Starting phenix.real_space_refine on Thu Mar 13 09:58:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t8e_41097/03_2025/8t8e_41097.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t8e_41097/03_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_41097/03_2025/8t8e_41097.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t8e_41097/03_2025/8t8e_41097.map" model { file = "/net/cci-nas-00/data/ceres_data/8t8e_41097/03_2025/8t8e_41097.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t8e_41097/03_2025/8t8e_41097.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.062 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 1, 'ARG:plan': 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: {'TYR:plan': 1, 'GLU:plan': 1, 'ASP:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 28 Time building chain proxies: 5.95, per 1000 atoms: 0.68 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: 2.26 Conformation dependent library (CDL) restraints added in 994.7 milliseconds 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: 0.90 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: 2.31 Time building geometry restraints manager: 2.67 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: 1.580 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.400 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.630 ------------------------------------------------------------------------------- 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= 0.199 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 : 12.90 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (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 TRP 0.006 0.001 TRP B 200 HIS 0.013 0.001 HIS C 513 PHE 0.014 0.001 PHE A1049 TYR 0.026 0.002 TYR B 295 ARG 0.003 0.000 ARG A 177 *********************** 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 : 1.001 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: 0.1922 time to fit residues: 33.0905 Evaluate side-chains 112 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 89 optimal weight: 0.0870 chunk 80 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 0.5980 chunk 61 optimal weight: 0.0010 chunk 96 optimal weight: 0.0470 overall best weight: 0.3062 ------------------------------------------------------------------------------- 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 = 0.4164 r_free = 0.4164 target = 0.177116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.133967 restraints weight = 10818.835| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.29 r_work: 0.3463 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8923 Z= 0.158 Angle : 0.576 7.673 12025 Z= 0.303 Chirality : 0.041 0.154 1357 Planarity : 0.004 0.048 1525 Dihedral : 5.082 26.332 1167 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer: Outliers : 2.87 % Allowed : 23.79 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.25 (0.24), residues: 1061 helix: -1.75 (0.20), residues: 542 sheet: -2.20 (0.59), residues: 75 loop : -2.55 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 220 HIS 0.004 0.001 HIS C 513 PHE 0.011 0.001 PHE A 973 TYR 0.011 0.001 TYR C 539 ARG 0.004 0.000 ARG C 195 *********************** 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 150 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 537 LEU cc_start: 0.8389 (mm) cc_final: 0.7929 (tp) REVERT: B 210 GLU cc_start: 0.8147 (mm-30) cc_final: 0.7890 (mm-30) REVERT: B 328 HIS cc_start: 0.6830 (OUTLIER) cc_final: 0.6529 (m-70) REVERT: B 361 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7752 (ttp-110) outliers start: 28 outliers final: 12 residues processed: 147 average time/residue: 0.1830 time to fit residues: 39.0040 Evaluate side-chains 126 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.015 ------------------------------------------------------------------------------- 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 64 ILE 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 B residue 200 TRP Chi-restraints excluded: chain B residue 239 VAL 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 456 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 56 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 0.0270 chunk 65 optimal weight: 0.0970 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 134 GLN C 544 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.176048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.133139 restraints weight = 11055.679| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.54 r_work: 0.3421 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.1559 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= 0.184 Angle : 0.575 11.526 12025 Z= 0.295 Chirality : 0.041 0.153 1357 Planarity : 0.003 0.044 1525 Dihedral : 4.894 25.383 1163 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 4.00 % Allowed : 24.31 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.24), residues: 1061 helix: -1.33 (0.21), residues: 544 sheet: -2.21 (0.59), residues: 75 loop : -2.54 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 220 HIS 0.010 0.001 HIS C 513 PHE 0.015 0.001 PHE C 284 TYR 0.017 0.001 TYR A 81 ARG 0.003 0.000 ARG C 195 *********************** 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 162 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 123 time to evaluate : 0.941 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 508 GLN cc_start: 0.7217 (mt0) cc_final: 0.6694 (pt0) REVERT: C 537 LEU cc_start: 0.8346 (mm) cc_final: 0.7738 (tp) REVERT: C 544 GLN cc_start: 0.8678 (tt0) cc_final: 0.8459 (tt0) REVERT: B 210 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7645 (mm-30) REVERT: B 328 HIS cc_start: 0.6772 (OUTLIER) cc_final: 0.6507 (m-70) REVERT: B 361 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7727 (ttp-110) REVERT: B 416 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.7658 (t80) outliers start: 39 outliers final: 21 residues processed: 156 average