Starting phenix.real_space_refine on Wed May 21 14:19:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8so0_40644/05_2025/8so0_40644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8so0_40644/05_2025/8so0_40644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79961 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8so0_40644/05_2025/8so0_40644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8so0_40644/05_2025/8so0_40644.map" model { file = "/net/cci-nas-00/data/ceres_data/8so0_40644/05_2025/8so0_40644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8so0_40644/05_2025/8so0_40644.cif" } resolution = 2.79961 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= 0.000 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 Zn 1 6.06 5 S 62 5.16 5 C 6794 2.51 5 N 1850 2.21 5 O 2048 1.98 5 H 10660 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 21416 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 581, 9162 Classifications: {'peptide': 581} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 554} Chain: "B" Number of atoms: 6849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 6849 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 14, 'TRANS': 408} Chain breaks: 4 Chain: "C" Number of atoms: 4897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 4897 Classifications: {'peptide': 308} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 10, 'TRANS': 294} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Planarities with less than four sites: {'MLL%COO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 506 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' FE': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 12.13, per 1000 atoms: 0.57 Number of scatterers: 21416 At special positions: 0 Unit cell: (101.994, 127.626, 106.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Fe 1 26.01 S 62 16.00 O 2048 8.00 N 1850 7.00 C 6794 6.00 H 10660 1.00 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: 5.66 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 402 " pdb="ZN ZN C 402 " - pdb=" NE2 HIS C 59 " 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2576 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 12 sheets defined 55.2% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 24 through 34 Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 43 through 50 Processing helix chain 'A' and resid 50 through 57 removed outlier: 3.560A pdb=" N PHE A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP A 57 " --> pdb=" O PRO A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 74 Processing helix chain 'A' and resid 82 through 88 removed outlier: 5.430A pdb=" N HIS A 87 " --> pdb=" O GLU A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 101 through 117 removed outlier: 3.745A pdb=" N HIS A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 127 Processing helix chain 'A' and resid 127 through 137 Processing helix chain 'A' and resid 140 through 148 removed outlier: 3.575A pdb=" N CYS A 148 " --> pdb=" O ARG A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 removed outlier: 3.711A pdb=" N CYS A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 175 Processing helix chain 'A' and resid 178 through 196 removed outlier: 4.426A pdb=" N GLY A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLU A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 217 through 235 removed outlier: 4.031A pdb=" N LEU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA A 224 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N VAL A 225 " --> pdb=" O ARG A 221 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLU A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 removed outlier: 4.402A pdb=" N GLU A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N ALA A 242 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 253 Processing helix chain 'A' and resid 256 through 266 Processing helix chain 'A' and resid 266 through 275 Processing helix chain 'A' and resid 275 through 282 Processing helix chain 'A' and resid 282 through 292 Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.796A pdb=" N LYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 313 Processing helix chain 'A' and resid 317 through 325 Processing helix chain 'A' and resid 325 through 335 removed outlier: 4.173A pdb=" N CYS A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N SER A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 350 removed outlier: 3.536A pdb=" N LYS A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N MET A 350 " --> pdb=" O ALA A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 364 removed outlier: 6.221A pdb=" N LYS A 358 " --> pdb=" O PRO A 354 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N ASP A 359 " --> pdb=" O ILE A 355 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N ASN A 360 " --> pdb=" O