Starting phenix.real_space_refine on Sat Aug 23 00:38:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t8e_41097/08_2025/8t8e_41097.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t8e_41097/08_2025/8t8e_41097.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8t8e_41097/08_2025/8t8e_41097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t8e_41097/08_2025/8t8e_41097.map" model { file = "/net/cci-nas-00/data/ceres_data/8t8e_41097/08_2025/8t8e_41097.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t8e_41097/08_2025/8t8e_41097.cif" } 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= 0.062 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 5634 2.51 5 N 1463 2.21 5 O 1613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s 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: 8755 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2703 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 341} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 3966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 488, 3966 Classifications: {'peptide': 488} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 20, 'TRANS': 467} Chain breaks: 4 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 2086 Classifications: {'peptide': 249} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 243} Chain breaks: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASP:plan': 4, 'TYR:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 1.79, per 1000 atoms: 0.20 Number of scatterers: 8755 At special positions: 0 Unit cell: (92.568, 81.928, 148.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 1613 8.00 N 1463 7.00 C 5634 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: 0.46 Conformation dependent library (CDL) restraints added in 294.6 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2086 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 3 sheets defined 50.1% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 114 through 125 removed outlier: 3.780A pdb=" N LEU A 119 " --> pdb=" O LYS A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 removed outlier: 3.922A pdb=" N PHE A 169 " --> pdb=" O GLN A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 removed outlier: 3.582A pdb=" N ILE A 204 " --> pdb=" O LYS A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 231 removed outlier: 3.725A pdb=" N PHE A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 247 removed outlier: 3.618A pdb=" N LYS A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N TYR A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N SER A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 951 through 959 Processing helix chain 'A' and resid 960 through 966 removed outlier: 3.527A pdb=" N TYR A 964 " --> pdb=" O ARG A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 981 removed outlier: 3.639A pdb=" N ASP A 978 " --> pdb=" O ASP A 974 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE A 979 " --> pdb=" O ALA A 975 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1020 through 1037 removed outlier: 3.622A pdb=" N LYS A1024 " --> pdb=" O SER A1020 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TRP A1036 " --> pdb=" O LEU A1032 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LYS A1037 " --> pdb=" O LEU A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1054 through 1071 removed outlier: 3.975A pdb=" N ILE A1060 " --> pdb=" O VAL A1056 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ASP A1071 " --> pdb=" O LYS A1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 41 removed outlier: 3.505A pdb=" N LEU C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN C 36 " --> pdb=" O PHE C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 53 removed outlier: 3.605A pdb=" N VAL C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 76 Processing helix chain 'C' and resid 84 through 91 removed outlier: 4.456A pdb=" N ASP C 91 " --> pdb=" O LEU C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 109 removed outlier: 3.531A pdb=" N ARG C 103 " --> pdb=" O THR C 99 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 105 " --> pdb=" O SER C 101 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS C 106 " --> pdb=" O ARG C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 116 removed outlier: 3.682A pdb=" N LEU C 115 " --> pdb=" O TYR C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 140 removed outlier: 3.566A pdb=" N ARG C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 209 removed outlier: 3.765A pdb=" N ASN C 209 " --> pdb=" O ASN C 205 " (cutoff:3.500A) Processing helix chain 'C' and resid 215 through 