Starting phenix.real_space_refine on Sat Aug 23 05:17:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u89_42018/08_2025/8u89_42018.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u89_42018/08_2025/8u89_42018.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u89_42018/08_2025/8u89_42018.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u89_42018/08_2025/8u89_42018.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u89_42018/08_2025/8u89_42018.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u89_42018/08_2025/8u89_42018.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.037 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mn 2 7.51 5 S 55 5.16 5 C 6361 2.51 5 N 1665 2.21 5 O 1845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9928 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 566, 4405 Classifications: {'peptide': 566} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 540} Chain: "B" Number of atoms: 3091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3091 Classifications: {'peptide': 373} Link IDs: {'PTRANS': 23, 'TRANS': 349} Chain: "C" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2430 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 289} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.84, per 1000 atoms: 0.19 Number of scatterers: 9928 At special positions: 0 Unit cell: (108.936, 113.208, 116.412, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Mn 2 24.99 S 55 16.00 O 1845 8.00 N 1665 7.00 C 6361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 250.5 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2380 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 3 sheets defined 75.9% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 24 through 34 Processing helix chain 'A' and resid 34 through 42 Processing helix chain 'A' and resid 45 through 50 Processing helix chain 'A' and resid 50 through 58 Processing helix chain 'A' and resid 62 through 73 Processing helix chain 'A' and resid 76 through 81 removed outlier: 3.937A pdb=" N GLY A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 removed outlier: 5.602A pdb=" N HIS A 87 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS A 88 " --> pdb=" O TYR A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 101 through 119 removed outlier: 3.547A pdb=" N LYS A 107 " --> pdb=" O VAL A 103 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N HIS A 117 " --> pdb=" O ARG A 113 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU A 118 " --> pdb=" O ALA A 114 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS A 119 " --> pdb=" O ILE A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 137 removed outlier: 4.167A pdb=" N GLU A 125 " --> pdb=" O PRO A 121 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N VAL A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) Proline residue: A 130 - end of helix Processing helix chain 'A' and resid 140 through 149 removed outlier: 3.713A pdb=" N ARG A 144 " --> pdb=" O TRP A 140 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLY A 149 " --> pdb=" O THR A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 175 Processing helix chain 'A' and resid 178 through 194 removed outlier: 4.750A pdb=" N GLY A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N GLU A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 204 Processing helix chain 'A' and resid 204 through 214 removed outlier: 3.654A pdb=" N MET A 208 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 234 removed outlier: 4.096A pdb=" N LEU A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL A 229 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LEU A 234 " --> pdb=" O ASN A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 244 removed outlier: 3.540A pdb=" N LEU A 240 " --> pdb=" O PRO A 236 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) removed outlier: 5.098A 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 292 removed outlier: 3.893A pdb=" N THR A 279 " --> pdb=" O GLY A 275 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS A 280 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N VAL A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 295 through 305 removed outlier: 3.750A pdb=" N LYS A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 312 removed outlier: 3.863A pdb=" N CYS A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 317 through 335 removed outlier: 4.890A pdb=" N LEU A 327 " --> pdb=" O MET A 323 " (cutoff:3.500A) Proline residue: A 328 - end of helix removed outlier: 3.604A pdb=" N GLU A 332 " --> pdb=" O PRO A 328 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N SER A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 removed outlier: 3.820A pdb=" N LYS A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 351 Processing helix chain 'A' and resid 352 through 357 Processing helix chain 'A' and resid 357 through 374 removed outlier: 4.748A pdb=" N LEU A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Proline residue: A 367 - end of helix Processing helix chain 'A' and resid 377 through 387 removed outlier: 4.009A pdb=" N ASN A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 393 removed outlier: 3.870A pdb=" N VAL A 391 " --> pdb=" O ASN A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 404 Processing helix chain 'A' and resid 404 through 412 Processing helix chain 'A' and resid 416 through 435 Proline residue: A 428 - end of helix Processing helix chain 'A' and resid 435 through 443 removed outlier: 3.586A pdb=" N GLU A 441 " --> pdb=" O GLU A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 450 Processing helix chain 'A' and resid 451 through 453 No H-bonds generated for 'chain 'A' and resid 451 through 453' Processing helix chain 'A' and resid 455 through 474 Processing helix chain 'A' and resid 474 through 482 removed outlier: 3.643A pdb=" N ALA A 478 " --> pdb=" O GLY A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 488 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 494 through 521 removed outlier: 4.392A pdb=" N GLU A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N VAL A 511 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY A 513 " --> pdb=" O SER A 509 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLN A 514 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 8.516A pdb=" N ASP A 515 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE A 516 " --> pdb=" O CYS A 512 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET A 521 " --> pdb=" O THR A 517 " (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 568 removed outlier: 4.233A pdb=" N ILE A 563 " --> pdb=" O GLU A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 586 Processing helix chain 'B' and resid 113 through 124 Processing helix chain 'B' and resid 138 through 159 Processing helix chain 'B' and resid 167 through 180 Processing helix chain 'B' and resid 195 through 199 removed outlier: 3.953A pdb=" N ASP B 199 " --> pdb=" O PRO B 196 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 223 removed outlier: 4.499A pdb=" N LEU B 212 " --> pdb=" O PRO B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 Processing helix chain 'B' and resid 236 through 246 removed outlier: 3.527A pdb=" N LEU B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 249 No H-bonds generated for 'chain 'B' and resid 247 through 249' Processing helix chain 'B' and resid 251 through 269 Processing helix chain 'B' and resid 272 through 290 Processing helix chain 'B' and resid 296 through 309 Processing helix chain 'B' and resid 316 through 326 Processing helix chain 'B' and resid 328 through 333 removed outlier: 3.772A pdb=" N VAL B 333 " --> pdb=" O LEU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 354 removed outlier: 4.221A pdb=" N TYR B 339 " --> pdb=" O SER B 335 " (cutoff:3.500A) Proline residue: B 341 - end of helix Processing helix chain 'B' and resid 357 through 368 Processing helix chain 'B' and resid 373 through 389 Processing helix chain 'B' and resid 392 through 413 removed outlier: 3.547A pdb=" N SER B 397 " --> pdb=" O PRO B 393 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS B 398 " --> pdb=" O SER B 394 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL B 399 " --> pdb=" O GLU B 395 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N GLU B 401 " --> pdb=" O SER B 397 " (cutoff:3.500A) Proline residue: B 402 - end of helix removed outlier: 3.693A pdb=" N LYS B 409 " --> pdb=" O ARG B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 424 Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 428 through 438 Processing helix chain 'B' and resid 438 through 453 Proline residue: B 444 - end of helix Proline residue: B 448 - end of helix removed outlier: 3.622A pdb=" N ASN B 453 " --> pdb=" O ALA B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 477 removed outlier: 3.533A pdb=" N HIS B 463 " --> pdb=" O ASN B 459 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASN