Starting phenix.real_space_refine on Fri May 16 01:48:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8izm_35865/05_2025/8izm_35865.cif Found real_map, /net/cci-nas-00/data/ceres_data/8izm_35865/05_2025/8izm_35865.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8izm_35865/05_2025/8izm_35865.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8izm_35865/05_2025/8izm_35865.map" model { file = "/net/cci-nas-00/data/ceres_data/8izm_35865/05_2025/8izm_35865.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8izm_35865/05_2025/8izm_35865.cif" } resolution = 3.01 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= 0.053 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1404 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 2 6.06 5 S 81 5.16 5 C 8105 2.51 5 N 2182 2.21 5 O 2372 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 43 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 12742 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 517 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "C" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 642 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 4, 'TRANS': 80} Chain: "D" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 387 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} Chain: "E" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 412 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "A" Number of atoms: 10782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1350, 10782 Classifications: {'peptide': 1350} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 67, 'TRANS': 1282} Chain breaks: 5 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 11097 SG CYS A1187 61.723 18.565 85.241 1.00108.17 S ATOM 11122 SG CYS A1190 63.227 21.089 88.334 1.00128.93 S ATOM 10755 SG CYS A1142 75.237 23.137 70.425 1.00 99.43 S ATOM 12460 SG CYS A1379 73.778 20.648 72.983 1.00109.11 S ATOM 12466 SG CYS A1380 71.860 24.070 72.475 1.00103.98 S Time building chain proxies: 8.85, per 1000 atoms: 0.69 Number of scatterers: 12742 At special positions: 0 Unit cell: (104.94, 148.4, 134.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 2 29.99 S 81 16.00 O 2372 8.00 N 2182 7.00 C 8105 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: 3.42 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3001 " pdb="ZN ZN A3001 " - pdb=" NE2 HIS A1374 " pdb="ZN ZN A3001 " - pdb=" ND1 HIS A1372 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1190 " pdb="ZN ZN A3001 " - pdb=" SG CYS A1187 " pdb=" ZN A3002 " pdb="ZN ZN A3002 " - pdb=" SG CYS A1142 " pdb="ZN ZN A3002 " - pdb=" SG CYS A1380 " pdb="ZN ZN A3002 " - pdb=" SG CYS A1379 " Number of angles added : 1 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3070 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 8 sheets defined 61.2% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.46 Creating SS restraints... Processing helix chain 'B' and resid 218 through 277 removed outlier: 4.097A pdb=" N GLY B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N MET B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL B 249 " --> pdb=" O GLN B 245 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N THR B 258 " --> pdb=" O ASN B 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 272 removed outlier: 3.788A pdb=" N GLY C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA C 230 " --> pdb=" O ARG C 226 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA C 244 " --> pdb=" O ASP C 240 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N GLN C 245 " --> pdb=" O LYS C 241 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY C 246 " --> pdb=" O VAL C 242 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER C 247 " --> pdb=" O LEU C 243 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR C 265 " --> pdb=" O THR C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 290 Processing helix chain 'D' and resid 219 through 243 removed outlier: 3.566A pdb=" N ARG D 226 " --> pdb=" O MET D 222 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP D 240 " --> pdb=" O GLU D 236 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LYS D 241 " --> pdb=" O GLN D 237 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU D 243 " --> pdb=" O VAL D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 267 removed outlier: 3.792A pdb=" N MET D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR D 265 " --> pdb=" O THR D 261 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE D 266 " --> pdb=" O THR D 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 219 through 271 removed outlier: 3.548A pdb=" N LYS E 241 " --> pdb=" O GLN E 237 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N MET E 248 " --> pdb=" O ALA E 244 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N MET E 269 " --> pdb=" O THR E 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 30 removed outlier: 3.629A pdb=" N LEU A 23 " --> pdb=" O VAL A 19 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY A 30 " --> pdb=" O TYR A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.700A pdb=" N LEU A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLY A 42 " --> pdb=" O PRO A 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 37 through 42' Processing helix chain 'A' and resid 43 through 47 Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 56 through 74 Processing helix chain 'A' and resid 75 through 79 Processing helix chain 'A' and resid 90 through 98 removed outlier: 4.059A pdb=" N LEU A 95 " --> pdb=" O PRO A 92 " (cutoff:3.500A) Proline residue: A 96 - end of helix Processing