224 Processing helix chain 'C' and resid 229 through 234 Processing helix chain 'C' and resid 235 through 237 No H-bonds generated for 'chain 'C' and resid 235 through 237' Processing helix chain 'C' and resid 240 through 259 removed outlier: 3.618A pdb=" N ILE C 246 " --> pdb=" O PRO C 242 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLN C 255 " --> pdb=" O PHE C 251 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ASP C 256 " --> pdb=" O SER C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 273 Processing helix chain 'C' and resid 274 through 276 No H-bonds generated for 'chain 'C' and resid 274 through 276' Processing helix chain 'C' and resid 279 through 287 removed outlier: 3.632A pdb=" N PHE C 285 " --> pdb=" O LEU C 281 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 301 removed outlier: 3.665A pdb=" N VAL C 301 " --> pdb=" O PHE C 297 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 347 removed outlier: 3.529A pdb=" N LYS C 346 " --> pdb=" O TYR C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 356 removed outlier: 3.587A pdb=" N ARG C 351 " --> pdb=" O SER C 347 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS C 353 " --> pdb=" O ALA C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 392 removed outlier: 3.592A pdb=" N PHE C 392 " --> pdb=" O LEU C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 403 Processing helix chain 'C' and resid 413 through 430 removed outlier: 5.145A pdb=" N GLU C 419 " --> pdb=" O PRO C 415 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU C 424 " --> pdb=" O GLY C 420 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS C 427 " --> pdb=" O SER C 423 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ASP C 428 " --> pdb=" O GLU C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 442 Processing helix chain 'C' and resid 444 through 458 Processing helix chain 'C' and resid 471 through 497 removed outlier: 3.925A pdb=" N LEU C 477 " --> pdb=" O GLU C 473 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP C 483 " --> pdb=" O ILE C 479 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 484 " --> pdb=" O GLU C 480 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N CYS C 485 " --> pdb=" O LYS C 481 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LEU C 486 " --> pdb=" O CYS C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 506 through 528 Processing helix chain 'C' and resid 538 through 547 removed outlier: 4.033A pdb=" N VAL C 542 " --> pdb=" O LEU C 538 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN C 544 " --> pdb=" O PRO C 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 220 Processing helix chain 'B' and resid 245 through 254 Processing helix chain 'B' and resid 270 through 274 removed outlier: 3.842A pdb=" N ARG B 274 " --> pdb=" O GLU B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 292 removed outlier: 3.508A pdb=" N LYS B 289 " --> pdb=" O ASN B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 300 through 316 Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.795A pdb=" N LEU B 337 " --> pdb=" O LYS B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 346 removed outlier: 3.524A pdb=" N SER B 346 " --> pdb=" O HIS B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 363 removed outlier: 3.783A pdb=" N TYR B 360 " --> pdb=" O PHE B 356 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG B 361 " --> pdb=" O PHE B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 364 through 365 No H-bonds generated for 'chain 'B' and resid 364 through 365' Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 369 through 378 removed outlier: 3.905A pdb=" N LEU B 374 " --> pdb=" O GLN B 370 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG B 375 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 398 removed outlier: 3.741A pdb=" N ILE B 393 " --> pdb=" O GLN B 389 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLU B 398 " --> pdb=" O LYS B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 416 removed outlier: 3.560A pdb=" N MET B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 440 removed outlier: 4.070A pdb=" N ILE B 440 " --> pdb=" O CYS B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 460 Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 99 removed outlier: 6.737A pdb=" N HIS A 155 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N VAL A 85 " --> pdb=" O ILE A 153 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ILE A 153 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LEU A 87 " --> pdb=" O LYS A 151 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LYS A 151 " --> pdb=" O LEU A 87 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A 154 " --> pdb=" O VAL A 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 989 through 995 Processing sheet with id=AA3, first strand: chain 'A' and resid 1043 through 1044 295 hydrogen bonds defined for protein. 