Starting phenix.real_space_refine on Wed Jun 18 18:28:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8so0_40644/06_2025/8so0_40644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8so0_40644/06_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_40644/06_2025/8so0_40644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8so0_40644/06_2025/8so0_40644.map" model { file = "/net/cci-nas-00/data/ceres_data/8so0_40644/06_2025/8so0_40644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8so0_40644/06_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-5710/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: 11.70, per 1000 atoms: 0.55 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: 5.37 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: 1.96 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: 8.39 Time building geometry restraints manager: 6.54 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: 11.040 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: 0.900 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 56.050 Find NCS groups from input model: 0.130 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: 0.000 Load rotamer database and sin/cos tables:12.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.360 ------------------------------------------------------------------------------- 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 : 1.594 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: 3.1967 time to fit residues: 708.0426 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 : 1.637 ------------------------------------------------------------------------------- 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 = 32)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.065121 restraints weight = 58260.809| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.36 r_work: 0.2754 rms_B_bonded: 2.63 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: 0.8686 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 : 1.654 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: 0.7554 (mp0) cc_final: 0.7250 (mp0) REVERT: A 399 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7750 (mt0) REVERT: A 425 GLU cc_start: 0.8774 (OUTLIER) cc_final: 0.8028 (mp0) REVERT: B 161 ASP cc_start: 0.8066 (m-30) cc_final: 0.7557 (p0) REVERT: B 280 PHE cc_start: 0.8462 (t80) cc_final: 0.7909 (OUTLIER) REVERT: B 324 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8967 (mm-40) REVERT: B 393 LYS cc_start: 0.8595 (mmmt) cc_final: 0.7908 (mmtm) REVERT: C 191 HIS cc_start: 0.7531 (m90) cc_final: 0.6653 (m170) REVERT: D 87 GLN cc_start: 0.7908 (mt0) cc_final: 0.7621 (mt0) outliers start: 20 outliers final: 10 residues processed: 115 average time/residue: 3.2213 time to fit residues: 397.4598 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 : 1.626 ------------------------------------------------------------------------------- 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: 0.0270 chunk 56 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.7244 ------------------------------------------------------------------------------- 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 = 0.3327 r_free = 0.3327 target = 0.088322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.065096 restraints weight = 58406.106| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.34 r_work: 0.2742 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2980 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= 0.164 Angle : 0.517 5.543 14848 Z= 0.279 Chirality : 0.039 0.152 1676 Planarity : 0.004 0.054 1920 Dihedral : 4.595 41.325 1460 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.50 % Allowed : 8.75 % Favored : 89.75 % 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: 1.15 (0.23), residues: 1326 helix: 1.34 (0.21), residues: 638 sheet: 0.30 (0.38), residues: 203 loop : 0.36 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 203 HIS 0.011 0.001 HIS C 299 PHE 0.025 0.002 PHE A 538 TYR 0.012 0.001 TYR B 178 ARG 0.008 0.000 ARG C 295 Details of bonding type rmsd hydrogen bonds : bond 0.05153 ( 529) hydrogen bonds : angle 4.85247 ( 1500) metal coordination : bond 0.00406 ( 1) covalent geometry : bond 0.00373 (10964) covalent geometry : angle 0.51667 (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: 18 poor density : 91 time to evaluate : 1.766 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: 0.8953 (mmm) cc_final: 0.8748 (mmm) REVERT: A 266 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8428 (mttt) REVERT: A 425 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: B 324 GLN cc_start: 0.9191 (mm-40) cc_final: 0.8982 (mm-40) REVERT: B 393 LYS cc_start: 0.8601 (mmmt) cc_final: 0.7934 (mmtm) REVERT: B 407 GLU cc_start: 0.6641 (mp0) cc_final: 0.6393 (mp0) REVERT: C 191 HIS cc_start: 0.7773 (m90) cc_final: 0.6879 (m170) REVERT: C 197 ASP cc_start: 0.8903 (m-30) cc_final: 0.8700 (m-30) REVERT: D 94 MET cc_start: 0.5877 (OUTLIER) cc_final: 0.5494 (mtm) REVERT: D 111 MET cc_start: 0.6240 (tpp) cc_final: 0.5730 (mmt) outliers start: 18 outliers final: 9 residues processed: 105 average time/residue: 3.2533 time to fit residues: 365.9129 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 : 1.759 ------------------------------------------------------------------------------- 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 4.9990 chunk 34 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 135 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.087878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.064618 