3.845A pdb=" N VAL A 79 " --> pdb=" O MET A 75 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 117 removed outlier: 3.611A pdb=" N TYR A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ILE A 104 " --> pdb=" O CYS A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 3.546A pdb=" N ASP A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 211 through 228 Processing helix chain 'A' and resid 229 through 232 removed outlier: 3.580A pdb=" N LYS A 232 " --> pdb=" O MET A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 233 through 250 removed outlier: 3.529A pdb=" N VAL A 237 " --> pdb=" O GLY A 233 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 266 removed outlier: 4.068A pdb=" N CYS A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.554A pdb=" N LEU A 263 " --> pdb=" O PRO A 259 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N PHE A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.705A pdb=" N PHE A 279 " --> pdb=" O ASP A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 299 removed outlier: 4.375A pdb=" N THR A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY A 292 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 309 removed outlier: 3.520A pdb=" N PHE A 306 " --> pdb=" O PRO A 302 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 308 " --> pdb=" O ILE A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 320 removed outlier: 3.682A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 removed outlier: 3.540A pdb=" N MET A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 346 Processing helix chain 'A' and resid 351 through 365 removed outlier: 3.543A pdb=" N ARG A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix removed outlier: 3.878A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 384 removed outlier: 3.983A pdb=" N VAL A 379 " --> pdb=" O ALA A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 408 removed outlier: 3.823A pdb=" N ILE A 395 " --> pdb=" O ILE A 391 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR A 396 " --> pdb=" O GLY A 392 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N THR A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 removed outlier: 3.595A pdb=" N VAL A 422 " --> pdb=" O THR A 418 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 426 " --> pdb=" O VAL A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 436 removed outlier: 3.556A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 433 " --> pdb=" O ALA A 430 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR A 434 " --> pdb=" O GLU A 431 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 435 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 466 removed outlier: 3.659A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN A 451 " --> pdb=" O ARG A 447 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'B' and resid 21 through 40 removed outlier: 3.502A pdb=" N ALA B 27 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLU B 40 " --> pdb=" O VAL B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 53 removed outlier: 3.816A pdb=" N ALA B 53 " --> pdb=" O LYS B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 86 removed outlier: 3.723A pdb=" N LEU B 59 " --> pdb=" O PRO B 55 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS B 64 " --> pdb=" O MET B 60 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE B 66 " --> pdb=" O MET B 62 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LEU B 68 " --> pdb=" O LYS B 64 " (cutoff:3.500A) Proline residue: B 69 - end of helix removed outlier: 3.706A pdb=" N SER B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL B 86 " --> pdb=" O LEU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 117 removed outlier: 3.641A pdb=" N VAL B 95 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 3.584A pdb=" N MET B 142 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ILE B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N PHE B 150 " --> pdb=" O ILE B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 158 Processing helix chain 'B' and resid 211 through 230 removed outlier: 3.551A pdb=" N GLY B 227 " --> pdb=" O GLY B 223 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY B 230 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 273 Proline residue: B 259 - end of helix removed outlier: 3.549A pdb=" N LEU B 263 " --> pdb=" O PRO B 259 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N PHE B 264 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LYS B 269 " --> pdb=" O LEU B 265 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLU B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 299 removed outlier: 3.729A pdb=" N THR B 291 " --> pdb=" O ALA B 287 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 309 removed outlier: 3.698A pdb=" N VAL B 308 " --> pdb=" O ILE B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 319 removed outlier: 3.524A pdb=" N PHE B 316 " --> pdb=" O ASN B 312 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY B 319 " --> pdb=" O ARG B 315 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 330 removed outlier: 3.692A pdb=" N LEU B 325 " --> pdb=" O ALA B 321 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 326 " --> pdb=" O GLN B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 349 removed outlier: 4.141A pdb=" N ARG B 342 " --> pdb=" O PRO B 338 