858 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: 0.82 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1759 1.33 - 1.45: 2062 1.45 - 1.57: 5036 1.57 - 1.69: 0 1.69 - 1.81: 66 Bond restraints: 8923 Sorted by residual: bond pdb=" C HIS B 240 " pdb=" O HIS B 240 " ideal model delta sigma weight residual 1.235 1.208 0.028 1.13e-02 7.83e+03 6.02e+00 bond pdb=" CA LEU C 538 " pdb=" C LEU C 538 " ideal model delta sigma weight residual 1.523 1.504 0.020 8.40e-03 1.42e+04 5.39e+00 bond pdb=" N HIS B 240 " pdb=" CA HIS B 240 " ideal model delta sigma weight residual 1.460 1.434 0.026 1.17e-02 7.31e+03 4.79e+00 bond pdb=" C PHE A 211 " pdb=" O PHE A 211 " ideal model delta sigma weight residual 1.235 1.217 0.018 1.26e-02 6.30e+03 2.10e+00 bond pdb=" CA TYR C 539 " pdb=" C TYR C 539 " ideal model delta sigma weight residual 1.524 1.542 -0.018 1.26e-02 6.30e+03 2.09e+00 ... (remaining 8918 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 11880 2.58 - 5.16: 130 5.16 - 7.74: 11 7.74 - 10.32: 3 10.32 - 12.90: 1 Bond angle restraints: 12025 Sorted by residual: angle pdb=" N TYR C 539 " pdb=" CA TYR C 539 " pdb=" C TYR C 539 " ideal model delta sigma weight residual 109.81 122.71 -12.90 2.21e+00 2.05e-01 3.41e+01 angle pdb=" N ILE C 68 " pdb=" CA ILE C 68 " pdb=" C ILE C 68 " ideal model delta sigma weight residual 112.29 106.90 5.39 9.40e-01 1.13e+00 3.29e+01 angle pdb=" N ILE B 437 " pdb=" CA ILE B 437 " pdb=" C ILE B 437 " ideal model delta sigma weight residual 111.91 107.25 4.66 8.90e-01 1.26e+00 2.74e+01 angle pdb=" N ILE B 450 " pdb=" CA ILE B 450 " pdb=" C ILE B 450 " ideal model delta sigma weight residual 113.71 108.78 4.93 9.50e-01 1.11e+00 2.69e+01 angle pdb=" N GLU A 968 " pdb=" CA GLU A 968 " pdb=" C GLU A 968 " ideal model delta sigma weight residual 112.94 107.11 5.83 1.41e+00 5.03e-01 1.71e+01 ... (remaining 12020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 4585 17.05 - 34.10: 607 34.10 - 51.15: 180 51.15 - 68.20: 20 68.20 - 85.26: 11 Dihedral angle restraints: 5403 sinusoidal: 2202 harmonic: 3201 Sorted by residual: dihedral pdb=" CA LYS C 308 " pdb=" C LYS C 308 " pdb=" N LEU C 309 " pdb=" CA LEU C 309 " ideal model delta harmonic sigma weight residual 180.00 -154.19 -25.81 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA TRP B 200 " pdb=" C TRP B 200 " pdb=" N HIS B 201 " pdb=" CA HIS B 201 " ideal model delta harmonic sigma weight residual 180.00 158.44 21.56 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA TYR B 347 " pdb=" C TYR B 347 " pdb=" N PHE B 348 " pdb=" CA PHE B 348 " ideal model delta harmonic sigma weight residual 180.00 158.75 21.25 0 5.00e+00 4.00e-02 1.81e+01 ... (remaining 5400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1271 0.085 - 0.169: 83 0.169 - 0.253: 2 0.253 - 0.338: 0 0.338 - 0.422: 1 Chirality restraints: 1357 Sorted by residual: chirality pdb=" CA TYR C 539 " pdb=" N TYR C 539 " pdb=" C TYR C 539 " pdb=" CB TYR C 539 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.46e+00 chirality pdb=" CA SER A 212 " pdb=" N SER A 212 " pdb=" C SER A 212 " pdb=" CB SER A 212 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA LYS A 987 " pdb=" N LYS A 987 " pdb=" C LYS A 987 " pdb=" CB LYS A 987 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.95e-01 ... (remaining 1354 not shown) Planarity restraints: 1525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A 210 " -0.015 2.00e-02 2.50e+03 3.13e-02 9.77e+00 pdb=" C TYR A 210 " 0.054 2.00e-02 2.50e+03 pdb=" O TYR A 210 " -0.020 2.00e-02 2.50e+03 pdb=" N PHE A 211 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 77 " -0.036 5.00e-02 4.00e+02 5.59e-02 4.99e+00 pdb=" N PRO A 78 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 78 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 78 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR B 444 " 0.011 2.00e-02 2.50e+03 2.10e-02 4.39e+00 pdb=" C THR B 444 " -0.036 2.00e-02 2.50e+03 pdb=" O THR B 444 " 0.014 2.00e-02 2.50e+03 pdb=" N THR B 445 " 0.012 2.00e-02 2.50e+03 ... (remaining 1522 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 775 2.74 - 3.28: 8893 3.28 - 3.82: 13661 3.82 - 4.36: 16897 4.36 - 4.90: 28621 Nonbonded interactions: 68847 Sorted by model distance: nonbonded pdb=" OE1 GLN C 255 " pdb=" OG SER C 279 " model vdw 2.199 3.040 nonbonded pdb=" O ALA