helix chain 'A' and resid 108 through 123 removed outlier: 3.704A pdb=" N LEU A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 141 Processing helix chain 'A' and resid 162 through 172 Processing helix chain 'A' and resid 175 through 199 Processing helix chain 'A' and resid 237 through 260 Processing helix chain 'A' and resid 265 through 285 removed outlier: 4.394A pdb=" N ARG A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 305 removed outlier: 3.914A pdb=" N ILE A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR A 300 " --> pdb=" O GLU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 329 Processing helix chain 'A' and resid 335 through 349 removed outlier: 3.835A pdb=" N GLN A 349 " --> pdb=" O ASP A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 361 through 368 removed outlier: 3.956A pdb=" N ILE A 364 " --> pdb=" O LEU A 361 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET A 365 " --> pdb=" O LEU A 362 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG A 366 " --> pdb=" O CYS A 363 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N TRP A 368 " --> pdb=" O MET A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 386 removed outlier: 3.699A pdb=" N LYS A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL A 382 " --> pdb=" O ALA A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 413 Processing helix chain 'A' and resid 430 through 439 Processing helix chain 'A' and resid 444 through 450 removed outlier: 3.658A pdb=" N LYS A 450 " --> pdb=" O GLU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 456 removed outlier: 3.536A pdb=" N ILE A 455 " --> pdb=" O ASN A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 492 removed outlier: 3.933A pdb=" N VAL A 491 " --> pdb=" O TRP A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 503 removed outlier: 3.601A pdb=" N ILE A 497 " --> pdb=" O ARG A 493 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N GLN A 499 " --> pdb=" O SER A 495 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ARG A 500 " --> pdb=" O LEU A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 522 Processing helix chain 'A' and resid 527 through 532 Processing helix chain 'A' and resid 532 through 537 Processing helix chain 'A' and resid 538 through 543 removed outlier: 3.914A pdb=" N ARG A 542 " --> pdb=" O GLY A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 585 Processing helix chain 'A' and resid 586 through 590 removed outlier: 3.731A pdb=" N MET A 590 " --> pdb=" O GLY A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 611 Processing helix chain 'A' and resid 672 through 677 removed outlier: 3.680A pdb=" N ASN A 676 " --> pdb=" O LYS A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 694 Processing helix chain 'A' and resid 700 through 708 removed outlier: 3.555A pdb=" N LEU A 704 " --> pdb=" O GLU A 700 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 768 removed outlier: 3.516A pdb=" N TRP A 753 " --> pdb=" O CYS A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 820 removed outlier: 4.173A pdb=" N LEU A 808 " --> pdb=" O LYS A 804 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE A 809 " --> pdb=" O ALA A 805 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 858 removed outlier: 3.822A pdb=" N ASN A 855 " --> pdb=" O GLN A 851 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LYS A 858 " --> pdb=" O LYS A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 887 Processing helix chain 'A' and resid 890 through 912 Processing helix chain 'A' and resid 920 through 928 Processing helix chain 'A' and resid 929 through 939 removed outlier: 3.577A pdb=" N ILE A 933 " --> pdb=" O HIS A 929 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 944 Processing helix chain 'A' and resid 951 through 955 Processing helix chain 'A' and resid 961 through 977 removed outlier: 3.621A pdb=" N SER A 965 " --> pdb=" O ASP A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 989 removed outlier: 3.821A pdb=" N LEU A 984 " --> pdb=" O ASP A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1003 removed outlier: 3.516A pdb=" N ALA A1001 " --> pdb=" O TRP A 997 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A1003 " --> pdb=" O THR A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1014 through 1031 Processing helix chain 'A' and resid 1043 through 1057 Processing helix chain 'A' and resid 1062 through 1073 Processing helix chain 'A' and resid 1073 through 1084 Processing helix chain 'A' and resid 1088 through 1099 Processing helix chain 'A' and resid 1102 through 1111 Processing helix chain 'A' and resid 1111 through 1121 Processing helix chain 'A' and resid 1131 through 1137 removed outlier: 3.646A pdb=" N LEU A1134 " --> pdb=" O GLN A1131 " (cutoff:3.500A) Processing helix chain 'A' and resid 1142 through 1155 Processing helix chain 'A' and resid 1155 through 1160 Processing helix chain 'A' and resid 1171 through 1176 Processing helix chain 'A' and resid 1187 through 1192 Processing helix chain 'A' and resid 1242 through 1259 Processing helix chain 'A' and resid 1263 through 1268 Processing helix chain 'A' and resid 1269 through 1275 Processing helix chain 'A' and resid 1280 through 1288 Processing helix chain 'A' and resid 1317 through 1321 removed outlier: 3.658A pdb=" N PHE A1320 " --> pdb=" O PHE A1317 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A1321 " --> pdb=" O SER A1318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1317 through 1321' Processing helix chain 'A' and resid 1338 through 1358 Processing sheet with id=AA1, first strand: chain 'B' and resid 282 