B 477 " --> pdb=" O PHE B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 24 through 40 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 129 through 138 Processing helix chain 'C' and resid 140 through 151 removed outlier: 3.588A pdb=" N LYS C 144 " --> pdb=" O ALA C 140 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP C 151 " --> pdb=" O THR C 147 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 182 Processing helix chain 'C' and resid 193 through 201 removed outlier: 3.729A 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 sheet with id=AA1, first strand: chain 'C' and resid 47 through 48 Processing sheet with id=AA2, first strand: chain 'C' and resid 111 through 113 removed outlier: 3.530A pdb=" N ALA C 273 " --> pdb=" O PHE C 289 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 202 through 203 removed outlier: 6.698A pdb=" N ASP C 202 " --> pdb=" O PHE C 220 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1683 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.11 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1831 1.33 - 1.45: 2460 1.45 - 1.57: 5768 1.57 - 1.70: 1 1.70 - 1.82: 82 Bond restraints: 10142 Sorted by residual: bond pdb=" C PRO A 276 " pdb=" O PRO A 276 " ideal model delta sigma weight residual 1.238 1.201 0.037 1.24e-02 6.50e+03 8.88e+00 bond pdb=" N VAL C 159 " pdb=" CA VAL C 159 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.24e-02 6.50e+03 8.37e+00 bond pdb=" N ASP A 293 " pdb=" CA ASP A 293 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.19e-02 7.06e+03 8.20e+00 bond pdb=" N GLU A 204 " pdb=" CA GLU A 204 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.25e-02 6.40e+03 8.15e+00 bond pdb=" N VAL A 274 " pdb=" CA VAL A 274 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.17e-02 7.31e+03 7.90e+00 ... (remaining 10137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 13303 1.69 - 3.37: 350 3.37 - 5.06: 74 5.06 - 6.74: 22 6.74 - 8.43: 8 Bond angle restraints: 13757 Sorted by residual: angle pdb=" N MET C 66 " pdb=" CA MET C 66 " pdb=" C MET C 66 " ideal model delta sigma weight residual 110.97 105.27 5.70 1.09e+00 8.42e-01 2.73e+01 angle pdb=" N ASN A 539 " pdb=" CA ASN A 539 " pdb=" C ASN A 539 " ideal model delta sigma weight residual 111.36 105.69 5.67 1.09e+00 8.42e-01 2.71e+01 angle pdb=" C GLN A 571 " pdb=" N ASP A 572 " pdb=" CA ASP A 572 " ideal model delta sigma weight residual 121.39 114.47 6.92 1.66e+00 3.63e-01 1.74e+01 angle pdb=" C GLU A 100 " pdb=" N GLU A 101 " pdb=" CA GLU A 101 " ideal model delta sigma weight residual 120.75 114.47 6.28 1.51e+00 4.39e-01 1.73e+01 angle pdb=" N MET A 499 " pdb=" CA MET A 499 " pdb=" C MET A 499 " ideal model delta sigma weight residual 111.82 107.24 4.58 1.16e+00 7.43e-01 1.56e+01 ... (remaining 13752 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5360 17.91 - 35.82: 616 35.82 - 53.72: 154 53.72 - 71.63: 16 71.63 - 89.54: 13 Dihedral angle restraints: 6159 sinusoidal: 2502 harmonic: 3657 Sorted by residual: dihedral pdb=" CD ARG B 114 " pdb=" NE ARG B 114 " pdb=" CZ ARG B 114 " pdb=" NH1 ARG B 114 " ideal model delta sinusoidal sigma weight residual 0.00 -59.96 59.96 1 1.00e+01 1.00e-02 4.79e+01 dihedral pdb=" CD ARG A 113 " pdb=" NE ARG A 113 " pdb=" CZ ARG A 113 " pdb=" NH1 ARG A 113 " ideal model delta sinusoidal sigma weight residual 0.00 -44.45 44.45 1 1.00e+01 1.00e-02 2.75e+01 dihedral pdb=" CG ARG C 89 " pdb=" CD ARG C 89 " pdb=" NE ARG C 89 " pdb=" CZ ARG C 89 " ideal model delta sinusoidal sigma weight residual -90.00 -37.14 -52.86 2 1.50e+01 4.44e-03 1.36e+01 ... (remaining 6156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1234 0.050 - 0.100: 287 0.100 - 0.151: 35 0.151 - 0.201: 7 0.201 - 0.251: 1 Chirality restraints: 1564 Sorted by residual: chirality pdb=" CB VAL C 159 " pdb=" CA VAL C 159 " pdb=" CG1 VAL C 159 " pdb=" CG2 VAL C 159 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA ILE B 308 " pdb=" N ILE B 308 " pdb=" C ILE B 308 " pdb=" CB ILE B 308 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" CA LYS A 163 " pdb=" N LYS A 163 " pdb=" C LYS A 163 " pdb=" CB LYS A 163 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.78e-01 ... (remaining 1561 not shown) Planarity restraints: 1767 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 114 " -0.953 9.50e-02 1.11e+02 4.27e-01 1.10e+02 pdb=" NE ARG B 114 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARG B 114 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 