A 259 " pdb=" ND1 HIS A 263 " model vdw 2.214 3.120 nonbonded pdb=" OH TYR C 81 " pdb=" O GLU C 325 " model vdw 2.215 3.040 nonbonded pdb=" NZ LYS C 400 " pdb=" OG1 THR B 220 " model vdw 2.220 3.120 nonbonded pdb=" O GLU C 23 " pdb=" OH TYR C 126 " model vdw 2.247 3.040 ... (remaining 68842 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.740 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 0.029 8923 Z= 0.160 Angle : 0.694 12.904 12025 Z= 0.398 Chirality : 0.045 0.422 1357 Planarity : 0.004 0.056 1525 Dihedral : 16.794 85.255 3317 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.95 % Favored : 90.86 % Rotamer: Outliers : 1.03 % Allowed : 26.77 % Favored : 72.21 % 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: -3.74 (0.24), residues: 1061 helix: -2.29 (0.20), residues: 539 sheet: -2.02 (0.64), residues: 75 loop : -2.67 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 177 TYR 0.026 0.002 TYR B 295 PHE 0.014 0.001 PHE A1049 TRP 0.006 0.001 TRP B 200 HIS 0.013 0.001 HIS C 513 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 8923) covalent geometry : angle 0.69383 (12025) hydrogen bonds : bond 0.24334 ( 295) hydrogen bonds : angle 8.59001 ( 858) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 115 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 PHE cc_start: 0.7718 (OUTLIER) cc_final: 0.7503 (m-80) REVERT: C 545 MET cc_start: 0.8568 (ttm) cc_final: 0.8328 (mtp) outliers start: 10 outliers final: 2 residues processed: 120 average time/residue: 0.0777 time to fit residues: 13.3338 Evaluate side-chains 113 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 110 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain C residue 273 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.2980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 954 HIS ** C 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 513 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 = 0.4132 r_free = 0.4132 target = 0.174028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.129944 restraints weight = 10951.374| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.46 r_work: 0.3381 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8923 Z= 0.154 Angle : 0.607 7.315 12025 Z= 0.318 Chirality : 0.043 0.154 1357 Planarity : 0.004 0.047 1525 Dihedral : 5.291 26.100 1167 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer: Outliers : 3.08 % Allowed : 24.82 % Favored : 72.10 % 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: -3.28 (0.24), residues: 1061 helix: -1.82 (0.21), residues: 537 sheet: -2.29 (0.59), residues: 75 loop : -2.48 (0.27), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 195 TYR 0.014 0.002 TYR C 539 PHE 0.017 0.002 PHE A 973 TRP 0.011 0.001 TRP C 220 HIS 0.004 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 8923) covalent geometry : angle 0.60729 (12025) hydrogen bonds : bond 0.04245 ( 295) hydrogen bonds : angle 5.15555 ( 858) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 GLU cc_start: 0.8036 (mm-30) cc_final: 0.7774 (mm-30) REVERT: B 328 HIS cc_start: 0.6850 (OUTLIER) cc_final: 0.6531 (m-70) REVERT: B 361 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7786 (ttp-110) outliers start: 30 outliers final: 16 residues processed: 148 average time/residue: 0.0653 time to fit residues: 14.3948 Evaluate side-chains 129 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 307 TYR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain B residue 200 TRP Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 361 ARG Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 456 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 64 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 8 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 52 optimal weight: 0.0050 chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.174779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.133132 restraints weight = 10885.910| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.37 r_work: 0.3422 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8923 Z= 0.136 Angle : 0.577 7.486 12025 Z= 0.298 Chirality : 0.042 0.155 1357 Planarity : 0.003 0.044 1525 Dihedral : 5.038 25.625 1163 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 4.41 % Allowed : 24.21 % Favored : 71.38 % 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: -2.92 (0.24), residues: 1061 helix: -1.34 (0.22), residues: 540 sheet: -2.32 (0.59), residues: 75 loop : -2.54 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 195 TYR 0.017 0.001 TYR A 81 PHE 0.014 0.001 PHE A 973 TRP 0.011 0.001 TRP C 220 HIS 0.012 0.001 HIS C 513 