through 283 Processing sheet with id=AA2, first strand: chain 'C' and resid 274 through 276 removed outlier: 3.829A pdb=" N ILE C 275 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU A 392 " --> pdb=" O ILE C 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.075A pdb=" N ALA A 87 " --> pdb=" O LEU A 232 " (cutoff:3.500A) removed outlier: 8.166A pdb=" N TYR A 234 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N LEU A 89 " --> pdb=" O TYR A 234 " (cutoff:3.500A) removed outlier: 9.550A pdb=" N THR A 236 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 423 through 424 removed outlier: 3.646A pdb=" N ARG A 459 " --> pdb=" O THR A 424 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 563 through 566 Processing sheet with id=AA6, first strand: chain 'A' and resid 780 through 790 Processing sheet with id=AA7, first strand: chain 'A' and resid 835 through 838 removed outlier: 3.541A pdb=" N PHE A 836 " --> pdb=" O PHE A 843 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1180 through 1182 690 hydrogen bonds defined for protein. 2001 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: 4.62 Time building geometry restraints manager: 3.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2116 1.30 - 1.43: 3115 1.43 - 1.56: 7612 1.56 - 1.68: 1 1.68 - 1.81: 133 Bond restraints: 12977 Sorted by residual: bond pdb=" C LYS A 444 " pdb=" N TYR A 445 " ideal model delta sigma weight residual 1.335 1.445 -0.109 1.34e-02 5.57e+03 6.66e+01 bond pdb=" C LEU A 443 " pdb=" N LYS A 444 " ideal model delta sigma weight residual 1.331 1.436 -0.105 1.37e-02 5.33e+03 5.89e+01 bond pdb=" C GLY A 285 " pdb=" N ASP A 286 " ideal model delta sigma weight residual 1.333 1.428 -0.095 1.49e-02 4.50e+03 4.05e+01 bond pdb=" C LYS A 672 " pdb=" N TYR A 673 " ideal model delta sigma weight residual 1.334 1.245 0.089 1.43e-02 4.89e+03 3.90e+01 bond pdb=" C ILE A 364 " pdb=" N MET A 365 " ideal model delta sigma weight residual 1.334 1.412 -0.078 1.27e-02 6.20e+03 3.73e+01 ... (remaining 12972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 16693 2.39 - 4.78: 775 4.78 - 7.16: 104 7.16 - 9.55: 17 9.55 - 11.94: 2 Bond angle restraints: 17591 Sorted by residual: angle pdb=" N ARG A 414 " pdb=" CA ARG A 414 " pdb=" C ARG A 414 " ideal model delta sigma weight residual 113.72 102.25 11.47 1.52e+00 4.33e-01 5.69e+01 angle pdb=" C MET C 228 " pdb=" N ASP C 229 " pdb=" CA ASP C 229 " ideal model delta sigma weight residual 120.58 132.52 -11.94 1.71e+00 3.42e-01 4.87e+01 angle pdb=" N TYR A 412 " pdb=" CA TYR A 412 " pdb=" C TYR A 412 " ideal model delta sigma weight residual 111.28 103.89 7.39 1.09e+00 8.42e-01 4.59e+01 angle pdb=" N SER A 415 " pdb=" CA SER A 415 " pdb=" C SER A 415 " ideal model delta sigma weight residual 108.45 100.12 8.33 1.26e+00 6.30e-01 4.37e+01 angle pdb=" N GLU A 592 " pdb=" CA GLU A 592 " pdb=" C GLU A 592 " ideal model delta sigma weight residual 111.75 104.45 7.30 1.28e+00 6.10e-01 3.25e+01 ... (remaining 17586 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 7080 17.78 - 35.55: 696 35.55 - 53.33: 143 53.33 - 71.11: 27 71.11 - 88.88: 4 Dihedral angle restraints: 7950 sinusoidal: 3234 harmonic: 4716 Sorted by residual: dihedral pdb=" CA LEU A 849 " pdb=" C LEU A 849 " pdb=" N THR A 850 " pdb=" CA THR A 850 " ideal model delta harmonic sigma weight residual -180.00 -157.63 -22.37 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" C ASP A1268 " pdb=" N ASP A1268 " pdb=" CA ASP A1268 " pdb=" CB ASP A1268 " ideal model delta harmonic sigma weight residual -122.60 -132.09 9.49 0 2.50e+00 1.60e-01 1.44e+01 dihedral pdb=" CA ILE A 820 " pdb=" C ILE A 820 " pdb=" N GLY A 821 " pdb=" CA GLY A 821 " ideal model delta harmonic sigma weight residual 180.00 161.99 18.01 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 7947 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1686 0.064 - 0.127: 302 0.127 - 0.191: 56 0.191 - 0.255: 12 0.255 - 0.319: 5 Chirality restraints: 2061 Sorted by residual: chirality pdb=" CA MET A 107 " pdb=" N MET A 107 " pdb=" C MET A 107 " pdb=" CB MET A 107 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA ILE A 830 " pdb=" N ILE A 830 " pdb=" C ILE A 830 " pdb=" CB ILE A 830 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.30 2.00e-01 2.50e+01 2.24e+00 chirality pdb=" CA ILE A 738 " pdb=" N ILE A 738 " pdb=" C ILE A 738 " pdb=" CB ILE A 738 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 2058 not shown) Planarity restraints: 2226 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 443 " -0.021 2.00e-02 2.50e+03 4.35e-02 1.89e+01 pdb=" C LEU A 443 " 0.075 2.00e-02 2.50e+03 pdb=" O LEU A 443 " -0.031 2.00e-02 2.50e+03 pdb=" N LYS A 444 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A1244 " -0.018 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C SER A1244 " 0.057 2.00e-02 2.50e+03 pdb=" O SER A1244 " -0.020 2.00e-02 2.50e+03 pdb=" N LEU A1245 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 37 " 0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO A 38 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " 0.044 5.00e-02 4.00e+02 ... (remaining 2223 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 8 2.19 - 2.87: 5196 2.87 - 3.55: 19262 3.55 - 4.22: 30921 4.22 - 4.90: 52655 Nonbonded interactions: 108042 Sorted by model distance: nonbonded pdb=" OE2 GLU D 255 " pdb=" CB LYS E 260 " model vdw 1.514 3.440 nonbonded pdb=" OE2 GLU C 255 " pdb=" NZ LYS D 253 " model vdw 1.943 3.120 nonbonded pdb=" OE2 GLU C 255 " pdb=" CE LYS D 253 " model vdw 1.999 3.440 nonbonded pdb=" CG2 VAL C 259 " pdb=" CD1 LEU D 256 " model vdw 2.000 3.880 nonbonded pdb=" O GLY C 302 " pdb=" CE1 HIS A 426 " model vdw 2.044 3.260 ... (remaining 108037 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 Found NCS groups: ncs_group { reference = chain 'D' selection = (chain 'E' and resid 218 through 267) } 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: 8.