114 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 114 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 113 " 0.776 9.50e-02 1.11e+02 3.48e-01 7.35e+01 pdb=" NE ARG A 113 " -0.045 2.00e-02 2.50e+03 pdb=" CZ ARG A 113 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 113 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 113 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 273 " 0.013 2.00e-02 2.50e+03 2.72e-02 7.37e+00 pdb=" C ALA A 273 " -0.047 2.00e-02 2.50e+03 pdb=" O ALA A 273 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL A 274 " 0.016 2.00e-02 2.50e+03 ... (remaining 1764 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 120 2.65 - 3.21: 9438 3.21 - 3.78: 15969 3.78 - 4.34: 21181 4.34 - 4.90: 34820 Nonbonded interactions: 81528 Sorted by model distance: nonbonded pdb=" OD2 ASP C 85 " pdb="MN MN C 401 " model vdw 2.091 2.320 nonbonded pdb=" OD2 ASP C 85 " pdb="MN MN C 402 " model vdw 2.136 2.320 nonbonded pdb=" ND1 HIS C 241 " pdb="MN MN C 401 " model vdw 2.156 2.400 nonbonded pdb=" NE2 HIS C 167 " pdb="MN MN C 401 " model vdw 2.165 2.400 nonbonded pdb=" CD ARG B 114 " pdb=" OH TYR B 155 " model vdw 2.197 3.440 ... (remaining 81523 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: 1.120 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.960 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 10142 Z= 0.184 Angle : 0.698 8.431 13757 Z= 0.400 Chirality : 0.043 0.251 1564 Planarity : 0.014 0.427 1767 Dihedral : 16.176 89.540 3779 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.54 % Allowed : 20.24 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.25), residues: 1233 helix: 1.29 (0.19), residues: 810 sheet: -0.43 (0.94), residues: 37 loop : -0.51 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 89 TYR 0.015 0.001 TYR A 426 PHE 0.035 0.001 PHE B 396 TRP 0.011 0.001 TRP A 417 HIS 0.003 0.000 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00334 (10142) covalent geometry : angle 0.69849 (13757) hydrogen bonds : bond 0.11903 ( 574) hydrogen bonds : angle 5.02749 ( 1683) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 154 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.6736 (ttp-170) cc_final: 0.5824 (tpp-160) REVERT: A 226 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7757 (mt-10) REVERT: B 227 GLN cc_start: 0.8344 (tp-100) cc_final: 0.8112 (tm-30) outliers start: 6 outliers final: 2 residues processed: 157 average time/residue: 0.0845 time to fit residues: 18.6032 Evaluate side-chains 133 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 274 VAL Chi-restraints excluded: chain C residue 131 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 0.3980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.142399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.117674 restraints weight = 17382.505| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.57 r_work: 0.3515 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.0991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10142 Z= 0.120 Angle : 0.553 6.214 13757 Z= 0.280 Chirality : 0.040 0.160 1564 Planarity : 0.004 0.072 1767 Dihedral : 4.030 24.713 1342 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.18 % Allowed : 17.70 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.25), residues: 1233 helix: 1.52 (0.19), residues: 815 sheet: -0.70 (0.75), residues: 53 loop : -0.49 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 171 TYR 0.010 0.001 TYR B 430 PHE 0.029 0.001 PHE B 396 TRP 0.011 0.001 TRP A 417 HIS 0.003 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00278 (10142) covalent geometry : angle 0.55281 (13757) hydrogen bonds : bond 0.03314 ( 574) hydrogen bonds : angle 4.17758 ( 1683) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.270 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.7018 (ttp-170) cc_final: 0.6093 (mtt180) REVERT: A 195 VAL cc_start: 0.8674 (m) cc_final: 0.8226 (p) REVERT: A 226 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7967 (mt-10) outliers start: 24 outliers final: 11 residues processed: 161 average time/residue: 0.0712 time to fit residues: 16.8629 Evaluate side-chains 142 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 163 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 80 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 66 optimal weight: 8.9990 chunk 23 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.140202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.115665 