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 8923) covalent geometry : angle 0.57714 (12025) hydrogen bonds : bond 0.03662 ( 295) hydrogen bonds : angle 4.65984 ( 858) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 122 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.3078 (OUTLIER) cc_final: 0.2683 (mp) REVERT: B 210 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7622 (mm-30) REVERT: B 328 HIS cc_start: 0.6811 (OUTLIER) cc_final: 0.6487 (m-70) outliers start: 43 outliers final: 24 residues processed: 157 average time/residue: 0.0848 time to fit residues: 19.5925 Evaluate side-chains 136 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 307 TYR Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain B residue 200 TRP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 456 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 88 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 chunk 73 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 85 optimal weight: 0.1980 chunk 82 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 183 ASN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 389 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.170777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.127655 restraints weight = 11106.962| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.53 r_work: 0.3336 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8923 Z= 0.226 Angle : 0.656 10.437 12025 Z= 0.334 Chirality : 0.045 0.161 1357 Planarity : 0.004 0.042 1525 Dihedral : 5.348 25.150 1163 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 5.13 % Allowed : 24.62 % Favored : 70.26 % 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: -2.92 (0.24), residues: 1061 helix: -1.35 (0.22), residues: 540 sheet: -2.38 (0.57), residues: 75 loop : -2.50 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 980 TYR 0.016 0.002 TYR A 258 PHE 0.025 0.002 PHE C 258 TRP 0.008 0.001 TRP C 220 HIS 0.007 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00548 ( 8923) covalent geometry : angle 0.65554 (12025) hydrogen bonds : bond 0.04010 ( 295) hydrogen bonds : angle 4.75562 ( 858) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 106 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 92 CYS cc_start: 0.8284 (OUTLIER) cc_final: 0.7991 (m) REVERT: A 256 LEU cc_start: 0.3142 (OUTLIER) cc_final: 0.2887 (mp) REVERT: C 479 ILE cc_start: 0.8955 (tp) cc_final: 0.8615 (tp) REVERT: C 511 MET cc_start: 0.8215 (tmm) cc_final: 0.7693 (tmm) REVERT: C 537 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8003 (tp) REVERT: B 210 GLU cc_start: 0.7893 (mm-30) cc_final: 0.7679 (mm-30) REVERT: B 238 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.7322 (m-80) REVERT: B 316 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.7681 (pp) REVERT: B 328 HIS cc_start: 0.6977 (OUTLIER) cc_final: 0.6479 (m-70) outliers start: 50 outliers final: 31 residues processed: 148 average time/residue: 0.0870 time to fit residues: 18.6968 Evaluate side-chains 135 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 98 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1057 ASN Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 246 ILE Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 307 TYR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 478 ASN Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain B residue 200 TRP Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 238 PHE Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 267 TYR Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 456 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 90 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 52 optimal weight: 0.0670 chunk 57 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 102 optimal weight: 0.3980 chunk 54 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 508 GLN ** C 513 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 ASN B 389 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.176432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.134160 restraints weight = 10956.395| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 2.63 r_work: 0.3414 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8923 Z= 0.114 Angle : 0.553 8.328 12025 Z= 0.286 Chirality : 0.041 0.157 1357 Planarity : 0.003 0.041 1525 Dihedral : 4.898 25.429 1163 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 4.62 % Allowed : 25.74 % Favored : 69.64 % 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: -2.70 (0.25), residues: 1061 helix: -1.09 (0.22), residues: 550 sheet: -2.26 (0.57), residues: 75 loop : -2.56 