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.790 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 35.010 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 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 : 0.007 0.114 12984 Z= 0.491 Angle : 1.073 12.356 17592 Z= 0.738 Chirality : 0.054 0.319 2061 Planarity : 0.006 0.081 2226 Dihedral : 14.422 88.883 4880 Min Nonbonded Distance : 1.514 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.97 % Allowed : 20.39 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.20), residues: 1588 helix: -0.08 (0.17), residues: 890 sheet: -0.82 (0.55), residues: 81 loop : -0.82 (0.24), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 488 HIS 0.004 0.001 HIS A 60 PHE 0.029 0.002 PHE A 520 TYR 0.026 0.002 TYR A 550 ARG 0.008 0.001 ARG A 814 Details of bonding type rmsd hydrogen bonds : bond 0.17092 ( 690) hydrogen bonds : angle 6.98465 ( 2001) metal coordination : bond 0.05310 ( 7) metal coordination : angle 12.35639 ( 1) covalent geometry : bond 0.00690 (12977) covalent geometry : angle 1.06905 (17591) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 480 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 MET cc_start: 0.6702 (tpp) cc_final: 0.6468 (tpp) REVERT: C 248 MET cc_start: 0.5793 (mmt) cc_final: 0.5432 (mmt) REVERT: C 252 ILE cc_start: 0.8366 (mt) cc_final: 0.8053 (mt) REVERT: A 16 SER cc_start: 0.8457 (p) cc_final: 0.8209 (t) REVERT: A 66 ILE cc_start: 0.8533 (tt) cc_final: 0.8223 (pt) REVERT: A 77 LEU cc_start: 0.8509 (mm) cc_final: 0.8284 (mm) REVERT: A 107 MET cc_start: 0.6246 (ttp) cc_final: 0.5617 (ttp) REVERT: A 138 GLN cc_start: 0.7847 (tm-30) cc_final: 0.7638 (tm-30) REVERT: A 174 GLU cc_start: 0.7127 (pt0) cc_final: 0.6722 (pt0) REVERT: A 184 MET cc_start: 0.7283 (tmm) cc_final: 0.7065 (ttt) REVERT: A 186 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8200 (ttpp) REVERT: A 193 ILE cc_start: 0.8403 (mt) cc_final: 0.8181 (mm) REVERT: A 207 ILE cc_start: 0.7816 (mt) cc_final: 0.7465 (mt) REVERT: A 255 SER cc_start: 0.7972 (m) cc_final: 0.7708 (p) REVERT: A 360 GLU cc_start: 0.6726 (mm-30) cc_final: 0.6474 (mm-30) REVERT: A 420 TRP cc_start: 0.6194 (m-10) cc_final: 0.5963 (m100) REVERT: A 436 MET cc_start: 0.7575 (mtp) cc_final: 0.6164 (mmm) REVERT: A 442 GLU cc_start: 0.6073 (tt0) cc_final: 0.5696 (tt0) REVERT: A 453 LYS cc_start: 0.7852 (mttt) cc_final: 0.7626 (mtpp) REVERT: A 488 TRP cc_start: 0.8213 (p-90) cc_final: 0.7993 (p-90) REVERT: A 489 MET cc_start: 0.8107 (mtp) cc_final: 0.7496 (mtt) REVERT: A 493 ARG cc_start: 0.7232 (ttm170) cc_final: 0.6903 (ttt180) REVERT: A 523 ASP cc_start: 0.7203 (t0) cc_final: 0.6966 (t0) REVERT: A 539 GLU cc_start: 0.7323 (tp30) cc_final: 0.6923 (tp30) REVERT: A 553 LYS cc_start: 0.8337 (tttp) cc_final: 0.7983 (tttp) REVERT: A 568 THR cc_start: 0.7366 (p) cc_final: 0.6697 (t) REVERT: A 576 VAL cc_start: 0.7789 (p) cc_final: 0.7522 (m) REVERT: A 661 ILE cc_start: 0.5475 (OUTLIER) cc_final: 0.5125 (tp) REVERT: A 674 CYS cc_start: 0.7932 (p) cc_final: 0.7454 (p) REVERT: A 695 ILE cc_start: 0.8718 (mt) cc_final: 0.8469 (pt) REVERT: A 701 TRP cc_start: 0.8135 (p-90) cc_final: 0.7838 (p-90) REVERT: A 801 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7935 (tp40) REVERT: A 829 THR cc_start: 0.7734 (t) cc_final: 0.7402 (m) REVERT: A 840 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7810 (mmpt) REVERT: A 858 LYS cc_start: 0.8313 (ptpt) cc_final: 0.8096 (ptpp) REVERT: A 866 LEU cc_start: 0.7754 (mm) cc_final: 0.7523 (mt) REVERT: A 956 ASN cc_start: 0.7315 (p0) cc_final: 0.7072 (p0) REVERT: A 994 LYS cc_start: 0.8031 (mtmm) cc_final: 0.7830 (mtmm) REVERT: A 1049 GLU cc_start: 0.7443 (tp30) cc_final: 0.6989 (mm-30) REVERT: A 1099 ARG cc_start: 0.7861 (ttt-90) cc_final: 0.7628 (ttt180) REVERT: A 1104 LYS cc_start: 0.8147 (mttt) cc_final: 0.7881 (mttt) REVERT: A 1105 LYS cc_start: 0.8437 (mmmm) cc_final: 0.7981 (mmmm) REVERT: A 1176 VAL cc_start: 0.7557 (m) cc_final: 0.7189 (m) REVERT: A 1372 HIS cc_start: 0.7579 (m170) cc_final: 0.7351 (m170) outliers start: 14 outliers final: 4 residues processed: 491 average time/residue: 0.2775 time to fit residues: 189.2523 Evaluate side-chains 410 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 405 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain C residue 295 ASP Chi-restraints excluded: chain A residue 661 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 134 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 41 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 124 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 251 GLN C 251 GLN E 234 HIS E 245 GLN A 60 HIS A 172 ASN A 416 HIS ** A 426 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 780 ASN A 817 ASN ** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 ASN A 905 GLN A 914 GLN A1160 ASN A1177 HIS A1298 HIS A1322 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.149500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.131590 restraints weight = 22134.454| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.81 r_work: 0.3662 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12984 Z= 0.169 Angle : 0.655 11.609 17592 Z= 0.338 Chirality : 0.044 0.210 2061 Planarity : 0.005 0.063 2226 Dihedral : 4.457 31.085 