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN B 347 " --> pdb=" O CYS B 343 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B 349 " --> pdb=" O GLU B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 366 removed outlier: 4.172A pdb=" N PHE B 357 " --> pdb=" O ARG B 353 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 359 " --> pdb=" O THR B 355 " (cutoff:3.500A) Proline residue: B 360 - end of helix removed outlier: 4.410A pdb=" N THR B 364 " --> pdb=" O PRO B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 385 removed outlier: 3.567A pdb=" N VAL B 379 " --> pdb=" O ALA B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 401 Processing helix chain 'B' and resid 412 through 415 removed outlier: 3.881A pdb=" N GLY B 415 " --> pdb=" O PRO B 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 412 through 415' Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.780A pdb=" N VAL B 426 " --> pdb=" O VAL B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 432 removed outlier: 3.572A pdb=" N ASP B 432 " --> pdb=" O PRO B 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 429 through 432' Processing helix chain 'B' and resid 433 through 438 Processing helix chain 'B' and resid 439 through 466 removed outlier: 3.613A pdb=" N LEU B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ARG B 445 " --> pdb=" O TRP B 441 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N PHE B 446 " --> pdb=" O LEU B 442 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR B 448 " --> pdb=" O ASP B 444 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N MET B 449 " --> pdb=" O ARG B 445 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ASP B 455 " --> pdb=" O ASN B 451 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N THR B 459 " --> pdb=" O ASP B 455 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLY B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU B 463 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LYS B 464 " --> pdb=" O GLY B 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 40 removed outlier: 3.601A pdb=" N ALA C 27 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG C 39 " --> pdb=" O GLY C 35 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLU C 40 " --> pdb=" O VAL C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 53 removed outlier: 3.762A pdb=" N ALA C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 53 through 86 removed outlier: 3.657A pdb=" N LEU C 59 " --> pdb=" O PRO C 55 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS C 64 " --> pdb=" O MET C 60 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 66 " --> pdb=" O MET C 62 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU C 68 " --> pdb=" O LYS C 64 " (cutoff:3.500A) Proline residue: C 69 - end of helix removed outlier: 3.747A pdb=" N SER C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL C 86 " --> pdb=" O LEU C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 117 removed outlier: 3.612A pdb=" N VAL C 95 " --> pdb=" O GLY C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 3.537A pdb=" N MET C 142 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE C 146 " --> pdb=" O MET C 142 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 150 " --> pdb=" O ILE C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 155 through 158 Processing helix chain 'C' and resid 211 through 230 removed outlier: 3.558A pdb=" N GLY C 227 " --> pdb=" O GLY C 223 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY C 230 " --> pdb=" O ILE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 273 removed outlier: 3.503A pdb=" N GLN C 252 " --> pdb=" O MET C 248 " (cutoff:3.500A) Proline residue: C 259 - end of helix removed outlier: 3.676A pdb=" N PHE C 264 " --> pdb=" O LEU C 260 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS C 269 " --> pdb=" O LEU C 265 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU C 272 " --> pdb=" O GLY C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 299 removed outlier: 3.716A pdb=" N THR C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 300 through 309 removed outlier: 3.725A pdb=" N VAL C 308 " --> pdb=" O ILE C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 312 through 319 Processing helix chain 'C' and resid 320 through 330 removed outlier: 3.621A pdb=" N THR C 326 " --> pdb=" O GLN C 322 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 349 removed outlier: 4.243A pdb=" N ARG C 342 " --> pdb=" O PRO C 338 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU C 345 " --> pdb=" O PHE C 341 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ASN C 347 " --> pdb=" O CYS C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 366 removed outlier: 4.177A pdb=" N PHE C 357 " --> pdb=" O ARG C 353 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU C 359 " --> pdb=" O THR C 355 " (cutoff:3.500A) Proline residue: C 360 - end of helix removed outlier: 4.274A pdb=" N THR C 364 " --> pdb=" O PRO C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 385 removed outlier: 3.558A pdb=" N VAL C 379 " --> pdb=" O ALA C 375 " (cutoff:3.500A) Processing helix chain 'C' and resid 391 through 401 removed outlier: 3.622A pdb=" N THR C 396 " --> pdb=" O GLY C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 412 through 415 removed outlier: 3.911A pdb=" N GLY C 415 " --> pdb=" O PRO