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 195 TYR 0.011 0.001 TYR C 412 PHE 0.018 0.001 PHE C 258 TRP 0.011 0.001 TRP C 220 HIS 0.017 0.001 HIS C 513 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 8923) covalent geometry : angle 0.55326 (12025) hydrogen bonds : bond 0.03108 ( 295) hydrogen bonds : angle 4.31706 ( 858) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 122 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 508 GLN cc_start: 0.6970 (mt0) cc_final: 0.6384 (pt0) REVERT: C 537 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7872 (tp) REVERT: B 316 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7618 (pt) REVERT: B 328 HIS cc_start: 0.6756 (OUTLIER) cc_final: 0.6461 (m-70) outliers start: 45 outliers final: 26 residues processed: 160 average time/residue: 0.0868 time to fit residues: 20.1821 Evaluate side-chains 138 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 307 TYR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain B residue 200 TRP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 255 VAL Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 351 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 32 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 35 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 58 optimal weight: 0.0570 chunk 53 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 518 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.176158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.134210 restraints weight = 10971.871| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.63 r_work: 0.3416 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8923 Z= 0.125 Angle : 0.557 7.762 12025 Z= 0.288 Chirality : 0.041 0.156 1357 Planarity : 0.003 0.041 1525 Dihedral : 4.833 25.394 1163 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.82 % Favored : 92.18 % Rotamer: Outliers : 4.82 % Allowed : 26.46 % Favored : 68.72 % 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: -2.58 (0.25), residues: 1061 helix: -1.00 (0.22), residues: 549 sheet: -2.19 (0.58), residues: 75 loop : -2.47 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 230 TYR 0.020 0.001 TYR A 81 PHE 0.016 0.001 PHE C 258 TRP 0.010 0.001 TRP C 220 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8923) covalent geometry : angle 0.55721 (12025) hydrogen bonds : bond 0.03214 ( 295) hydrogen bonds : angle 4.25617 ( 858) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 119 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 CYS cc_start: 0.8250 (OUTLIER) cc_final: 0.8045 (m) REVERT: C 78 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7418 (pp) REVERT: C 537 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7863 (tp) REVERT: B 316 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7666 (pt) REVERT: B 328 HIS cc_start: 0.6787 (OUTLIER) cc_final: 0.6467 (m-70) outliers start: 47 outliers final: 28 residues processed: 158 average time/residue: 0.0815 time to fit residues: 18.9449 Evaluate side-chains 145 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 112 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1033 LEU Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 307 TYR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain B residue 200 TRP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 267 TYR Chi-restraints excluded: chain B residue 269 LYS Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 52 optimal weight: 0.0270 chunk 69 optimal weight: 2.9990 chunk 71 optimal weight: 0.0010 chunk 89 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 6 optimal weight: 0.0030 chunk 102 optimal weight: 0.8980 chunk 70 optimal weight: 0.4980 chunk 77 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 508 GLN B 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.178881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.135604 restraints weight = 10878.570| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.44 r_work: 0.3456 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8923 Z= 0.103 Angle : 0.540 7.346 12025 Z= 0.281 Chirality : 0.040 0.155 1357 Planarity : 0.003 0.042 1525 Dihedral : 4.623 24.722 1163 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 4.21 % Allowed : 26.87 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.38 (0.25), residues: 1061 helix: -0.83 (0.22), residues: 555 sheet: -1.97 (0.59), residues: 75 loop : -2.44 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 230 TYR 0.020 0.001 TYR A 81 PHE 0.015 0.001 PHE C 258 TRP 0.012 0.001 TRP C 220 HIS 0.003 0.001 HIS A 954 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 