LEU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 374 removed outlier: 3.938A pdb=" N LEU A 368 " --> pdb=" O HIS A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 387 removed outlier: 3.513A pdb=" N ASN A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 396 removed outlier: 3.845A pdb=" N GLU A 393 " --> pdb=" O ASP A 389 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N VAL A 394 " --> pdb=" O CYS A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 413 removed outlier: 4.402A pdb=" N LEU A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N GLN A 402 " --> pdb=" O ARG A 398 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N SER A 403 " --> pdb=" O GLN A 399 " (cutoff:3.500A) Proline residue: A 406 - end of helix Processing helix chain 'A' and resid 416 through 435 removed outlier: 3.581A pdb=" N TYR A 426 " --> pdb=" O ALA A 422 " (cutoff:3.500A) Proline residue: A 428 - end of helix Processing helix chain 'A' and resid 435 through 442 Processing helix chain 'A' and resid 443 through 452 removed outlier: 3.586A pdb=" N LEU A 451 " --> pdb=" O CYS A 447 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL A 452 " --> pdb=" O MET A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 482 removed outlier: 3.792A pdb=" N LYS A 467 " --> pdb=" O THR A 463 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LYS A 475 " --> pdb=" O GLU A 471 " (cutoff:3.500A) removed outlier: 8.707A pdb=" N GLU A 476 " --> pdb=" O LYS A 472 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TRP A 477 " --> pdb=" O PHE A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 487 Processing helix chain 'A' and resid 488 through 492 Processing helix chain 'A' and resid 494 through 520 removed outlier: 3.539A pdb=" N THR A 501 " --> pdb=" O HIS A 497 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU A 502 " --> pdb=" O ARG A 498 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N GLN A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ASP A 515 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ILE A 516 " --> pdb=" O CYS A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 529 Processing helix chain 'A' and resid 533 through 548 Processing helix chain 'A' and resid 552 through 559 Processing helix chain 'A' and resid 559 through 569 removed outlier: 3.534A pdb=" N ILE A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 569 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 587 Processing helix chain 'B' and resid 26 through 29 Processing helix chain 'B' and resid 145 through 149 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 281 through 286 Processing helix chain 'B' and resid 326 through 331 removed outlier: 3.580A pdb=" N LEU B 329 " --> pdb=" O HIS B 326 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER B 331 " --> pdb=" O TYR B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 339 Processing helix chain 'B' and resid 340 through 344 Processing helix chain 'B' and resid 382 through 386 Processing helix chain 'B' and resid 411 through 413 No H-bonds generated for 'chain 'B' and resid 411 through 413' Processing helix chain 'C' and resid 3 through 19 Processing helix chain 'C' and resid 24 through 40 removed outlier: 3.590A pdb=" N GLU C 37 " --> pdb=" O GLU C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 92 through 107 Processing helix chain 'C' and resid 120 through 127 Processing helix chain 'C' and resid 128 through 138 Processing helix chain 'C' and resid 140 through 151 removed outlier: 3.827A pdb=" N ASP C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 182 removed outlier: 3.672A pdb=" N ILE C 180 " --> pdb=" O THR C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.554A pdb=" N LEU C 199 " --> pdb=" O MET C 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 233 Processing helix chain 'C' and resid 264 through 268 Processing helix chain 'D' and resid 83 through 94 Processing helix chain 'D' and resid 97 through 111 Processing sheet with id=AA1, first strand: chain 'B' and resid 390 through 391 removed outlier: 4.087A pdb=" N THR B 390 " --> pdb=" O PHE B 14 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE B 441 " --> pdb=" O SER B 15 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL B 17 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LEU B 439 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N HIS B 421 " --> pdb=" O ALA B 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 31 through 36 removed outlier: 6.216A pdb=" N GLY B 46 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N VAL B 34 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA B 44 " --> pdb=" O VAL B 34 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE B 36 " --> pdb=" O LEU B 42 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU B 42 " --> pdb=" O PHE B 36 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N ARG B 51 " --> pdb=" O