C 412 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 412 through 415' Processing helix chain 'C' and resid 416 through 427 removed outlier: 3.777A pdb=" N VAL C 426 " --> pdb=" O VAL C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 432 removed outlier: 3.591A pdb=" N ASP C 432 " --> pdb=" O PRO C 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 429 through 432' Processing helix chain 'C' and resid 433 through 438 Processing helix chain 'C' and resid 439 through 466 removed outlier: 3.598A pdb=" N LEU C 443 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N ARG C 445 " --> pdb=" O TRP C 441 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N PHE C 446 " --> pdb=" O LEU C 442 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR C 448 " --> pdb=" O ASP C 444 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP C 455 " --> pdb=" O ASN C 451 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N THR C 459 " --> pdb=" O ASP C 455 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU C 463 " --> pdb=" O THR C 459 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LYS C 464 " --> pdb=" O GLY C 460 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 Processing sheet with id=AA2, first strand: chain 'B' and resid 160 through 161 Processing sheet with id=AA3, first strand: chain 'B' and resid 164 through 167 Processing sheet with id=AA4, first strand: chain 'C' and resid 160 through 161 Processing sheet with id=AA5, first strand: chain 'C' and resid 164 through 167 595 hydrogen bonds defined for protein. 1761 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: 2.66 Time building geometry restraints manager: 2.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1816 1.33 - 1.45: 1998 1.45 - 1.57: 5666 1.57 - 1.69: 0 1.69 - 1.81: 123 Bond restraints: 9603 Sorted by residual: bond pdb=" N LEU C 372 " pdb=" CA LEU C 372 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.23e-02 6.61e+03 5.17e+00 bond pdb=" N LEU B 30 " pdb=" CA LEU B 30 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.33e-02 5.65e+03 4.97e+00 bond pdb=" N CYS A 100 " pdb=" CA CYS A 100 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.31e-02 5.83e+03 4.78e+00 bond pdb=" N LYS A 269 " pdb=" CA LYS A 269 " ideal model delta sigma weight residual 1.456 1.484 -0.028 1.28e-02 6.10e+03 4.65e+00 bond pdb=" N LEU B 372 " pdb=" CA LEU B 372 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.23e-02 6.61e+03 4.52e+00 ... (remaining 9598 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.74: 12305 1.74 - 3.47: 604 3.47 - 5.20: 71 5.20 - 6.94: 30 6.94 - 8.67: 17 Bond angle restraints: 13027 Sorted by residual: angle pdb=" N GLN A 122 " pdb=" CA GLN A 122 " pdb=" C GLN A 122 " ideal model delta sigma weight residual 110.44 102.53 7.91 1.20e+00 6.94e-01 4.35e+01 angle pdb=" CA LYS A 123 " pdb=" C LYS A 123 " pdb=" N VAL A 124 " ideal model delta sigma weight residual 117.17 122.37 -5.20 1.18e+00 7.18e-01 1.94e+01 angle pdb=" C VAL A 120 " pdb=" N THR A 121 " pdb=" CA THR A 121 " ideal model delta sigma weight residual 122.40 128.71 -6.31 1.45e+00 4.76e-01 1.89e+01 angle pdb=" CA GLN A 413 " pdb=" CB GLN A 413 " pdb=" CG GLN A 413 " ideal model delta sigma weight residual 114.10 122.73 -8.63 2.00e+00 2.50e-01 1.86e+01 angle pdb=" C ASP C 388 " pdb=" N LEU C 389 " pdb=" CA LEU C 389 " ideal model delta sigma weight residual 121.54 128.96 -7.42 1.91e+00 2.74e-01 1.51e+01 ... (remaining 13022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5202 17.90 - 35.79: 437 35.79 - 53.68: 84 53.68 - 71.58: 17 71.58 - 89.47: 10 Dihedral angle restraints: 5750 sinusoidal: 2192 harmonic: 3558 Sorted by residual: dihedral pdb=" CA GLU A 272 " pdb=" C GLU A 272 " pdb=" N VAL A 273 " pdb=" CA VAL A 273 " ideal model delta harmonic sigma weight residual -180.00 -158.11 -21.89 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA LEU B 384 " pdb=" C LEU B 384 " pdb=" N ASN B 385 " pdb=" CA ASN B 385 " ideal model delta harmonic sigma weight residual 180.00 160.31 19.69 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" CA LEU C 384 " pdb=" C LEU C 384 " pdb=" N ASN C 385 " pdb=" CA ASN C 385 " ideal model delta harmonic sigma weight residual 180.00 160.67 19.33 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 5747 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1388 0.070 - 0.141: 237 0.141 - 0.211: 21 0.211 - 0.281: 7 0.281 - 0.352: 1 Chirality restraints: 1654 Sorted by residual: chirality pdb=" CB VAL A 411 " pdb=" CA VAL A 411 " pdb=" CG1 VAL A 411 " pdb=" CG2 VAL A 411 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" CB ILE A 278 " pdb=" CA ILE A 278 " pdb=" CG1 ILE A 278 " pdb=" CG2 ILE A 278 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CB VAL A 426 " pdb=" CA VAL A 426 " pdb=" CG1 VAL A 426 " pdb=" CG2 VAL A 426 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.58e+00 ... (remaining 1651 not shown) Planarity restraints: 1585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 301 " -0.047 5.00e-02 4.00e+02 7.01e-02 7.86e+00 pdb=" N PRO B 302 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 302 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 302 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 301 " -0.046 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO C 302 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO C 302 