1742 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.69 % Allowed : 20.60 % Favored : 75.71 % 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: 0.66 (0.21), residues: 1588 helix: 1.24 (0.17), residues: 885 sheet: -0.33 (0.55), residues: 89 loop : -0.54 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 677 HIS 0.015 0.001 HIS E 234 PHE 0.024 0.002 PHE A 717 TYR 0.016 0.002 TYR A 895 ARG 0.007 0.001 ARG A 514 Details of bonding type rmsd hydrogen bonds : bond 0.05040 ( 690) hydrogen bonds : angle 4.56144 ( 2001) metal coordination : bond 0.02717 ( 7) metal coordination : angle 4.53657 ( 1) covalent geometry : bond 0.00376 (12977) covalent geometry : angle 0.65446 (17591) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 449 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 234 HIS cc_start: 0.8214 (m90) cc_final: 0.8009 (m90) REVERT: B 275 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7181 (mp) REVERT: C 248 MET cc_start: 0.6748 (mmt) cc_final: 0.6276 (mmt) REVERT: C 276 MET cc_start: 0.7478 (ttp) cc_final: 0.7250 (ttp) REVERT: E 222 MET cc_start: 0.8343 (mmm) cc_final: 0.7876 (mpp) REVERT: A 15 ASN cc_start: 0.8178 (m-40) cc_final: 0.7837 (m-40) REVERT: A 50 LYS cc_start: 0.8644 (tttm) cc_final: 0.8380 (ttmm) REVERT: A 66 ILE cc_start: 0.8587 (tt) cc_final: 0.8299 (pt) REVERT: A 76 SER cc_start: 0.8260 (p) cc_final: 0.7781 (p) REVERT: A 77 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8597 (mm) REVERT: A 94 ILE cc_start: 0.8220 (tt) cc_final: 0.7858 (tp) REVERT: A 107 MET cc_start: 0.6810 (ttp) cc_final: 0.6133 (ttp) REVERT: A 137 ASN cc_start: 0.8281 (t0) cc_final: 0.7968 (t0) REVERT: A 138 GLN cc_start: 0.8567 (tm-30) cc_final: 0.7942 (tm-30) REVERT: A 184 MET cc_start: 0.8019 (tmm) cc_final: 0.7467 (ttt) REVERT: A 207 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7992 (mt) REVERT: A 313 LYS cc_start: 0.8555 (tttp) cc_final: 0.8240 (ttmm) REVERT: A 322 ASN cc_start: 0.7742 (t0) cc_final: 0.7516 (m-40) REVERT: A 398 MET cc_start: 0.8151 (mmm) cc_final: 0.7928 (mmt) REVERT: A 420 TRP cc_start: 0.7427 (m-10) cc_final: 0.6659 (m100) REVERT: A 428 ASN cc_start: 0.7655 (p0) cc_final: 0.7372 (p0) REVERT: A 442 GLU cc_start: 0.7363 (tt0) cc_final: 0.7094 (tt0) REVERT: A 444 LYS cc_start: 0.8267 (mttt) cc_final: 0.8029 (mtpp) REVERT: A 457 MET cc_start: 0.7553 (mpp) cc_final: 0.7051 (mtm) REVERT: A 494 ARG cc_start: 0.7614 (ttt180) cc_final: 0.7362 (mtt180) REVERT: A 539 GLU cc_start: 0.7658 (tp30) cc_final: 0.7290 (tp30) REVERT: A 553 LYS cc_start: 0.8472 (tttp) cc_final: 0.8258 (tttp) REVERT: A 576 VAL cc_start: 0.8256 (p) cc_final: 0.7912 (m) REVERT: A 579 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7237 (mm-30) REVERT: A 661 ILE cc_start: 0.6360 (OUTLIER) cc_final: 0.6089 (tt) REVERT: A 674 CYS cc_start: 0.8208 (p) cc_final: 0.7857 (m) REVERT: A 675 LEU cc_start: 0.8785 (mt) cc_final: 0.8570 (mt) REVERT: A 692 MET cc_start: 0.8369 (mtm) cc_final: 0.8127 (mtp) REVERT: A 707 MET cc_start: 0.8402 (mtt) cc_final: 0.8186 (mtp) REVERT: A 801 GLN cc_start: 0.8408 (mm-40) cc_final: 0.8169 (tp40) REVERT: A 965 SER cc_start: 0.8696 (t) cc_final: 0.8454 (m) REVERT: A 972 ARG cc_start: 0.8100 (mtt180) cc_final: 0.7824 (mtt180) REVERT: A 982 TRP cc_start: 0.8010 (p-90) cc_final: 0.7681 (p-90) REVERT: A 1006 THR cc_start: 0.8341 (m) cc_final: 0.7904 (p) REVERT: A 1020 LYS cc_start: 0.8531 (mttt) cc_final: 0.8278 (mttm) REVERT: A 1021 LYS cc_start: 0.8346 (mmtp) cc_final: 0.8129 (mptt) REVERT: A 1104 LYS cc_start: 0.8549 (mttt) cc_final: 0.8253 (mttt) REVERT: A 1112 TYR cc_start: 0.8362 (t80) cc_final: 0.8142 (t80) REVERT: A 1176 VAL cc_start: 0.8046 (m) cc_final: 0.7451 (m) REVERT: A 1249 LEU cc_start: 0.8544 (mt) cc_final: 0.8283 (mm) REVERT: A 1282 GLU cc_start: 0.7705 (mp0) cc_final: 0.7258 (mp0) REVERT: A 1410 ASP cc_start: 0.7937 (p0) cc_final: 0.7516 (p0) outliers start: 53 outliers final: 14 residues processed: 475 average time/residue: 0.2780 time to fit residues: 182.8131 Evaluate side-chains 427 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 409 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 262 THR Chi-restraints excluded: chain E residue 232 LEU Chi-restraints excluded: chain E residue 253 LYS Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 132 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 661 ILE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 760 THR Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1234 SER Chi-restraints excluded: chain A residue 1365 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 23 optimal weight: 0.7980 chunk 149 optimal weight: 0.0470 chunk 4 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 17 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 119 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN A 438 HIS A 451 ASN ** A 780 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1120 ASN A1322 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.144162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.125440 restraints weight = 21839.566| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.84 r_work: 0.3584 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12984 Z= 0.151 Angle : 0.611 11.551 17592 Z= 0.315 Chirality : 0.044 0.318 2061 Planarity : 0.005 0.057 2226 Dihedral : 4.218 32.721 1737 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.06 % Allowed : 23.31 % Favored : 73.63 % 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: 1.02 (0.21), residues: 1588 helix: 1.55 (0.17), residues: 884 sheet: -0.30 (0.53), residues: 89 loop : -0.39 