restraints weight = 58881.640| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.34 r_work: 0.2734 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2608 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10965 Z= 0.181 Angle : 0.519 6.023 14848 Z= 0.281 Chirality : 0.039 0.149 1676 Planarity : 0.004 0.044 1920 Dihedral : 4.623 42.515 1460 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.25 % Allowed : 8.25 % 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: 0.95 (0.23), residues: 1326 helix: 1.25 (0.21), residues: 643 sheet: 0.17 (0.38), residues: 198 loop : 0.15 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 203 HIS 0.007 0.001 HIS C 299 PHE 0.027 0.002 PHE A 538 TYR 0.013 0.001 TYR B 244 ARG 0.004 0.001 ARG B 389 Details of bonding type rmsd hydrogen bonds : bond 0.04745 ( 529) hydrogen bonds : angle 4.75344 ( 1500) metal coordination : bond 0.00534 ( 1) covalent geometry : bond 0.00414 (10964) covalent geometry : angle 0.51855 (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 112 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 2.971 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: A 245 MET cc_start: 0.8959 (mmm) cc_final: 0.8649 (mmm) REVERT: A 266 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8438 (mttt) REVERT: A 399 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7713 (mt0) REVERT: A 425 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: B 280 PHE cc_start: 0.8456 (t80) cc_final: 0.7874 (t80) REVERT: B 393 LYS cc_start: 0.8611 (mmmt) cc_final: 0.7981 (mptp) outliers start: 27 outliers final: 10 residues processed: 103 average time/residue: 3.5716 time to fit residues: 395.3221 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 : 1.715 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 121 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 120 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 GLN 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 = 0.087811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.064585 restraints weight = 59011.338| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 2.34 r_work: 0.2734 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3445 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= 0.178 Angle : 0.515 5.788 14848 Z= 0.278 Chirality : 0.039 0.149 1676 Planarity : 0.005 0.063 1920 Dihedral : 4.622 42.714 1460 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.67 % Allowed : 9.58 % Favored : 88.75 % 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: 0.84 (0.23), residues: 1326 helix: 1.22 (0.21), residues: 644 sheet: -0.04 (0.36), residues: 213 loop : 0.08 (0.28), residues: 469 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 0.026 0.002 PHE A 538 TYR 0.012 0.001 TYR B 244 ARG 0.008 0.001 ARG B 389 Details of bonding type rmsd hydrogen bonds : bond 0.04638 ( 529) hydrogen bonds : angle 4.73369 ( 1500) metal coordination : bond 0.00534 ( 1) covalent geometry : bond 0.00409 (10964) covalent geometry : angle 0.51486 (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 106 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 3.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 245 MET cc_start: 0.8961 (mmm) cc_final: 0.8665 (mmm) REVERT: A 266 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8449 (mttt) REVERT: A 425 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.7945 (mp0) REVERT: B 393 LYS cc_start: 0.8629 (mmmt) cc_final: 0.7999 (mptp) REVERT: B 398 CYS cc_start: 0.8114 (t) cc_final: 0.6847 (p) REVERT: C 191 HIS cc_start: 0.7838 (m90) cc_final: 0.7165 (m-70) outliers start: 20 outliers final: 10 residues processed: 99 average time/residue: 3.4565 time to fit residues: 366.0441 Evaluate side-chains 92 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 1.912 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 106 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: 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 = 0.3307 r_free = 0.3307 target = 0.087167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.063936 restraints weight = 58730.764| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.34 r_work: 0.2732 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.3598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10965 Z= 0.210 Angle : 0.533 6.452 14848 Z= 0.289 Chirality : 0.040 0.149 1676 Planarity : 0.005 0.052 1920 Dihedral : 4.694 43.614 1460 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.25 % Allowed : 9.00 % Favored : 88.75 % 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: 0.70 (0.23), residues: 1326 helix: 1.15 (0.21), residues: 644 sheet: -0.14 (0.36), residues: 213 loop : -0.02 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 203 HIS 0.007 0.001 HIS C 299 PHE 0.027 0.002 PHE A 538 TYR 0.014 0.001 TYR B 178 ARG 0.007 0.001 ARG B 389 Details of bonding type rmsd hydrogen bonds : bond 0.04777 ( 529) hydrogen bonds : angle 4.74695 ( 1500) metal coordination : bond 0.00622 ( 1) covalent geometry : bond 0.00484 (10964) covalent geometry : angle 0.53297 (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 106 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 1.