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 302 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 301 " -0.042 5.00e-02 4.00e+02 6.21e-02 6.17e+00 pdb=" N PRO A 302 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 302 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 302 " -0.035 5.00e-02 4.00e+02 ... (remaining 1582 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 82 2.65 - 3.21: 8339 3.21 - 3.77: 14585 3.77 - 4.34: 20502 4.34 - 4.90: 33380 Nonbonded interactions: 76888 Sorted by model distance: nonbonded pdb=" OD1 ASP A 368 " pdb="NA NA A 603 " model vdw 2.083 2.470 nonbonded pdb=" OD1 ASN A 366 " pdb="NA NA A 603 " model vdw 2.228 2.470 nonbonded pdb=" O ASN A 366 " pdb="NA NA A 601 " model vdw 2.293 2.470 nonbonded pdb=" O PRO B 69 " pdb=" OG SER B 73 " model vdw 2.301 3.040 nonbonded pdb=" O ALA A 456 " pdb=" OG1 THR A 459 " model vdw 2.317 3.040 ... (remaining 76883 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 121 or resid 137 through 474)) selection = chain 'B' selection = chain 'C' } 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: 1.210 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.300 Find NCS groups from input model: 0.340 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 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 : 0.006 0.063 9603 Z= 0.346 Angle : 0.904 8.675 13027 Z= 0.500 Chirality : 0.055 0.352 1654 Planarity : 0.007 0.070 1585 Dihedral : 14.423 89.473 3454 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 11.31 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.06 (0.15), residues: 1223 helix: -4.16 (0.08), residues: 954 sheet: -2.40 (0.81), residues: 54 loop : -1.89 (0.34), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 276 HIS 0.003 0.001 HIS C 41 PHE 0.022 0.003 PHE B 159 TYR 0.024 0.002 TYR C 373 ARG 0.003 0.001 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 299 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.9037 (mp) cc_final: 0.8808 (tp) REVERT: A 112 LEU cc_start: 0.8818 (mt) cc_final: 0.8537 (mt) REVERT: A 277 GLU cc_start: 0.8270 (tp30) cc_final: 0.7885 (tp30) REVERT: B 19 TRP cc_start: 0.7039 (t60) cc_final: 0.5389 (m100) REVERT: B 93 ARG cc_start: 0.8504 (mtt180) cc_final: 0.7722 (mtt180) REVERT: B 140 ASP cc_start: 0.7915 (m-30) cc_final: 0.7557 (m-30) REVERT: B 228 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7889 (mmmt) REVERT: B 280 ARG cc_start: 0.8240 (ttp80) cc_final: 0.7459 (tpt170) REVERT: B 354 ILE cc_start: 0.8661 (mt) cc_final: 0.8310 (mm) REVERT: B 444 ASP cc_start: 0.8898 (t0) cc_final: 0.8466 (t0) REVERT: B 465 LEU cc_start: 0.8761 (mt) cc_final: 0.8457 (mt) REVERT: C 97 TYR cc_start: 0.9153 (t80) cc_final: 0.8689 (t80) REVERT: C 397 ILE cc_start: 0.9506 (mm) cc_final: 0.9256 (mm) REVERT: C 446 PHE cc_start: 0.8519 (m-80) cc_final: 0.8242 (m-80) outliers start: 0 outliers final: 0 residues processed: 299 average time/residue: 0.2226 time to fit residues: 90.7756 Evaluate side-chains 198 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 62 optimal weight: 0.1980 chunk 49 optimal weight: 2.9990 chunk 96 optimal weight: 0.8980 chunk 37 optimal weight: 7.9990 chunk 58 optimal weight: 0.6980 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 ASN B 348 ASN C 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.130273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.095610 restraints weight = 15285.927| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.03 r_work: 0.2956 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9603 Z= 0.156 Angle : 0.601 8.191 13027 Z= 0.305 Chirality : 0.040 0.148 1654 Planarity : 0.005 0.037 1585 Dihedral : 4.580 18.303 1302 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.21 % Allowed : 16.20 % Favored : 81.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.08 (0.20), residues: 1223 helix: -1.78 (0.14), residues: 953 sheet: -2.19 (0.77), residues: 54 loop : -2.05 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 441 HIS 0.000 0.000 HIS A 296 PHE 0.019 0.002 PHE C 306 TYR 0.010 0.001 TYR B 305 ARG 0.006 0.001 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 224 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: A 30 LEU cc_start: 0.9059 (mp) cc_final: 0.8754 (tp) REVERT: A 40 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7343 (mp0) REVERT: A 112 LEU cc_start: 0.8350 (mt) cc_final: 0.8101 (mt) REVERT: A 205 MET cc_start: 0.8566 (pmm) cc_final: 0.8334 (ptm) REVERT: A 277 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7274 (tp30) REVERT: A 463 GLU cc_start: 0.8566 (tt0) cc_final: 0.7872 (tm-30) REVERT: A 473 MET cc_start: 0.4468 (mtt) cc_final: 0.4162 (ptp) REVERT: B 19 TRP cc_start: 0.7200 (t60) cc_final: 0.5420 (m100) REVERT: B 220 LEU cc_start: 0.9232 (tt) cc_final: 0.8353 (mt) REVERT: B 320 MET cc_start: 0.8354 (mmm) cc_final: 0.8041 (mpp) REVERT: B 354 ILE cc_start: 0.8638 (mt) cc_final: 0.8344 (mm) REVERT: B 368 ASP cc_start: 0.9264 (m-30) cc_final: 0.8958 (m-30) REVERT: B 449 MET cc_start: 0.8445 (tmm) cc_final: 0.8170 (tmm) REVERT: C 97 TYR cc_start: 0.8969 (t80) cc_final: 0.8634 (t80) REVERT: C 206 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.7503 (t80) REVERT: C 446 PHE cc_start: 0.8877 (m-80) cc_final: 0.8660 (m-80) outliers start: 23 outliers final: 13 residues processed: 235 average time/residue: 0.1851 time to fit residues: 