8923) covalent geometry : angle 0.54025 (12025) hydrogen bonds : bond 0.02906 ( 295) hydrogen bonds : angle 4.08254 ( 858) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 125 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 CYS cc_start: 0.8330 (OUTLIER) cc_final: 0.7984 (m) REVERT: C 78 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7310 (pp) REVERT: C 483 ASP cc_start: 0.8243 (m-30) cc_final: 0.7989 (m-30) REVERT: C 537 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8014 (tp) REVERT: B 316 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7452 (pt) REVERT: B 317 ASP cc_start: 0.7919 (p0) cc_final: 0.7680 (p0) REVERT: B 328 HIS cc_start: 0.6704 (OUTLIER) cc_final: 0.6440 (m-70) REVERT: B 456 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8150 (mt) outliers start: 41 outliers final: 26 residues processed: 159 average time/residue: 0.0846 time to fit residues: 19.7161 Evaluate side-chains 150 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 307 TYR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain B residue 200 TRP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 316 LEU Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 456 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 78 optimal weight: 10.0000 chunk 101 optimal weight: 0.1980 chunk 58 optimal weight: 0.0050 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 81 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 96 optimal weight: 0.0040 overall best weight: 0.3406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 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 = 0.4179 r_free = 0.4179 target = 0.178983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.136120 restraints weight = 10830.091| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.39 r_work: 0.3452 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8923 Z= 0.107 Angle : 0.546 8.009 12025 Z= 0.281 Chirality : 0.041 0.180 1357 Planarity : 0.003 0.041 1525 Dihedral : 4.527 24.040 1163 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.41 % Allowed : 27.28 % Favored : 68.31 % 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: -2.19 (0.25), residues: 1061 helix: -0.69 (0.22), residues: 554 sheet: -1.95 (0.60), residues: 75 loop : -2.31 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 230 TYR 0.021 0.001 TYR A 81 PHE 0.014 0.001 PHE C 258 TRP 0.015 0.001 TRP C 220 HIS 0.005 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00241 ( 8923) covalent geometry : angle 0.54573 (12025) hydrogen bonds : bond 0.02953 ( 295) hydrogen bonds : angle 4.02097 ( 858) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 120 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 CYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8079 (m) REVERT: C 78 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7361 (pp) REVERT: C 483 ASP cc_start: 0.8257 (m-30) cc_final: 0.7957 (m-30) REVERT: C 537 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8019 (tp) REVERT: B 317 ASP cc_start: 0.7960 (p0) cc_final: 0.7688 (p0) REVERT: B 328 HIS cc_start: 0.6705 (OUTLIER) cc_final: 0.6462 (m-70) REVERT: B 456 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8172 (mt) outliers start: 43 outliers final: 31 residues processed: 155 average time/residue: 0.0849 time to fit residues: 19.3016 Evaluate side-chains 152 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 116 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 CYS Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 78 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 307 TYR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 537 LEU Chi-restraints excluded: chain B residue 200 TRP Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 456 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 68 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 5 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.168504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.126126 restraints weight = 11104.198| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.49 r_work: 0.3309 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 8923 Z= 0.345 Angle : 0.773 8.953 12025 Z= 0.390 Chirality : 0.050 0.215 1357 Planarity : 0.004 0.037 1525 Dihedral : 5.492 25.426 1163 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 4.21 % Allowed : 27.69 % Favored : 68.10 % 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: -2.79 (0.24), residues: 1061 helix: -1.27 (0.21), residues: 553 sheet: -2.16 (0.58), residues: 75 loop : -2.47 (0.28), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 980 TYR 0.025 0.003 TYR B 295 PHE 0.025 