restraints weight = 17520.867| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.56 r_work: 0.3453 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10142 Z= 0.126 Angle : 0.546 6.387 13757 Z= 0.274 Chirality : 0.040 0.170 1564 Planarity : 0.004 0.038 1767 Dihedral : 3.896 18.702 1339 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.36 % Allowed : 18.15 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.25), residues: 1233 helix: 1.59 (0.19), residues: 814 sheet: -0.79 (0.71), residues: 53 loop : -0.52 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 89 TYR 0.010 0.001 TYR A 495 PHE 0.023 0.001 PHE B 396 TRP 0.010 0.001 TRP A 417 HIS 0.003 0.001 HIS B 463 Details of bonding type rmsd covalent geometry : bond 0.00295 (10142) covalent geometry : angle 0.54598 (13757) hydrogen bonds : bond 0.03228 ( 574) hydrogen bonds : angle 4.08397 ( 1683) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 195 VAL cc_start: 0.8671 (m) cc_final: 0.8268 (p) REVERT: A 226 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7930 (mt-10) REVERT: B 244 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8382 (mt) REVERT: B 351 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8382 (mm) REVERT: B 474 MET cc_start: 0.8051 (mtp) cc_final: 0.7816 (mtm) REVERT: C 174 ILE cc_start: 0.6645 (OUTLIER) cc_final: 0.6282 (tp) outliers start: 26 outliers final: 13 residues processed: 159 average time/residue: 0.0722 time to fit residues: 17.1903 Evaluate side-chains 139 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 174 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 64 optimal weight: 6.9990 chunk 57 optimal weight: 0.9980 chunk 104 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.140603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.116027 restraints weight = 17640.171| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 2.58 r_work: 0.3454 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10142 Z= 0.114 Angle : 0.535 6.869 13757 Z= 0.267 Chirality : 0.040 0.170 1564 Planarity : 0.004 0.039 1767 Dihedral : 3.839 18.518 1339 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.36 % Allowed : 18.97 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.25), residues: 1233 helix: 1.62 (0.19), residues: 816 sheet: -0.82 (0.72), residues: 53 loop : -0.45 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 89 TYR 0.009 0.001 TYR A 155 PHE 0.033 0.001 PHE B 396 TRP 0.010 0.001 TRP A 417 HIS 0.003 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00267 (10142) covalent geometry : angle 0.53528 (13757) hydrogen bonds : bond 0.02979 ( 574) hydrogen bonds : angle 4.05167 ( 1683) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: A 195 VAL cc_start: 0.8703 (m) cc_final: 0.8316 (p) REVERT: A 226 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7892 (mt-10) REVERT: B 244 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8399 (mt) REVERT: B 351 LEU cc_start: 0.8605 (OUTLIER) cc_final: 0.8373 (mm) REVERT: B 455 LYS cc_start: 0.6392 (mmmt) cc_final: 0.6108 (mtmt) REVERT: B 474 MET cc_start: 0.8081 (mtp) cc_final: 0.7829 (mtm) REVERT: C 174 ILE cc_start: 0.6772 (OUTLIER) cc_final: 0.6391 (tp) outliers start: 26 outliers final: 16 residues processed: 159 average time/residue: 0.0731 time to fit residues: 17.3106 Evaluate side-chains 143 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 ASN Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 174 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 105 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 7 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.140079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.115556 restraints weight = 17594.318| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.57 r_work: 0.3457 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10142 Z= 0.119 Angle : 0.543 7.378 13757 Z= 0.271 Chirality : 0.040 0.166 1564 Planarity : 0.004 0.035 1767 Dihedral : 3.828 18.082 1339 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.63 % Allowed : 18.87 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.25), residues: 1233 helix: 1.65 (0.19), residues: 816 sheet: -0.74 (0.72), residues: 53 loop : -0.47 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 89 TYR 0.010 0.001 TYR A 495 PHE 0.025 0.001 PHE B 396 TRP 0.010 0.001 TRP A 417 HIS 0.003 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00279 (10142) covalent geometry : angle 0.54322 (13757) hydrogen bonds : bond 