63.0027 Evaluate side-chains 193 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 373 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 109 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 48 optimal weight: 3.9990 chunk 62 optimal weight: 7.9990 chunk 53 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 347 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.127051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.091860 restraints weight = 15253.538| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.02 r_work: 0.2896 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8808 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9603 Z= 0.226 Angle : 0.588 8.739 13027 Z= 0.297 Chirality : 0.040 0.160 1654 Planarity : 0.004 0.028 1585 Dihedral : 4.279 18.724 1302 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.07 % Allowed : 18.50 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.23), residues: 1223 helix: -0.50 (0.16), residues: 957 sheet: -1.90 (0.76), residues: 54 loop : -1.84 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 441 HIS 0.002 0.001 HIS A 296 PHE 0.018 0.002 PHE A 240 TYR 0.013 0.001 TYR A 305 ARG 0.004 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: A 112 LEU cc_start: 0.8413 (mt) cc_final: 0.8150 (mt) REVERT: A 205 MET cc_start: 0.8550 (pmm) cc_final: 0.8306 (ptm) REVERT: A 277 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8180 (tp30) REVERT: A 345 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7189 (mp0) REVERT: A 463 GLU cc_start: 0.8590 (tt0) cc_final: 0.8153 (tm-30) REVERT: A 473 MET cc_start: 0.4584 (mtt) cc_final: 0.4189 (ptp) REVERT: B 19 TRP cc_start: 0.7247 (t60) cc_final: 0.5463 (m100) REVERT: B 220 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8352 (mt) REVERT: B 280 ARG cc_start: 0.8586 (ttp80) cc_final: 0.7598 (tpt170) REVERT: B 320 MET cc_start: 0.8354 (mmm) cc_final: 0.7790 (mpp) REVERT: B 354 ILE cc_start: 0.8653 (mt) cc_final: 0.8438 (mm) REVERT: B 473 MET cc_start: 0.6031 (ptt) cc_final: 0.5750 (ptt) REVERT: C 89 LYS cc_start: 0.7981 (mmtp) cc_final: 0.7606 (mptt) REVERT: C 97 TYR cc_start: 0.8958 (t80) cc_final: 0.8632 (t80) REVERT: C 206 TYR cc_start: 0.8687 (OUTLIER) cc_final: 0.7374 (t80) outliers start: 32 outliers final: 18 residues processed: 205 average time/residue: 0.2056 time to fit residues: 60.7132 Evaluate side-chains 186 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 276 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 373 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 75 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 39 optimal weight: 10.0000 chunk 105 optimal weight: 0.2980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 HIS B 472 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.129092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.096383 restraints weight = 15166.679| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.97 r_work: 0.2937 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9603 Z= 0.152 Angle : 0.539 10.207 13027 Z= 0.269 Chirality : 0.039 0.151 1654 Planarity : 0.003 0.027 1585 Dihedral : 4.057 17.913 1302 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.55 % Allowed : 19.27 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.25), residues: 1223 helix: 0.23 (0.17), residues: 957 sheet: -1.62 (0.76), residues: 54 loop : -1.92 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 441 HIS 0.001 0.000 HIS B 41 PHE 0.022 0.001 PHE A 306 TYR 0.016 0.001 TYR C 98 ARG 0.005 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 202 ILE cc_start: 0.8631 (mm) cc_final: 0.8373 (mm) REVERT: A 277 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.7979 (tp30) REVERT: A 473 MET cc_start: 0.4625 (mtt) cc_final: 0.4212 (ptp) REVERT: B 19 TRP cc_start: 0.7341 (t60) cc_final: 0.5405 (m100) REVERT: B 164 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8725 (p) REVERT: B 220 LEU cc_start: 0.9246 (tt) cc_final: 0.8339 (mt) REVERT: B 280 ARG cc_start: 0.8502 (ttp80) cc_final: 0.7564 (tpt170) REVERT: B 320 MET cc_start: 0.8232 (mmm) cc_final: 0.7697 (mpp) REVERT: B 354 ILE cc_start: 0.8626 (mt) cc_final: 0.8421 (mm) REVERT: B 449 MET cc_start: 0.8374 (tmm) cc_final: 0.8035 (tmm) REVERT: B 472 GLN cc_start: 0.7442 (mt0) cc_final: 0.7146 (mm110) REVERT: C 48 GLU cc_start: 0.7972 (tp30) cc_final: 0.7761 (tp30) REVERT: C 206 TYR cc_start: 0.8620 (OUTLIER) cc_final: 0.7495 (t80) outliers start: 37 outliers final: 24 residues processed: 194 average time/residue: 0.1883 time to fit residues: 53.4797 Evaluate side-chains 183 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 156 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 276 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 304 ILE Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 373 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 77 optimal weight: 4.9990 chunk 117 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 0.3980 chunk 59 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 33 optimal weight: 0.4980 chunk 120 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.128002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.092969 restraints weight = 15231.887| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.95 r_work: 0.2926 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9603 Z= 0.182 Angle : 