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 982 HIS 0.004 0.001 HIS A 13 PHE 0.017 0.002 PHE A1197 TYR 0.012 0.001 TYR A 895 ARG 0.006 0.001 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.04667 ( 690) hydrogen bonds : angle 4.30771 ( 2001) metal coordination : bond 0.02145 ( 7) metal coordination : angle 0.34324 ( 1) covalent geometry : bond 0.00331 (12977) covalent geometry : angle 0.61128 (17591) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 439 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 MET cc_start: 0.6468 (tpp) cc_final: 0.6084 (tpp) REVERT: C 248 MET cc_start: 0.6599 (mmt) cc_final: 0.6323 (mmt) REVERT: C 276 MET cc_start: 0.7479 (ttp) cc_final: 0.7234 (ttp) REVERT: E 248 MET cc_start: 0.7352 (mtp) cc_final: 0.6973 (mtp) REVERT: A 15 ASN cc_start: 0.8206 (m-40) cc_final: 0.7764 (m-40) REVERT: A 32 LEU cc_start: 0.8738 (mm) cc_final: 0.8534 (mt) REVERT: A 50 LYS cc_start: 0.8688 (tttm) cc_final: 0.8432 (ttmm) REVERT: A 66 ILE cc_start: 0.8623 (tt) cc_final: 0.8354 (pt) REVERT: A 69 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7645 (mm-30) REVERT: A 107 MET cc_start: 0.6837 (ttp) cc_final: 0.6120 (ttp) REVERT: A 137 ASN cc_start: 0.8323 (t0) cc_final: 0.8051 (t0) REVERT: A 138 GLN cc_start: 0.8482 (tm-30) cc_final: 0.8210 (tm-30) REVERT: A 184 MET cc_start: 0.7984 (tmm) cc_final: 0.7501 (ttt) REVERT: A 207 ILE cc_start: 0.8316 (mt) cc_final: 0.8098 (mt) REVERT: A 225 TYR cc_start: 0.8056 (t80) cc_final: 0.7716 (t80) REVERT: A 279 ASP cc_start: 0.8126 (m-30) cc_final: 0.7894 (m-30) REVERT: A 360 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7223 (mm-30) REVERT: A 366 ARG cc_start: 0.8463 (mmt90) cc_final: 0.8138 (mmt90) REVERT: A 394 PHE cc_start: 0.7867 (t80) cc_final: 0.7412 (t80) REVERT: A 428 ASN cc_start: 0.8097 (p0) cc_final: 0.7787 (p0) REVERT: A 437 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7547 (ttt180) REVERT: A 442 GLU cc_start: 0.7817 (tt0) cc_final: 0.7526 (tt0) REVERT: A 457 MET cc_start: 0.8130 (mpp) cc_final: 0.7697 (mtm) REVERT: A 494 ARG cc_start: 0.7691 (ttt180) cc_final: 0.7384 (mtt180) REVERT: A 503 ASP cc_start: 0.7921 (m-30) cc_final: 0.7615 (m-30) REVERT: A 539 GLU cc_start: 0.7669 (tp30) cc_final: 0.7320 (tp30) REVERT: A 550 TYR cc_start: 0.8656 (m-80) cc_final: 0.8434 (m-80) REVERT: A 553 LYS cc_start: 0.8514 (tttp) cc_final: 0.8312 (tttp) REVERT: A 555 LYS cc_start: 0.8428 (mttp) cc_final: 0.7876 (mttt) REVERT: A 579 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7242 (mm-30) REVERT: A 674 CYS cc_start: 0.8331 (p) cc_final: 0.8006 (m) REVERT: A 707 MET cc_start: 0.8463 (mtt) cc_final: 0.8214 (mtp) REVERT: A 801 GLN cc_start: 0.8394 (mm-40) cc_final: 0.8085 (tp40) REVERT: A 883 ARG cc_start: 0.8182 (mpt180) cc_final: 0.7803 (mpt180) REVERT: A 886 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8278 (mt-10) REVERT: A 965 SER cc_start: 0.8790 (t) cc_final: 0.8432 (p) REVERT: A 996 LYS cc_start: 0.8572 (mttm) cc_final: 0.8174 (mtmm) REVERT: A 1006 THR cc_start: 0.8652 (m) cc_final: 0.8203 (p) REVERT: A 1020 LYS cc_start: 0.8585 (mttt) cc_final: 0.8282 (mttp) REVERT: A 1021 LYS cc_start: 0.8463 (mmtp) cc_final: 0.8201 (mmtm) REVERT: A 1049 GLU cc_start: 0.8229 (tp30) cc_final: 0.8007 (tp30) REVERT: A 1112 TYR cc_start: 0.8454 (t80) cc_final: 0.8175 (t80) REVERT: A 1174 GLU cc_start: 0.8280 (tt0) cc_final: 0.7601 (tt0) REVERT: A 1207 ARG cc_start: 0.7422 (ttm110) cc_final: 0.7194 (ttm170) REVERT: A 1282 GLU cc_start: 0.7733 (mp0) cc_final: 0.7234 (mp0) REVERT: A 1403 GLN cc_start: 0.8531 (mm110) cc_final: 0.8299 (mm110) outliers start: 44 outliers final: 15 residues processed: 459 average time/residue: 0.2865 time to fit residues: 182.9160 Evaluate side-chains 414 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 399 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1274 SER Chi-restraints excluded: chain A residue 1396 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 126 optimal weight: 2.9990 chunk 143 optimal weight: 0.7980 chunk 140 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 chunk 86 optimal weight: 0.2980 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 110 optimal weight: 0.4980 chunk 22 optimal weight: 4.9990 chunk 12 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: ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 GLN D 245 GLN A 105 GLN A 122 ASN A 172 ASN A 229 HIS A 438 HIS A 451 ASN ** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 920 GLN A1120 ASN A1322 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.142806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.124334 restraints weight = 21492.980| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.80 r_work: 0.3576 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12984 Z= 0.129 Angle : 0.601 11.265 17592 Z= 0.306 Chirality : 0.043 0.231 2061 Planarity : 0.005 0.054 2226 Dihedral : 4.082 24.023 1733 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 2.64 % Allowed : 26.17 % Favored : 71.19 % 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: 1.14 (0.21), residues: 1588 helix: 1.60 (0.17), residues: 893 sheet: -0.07 (0.55), residues: 89 loop : -0.32 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 982 HIS 0.006 0.001 HIS B 234 PHE 0.020 0.001 PHE A1197 TYR 0.014 0.001 TYR A 679 ARG 0.007 0.001 ARG A 742 Details of bonding type rmsd hydrogen bonds : bond 0.04221 ( 690) hydrogen bonds : angle 4.19179 ( 2001) metal coordination : bond 0.01644 ( 7) metal coordination : angle 0.24394 ( 1) covalent geometry : bond 0.00284 (12977) covalent geometry : angle 0.60118 (17591) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 415 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 MET cc_start: 0.6426 (tpp) cc_final: 0.6052 (tpp) REVERT: B 274 LYS cc_start: 0.7966 (OUTLIER) cc_final: 0.7721 (mmtp) REVERT: C 228 MET cc_start: 0.5444 (mmm) cc_final: 0.5243 (mmt) REVERT: C 276 MET cc_start: 0.7336 (ttp) cc_final: 0.7063 (ttp) REVERT: D 221 ILE cc_start: 0.8385 (tp) cc_final: 0.8048 (tp) REVERT: E 222 MET cc_start: 0.8181 (mmm) cc_final: 0.7775 (mpp) REVERT: E 248 MET cc_start: 0.7450 (mtp) cc_final: 0.7099 (mtp) REVERT: A 50 LYS cc_start: 0.8708 (tttm) cc_final: 0.8428 (ttmm) REVERT: A 64 LYS cc_start: 0.8466 (ttpp) cc_final: 0.8258 (ttpp) REVERT: A 66 ILE cc_start: 0.8578 (tt) cc_final: 0.8299 (pt) REVERT: A 69 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7600 (mm-30) REVERT: A 94 ILE cc_start: 0.8148 (tt) cc_final: 0.7811 (tp) REVERT: A 107 MET cc_start: 0.6806 (ttp) cc_final: 0.6046 (ttp) REVERT: A 137 ASN cc_start: 0.8338 (t0) cc_final: 0.8095 (t0) REVERT: A 138 GLN cc_start: 0.8466 (tm-30) cc_final: 0.8045 (tm-30) REVERT: A 184 MET cc_start: 0.8018 (tmm) cc_final: 0.7478 (ttt) REVERT: A 207 ILE cc_start: 0.8364 (OUTLIER) cc_final: 0.8120 (mt) REVERT: A 214 LEU cc_start: 0.8565 (tp) cc_final: 0.8363 (tt) REVERT: A 279 ASP cc_start: 0.8106 (m-30) cc_final: 0.7865 (m-30) REVERT: A 360 GLU cc_start: 0.7483 (mm-30) cc_final: 0.7175 (mm-30) REVERT: A 366 ARG cc_start: 0.8440 (mmt90) cc_final: 0.8104 (mmt90) REVERT: A 394 PHE cc_start: 0.8084 (t80) cc_final: 0.7789 (t80) REVERT: A 428 ASN cc_start: 0.8095 (p0) cc_final: 0.7885 (p0) REVERT: A 437 ARG cc_start: 0.8106 (ttp80) cc_final: 0.7675 (ttt180) REVERT: A 442 GLU cc_start: 0.7838 (tt0) cc_final: 0.7580 (tt0) REVERT: A 457 MET cc_start: 0.8057 (mpp) cc_final: 0.7739 (mtm) REVERT: A 499 GLN cc_start: 0.8345 (tp40) cc_final: 0.7824 (tp40) REVERT: A 503 ASP cc_start: 0.7901 (m-30) cc_final: 0.7459 (m-30) REVERT: A 539 GLU cc_start: 0.7656 (tp30) cc_final: 0.7316 (tp30) REVERT: A 553 LYS cc_start: 0.8544 (tttp) cc_final: 0.8328 (tttm) REVERT: A 579 GLU cc_start: 0.7521 (mm-30) cc_final: 0.7300 (mm-30) REVERT: A 659 PHE cc_start: 0.5974 (OUTLIER) cc_final: 0.5770 (m-10) REVERT: A 710 THR cc_start: 0.8719 (m) cc_final: 0.8154 (p) REVERT: A 797 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7699 (mm-30) REVERT: A 801 GLN cc_start: 0.8327 (mm-40) cc_final: 0.8018 (tp40) REVERT: A 826 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7679 (mp0) REVERT: A 883 ARG cc_start: 0.8214 (mpt180) cc_final: 0.7750 (mpt180) REVERT: A 886 GLU cc_start: 0.8462 (mt-10) cc_final: 0.8141 (mt-10) REVERT: A 933 ILE cc_start: 0.8806 (mt) cc_final: 0.8589 (mp) REVERT: A 965 SER cc_start: 0.8774 (t) cc_final: 0.8447 (m) REVERT: A 996 LYS cc_start: 0.8510 (mttm) cc_final: 0.8181 (mtmm) REVERT: A 1006 THR cc_start: 0.8674 (m) cc_final: 0.8208 (p) REVERT: A 1021 LYS cc_start: 0.8450 (mmtp) cc_final: 0.8175 (mmtm) REVERT: A 1030 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8474 (mtp85) REVERT: A 1041 SER cc_start: 0.8484 (t) cc_final: 0.8273 (t) REVERT: A 1112 TYR cc_start: 0.8434 (t80) cc_final: 0.8180 (t80) REVERT: A 1141 THR cc_start: 0.8761 (m) cc_final: 0.8182 (p) REVERT: A 1174 GLU cc_start: 0.8253 (tt0) cc_final: 0.7647 (tt0) REVERT: A 1249 LEU cc_start: 0.8564 (mt) cc_final: 0.8324 (mm) REVERT: A 1282 GLU cc_start: 0.7800 (mp0) cc_final: 0.7314 (mp0) REVERT: A 1320 PHE cc_start: 0.7747 (m-10) cc_final: 0.7501 (m-10) REVERT: A 1393 LEU cc_start: 0.8159 (tp) cc_final: 0.7948 (tt) outliers start: 38 outliers final: 20 residues processed: 431 average time/residue: 0.2705 time to fit residues: 161.4361 Evaluate side-chains 420 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 396 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 420 TRP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1030 ARG Chi-restraints excluded: chain A residue 1055 LEU Chi-restraints excluded: chain A residue 1234 SER Chi-restraints excluded: chain A residue 1235 MET Chi-restraints excluded: chain A residue 1354 ILE Chi-restraints excluded: chain A residue 1389 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 99 optimal weight: 0.5980 chunk 50 optimal weight: 0.9990 chunk 131 optimal weight: 0.0370 chunk 28 optimal weight: 2.9990 chunk 137 optimal weight: 0.0980 chunk 4 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 106 optimal weight: 1.9990 overall best weight: 0.5260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 GLN A 172 ASN A 451 ASN ** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1322 HIS ** A1328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.147709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.128545 restraints weight = 21259.952| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.88 r_work: 0.3567 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.5275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12984 Z= 0.124 Angle : 0.595 10.257 17592 Z= 0.302 Chirality : 0.042 0.226 2061 Planarity : 0.004 0.052 2226 Dihedral : 4.018 23.388 1733 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 3.62 % Allowed : 25.26 % Favored : 71.12 % 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: 1.18 (0.21), residues: 1588 helix: 1.63 (0.18), residues: 895 sheet: 0.03 (0.59), residues: 81 loop : -0.31 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 982 HIS 0.008 0.001 HIS B 234 PHE 0.022 0.001 PHE A1197 TYR 0.016 0.001 TYR A 447 ARG 0.006 0.000 ARG A 742 Details of bonding type rmsd hydrogen bonds : bond 0.04091 ( 690) hydrogen bonds : angle 4.07655 ( 2001) metal coordination : bond 0.01680 ( 7) metal