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 266 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8478 (mttt) REVERT: A 399 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7674 (mt0) REVERT: A 425 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7958 (mp0) REVERT: B 393 LYS cc_start: 0.8658 (mmmt) cc_final: 0.7986 (mmtm) REVERT: B 398 CYS cc_start: 0.8172 (t) cc_final: 0.6947 (p) REVERT: C 191 HIS cc_start: 0.7862 (m90) cc_final: 0.7219 (m-70) outliers start: 27 outliers final: 10 residues processed: 98 average time/residue: 3.1626 time to fit residues: 332.4904 Evaluate side-chains 92 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 1.912 ------------------------------------------------------------------------------- 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 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 B residue 408 ILE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 282 LEU 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: 1.9990 chunk 81 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 80 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.3331 r_free = 0.3331 target = 0.088404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.065256 restraints weight = 58487.217| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.35 r_work: 0.2751 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2627 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 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 0.036 10965 Z= 0.122 Angle : 0.488 5.958 14848 Z= 0.262 Chirality : 0.038 0.148 1676 Planarity : 0.004 0.057 1920 Dihedral : 4.540 43.199 1460 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.58 % Allowed : 9.83 % 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: 0.92 (0.24), residues: 1326 helix: 1.34 (0.21), residues: 644 sheet: 0.12 (0.38), residues: 198 loop : -0.03 (0.28), residues: 484 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 0.024 0.001 PHE A 538 TYR 0.011 0.001 TYR B 244 ARG 0.006 0.000 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.04149 ( 529) hydrogen bonds : angle 4.57612 ( 1500) metal coordination : bond 0.00332 ( 1) covalent geometry : bond 0.00273 (10964) covalent geometry : angle 0.48774 (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 101 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8271 (mp) REVERT: A 245 MET cc_start: 0.8947 (mmm) cc_final: 0.8737 (mmm) REVERT: A 266 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8448 (mttt) REVERT: A 425 GLU cc_start: 0.8704 (OUTLIER) cc_final: 0.7877 (mp0) REVERT: B 393 LYS cc_start: 0.8637 (mmmt) cc_final: 0.7977 (mmtm) REVERT: B 398 CYS cc_start: 0.8167 (t) cc_final: 0.6967 (p) REVERT: C 191 HIS cc_start: 0.7812 (m90) cc_final: 0.7189 (m-70) outliers start: 19 outliers final: 10 residues processed: 96 average time/residue: 3.2962 time to fit residues: 339.9758 Evaluate side-chains 92 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 1.915 ------------------------------------------------------------------------------- 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 196 LEU 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 B residue 408 ILE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 282 LEU 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: 0.9990 chunk 75 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3322 r_free = 0.3322 target = 0.087909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.064710 restraints weight = 59016.527| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 2.35 r_work: 0.2750 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10965 Z= 0.160 Angle : 0.495 5.756 14848 Z= 0.267 Chirality : 0.039 0.147 1676 Planarity : 0.004 0.047 1920 Dihedral : 4.538 42.871 1460 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.50 % Allowed : 9.92 % 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: 0.85 (0.23), residues: 1326 helix: 1.31 (0.21), residues: 644 sheet: -0.13 (0.36), residues: 213 loop : 0.03 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 203 HIS 0.005 0.001 HIS C 299 PHE 0.025 0.002 PHE A 538 TYR 0.012 0.001 TYR B 244 ARG 0.006 0.000 ARG B 389 Details of bonding type rmsd hydrogen bonds : bond 0.04300 ( 529) hydrogen bonds : angle 4.59000 ( 1500) metal coordination : bond 0.00450 ( 1) covalent geometry : bond 0.00367 (10964) covalent geometry : angle 0.49520 (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 99 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8254 (mp) REVERT: A 245 MET cc_start: 0.8970 (mmm) cc_final: 0.8688 (mmm) REVERT: A 266 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8462 (mttt) REVERT: A 425 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: B 393 LYS cc_start: 0.8634 (mmmt) cc_final: 0.7976 (mmtm) REVERT: B 398 CYS cc_start: 0.8180 (t) cc_final: 0.6983 (p) REVERT: C 191 HIS cc_start: 0.7812 (m90) cc_final: 0.7189 (m-70) REVERT: C 204 ASP cc_start: 0.7870 (t0) cc_final: 0.7667 (t0) outliers start: 18 outliers final: 10 residues processed: 95 average time/residue: 3.7649 time to fit residues: 388.1771 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 : 1.943 ------------------------------------------------------------------------------- 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 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 B residue 408 ILE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 282 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3319 r_free = 0.3319 target = 0.087639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.064488 restraints weight = 58653.037| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.34 r_work: 0.2745 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10965 Z= 0.178 Angle : 0.511 5.624 14848 Z= 0.277 Chirality : 0.039 0.149 1676 Planarity : 0.004 0.067 1920 Dihedral : 4.588 43.036 1460 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.42 % Allowed : 10.08 % 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: 0.80 (0.23), residues: 1326 helix: 1.27 (0.21), residues: 644 sheet: -0.21 (0.36), residues: 216 loop : 0.02 (0.28), residues: 466 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 0.012 0.001 TYR B 178 ARG 0.009 0.000 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 529) hydrogen bonds : angle 4.62796 ( 1500) metal coordination : bond 0.00518 ( 1) covalent geometry : bond 0.00411 (10964) covalent geometry : angle 0.51111 (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 101 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 1.