0.548 10.697 13027 Z= 0.272 Chirality : 0.040 0.147 1654 Planarity : 0.003 0.031 1585 Dihedral : 3.995 18.479 1302 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.55 % Allowed : 19.65 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.25), residues: 1223 helix: 0.55 (0.18), residues: 960 sheet: -1.45 (0.76), residues: 54 loop : -1.82 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 441 HIS 0.001 0.000 HIS A 296 PHE 0.022 0.001 PHE B 357 TYR 0.017 0.001 TYR C 98 ARG 0.006 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 277 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.7951 (tp30) REVERT: A 419 MET cc_start: 0.8434 (tpt) cc_final: 0.8147 (tpt) REVERT: A 473 MET cc_start: 0.4650 (mtt) cc_final: 0.4175 (ptp) REVERT: B 19 TRP cc_start: 0.7438 (t60) cc_final: 0.5417 (m100) REVERT: B 220 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8254 (mt) REVERT: B 280 ARG cc_start: 0.8586 (ttp80) cc_final: 0.7730 (tpt170) REVERT: B 320 MET cc_start: 0.8230 (mmm) cc_final: 0.7660 (mpp) REVERT: B 449 MET cc_start: 0.8343 (tmm) cc_final: 0.8008 (tmm) REVERT: B 472 GLN cc_start: 0.7361 (mt0) cc_final: 0.7074 (mm110) REVERT: C 60 MET cc_start: 0.9247 (mmm) cc_final: 0.8988 (mmp) REVERT: C 206 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.7345 (t80) REVERT: C 320 MET cc_start: 0.7716 (mmm) cc_final: 0.7251 (mmm) outliers start: 37 outliers final: 26 residues processed: 191 average time/residue: 0.1862 time to fit residues: 51.4127 Evaluate side-chains 191 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 162 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 276 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 373 TYR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 373 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 89 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 78 optimal weight: 2.9990 chunk 21 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 296 HIS B 393 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.125506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.090250 restraints weight = 15304.461| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.93 r_work: 0.2880 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 9603 Z= 0.295 Angle : 0.599 9.220 13027 Z= 0.299 Chirality : 0.042 0.202 1654 Planarity : 0.004 0.031 1585 Dihedral : 4.145 18.642 1302 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.03 % Allowed : 20.81 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.25), residues: 1223 helix: 0.58 (0.17), residues: 961 sheet: -1.52 (0.75), residues: 54 loop : -1.68 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 441 HIS 0.007 0.001 HIS A 296 PHE 0.021 0.002 PHE A 240 TYR 0.026 0.002 TYR C 98 ARG 0.007 0.001 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 166 time to evaluate : 1.210 Fit side-chains revert: symmetry clash REVERT: A 277 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7994 (tp30) REVERT: A 463 GLU cc_start: 0.8613 (tt0) cc_final: 0.8227 (tm-30) REVERT: B 19 TRP cc_start: 0.7360 (t60) cc_final: 0.5380 (m100) REVERT: B 220 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8235 (mt) REVERT: B 280 ARG cc_start: 0.8631 (ttp80) cc_final: 0.7772 (tpt170) REVERT: B 320 MET cc_start: 0.8254 (mmm) cc_final: 0.7614 (mpp) REVERT: B 472 GLN cc_start: 0.7435 (mt0) cc_final: 0.7171 (mm110) REVERT: C 23 SER cc_start: 0.9078 (t) cc_final: 0.8811 (p) REVERT: C 312 ASN cc_start: 0.8398 (OUTLIER) cc_final: 0.7923 (t0) REVERT: C 320 MET cc_start: 0.7643 (mmm) cc_final: 0.7152 (mmm) REVERT: C 341 PHE cc_start: 0.8621 (OUTLIER) cc_final: 0.8341 (m-10) outliers start: 42 outliers final: 30 residues processed: 192 average time/residue: 0.1809 time to fit residues: 51.6715 Evaluate side-chains 190 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 156 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 276 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain B residue 21 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 465 LEU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 341 PHE Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 433 VAL Chi-restraints excluded: chain C residue 448 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 115 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 44 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 36 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 2 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.128066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.093877 restraints weight = 15274.073| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.11 r_work: 0.2921 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9603 Z= 0.164 Angle : 0.539 8.474 13027 Z= 0.268 Chirality : 0.039 0.155 1654 Planarity : 0.003 0.034 1585 Dihedral : 3.951 17.642 1302 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.97 % Allowed : 22.24 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.25), residues: 1223 helix: 0.88 (0.18), residues: 955 sheet: -1.49 (0.74), residues: 54 loop : -1.72 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 441 HIS 0.005 0.001 HIS A 296 PHE 0.025 0.001 PHE B 357 TYR 0.025 0.001 TYR C 98 ARG 0.007 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 1.081 Fit side-chains revert: symmetry clash REVERT: A 277 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7925 (tp30) REVERT: A 463 GLU cc_start: 0.8524 (tt0) cc_final: 0.8177 (tm-30) REVERT: B 19 TRP cc_start: 0.7430 (t60) cc_final: 0.5389 (m100) REVERT: B 220 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8223 (mt) REVERT: B 280 ARG cc_start: 0.8576 (ttp80) cc_final: 0.7747 (tpt170) REVERT: B 320 MET cc_start: 0.8124 (mmm) cc_final: 0.7515 (mpp) REVERT: B 449 MET cc_start: 0.8393 (tmm) cc_final: 0.8042 (tmm) REVERT: B 472 GLN cc_start: 0.7349 (mt0) cc_final: 0.7135 (mm110) REVERT: C 23 SER cc_start: 0.9055 (t) cc_final: 0.8848 (p) REVERT: C 206 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.7307 (t80) REVERT: C 312 ASN cc_start: 0.8280 (OUTLIER) cc_final: 0.7819 (t0) REVERT: C 320 MET cc_start: 0.7715 (mmm) cc_final: 0.7254 (mmm) REVERT: C 399 ILE cc_start: 0.9413 (OUTLIER) cc_final: 0.9176 (mp) outliers start: 31 outliers final: 21 residues processed: 189 average time/residue: 0.1889 time to fit residues: 51.7680 Evaluate side-chains 187 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 161 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 276 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 19 TRP Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 399 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 84 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 chunk 46 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.128559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.094483 restraints weight = 15385.711| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.10 r_work: 0.2928 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9603 Z= 0.163 Angle : 0.549 8.215 13027 Z= 0.270 Chirality : 0.039 0.176 1654 Planarity : 0.003 0.034 1585 Dihedral : 3.902 17.325 1302 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.55 % Allowed : 22.15 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1223 helix: 1.04 (0.18), residues: 955 sheet: -1.44 (0.74), residues: 54 loop : -1.76 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP B 441 HIS 0.005 0.001 HIS A 296 PHE 0.021 0.001 PHE C 357 TYR 0.025 0.001 TYR C 98 ARG 0.007 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 172 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 97 TYR cc_start: 0.8435 (t80) cc_final: 0.8170 (t80) REVERT: A 277 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7825 (tp30) REVERT: A 280 ARG cc_start: 0.6133 (mtt180) cc_final: 0.4820 (tpt-90) REVERT: A 463 GLU cc_start: 0.8522 (tt0) cc_final: 0.8131 (tm-30) REVERT: B 19 TRP cc_start: 0.7434 (t60) cc_final: 0.5407 (m100) REVERT: B 220 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8194 (mt) REVERT: B 280 ARG cc_start: 0.8562 (ttp80) cc_final: 0.7730 (tpt170) REVERT: B 320 MET cc_start: 0.8087 (mmm) cc_final: 0.7590 (mpp) REVERT: B 447 ARG cc_start: 0.8537 (mtm-85) cc_final: 0.8252 (mtm-85) REVERT: B 449 MET cc_start: 0.8351 (tmm) cc_final: 0.7997 (tmm) REVERT: B 472 GLN cc_start: 0.7335 (mt0) cc_final: 0.7131 (mm110) REVERT: C 206 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.7268 (t80) REVERT: C 312 ASN cc_start: 0.8284 (OUTLIER) cc_final: 0.7822 (t0) REVERT: C 320 MET cc_start: 0.7710 (mmm) cc_final: 0.7228 (mmm) REVERT: C 399 ILE cc_start: 0.9405 (OUTLIER) cc_final: 0.9156 (mp) outliers start: 37 outliers final: 27 residues processed: 195 average time/residue: 0.1973 time to fit residues: 55.8108 Evaluate side-chains 197 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 165 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 276 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 112 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 46 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 38 optimal weight: 7.9990 chunk 76 optimal weight: 1.9990 chunk 10 optimal weight: 30.0000 chunk 72 optimal weight: 0.8980 chunk 110 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.129807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.097154 restraints weight = 15243.145| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 1.99 r_work: 0.2947 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9603 Z= 0.148 Angle : 0.551 9.851 13027 Z= 0.268 Chirality : 0.039 0.214 1654 Planarity : 0.003 0.036 1585 Dihedral : 3.793 16.334 1302 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.97 % Allowed : 23.01 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1223 helix: 1.19 (0.18), residues: 960 sheet: -1.33 (0.74), residues: 54 loop : -1.70 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 441 HIS 0.005 0.001 HIS A 296 PHE 0.029 0.001 PHE B 357 TYR 0.027 0.002 TYR C 98 ARG 0.007 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 173 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 97 TYR cc_start: 0.8423 (t80) cc_final: 0.8192 (t80) REVERT: A 164 THR cc_start: 0.8868 (OUTLIER) cc_final: 0.8554 (t) REVERT: A 277 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7866 (tp30) REVERT: A 280 ARG cc_start: 0.6095 (mtt180) cc_final: 0.4788 (tpt-90) REVERT: B 19 TRP cc_start: 0.7427 (t60) cc_final: 0.5360 (m100) REVERT: B 205 MET cc_start: 0.8411 (tpt) cc_final: 0.8115 (mtt) REVERT: B 220 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8159 (mt) REVERT: B 280 ARG cc_start: 0.8548 (ttp80) cc_final: 0.7720 (tpt170) REVERT: B 320 MET cc_start: 0.8042 (mmm) cc_final: 0.7513 (mpp) REVERT: B 447 ARG cc_start: 0.8483 (mtm-85) cc_final: 0.8209 (mtm-85) REVERT: B 449 MET