time/residue: 0.1749 time to fit residues: 39.7084 Evaluate side-chains 135 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 111 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 992 LEU 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 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 361 LEU Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 478 ASN 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 267 TYR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 33 optimal weight: 0.0050 chunk 70 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 104 optimal weight: 0.0870 chunk 49 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 overall best weight: 0.5572 ------------------------------------------------------------------------------- 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 = 0.176227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.134152 restraints weight = 10900.194| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 2.62 r_work: 0.3430 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1781 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= 0.182 Angle : 0.555 9.612 12025 Z= 0.288 Chirality : 0.041 0.155 1357 Planarity : 0.003 0.043 1525 Dihedral : 4.805 25.361 1163 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.72 % Allowed : 24.21 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.24), residues: 1061 helix: -1.15 (0.21), residues: 556 sheet: -2.20 (0.58), residues: 75 loop : -2.53 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 220 HIS 0.003 0.001 HIS A 93 PHE 0.025 0.001 PHE C 258 TYR 0.011 0.001 TYR C 539 ARG 0.002 0.000 ARG A 177 *********************** 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 162 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 116 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 CYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7813 (m) REVERT: A 256 LEU cc_start: 0.3154 (OUTLIER) cc_final: 0.2820 (mp) REVERT: C 119 ASP cc_start: 0.7072 (p0) cc_final: 0.6871 (p0) REVERT: C 508 GLN cc_start: 0.7106 (mt0) cc_final: 0.6555 (pt0) REVERT: B 210 GLU cc_start: 0.7834 (mm-30) cc_final: 0.7619 (mm-30) REVERT: B 238 PHE cc_start: 0.7591 (OUTLIER) cc_final: 0.7236 (m-80) REVERT: B 316 LEU cc_start: 0.7914 (OUTLIER) cc_final: 0.7572 (pt) REVERT: B 328 HIS cc_start: 0.6811 (OUTLIER) cc_final: 0.6545 (m-70) REVERT: B 416 TYR cc_start: 0.8355 (OUTLIER) cc_final: 0.7296 (t80) outliers start: 46 outliers final: 23 residues processed: 155 average time/residue: 0.1780 time to fit residues: 39.8833 Evaluate side-chains 139 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.935 ------------------------------------------------------------------------------- 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 256 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1056 VAL Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain C residue 99 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 361 LEU Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 478 ASN 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 255 VAL Chi-restraints excluded: chain B residue 267 TYR Chi-restraints excluded: chain B residue 269 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 83 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 52 optimal weight: 0.0570 chunk 65 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 overall best weight: 1.3704 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.171043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.128715 restraints weight = 11044.501| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.64 r_work: 0.3337 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 8923 Z= 0.342 Angle : 0.649 9.356 12025 Z= 0.331 Chirality : 0.044 0.156 1357 Planarity : 0.004 0.042 1525 Dihedral : 5.193 24.817 1163 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 4.62 % Allowed : 24.62 % Favored : 70.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.24), residues: 1061 helix: -1.22 (0.21), residues: 545 sheet: -2.24 (0.57), residues: 75 loop : -2.47 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 220 HIS 0.008 0.001 HIS B 201 PHE 0.019 0.002 PHE C 413 TYR 0.017 0.002 TYR A 258 ARG 0.003 0.000 ARG A 980 *********************** 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 158 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 113 time to evaluate : 0.959 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 LEU cc_start: 0.2980 (OUTLIER) cc_final: 0.2770 (mp) REVERT: C 26 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7327 (mm-30) REVERT: B 230 ARG cc_start: 0.5036 (ttt-90) cc_final: 0.4815 (ttp80) REVERT: B 316 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7690 (pp) REVERT: B 317 ASP cc_start: 0.8076 (p0) cc_final: 0.7636 (p0) REVERT: B 328 HIS cc_start: 0.6887 (OUTLIER) cc_final: 0.6527 (m-70) outliers start: 45 outliers final: 34 residues processed: 151 average time/residue: 0.1752 time to fit residues: 38.4841 Evaluate side-chains 144 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 247 THR Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 992 LEU 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 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 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 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 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 241 LEU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 257 GLN 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 373 LEU Chi-restraints excluded: chain B residue 416 TYR Chi-restraints excluded: chain B residue 456 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 64 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 chunk 57 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 chunk 8 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 183 ASN ** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 508 GLN B 322 