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8274 (mp) REVERT: A 245 MET cc_start: 0.8970 (mmm) cc_final: 0.8689 (mmm) REVERT: A 266 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8472 (mttt) REVERT: A 399 GLN cc_start: 0.8388 (OUTLIER) cc_final: 0.7634 (mt0) REVERT: A 425 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.7918 (mp0) REVERT: B 393 LYS cc_start: 0.8643 (mmmt) cc_final: 0.7988 (mmtm) REVERT: B 398 CYS cc_start: 0.8196 (t) cc_final: 0.6989 (p) REVERT: C 191 HIS cc_start: 0.7824 (m90) cc_final: 0.7196 (m-70) REVERT: C 204 ASP cc_start: 0.7839 (t0) cc_final: 0.7636 (t0) outliers start: 17 outliers final: 11 residues processed: 97 average time/residue: 3.0891 time to fit residues: 321.9157 Evaluate side-chains 91 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 2.071 ------------------------------------------------------------------------------- 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 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 399 GLN 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 B residue 408 ILE Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 175 ASP Chi-restraints excluded: chain C residue 282 LEU 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: 0.0970 chunk 71 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 9 optimal weight: 0.0370 chunk 22 optimal weight: 2.9990 chunk 87 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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 = 0.3338 r_free = 0.3338 target = 0.088852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.065806 restraints weight = 58526.486| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 2.34 r_work: 0.2767 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2643 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10965 Z= 0.105 Angle : 0.473 5.634 14848 Z= 0.253 Chirality : 0.038 0.144 1676 Planarity : 0.004 0.057 1920 Dihedral : 4.406 42.791 1460 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.08 % Allowed : 10.67 % Favored : 88.25 % 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: 1.03 (0.24), residues: 1326 helix: 1.45 (0.21), residues: 645 sheet: 0.06 (0.37), residues: 203 loop : 0.06 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 203 HIS 0.003 0.001 HIS C 63 PHE 0.024 0.001 PHE A 538 TYR 0.011 0.001 TYR B 244 ARG 0.008 0.000 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.03812 ( 529) hydrogen bonds : angle 4.45212 ( 1500) metal coordination : bond 0.00192 ( 1) covalent geometry : bond 0.00235 (10964) covalent geometry : angle 0.47299 (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 95 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8226 (mp) REVERT: A 266 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8433 (mttt) REVERT: A 425 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: B 393 LYS cc_start: 0.8628 (mmmt) cc_final: 0.7974 (mmtm) REVERT: B 398 CYS cc_start: 0.8177 (t) cc_final: 0.6980 (p) REVERT: C 191 HIS cc_start: 0.7779 (m90) cc_final: 0.7118 (m170) REVERT: C 204 ASP cc_start: 0.7713 (t0) cc_final: 0.7507 (t0) outliers start: 13 outliers final: 7 residues processed: 90 average time/residue: 2.8894 time to fit residues: 281.5790 Evaluate side-chains 87 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 PHE Chi-restraints excluded: chain A residue 196 LEU 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 175 ASP Chi-restraints excluded: chain C residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 132 optimal weight: 9.9990 chunk 71 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 106 optimal weight: 0.8980 chunk 100 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 = 0.3326 r_free = 0.3326 target = 0.087928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.064727 restraints weight = 58547.651| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 2.32 r_work: 0.2767 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2642 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3876 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= 0.178 Angle : 0.506 5.455 14848 Z= 0.273 Chirality : 0.039 0.147 1676 Planarity : 0.004 0.056 1920 Dihedral : 4.528 42.567 1460 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.17 % Allowed : 10.67 % Favored : 88.17 % 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: 0.89 (0.24), residues: 1326 helix: 1.37 (0.21), residues: 644 sheet: -0.22 (0.36), residues: 216 loop : 0.05 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 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 178 ARG 0.008 0.000 ARG A 527 Details of bonding type rmsd hydrogen bonds : bond 0.04323 ( 529) hydrogen bonds : angle 4.56654 ( 1500) metal coordination : bond 0.00483 ( 1) covalent geometry : bond 0.00411 (10964) covalent geometry : angle 0.50647 (14848) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16490.61 seconds wall clock time: 284 minutes 9.92 seconds (17049.92 seconds total)