ASP B 47 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL B 52 " --> pdb=" O THR B 76 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N THR B 76 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE B 54 " --> pdb=" O TYR B 74 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 83 through 85 removed outlier: 3.520A pdb=" N GLU B 83 " --> pdb=" O ILE B 92 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 101 removed outlier: 3.681A pdb=" N LYS B 98 " --> pdb=" O THR B 114 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG B 170 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS B 123 " --> pdb=" O PRO B 168 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N SER B 125 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ALA B 166 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ARG B 127 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N VAL B 164 " --> pdb=" O ARG B 127 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N LYS B 129 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 8.652A pdb=" N LEU B 162 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 9.105A pdb=" N MET B 160 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 182 through 185 removed outlier: 6.755A pdb=" N ILE B 200 " --> pdb=" O ILE B 214 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N HIS B 204 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N ARG B 210 " --> pdb=" O HIS B 204 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.837A pdb=" N ALA B 231 " --> pdb=" O SER B 245 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 290 through 293 removed outlier: 3.502A pdb=" N ASP B 290 " --> pdb=" O ARG B 303 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 348 through 350 removed outlier: 3.512A pdb=" N ARG B 375 " --> pdb=" O ASP B 370 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 397 through 398 Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 48 removed outlier: 6.181A pdb=" N GLN C 46 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N VAL C 237 " --> pdb=" O VAL C 257 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N ILE C 259 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG C 239 " --> pdb=" O ILE C 259 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 111 through 113 Processing sheet with id=AB3, first strand: chain 'C' and resid 202 through 203 529 hydrogen bonds defined for protein. 1500 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: 8.40 Time building geometry restraints manager: 6.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10627 1.03 - 1.23: 33 1.23 - 1.42: 4565 1.42 - 1.61: 6308 1.61 - 1.81: 91 Bond restraints: 21624 Sorted by residual: bond pdb=" C MLL C 309 " pdb=" OXT MLL C 309 " ideal model delta sigma weight residual 1.231 1.366 -0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" N ASP C 2 " pdb=" CA ASP C 2 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.87e+00 bond pdb=" N ASP C 2 " pdb=" H ASP C 2 " ideal model delta sigma weight residual 0.860 0.889 -0.029 2.00e-02 2.50e+03 2.14e+00 bond pdb=" CA ILE B 419 " pdb=" CB ILE B 419 " ideal model delta sigma weight residual 1.528 1.539 -0.011 1.34e-02 5.57e+03 7.28e-01 bond pdb=" CA LEU C 186 " pdb=" CB LEU C 186 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.21e-02 6.83e+03 5.36e-01 ... (remaining 21619 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 38283 1.34 - 2.69: 734 2.69 - 4.03: 51 4.03 - 5.38: 6 5.38 - 6.72: 2 Bond angle restraints: 39076 Sorted by residual: angle pdb=" N VAL C 58 " pdb=" CA VAL C 58 " pdb=" C VAL C 58 " ideal model delta sigma weight residual 112.12 109.04 3.08 8.40e-01 1.42e+00 1.34e+01 angle pdb=" CA MLL C 309 " pdb=" C MLL C 309 " pdb=" OXT MLL C 309 " ideal model delta sigma weight residual 121.00 114.28 6.72 3.00e+00 1.11e-01 5.02e+00 angle pdb=" N ASP D 95 " pdb=" CA ASP D 95 " pdb=" C ASP D 95 " ideal model delta sigma weight residual 111.24 114.06 -2.82 1.29e+00 6.01e-01 4.76e+00 angle pdb=" N MLL C 309 " pdb=" CA MLL C 309 " pdb=" CB MLL C 309 " ideal model delta sigma weight residual 110.50 114.07 -3.57 1.70e+00 3.46e-01 4.41e+00 angle pdb=" CA MLL C 309 " pdb=" C MLL C 309 " pdb=" O MLL C 309 " ideal model delta sigma weight residual 121.00 127.12 -6.12 3.00e+00 1.11e-01 4.17e+00 ... (remaining 39071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.94: 9652 15.94 - 31.87: 312 31.87 - 47.81: 121 47.81 - 63.74: 47 63.74 - 79.68: 27 Dihedral angle restraints: 10159 sinusoidal: 5554 harmonic: 4605 Sorted by residual: dihedral pdb=" CA TYR C 127 " pdb=" C TYR C 127 " pdb=" N GLY C 128 " pdb=" CA GLY C 128 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA ASP D 95 " pdb=" C ASP D 95 " pdb=" N LEU D 96 " pdb=" CA LEU D 96 " ideal model delta harmonic sigma weight residual -180.00 -164.62 -15.38 0 5.00e+00 4.00e-02 9.46e+00 dihedral pdb=" CA ARG C 239 " pdb=" CB ARG C 239 " pdb=" CG ARG C 239 " pdb=" CD ARG C 239 " ideal model delta sinusoidal sigma weight residual -60.00 -113.65 53.65 3 1.50e+01 4.44e-03 9.22e+00 ... (remaining 10156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1050 0.025 - 0.050: 391 0.050 - 0.076: 130 0.076 - 0.101: 49 0.101 - 0.126: 56 Chirality restraints: 1676 Sorted by residual: chirality pdb=" CA ILE B 430 " pdb=" N ILE B 430 " pdb=" C ILE B 430 " pdb=" CB ILE B 430 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 chirality pdb=" CA VAL B 34 " pdb=" N VAL B 34 " pdb=" C VAL B 34 " pdb=" CB VAL B 34 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA ILE B 171 " pdb=" N ILE B 171 " pdb=" C ILE B 171 " pdb=" CB ILE B 171 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.68e-01 ... (remaining 1673 not shown) Planarity restraints: 3202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 538 " -0.010 2.00e-02 2.50e+03 6.35e-03 1.21e+00 pdb=" CG PHE A 538 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE A 538 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 538 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 538 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 538 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 538 " -0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE A 538 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 PHE A 538 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 538 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 538 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 538 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 284 " 0.016 5.00e-02 4.00e+02 2.39e-02 9.15e-01 pdb=" N PRO A 285 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 285 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 285 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 366 " 0.015 5.00e-02 4.00e+02 2.23e-02 7.94e-01 pdb=" N PRO A 367 " -0.039 5.00e-02 4.00e+02 pdb=" CA PRO A 367 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 367 " 0.013 5.00e-02 4.00e+02 ... (remaining 3199 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.06: 338 2.06 - 2.70: 34259 2.70 - 3.33: 64212 3.33 - 3.97: 82755 3.97 - 4.60: 131027 Nonbonded interactions: 312591 Sorted by model distance: nonbonded pdb=" OXT MLL C 309 " pdb=" C10 MLL C 309 " model vdw 1.427 3.100 nonbonded pdb=" OD1 ASP B 196 " pdb=" H ARG B 199 " model vdw 1.557 2.450 nonbonded pdb=" OE1 GLU A 379 " pdb=" H GLU A 379 " model vdw 1.622 2.450 nonbonded pdb=" O HIS C 252 " pdb="HD21 ASN C 255 " model vdw 1.629 2.450 nonbonded pdb=" HH TYR B 86 " pdb=" OD2 ASP C 131 " model vdw 1.632 2.450 ... (remaining 312586 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 10.600 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: 0.350 Extract box with map and model: 0.920 Check model and map are aligned: 0.160 Set scattering table: 0.230 Process input model: 56.440 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 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 : 0.002 0.135 10965 Z= 0.105 Angle : 0.411 6.720 14848 Z= 0.220 Chirality : 0.037 0.126 1676 Planarity : 0.003 0.024 1920 Dihedral : 8.085 76.670 4099 Min Nonbonded Distance : 1.427 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.08 % Allowed : 0.83 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 1.96 (0.24), residues: 1326 helix: 2.00 (0.22), residues: 629 sheet: 0.87 (0.37), residues: 212 loop : 0.73 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 350 HIS 0.003 0.001 HIS C 118 PHE 0.019 0.001 PHE A 538 TYR 0.008 0.001 TYR C 265 ARG 0.002 0.000 ARG B 371 Details of bonding type rmsd hydrogen bonds : bond 0.24794 ( 529) hydrogen bonds : angle 6.85837 ( 1500) metal coordination : bond 0.00091 ( 1) covalent geometry : bond 0.00218 (10964) covalent geometry : angle 0.41136 (14848) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 ASP cc_start: 0.7857 (m-30) cc_final: 0.7549 (p0) REVERT: B 315 MET cc_start: 0.8072 (mtt) cc_final: 0.7822 (ttt) outliers start: 1 outliers final: 2 residues processed: 208 average time/residue: 3.2437 time to fit residues: 719.3501 Evaluate side-chains 90 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 88 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ILE Chi-restraints excluded: chain B residue 326 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 104 optimal weight: 0.3980 chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 HIS A 569 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.088612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.065121 restraints weight = 58260.868| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.36 r_work: 0.2754 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10965 Z= 0.192 Angle : 0.574 7.508 14848 Z= 0.313 Chirality : 0.040 0.152 1676 Planarity : 0.005 0.040 1920 Dihedral : 4.612 43.088 1462 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.67 % Allowed : 8.17 % Favored : 90.