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.172571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.130028 restraints weight = 10927.377| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.61 r_work: 0.3366 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8923 Z= 0.271 Angle : 0.602 9.104 12025 Z= 0.309 Chirality : 0.043 0.159 1357 Planarity : 0.003 0.040 1525 Dihedral : 5.101 25.091 1163 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 5.23 % Allowed : 24.92 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.24), residues: 1061 helix: -1.20 (0.21), residues: 557 sheet: -2.19 (0.58), residues: 75 loop : -2.53 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 200 HIS 0.009 0.001 HIS C 513 PHE 0.016 0.002 PHE C 258 TYR 0.013 0.002 TYR A 258 ARG 0.002 0.000 ARG A 980 *********************** 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 167 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 116 time to evaluate : 0.909 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 26 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7402 (mm-30) REVERT: B 316 LEU cc_start: 0.8196 (OUTLIER) cc_final: 0.7965 (pp) REVERT: B 328 HIS cc_start: 0.6737 (OUTLIER) cc_final: 0.6362 (m-70) outliers start: 51 outliers final: 35 residues processed: 156 average time/residue: 0.1794 time to fit residues: 41.0520 Evaluate side-chains 144 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 160 LYS Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 247 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 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 361 LEU Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain C residue 482 CYS Chi-restraints excluded: chain C residue 490 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 241 LEU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 257 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 71 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 chunk 80 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 37 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS C 201 ASN C 383 GLN C 508 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.174641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.132005 restraints weight = 11019.537| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.56 r_work: 0.3405 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8923 Z= 0.196 Angle : 0.581 9.054 12025 Z= 0.299 Chirality : 0.041 0.157 1357 Planarity : 0.003 0.041 1525 Dihedral : 4.914 24.770 1163 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 4.72 % Allowed : 26.26 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.64 (0.25), residues: 1061 helix: -1.10 (0.21), residues: 562 sheet: -2.02 (0.59), residues: 75 loop : -2.50 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 200 HIS 0.003 0.001 HIS B 201 PHE 0.016 0.001 PHE C 258 TYR 0.011 0.001 TYR C 412 ARG 0.003 0.000 ARG A 177 *********************** 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 160 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 114 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7479 (pp) REVERT: B 230 ARG cc_start: 0.4944 (ttt-90) cc_final: 0.4499 (ttp80) REVERT: B 316 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7757 (pt) REVERT: B 317 ASP cc_start: 0.8015 (p0) cc_final: 0.7791 (p0) REVERT: B 328 HIS cc_start: 0.6786 (OUTLIER) cc_final: 0.6423 (m-70) outliers start: 46 outliers final: 32 residues processed: 151 average time/residue: 0.1891 time to fit residues: 41.4621 Evaluate side-chains 141 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 106 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 968 GLU 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 78 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 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 361 LEU Chi-restraints excluded: chain C residue 444 ASP Chi-restraints excluded: chain C residue 446 VAL 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 241 LEU Chi-restraints excluded: chain B residue 243 CYS Chi-restraints excluded: chain B residue 257 GLN 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 41 optimal weight: 0.3980 chunk 59 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 62 optimal weight: 0.0980 chunk 104 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 7 optimal weight: 10.0000 chunk 94 optimal weight: 0.4980 chunk 49 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.4150 r_free = 0.4150 target = 0.175949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.133293 restraints weight = 11018.468| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.52 r_work: 0.3423 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8923 Z= 0.175 Angle : 0.573 10.042 12025 Z= 0.294 Chirality : 0.041 0.179 1357 Planarity : 0.003 0.041 1525 Dihedral : 4.776 24.477 1163 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 3.90 % Allowed : 26.87 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.25), residues: 1061 helix: -0.91 (0.22), residues: 557 sheet: -2.05 (0.59), residues: 75 loop : -2.41 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 200 HIS 0.004 0.001 HIS A 95 PHE 0.022 0.001 PHE C 284 TYR 0.021 0.001 TYR A 81 ARG 0.002 0.000 ARG C 195 *********************** 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 152 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 114 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7499 (pp) REVERT: B 230 ARG cc_start: 0.4938 (ttt-90) cc_final: 0.4500 (ttp80) REVERT: B 316 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7657 (pt) REVERT: B 317 ASP cc_start: 0.7887 (p0) cc_final: 0.7650 (p0) REVERT: B 328 HIS cc_start: 0.6829 (OUTLIER) cc_final: 0.6536 (m-70) REVERT: B 416 TYR cc_start: 0.8392 (OUTLIER) cc_final: 0.7367 (t80) outliers start: 38 outliers final: 25 residues processed: 145 average time/residue: 0.1963 time to fit residues: 41.0009 Evaluate side-chains 139 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 110 