cc_start: 0.8359 (tmm) cc_final: 0.8022 (tmm) REVERT: C 60 MET cc_start: 0.9208 (mmm) cc_final: 0.8929 (mmp) REVERT: C 206 TYR cc_start: 0.8555 (OUTLIER) cc_final: 0.7341 (t80) REVERT: C 312 ASN cc_start: 0.8298 (OUTLIER) cc_final: 0.7862 (t0) REVERT: C 320 MET cc_start: 0.7704 (mmm) cc_final: 0.7252 (mmm) REVERT: C 399 ILE cc_start: 0.9394 (OUTLIER) cc_final: 0.9146 (mp) outliers start: 31 outliers final: 21 residues processed: 193 average time/residue: 0.2038 time to fit residues: 57.4615 Evaluate side-chains 188 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 276 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 45 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 37 optimal weight: 20.0000 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.129939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.095208 restraints weight = 15289.302| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.97 r_work: 0.2956 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9603 Z= 0.151 Angle : 0.559 9.637 13027 Z= 0.271 Chirality : 0.040 0.212 1654 Planarity : 0.003 0.036 1585 Dihedral : 3.769 15.813 1302 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.97 % Allowed : 23.11 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1223 helix: 1.25 (0.18), residues: 962 sheet: -1.27 (0.74), residues: 54 loop : -1.72 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 441 HIS 0.005 0.001 HIS A 296 PHE 0.024 0.001 PHE A 306 TYR 0.026 0.002 TYR C 98 ARG 0.007 0.000 ARG A 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2446 Ramachandran restraints generated. 1223 Oldfield, 0 Emsley, 1223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 1.055 Fit side-chains revert: symmetry clash REVERT: A 97 TYR cc_start: 0.8413 (t80) cc_final: 0.8191 (t80) REVERT: A 277 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7912 (tp30) REVERT: A 280 ARG cc_start: 0.6045 (mtt180) cc_final: 0.4782 (tpt-90) REVERT: B 19 TRP cc_start: 0.7443 (t60) cc_final: 0.5349 (m100) REVERT: B 205 MET cc_start: 0.8425 (tpt) cc_final: 0.8186 (tpt) REVERT: B 220 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8160 (mt) REVERT: B 280 ARG cc_start: 0.8525 (ttp80) cc_final: 0.7763 (tpt170) REVERT: B 320 MET cc_start: 0.8043 (mmm) cc_final: 0.7532 (mpp) REVERT: B 447 ARG cc_start: 0.8502 (mtm-85) cc_final: 0.8199 (mtm-85) REVERT: B 449 MET cc_start: 0.8361 (tmm) cc_final: 0.8025 (tmm) REVERT: C 206 TYR cc_start: 0.8541 (OUTLIER) cc_final: 0.7324 (t80) REVERT: C 312 ASN cc_start: 0.8279 (OUTLIER) cc_final: 0.7840 (t0) REVERT: C 320 MET cc_start: 0.7683 (mmm) cc_final: 0.7251 (mmm) REVERT: C 347 ASN cc_start: 0.7868 (m-40) cc_final: 0.7578 (m-40) REVERT: C 399 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9130 (mp) outliers start: 31 outliers final: 24 residues processed: 189 average time/residue: 0.1890 time to fit residues: 51.8869 Evaluate side-chains 194 residues out of total 1043 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 165 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 276 TRP Chi-restraints excluded: chain A residue 277 GLU Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 345 GLU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 423 LEU Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 220 LEU Chi-restraints excluded: chain B residue 266 ILE Chi-restraints excluded: chain B residue 286 MET Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 206 TYR Chi-restraints excluded: chain C residue 308 VAL Chi-restraints excluded: chain C residue 312 ASN Chi-restraints excluded: chain C residue 328 LEU Chi-restraints excluded: chain C residue 332 SER Chi-restraints excluded: chain C residue 339 VAL Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 367 MET Chi-restraints excluded: chain C residue 373 TYR Chi-restraints excluded: chain C residue 399 ILE Chi-restraints excluded: chain C residue 433 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 82 optimal weight: 3.9990 chunk 43 optimal weight: 0.0020 chunk 16 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 113 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 14 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 117 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 25 optimal weight: 0.5980 overall best weight: 1.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 296 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.128976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.094108 restraints weight = 15196.283| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 1.95 r_work: 0.2941 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.4143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9603 Z= 0.182 Angle : 0.581 9.757 13027 Z= 0.282 Chirality : 0.040 0.205 1654 Planarity : 0.003 0.035 1585 Dihedral : 3.847 16.593 1302 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.97 % Allowed : 23.01 % Favored : 74.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.26), residues: 1223 helix: 1.18 (0.18), residues: 964 sheet: -1.26 (0.74), residues: 54 loop : -1.84 (0.41), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 441 HIS 0.005 0.001 HIS A 296 PHE 0.028 0.001 PHE B 357 TYR 0.027 0.002 TYR C 98 ARG 0.008 0.000 ARG A 342 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5071.05 seconds wall clock time: 90 minutes 31.84 seconds (5431.84 seconds total)