0.003 PHE B 202 TRP 0.011 0.002 TRP C 220 HIS 0.010 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00837 ( 8923) covalent geometry : angle 0.77328 (12025) hydrogen bonds : bond 0.04437 ( 295) hydrogen bonds : angle 4.80503 ( 858) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 115 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 26 GLU cc_start: 0.7594 (mm-30) cc_final: 0.7337 (mm-30) REVERT: C 511 MET cc_start: 0.8502 (tpp) cc_final: 0.8253 (tpp) REVERT: B 317 ASP cc_start: 0.8074 (p0) cc_final: 0.7656 (p0) REVERT: B 328 HIS cc_start: 0.6959 (OUTLIER) cc_final: 0.6375 (m-70) outliers start: 41 outliers final: 30 residues processed: 148 average time/residue: 0.0852 time to fit residues: 18.3673 Evaluate side-chains 140 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain A residue 1057 ASN Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 307 TYR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 361 LEU Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 257 GLN Chi-restraints excluded: chain B residue 267 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 456 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 102 optimal weight: 0.5980 chunk 1 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 201 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.175036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.132626 restraints weight = 10882.297| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.44 r_work: 0.3409 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8923 Z= 0.135 Angle : 0.617 9.806 12025 Z= 0.314 Chirality : 0.043 0.161 1357 Planarity : 0.003 0.035 1525 Dihedral : 5.045 24.315 1163 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 2.77 % Allowed : 29.44 % Favored : 67.79 % 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: -2.49 (0.25), residues: 1061 helix: -0.97 (0.22), residues: 559 sheet: -2.01 (0.59), residues: 75 loop : -2.43 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 375 TYR 0.020 0.001 TYR A 81 PHE 0.021 0.001 PHE A 96 TRP 0.011 0.002 TRP C 220 HIS 0.004 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8923) covalent geometry : angle 0.61695 (12025) hydrogen bonds : bond 0.03346 ( 295) hydrogen bonds : angle 4.35089 ( 858) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2122 Ramachandran restraints generated. 1061 Oldfield, 0 Emsley, 1061 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 113 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: B 328 HIS cc_start: 0.6745 (OUTLIER) cc_final: 0.6260 (m-70) outliers start: 27 outliers final: 25 residues processed: 134 average time/residue: 0.0829 time to fit residues: 16.1170 Evaluate side-chains 137 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 111 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 206 LEU Chi-restraints excluded: chain C residue 230 THR Chi-restraints excluded: chain C residue 259 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 307 TYR Chi-restraints excluded: chain C residue 330 ASP Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 267 TYR Chi-restraints excluded: chain B residue 284 VAL Chi-restraints excluded: chain B residue 315 ILE Chi-restraints excluded: chain B residue 328 HIS Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 416 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 78 optimal weight: 0.0570 chunk 101 optimal weight: 0.0040 chunk 1 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 overall best weight: 0.4110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.177648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.135722 restraints weight = 10781.259| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.46 r_work: 0.3449 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8923 Z= 0.116 Angle : 0.591 9.477 12025 Z= 0.299 Chirality : 0.041 0.156 1357 Planarity : 0.003 0.036 1525 Dihedral : 4.762 24.287 1163 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 3.18 % Allowed : 28.82 % Favored : 68.00 % 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: -2.28 (0.25), residues: 1061 helix: -0.73 (0.22), residues: 554 sheet: -1.98 (0.60), residues: 75 loop : -2.41 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 375 TYR 0.021 0.001 TYR A 81 PHE 0.016 0.001 PHE A 96 TRP 0.013 0.002 TRP B 200 HIS 0.003 0.001 HIS B 201 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8923) covalent geometry : angle 0.59092 (12025) hydrogen bonds : bond 0.03094 ( 295) hydrogen bonds : angle 4.17445 ( 858) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2017.18 seconds wall clock time: 35 minutes 33.96 seconds (2133.96 seconds total)