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 1.39 (0.23), residues: 1326 helix: 1.42 (0.21), residues: 636 sheet: 0.58 (0.38), residues: 203 loop : 0.60 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 203 HIS 0.004 0.001 HIS A 119 PHE 0.029 0.002 PHE A 538 TYR 0.012 0.001 TYR B 178 ARG 0.011 0.001 ARG B 153 Details of bonding type rmsd hydrogen bonds : bond 0.06178 ( 529) hydrogen bonds : angle 5.27209 ( 1500) metal coordination : bond 0.00334 ( 1) covalent geometry : bond 0.00430 (10964) covalent geometry : angle 0.57354 (14848) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 1.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 GLU cc_start: 0.7553 (mp0) cc_final: 0.7256 (mp0) REVERT: A 399 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7755 (mt0) REVERT: A 425 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8038 (mp0) REVERT: B 161 ASP cc_start: 0.8074 (m-30) cc_final: 0.7564 (p0) REVERT: B 280 PHE cc_start: 0.8464 (t80) cc_final: 0.7919 (OUTLIER) REVERT: B 324 GLN cc_start: 0.9178 (mm-40) cc_final: 0.8972 (mm-40) REVERT: B 393 LYS cc_start: 0.8601 (mmmt) cc_final: 0.7917 (mmtm) REVERT: C 191 HIS cc_start: 0.7523 (m90) cc_final: 0.6651 (m170) REVERT: D 87 GLN cc_start: 0.7939 (mt0) cc_final: 0.7649 (mt0) outliers start: 20 outliers final: 10 residues processed: 115 average time/residue: 3.1250 time to fit residues: 384.8642 Evaluate side-chains 92 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain D residue 94 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 5 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 129 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.086686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.063342 restraints weight = 58731.292| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.33 r_work: 0.2710 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 10965 Z= 0.273 Angle : 0.592 5.702 14848 Z= 0.324 Chirality : 0.042 0.157 1676 Planarity : 0.005 0.053 1920 Dihedral : 4.895 42.407 1460 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.75 % Allowed : 8.75 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.73 (0.23), residues: 1326 helix: 1.01 (0.21), residues: 642 sheet: 0.19 (0.37), residues: 203 loop : 0.08 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 203 HIS 0.013 0.002 HIS C 299 PHE 0.028 0.002 PHE A 538 TYR 0.017 0.002 TYR B 178 ARG 0.006 0.001 ARG C 89 Details of bonding type rmsd hydrogen bonds : bond 0.06058 ( 529) hydrogen bonds : angle 5.11424 ( 1500) metal coordination : bond 0.00815 ( 1) covalent geometry : bond 0.00630 (10964) covalent geometry : angle 0.59199 (14848) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 1.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8444 (mttt) REVERT: A 399 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7721 (mt0) REVERT: A 425 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8034 (mp0) REVERT: B 393 LYS cc_start: 0.8608 (mmmt) cc_final: 0.7937 (mmtm) REVERT: B 407 GLU cc_start: 0.6798 (mp0) cc_final: 0.6579 (mp0) REVERT: C 191 HIS cc_start: 0.7874 (m90) cc_final: 0.7146 (m-70) REVERT: D 94 MET cc_start: 0.5928 (OUTLIER) cc_final: 0.5588 (mtm) outliers start: 21 outliers final: 10 residues processed: 105 average time/residue: 3.1372 time to fit residues: 352.6008 Evaluate side-chains 92 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 1.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 399 GLN Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 94 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 132 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 GLN D 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.088141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.064891 restraints weight = 58794.265| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.34 r_work: 0.2745 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10965 Z= 0.154 Angle : 0.515 6.286 14848 Z= 0.279 Chirality : 0.039 0.149 1676 Planarity : 0.004 0.051 1920 Dihedral : 4.685 43.184 1460 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.83 % Allowed : 8.75 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.89 (0.23), residues: 1326 helix: 1.21 (0.21), residues: 643 sheet: 0.30 (0.38), residues: 193 loop : 0.05 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 203 HIS 0.006 0.001 HIS C 299 PHE 0.062 0.002 PHE A 76 TYR 0.013 0.001 TYR B 244 ARG 0.005 0.000 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.04617 ( 529) hydrogen bonds : angle 4.78702 ( 1500) metal coordination : bond 0.00464 ( 1) covalent geometry : bond 0.00351 (10964) covalent geometry : angle 0.51493 (14848) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.8939 (mmm) cc_final: 0.8713 (mmm) REVERT: A 266 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8453 (mttt) REVERT: A 425 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7933 (mp0) REVERT: B 280 PHE cc_start: 0.8497 (t80) cc_final: 0.7909 (t80) REVERT: B 393 LYS cc_start: 0.8617 (mmmt) cc_final: 0.7986 (mptp) REVERT: B 398 CYS cc_start: 0.8043 (t) cc_final: 0.6761 (p) REVERT: C 191 HIS cc_start: 0.7818 (m90) cc_final: 0.7131 (m-70) REVERT: D 94 MET cc_start: 0.5859 (OUTLIER) cc_final: 0.5440 (mtm) outliers start: 22 outliers final: 7 residues processed: 99 average time/residue: 3.0332 time to fit residues: 322.2092 Evaluate side-chains 90 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 94 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 80 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 47 optimal weight: 0.0570 chunk 101 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 overall best weight: 1.7704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 ASN C 61 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.087681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.064504 restraints weight = 58910.399| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.34 r_work: 0.2743 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2618 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10965 Z= 0.171 Angle : 0.512 5.694 14848 Z= 0.277 Chirality : 0.039 0.149 1676 Planarity : 0.004 0.053 1920 Dihedral : 4.631 43.230 1460 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.67 % Allowed : 9.50 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.79 (0.23), residues: 1326 helix: 1.21 (0.21), residues: 643 sheet: -0.04 (0.36), residues: 208 loop : 0.01 (0.28), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 203 HIS 0.006 0.001 HIS C 299 PHE 0.025 0.002 PHE A 538 TYR 0.013 0.001 TYR B 244 ARG 0.006 0.000 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.04626 ( 529) hydrogen bonds : angle 4.73377 ( 1500) metal coordination : bond 0.00482 ( 1) covalent geometry : bond 0.00394 (10964) covalent geometry : angle 0.51167 (14848) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.8947 (mmm) cc_final: 0.8645 (mmm) REVERT: A 266 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8453 (mttt) REVERT: A 425 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: B 393 LYS cc_start: 0.8622 (mmmt) cc_final: 0.7994 (mptp) REVERT: B 398 CYS cc_start: 0.8115 (t) cc_final: 0.6843 (p) REVERT: C 191 HIS cc_start: 0.7838 (m90) cc_final: 0.7135 (m-70) REVERT: D 94 MET cc_start: 0.5800 (OUTLIER) cc_final: 0.5480 (mtm) outliers start: 20 outliers final: 9 residues processed: 104 average time/residue: 3.0718 time to fit residues: 342.4799 Evaluate side-chains 93 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 1.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 94 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.086915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.063615 restraints weight = 58659.213| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.34 r_work: 0.2726 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2604 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.3589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10965 Z= 0.224 Angle : 0.544 6.170 14848 Z= 0.296 Chirality : 0.040 0.150 1676 Planarity : 0.005 0.054 1920 Dihedral : 4.770 43.505 1460 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.92 % Allowed : 9.17 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.60 (0.23), residues: 1326 helix: 1.08 (0.21), residues: 644 sheet: -0.23 (0.36), residues: 216 loop : -0.08 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 203 HIS 0.008 0.001 HIS C 299 PHE 0.027 0.002 PHE A 538 TYR 0.015 0.002 TYR B 178 ARG 0.007 0.001 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.04936 ( 529) hydrogen bonds : angle 4.82357 ( 1500) metal coordination : bond 0.00647 ( 1) covalent geometry : bond 0.00515 (10964) covalent geometry : angle 0.54391 (14848) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8481 (mttt) REVERT: A 425 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: B 393 LYS cc_start: 0.8672 (mmmt) cc_final: 0.8004 (mmtm) REVERT: B 398 CYS cc_start: 0.8176 (t) cc_final: 0.6957 (p) REVERT: C 191 HIS cc_start: 0.7856 (m90) cc_final: 0.7173 (m-70) REVERT: D 94 MET cc_start: 0.5810 (OUTLIER) cc_final: 0.5461 (mtm) outliers start: 23 outliers final: 8 residues processed: 95 average time/residue: 3.2228 time to fit residues: 328.3470 Evaluate side-chains 87 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 94 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 48 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 80 optimal weight: 0.5980 chunk 79 optimal weight: 0.8980 chunk 118 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 103 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.087859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.064715 restraints weight = 58647.601| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.34 r_work: 0.2748 