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 968 GLU 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 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 361 LEU Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain B residue 200 TRP Chi-restraints excluded: chain B residue 239 VAL 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.0770 chunk 33 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 71 optimal weight: 0.0470 chunk 98 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 overall best weight: 0.4636 ------------------------------------------------------------------------------- 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 = 0.4157 r_free = 0.4157 target = 0.176796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.134406 restraints weight = 10917.909| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.39 r_work: 0.3448 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.2265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8923 Z= 0.168 Angle : 0.565 9.024 12025 Z= 0.291 Chirality : 0.041 0.165 1357 Planarity : 0.003 0.041 1525 Dihedral : 4.676 24.061 1163 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 3.38 % Allowed : 27.49 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.34 (0.25), residues: 1061 helix: -0.82 (0.22), residues: 557 sheet: -2.01 (0.60), residues: 75 loop : -2.37 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 200 HIS 0.003 0.001 HIS B 201 PHE 0.019 0.001 PHE C 284 TYR 0.021 0.001 TYR A 81 ARG 0.003 0.000 ARG B 318 *********************** 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 150 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 117 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 78 LEU cc_start: 0.7889 (OUTLIER) cc_final: 0.7500 (pp) REVERT: C 483 ASP cc_start: 0.8232 (m-30) cc_final: 0.8032 (m-30) REVERT: B 220 THR cc_start: 0.8481 (t) cc_final: 0.8234 (t) REVERT: B 230 ARG cc_start: 0.5031 (ttt-90) cc_final: 0.4598 (ttp80) REVERT: B 317 ASP cc_start: 0.7955 (p0) cc_final: 0.7735 (p0) REVERT: B 328 HIS cc_start: 0.6755 (OUTLIER) cc_final: 0.6488 (m-70) REVERT: B 416 TYR cc_start: 0.8368 (OUTLIER) cc_final: 0.7378 (t80) outliers start: 33 outliers final: 27 residues processed: 144 average time/residue: 0.2164 time to fit residues: 45.4401 Evaluate side-chains 144 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 968 GLU 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 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 361 LEU Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain B residue 200 TRP Chi-restraints excluded: chain B residue 239 VAL 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 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 74 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 65 optimal weight: 0.0470 chunk 38 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- 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 = 0.4141 r_free = 0.4141 target = 0.174993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.132879 restraints weight = 10913.383| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.48 r_work: 0.3406 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8923 Z= 0.216 Angle : 0.593 9.770 12025 Z= 0.301 Chirality : 0.042 0.156 1357 Planarity : 0.003 0.037 1525 Dihedral : 4.788 23.667 1163 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.08 % Allowed : 27.49 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.25), residues: 1061 helix: -0.88 (0.22), residues: 558 sheet: -2.05 (0.59), residues: 75 loop : -2.36 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 200 HIS 0.004 0.001 HIS B 201 PHE 0.017 0.001 PHE C 284 TYR 0.021 0.001 TYR A 81 ARG 0.002 0.000 ARG B 318 ********************** 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 143 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 113 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 78 LEU cc_start: 0.7923 (OUTLIER) cc_final: 0.7473 (pp) REVERT: B 220 THR cc_start: 0.8517 (t) cc_final: 0.8073 (t) REVERT: B 230 ARG cc_start: 0.5119 (ttt-90) cc_final: 0.4654 (ttp80) REVERT: B 328 HIS cc_start: 0.6830 (OUTLIER) cc_final: 0.6565 (m-70) outliers start: 30 outliers final: 27 residues processed: 137 average time/residue: 0.1877 time to fit residues: 36.9289 Evaluate side-chains 141 residues out of total 991 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 968 GLU 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 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 361 LEU Chi-restraints excluded: chain C residue 446 VAL Chi-restraints excluded: chain B residue 200 TRP 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 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 66 optimal weight: 4.9990 chunk 92 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 15 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 50 optimal weight: 0.5980 chunk 101 optimal weight: 0.4980 chunk 53 optimal weight: 0.5980 chunk 4 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4147 r_free = 0.4147 target = 0.175537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.133115 restraints weight = 10913.348| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.58 r_work: 0.3423 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8923 Z= 0.206 Angle : 0.580 9.143 12025 Z= 0.298 Chirality : 0.042 0.155 1357 Planarity : 0.003 0.037 1525 Dihedral : 4.784 23.508 1163 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer: Outliers : 2.97 % Allowed : 28.00 % Favored : 69.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.25), residues: 1061 helix: -0.83 (0.22), residues: 558 sheet: -2.05 (0.60), residues: 75 loop : -2.34 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 220 HIS 0.003 0.001 HIS B 201 PHE 0.017 0.001 PHE C 284 TYR 0.020 0.001 TYR A 81 ARG 0.002 0.000 ARG B 318 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4098.25 seconds wall clock time: 71 minutes 28.29 seconds (4288.29 seconds total)