0.03019 ( 574) hydrogen bonds : angle 4.04736 ( 1683) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 195 VAL cc_start: 0.8702 (m) cc_final: 0.8329 (p) REVERT: A 226 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7913 (mt-10) REVERT: A 487 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8468 (mp) REVERT: B 244 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8392 (mt) REVERT: B 351 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8415 (mm) REVERT: B 474 MET cc_start: 0.8167 (mtp) cc_final: 0.7910 (mtm) REVERT: C 174 ILE cc_start: 0.6838 (OUTLIER) cc_final: 0.6484 (tp) outliers start: 29 outliers final: 19 residues processed: 154 average time/residue: 0.0709 time to fit residues: 16.7167 Evaluate side-chains 144 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 174 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 100 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 29 optimal weight: 0.0670 chunk 24 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 106 optimal weight: 0.7980 chunk 73 optimal weight: 0.8980 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 168 GLN ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.141120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.116518 restraints weight = 17723.592| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.62 r_work: 0.3468 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10142 Z= 0.105 Angle : 0.541 7.830 13757 Z= 0.268 Chirality : 0.039 0.173 1564 Planarity : 0.004 0.034 1767 Dihedral : 3.766 17.983 1339 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.09 % Allowed : 19.96 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.42 (0.25), residues: 1233 helix: 1.70 (0.19), residues: 814 sheet: -0.61 (0.74), residues: 53 loop : -0.47 (0.34), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 89 TYR 0.010 0.001 TYR A 426 PHE 0.023 0.001 PHE B 396 TRP 0.010 0.001 TRP A 417 HIS 0.004 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00239 (10142) covalent geometry : angle 0.54074 (13757) hydrogen bonds : bond 0.02825 ( 574) hydrogen bonds : angle 4.00905 ( 1683) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 195 VAL cc_start: 0.8630 (m) cc_final: 0.8261 (p) REVERT: A 277 GLU cc_start: 0.8226 (tp30) cc_final: 0.7568 (tp30) REVERT: A 487 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8429 (mp) REVERT: B 244 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8396 (mt) REVERT: B 351 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8328 (mm) REVERT: B 474 MET cc_start: 0.8255 (mtp) cc_final: 0.7977 (mtm) REVERT: C 174 ILE cc_start: 0.6876 (OUTLIER) cc_final: 0.6515 (tp) outliers start: 23 outliers final: 16 residues processed: 156 average time/residue: 0.0693 time to fit residues: 16.5475 Evaluate side-chains 144 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 174 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 56 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 81 optimal weight: 0.3980 chunk 58 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.140851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.116551 restraints weight = 17636.339| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.55 r_work: 0.3468 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10142 Z= 0.113 Angle : 0.547 8.191 13757 Z= 0.272 Chirality : 0.040 0.166 1564 Planarity : 0.003 0.034 1767 Dihedral : 3.768 17.699 1339 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.90 % Allowed : 19.87 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.25), residues: 1233 helix: 1.63 (0.19), residues: 818 sheet: -0.58 (0.75), residues: 53 loop : -0.47 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 89 TYR 0.011 0.001 TYR A 426 PHE 0.037 0.001 PHE B 396 TRP 0.010 0.001 TRP A 417 HIS 0.003 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00267 (10142) covalent geometry : angle 0.54709 (13757) hydrogen bonds : bond 0.02875 ( 574) hydrogen bonds : angle 4.00698 ( 1683) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: A 195 VAL cc_start: 0.8616 (m) cc_final: 0.8273 (p) REVERT: A 277 GLU cc_start: 0.8193 (tp30) cc_final: 0.7558 (tp30) REVERT: A 487 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8428 (mp) REVERT: B 244 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8418 (mt) REVERT: B 351 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8353 (mm) REVERT: B 474 MET cc_start: 0.8049 (mtp) cc_final: 0.7810 (mtm) REVERT: C 66 MET cc_start: 0.8536 (mmm) cc_final: 0.8312 (mmp) REVERT: C 174 ILE cc_start: 0.6952 (OUTLIER) cc_final: 0.6642 (tp) outliers start: 32 outliers final: 21 residues processed: 156 average time/residue: 0.0729 time to fit residues: 17.6995 Evaluate side-chains 147 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 174 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 16 optimal weight: 0.9990 chunk 121 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 104 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 7 optimal weight: 8.