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2626 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10965 Z= 0.145 Angle : 0.500 5.850 14848 Z= 0.270 Chirality : 0.038 0.147 1676 Planarity : 0.004 0.055 1920 Dihedral : 4.619 43.305 1460 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.42 % Allowed : 9.75 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.76 (0.23), residues: 1326 helix: 1.23 (0.21), residues: 644 sheet: -0.07 (0.37), residues: 206 loop : -0.07 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 203 HIS 0.004 0.001 HIS C 299 PHE 0.025 0.001 PHE A 538 TYR 0.012 0.001 TYR B 244 ARG 0.007 0.000 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 529) hydrogen bonds : angle 4.65505 ( 1500) metal coordination : bond 0.00437 ( 1) covalent geometry : bond 0.00329 (10964) covalent geometry : angle 0.50014 (14848) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 1.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.8947 (mmm) cc_final: 0.8663 (mmm) REVERT: A 266 LYS cc_start: 0.8908 (OUTLIER) cc_final: 0.8452 (mttt) REVERT: A 425 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7889 (mp0) REVERT: B 393 LYS cc_start: 0.8648 (mmmt) cc_final: 0.7989 (mmtm) REVERT: B 398 CYS cc_start: 0.8157 (t) cc_final: 0.6946 (p) REVERT: C 191 HIS cc_start: 0.7834 (m90) cc_final: 0.7258 (m-70) REVERT: D 94 MET cc_start: 0.5759 (OUTLIER) cc_final: 0.5395 (mtm) REVERT: D 111 MET cc_start: 0.6323 (tpp) cc_final: 0.6034 (mmt) outliers start: 17 outliers final: 9 residues processed: 94 average time/residue: 3.1443 time to fit residues: 317.9466 Evaluate side-chains 93 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 1.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 94 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 103 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.088140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.065058 restraints weight = 59025.807| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.34 r_work: 0.2755 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10965 Z= 0.138 Angle : 0.483 5.542 14848 Z= 0.260 Chirality : 0.038 0.146 1676 Planarity : 0.004 0.063 1920 Dihedral : 4.517 42.991 1460 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.50 % Allowed : 9.67 % Favored : 88.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.86 (0.23), residues: 1326 helix: 1.33 (0.21), residues: 644 sheet: -0.07 (0.37), residues: 206 loop : -0.04 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 203 HIS 0.004 0.001 HIS C 299 PHE 0.024 0.001 PHE A 538 TYR 0.012 0.001 TYR B 244 ARG 0.007 0.000 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 529) hydrogen bonds : angle 4.54589 ( 1500) metal coordination : bond 0.00396 ( 1) covalent geometry : bond 0.00316 (10964) covalent geometry : angle 0.48329 (14848) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 1.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8263 (mp) REVERT: A 245 MET cc_start: 0.8942 (mmm) cc_final: 0.8652 (mmm) REVERT: A 266 LYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8434 (mttt) REVERT: A 425 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.7879 (mp0) REVERT: B 280 PHE cc_start: 0.8512 (t80) cc_final: 0.7959 (t80) REVERT: B 393 LYS cc_start: 0.8635 (mmmt) cc_final: 0.7983 (mmtm) REVERT: B 398 CYS cc_start: 0.8120 (t) cc_final: 0.6918 (p) REVERT: C 191 HIS cc_start: 0.7820 (m90) cc_final: 0.7177 (m-70) REVERT: D 94 MET cc_start: 0.5636 (OUTLIER) cc_final: 0.5280 (mtm) outliers start: 18 outliers final: 8 residues processed: 93 average time/residue: 3.0715 time to fit residues: 306.7793 Evaluate side-chains 90 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 94 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.087210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.064093 restraints weight = 58687.097| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.32 r_work: 0.2742 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10965 Z= 0.213 Angle : 0.531 5.543 14848 Z= 0.289 Chirality : 0.040 0.151 1676 Planarity : 0.005 0.050 1920 Dihedral : 4.686 43.297 1460 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.58 % Allowed : 9.92 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.63 (0.23), residues: 1326 helix: 1.16 (0.21), residues: 644 sheet: -0.27 (0.36), residues: 216 loop : -0.11 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 203 HIS 0.007 0.001 HIS C 299 PHE 0.027 0.002 PHE A 538 TYR 0.015 0.001 TYR B 178 ARG 0.007 0.001 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.04695 ( 529) hydrogen bonds : angle 4.70098 ( 1500) metal coordination : bond 0.00629 ( 1) covalent geometry : bond 0.00497 (10964) covalent geometry : angle 0.53072 (14848) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 1.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8255 (mp) REVERT: A 266 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8479 (mttt) REVERT: A 425 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: B 88 LYS cc_start: 0.8466 (mttp) cc_final: 0.8249 (mmtm) REVERT: B 315 MET cc_start: 0.8419 (mtt) cc_final: 0.8132 (ttt) REVERT: B 393 LYS cc_start: 0.8676 (mmmt) cc_final: 0.8024 (mmtm) REVERT: B 398 CYS cc_start: 0.8162 (t) cc_final: 0.6946 (p) REVERT: C 191 HIS cc_start: 0.7855 (m90) cc_final: 0.7196 (m-70) REVERT: C 204 ASP cc_start: 0.7842 (t0) cc_final: 0.7617 (t0) REVERT: D 94 MET cc_start: 0.5692 (OUTLIER) cc_final: 0.5310 (mtm) outliers start: 19 outliers final: 9 residues processed: 95 average time/residue: 3.0168 time to fit residues: 308.2224 Evaluate side-chains 93 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 94 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 99 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 71 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 9 optimal weight: 0.3980 chunk 22 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.088287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.065147 restraints weight = 58649.276| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 2.34 r_work: 0.2774 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10965 Z= 0.134 Angle : 0.487 5.689 14848 Z= 0.263 Chirality : 0.038 0.147 1676 Planarity : 0.004 0.063 1920 Dihedral : 4.548 43.341 1460 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.25 % Allowed : 10.17 % Favored : 88.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.83 (0.24), residues: 1326 helix: 1.32 (0.21), residues: 644 sheet: -0.05 (0.37), residues: 206 loop : -0.08 (0.28), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 203 HIS 0.004 0.001 HIS C 299 PHE 0.025 0.001 PHE A 538 TYR 0.012 0.001 TYR B 244 ARG 0.008 0.000 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.04116 ( 529) hydrogen bonds : angle 4.55654 ( 1500) metal coordination : bond 0.00368 ( 1) covalent geometry : bond 0.00303 (10964) covalent geometry : angle 0.48747 (14848) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2652 Ramachandran restraints generated. 1326 Oldfield, 0 Emsley, 1326 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 1.839 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8243 (mp) REVERT: A 245 MET cc_start: 0.8945 (mmm) cc_final: 0.8662 (mmm) REVERT: A 266 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8457 (mttt) REVERT: A 425 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7886 (mp0) REVERT: B 88 LYS cc_start: 0.8468 (mttp) cc_final: 0.8231 (mmtm) REVERT: B 315 MET cc_start: 0.8405 (mtt) cc_final: 0.8104 (ttt) REVERT: B 393 LYS cc_start: 0.8669 (mmmt) cc_final: 0.8017 (mmtm) REVERT: B 398 CYS cc_start: 0.8147 (t) cc_final: 0.6895 (p) REVERT: C 191 HIS cc_start: 0.7810 (m90) cc_final: 0.7204 (m170) REVERT: C 204 ASP cc_start: 0.7775 (t0) cc_final: 0.7561 (t0) REVERT: D 94 MET cc_start: 0.5616 (OUTLIER) cc_final: 0.5233 (mtm) REVERT: D 111 MET cc_start: 0.6325 (tpp) cc_final: 0.5940 (mmt) outliers start: 15 outliers final: 8 residues processed: 92 average time/residue: 3.0584 time to fit residues: 302.2329 Evaluate side-chains 91 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 1.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 308 GLU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 425 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 304 ASP Chi-restraints excluded: chain B residue 326 HIS Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 282 LEU Chi-restraints excluded: chain D residue 94 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 28 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 132 optimal weight: 4.9990 chunk 71 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.087545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.064389 restraints weight = 58785.317| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.33 r_work: 0.2749 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8718 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10965 Z= 0.193 Angle : 0.517 5.470 14848 Z= 0.281 Chirality : 0.039 0.149 1676 Planarity : 0.005 0.058 1920 Dihedral : 4.634 43.342 1460 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.08 % Allowed : 10.58 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.69 (0.23), residues: 1326 helix: 1.21 (0.21), residues: 644 sheet: -0.24 (0.36), residues: 216 loop : -0.09 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 203 HIS 0.007 0.001 HIS C 299 PHE 0.026 0.002 PHE A 538 TYR 0.013 0.001 TYR B 178 ARG 0.008 0.001 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.04482 ( 529) hydrogen bonds : angle 4.64014 ( 1500) metal coordination : bond 0.00550 ( 1) covalent geometry : bond 0.00449 (10964) covalent geometry : angle 0.51715 (14848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15702.60 seconds wall clock time: 269 minutes 13.44 seconds (16153.44 seconds total)