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.140107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.115618 restraints weight = 17514.581| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.57 r_work: 0.3458 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10142 Z= 0.123 Angle : 0.560 8.679 13757 Z= 0.278 Chirality : 0.040 0.171 1564 Planarity : 0.004 0.036 1767 Dihedral : 3.820 17.710 1339 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.63 % Allowed : 20.51 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.25), residues: 1233 helix: 1.61 (0.19), residues: 819 sheet: -0.68 (0.75), residues: 53 loop : -0.45 (0.34), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 253 TYR 0.012 0.001 TYR A 426 PHE 0.032 0.001 PHE B 396 TRP 0.010 0.001 TRP A 417 HIS 0.004 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00295 (10142) covalent geometry : angle 0.55975 (13757) hydrogen bonds : bond 0.02973 ( 574) hydrogen bonds : angle 4.00757 ( 1683) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: A 195 VAL cc_start: 0.8636 (m) cc_final: 0.8304 (p) REVERT: A 277 GLU cc_start: 0.8219 (tp30) cc_final: 0.7603 (tp30) REVERT: A 487 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8469 (mp) REVERT: B 174 MET cc_start: 0.7195 (tmm) cc_final: 0.6965 (tmm) REVERT: B 226 PHE cc_start: 0.5204 (t80) cc_final: 0.4999 (t80) REVERT: B 244 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8398 (mt) REVERT: B 351 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8385 (mm) REVERT: B 474 MET cc_start: 0.8033 (mtp) cc_final: 0.7793 (mtm) REVERT: C 174 ILE cc_start: 0.6967 (OUTLIER) cc_final: 0.6649 (tp) outliers start: 29 outliers final: 24 residues processed: 145 average time/residue: 0.0757 time to fit residues: 17.0333 Evaluate side-chains 148 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 174 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 113 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 64 optimal weight: 0.0980 chunk 9 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.141498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.116784 restraints weight = 17701.089| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.60 r_work: 0.3475 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10142 Z= 0.109 Angle : 0.559 9.082 13757 Z= 0.278 Chirality : 0.039 0.171 1564 Planarity : 0.004 0.035 1767 Dihedral : 3.774 17.589 1339 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.63 % Allowed : 20.87 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.25), residues: 1233 helix: 1.63 (0.19), residues: 823 sheet: -0.76 (0.74), residues: 53 loop : -0.41 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 253 TYR 0.014 0.001 TYR A 426 PHE 0.030 0.001 PHE B 396 TRP 0.011 0.001 TRP A 417 HIS 0.005 0.001 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00258 (10142) covalent geometry : angle 0.55920 (13757) hydrogen bonds : bond 0.02804 ( 574) hydrogen bonds : angle 3.94310 ( 1683) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 136 time to evaluate : 0.359 Fit side-chains revert: symmetry clash REVERT: A 195 VAL cc_start: 0.8601 (m) cc_final: 0.8269 (p) REVERT: A 277 GLU cc_start: 0.8166 (tp30) cc_final: 0.7607 (tp30) REVERT: A 350 MET cc_start: 0.7661 (mtt) cc_final: 0.6991 (mtt) REVERT: A 487 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8431 (mp) REVERT: B 174 MET cc_start: 0.7118 (tmm) cc_final: 0.6868 (tmm) REVERT: B 244 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8409 (mt) REVERT: B 317 GLU cc_start: 0.7107 (tp30) cc_final: 0.6790 (tp30) REVERT: B 351 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8345 (mm) REVERT: B 474 MET cc_start: 0.8009 (mtp) cc_final: 0.7771 (mtm) REVERT: C 174 ILE cc_start: 0.7030 (OUTLIER) cc_final: 0.6718 (tp) outliers start: 29 outliers final: 24 residues processed: 158 average time/residue: 0.0751 time to fit residues: 18.4265 Evaluate side-chains 151 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 244 LEU Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 351 LEU Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 174 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 65 optimal weight: 2.9990 chunk 122 optimal weight: 0.5980 chunk 94 optimal weight: 5.9990 chunk 30 optimal weight: 0.3980 chunk 78 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 5 optimal weight: 0.0030 chunk 43 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 GLN ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.141866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.117563 restraints weight = 17440.447| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.55 r_work: 0.3486 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10142 Z= 0.106 Angle : 0.566 9.433 13757 Z= 0.280 Chirality : 0.039 0.178 1564 Planarity : 0.004 0.035 1767 Dihedral : 3.746 17.572 1339 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.45 % Allowed : 21.23 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.25), residues: 1233 helix: 1.62 (0.19), residues: 825 sheet: -0.97 (0.73), residues: 53 loop : -0.41 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 253 TYR 0.024 0.001 TYR A 426 PHE 0.030 0.001 PHE B 396 TRP 0.011 0.001 TRP A 417 HIS 0.005 0.000 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00244 (10142) covalent geometry : angle 0.56603 (13757) hydrogen bonds : bond 0.02785 ( 574) hydrogen bonds : angle 3.94620 ( 1683) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2466 Ramachandran restraints generated. 1233 Oldfield, 0 Emsley, 1233 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.399 Fit side-chains revert: symmetry clash REVERT: A 195 VAL cc_start: 0.8644 (m) cc_final: 0.8308 (p) REVERT: A 277 GLU cc_start: 0.8035 (tp30) cc_final: 0.7542 (tp30) REVERT: A 350 MET cc_start: 0.7832 (mtt) cc_final: 0.7189 (mtt) REVERT: A 487 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8412 (mp) REVERT: B 174 MET cc_start: 0.7105 (tmm) cc_final: 0.6860 (tmm) REVERT: B 317 GLU cc_start: 0.7062 (tp30) cc_final: 0.6781 (tp30) REVERT: B 474 MET cc_start: 0.8092 (mtp) cc_final: 0.7856 (mtm) REVERT: C 174 ILE cc_start: 0.7055 (OUTLIER) cc_final: 0.6789 (tp) outliers start: 27 outliers final: 23 residues processed: 151 average time/residue: 0.0775 time to fit residues: 17.9818 Evaluate side-chains 150 residues out of total 1105 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ILE Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 67 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 208 MET Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 289 ASN Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 563 ILE Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 139 LEU Chi-restraints excluded: chain B residue 240 VAL Chi-restraints excluded: chain B residue 350 PHE Chi-restraints excluded: chain B residue 358 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 174 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 50 optimal weight: 0.7980 chunk 61 optimal weight: 0.0170 chunk 89 optimal weight: 4.9990 chunk 90 optimal weight: 0.0770 chunk 70 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 108 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN ** B 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 241 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.141848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.117517 restraints weight = 17587.060| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.57 r_work: 0.3481 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10142 Z= 0.131 Angle : 0.853 59.165 13757 Z= 0.491 Chirality : 0.042 0.634 1564 Planarity : 0.004 0.035 1767 Dihedral : 3.893 38.547 1339 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.68 % Favored : 97.24 % Rotamer: Outliers : 2.27 % Allowed : 21.32 % Favored : 76.41 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.25), residues: 1233 helix: 1.61 (0.19), residues: 825 sheet: -0.99 (0.73), residues: 53 loop : -0.41 (0.34), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 253 TYR 0.020 0.001 TYR A 426 PHE 0.028 0.001 PHE B 396 TRP 0.010 0.001 TRP A 417 HIS 0.004 0.000 HIS B 293 Details of bonding type rmsd covalent geometry : bond 0.00272 (10142) covalent geometry : angle 0.85291 (13757) hydrogen bonds : bond 0.03023 ( 574) hydrogen bonds : angle 3.96260 ( 1683) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1979.38 seconds wall clock time: 34 minutes 40.65 seconds (2080.65 seconds total)