coordination : angle 0.19254 ( 1) covalent geometry : bond 0.00272 (12977) covalent geometry : angle 0.59460 (17591) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 406 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 MET cc_start: 0.6352 (tpp) cc_final: 0.5978 (tpp) REVERT: B 269 MET cc_start: 0.7023 (mmm) cc_final: 0.6728 (mmm) REVERT: C 276 MET cc_start: 0.7218 (ttp) cc_final: 0.6963 (ttp) REVERT: D 245 GLN cc_start: 0.8497 (OUTLIER) cc_final: 0.8262 (pm20) REVERT: E 222 MET cc_start: 0.8236 (mmm) cc_final: 0.7825 (mpp) REVERT: A 66 ILE cc_start: 0.8548 (tt) cc_final: 0.8282 (pt) REVERT: A 69 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7560 (mm-30) REVERT: A 94 ILE cc_start: 0.8140 (tt) cc_final: 0.7786 (tp) REVERT: A 104 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7420 (ttm110) REVERT: A 137 ASN cc_start: 0.8363 (t0) cc_final: 0.8129 (t0) REVERT: A 138 GLN cc_start: 0.8471 (tm-30) cc_final: 0.8243 (tm-30) REVERT: A 165 GLU cc_start: 0.7857 (mp0) cc_final: 0.7041 (mp0) REVERT: A 207 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8117 (mt) REVERT: A 214 LEU cc_start: 0.8574 (tp) cc_final: 0.8361 (tt) REVERT: A 279 ASP cc_start: 0.8105 (m-30) cc_final: 0.7865 (m-30) REVERT: A 313 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8269 (tttm) REVERT: A 337 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7539 (mt-10) REVERT: A 360 GLU cc_start: 0.7528 (mm-30) cc_final: 0.7206 (mm-30) REVERT: A 366 ARG cc_start: 0.8509 (mmt90) cc_final: 0.8139 (mmt90) REVERT: A 428 ASN cc_start: 0.8120 (p0) cc_final: 0.7915 (p0) REVERT: A 437 ARG cc_start: 0.8210 (ttp80) cc_final: 0.7762 (ttt180) REVERT: A 442 GLU cc_start: 0.7828 (tt0) cc_final: 0.7604 (tt0) REVERT: A 457 MET cc_start: 0.8214 (mpp) cc_final: 0.7916 (mtm) REVERT: A 489 MET cc_start: 0.8403 (mtp) cc_final: 0.8107 (ttm) REVERT: A 499 GLN cc_start: 0.8359 (tp40) cc_final: 0.7777 (tp40) REVERT: A 503 ASP cc_start: 0.7865 (m-30) cc_final: 0.7427 (m-30) REVERT: A 539 GLU cc_start: 0.7685 (tp30) cc_final: 0.7341 (tp30) REVERT: A 553 LYS cc_start: 0.8556 (tttp) cc_final: 0.8330 (tttm) REVERT: A 579 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7294 (mm-30) REVERT: A 659 PHE cc_start: 0.6189 (OUTLIER) cc_final: 0.5863 (m-10) REVERT: A 710 THR cc_start: 0.8675 (m) cc_final: 0.8150 (p) REVERT: A 793 LEU cc_start: 0.8388 (mt) cc_final: 0.8132 (mp) REVERT: A 797 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7659 (mm-30) REVERT: A 801 GLN cc_start: 0.8292 (mm-40) cc_final: 0.8080 (tp40) REVERT: A 883 ARG cc_start: 0.8192 (mpt180) cc_final: 0.7729 (mpt180) REVERT: A 886 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8197 (mt-10) REVERT: A 933 ILE cc_start: 0.8832 (mt) cc_final: 0.8608 (mp) REVERT: A 965 SER cc_start: 0.8763 (t) cc_final: 0.8444 (m) REVERT: A 996 LYS cc_start: 0.8423 (mttm) cc_final: 0.8114 (mtmm) REVERT: A 1006 THR cc_start: 0.8686 (m) cc_final: 0.8271 (p) REVERT: A 1021 LYS cc_start: 0.8458 (mmtp) cc_final: 0.8186 (mmtm) REVERT: A 1030 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7913 (ttm110) REVERT: A 1048 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7894 (tm-30) REVERT: A 1112 TYR cc_start: 0.8456 (t80) cc_final: 0.8201 (t80) REVERT: A 1141 THR cc_start: 0.8792 (m) cc_final: 0.8498 (t) REVERT: A 1174 GLU cc_start: 0.8300 (tt0) cc_final: 0.7974 (tt0) REVERT: A 1196 LYS cc_start: 0.7707 (mmmt) cc_final: 0.7403 (mmmt) REVERT: A 1249 LEU cc_start: 0.8584 (mt) cc_final: 0.8334 (mm) REVERT: A 1282 GLU cc_start: 0.7894 (mp0) cc_final: 0.7299 (mp0) REVERT: A 1373 LEU cc_start: 0.7611 (tp) cc_final: 0.7385 (mp) REVERT: A 1393 LEU cc_start: 0.8277 (tp) cc_final: 0.8071 (tt) REVERT: A 1403 GLN cc_start: 0.8547 (mm110) cc_final: 0.8310 (mm110) outliers start: 52 outliers final: 27 residues processed: 426 average time/residue: 0.2803 time to fit residues: 166.7414 Evaluate side-chains 433 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 400 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 245 GLN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 313 LYS Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 420 TRP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 444 LYS Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1030 ARG Chi-restraints excluded: chain A residue 1235 MET Chi-restraints excluded: chain A residue 1354 ILE Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1396 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 80 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 137 optimal weight: 0.8980 chunk 139 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 93 optimal weight: 0.0970 chunk 134 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 GLN A 172 ASN A 451 ASN ** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 HIS ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1120 ASN A1322 HIS A1328 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.142070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.123235 restraints weight = 21976.990| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.88 r_work: 0.3553 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12984 Z= 0.125 Angle : 0.597 10.714 17592 Z= 0.303 Chirality : 0.042 0.232 2061 Planarity : 0.004 0.051 2226 Dihedral : 4.013 24.230 1733 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.83 % Allowed : 25.05 % Favored : 71.12 % 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: 1.23 (0.21), residues: 1588 helix: 1.65 (0.18), residues: 891 sheet: 0.09 (0.60), residues: 81 loop : -0.24 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 182 HIS 0.008 0.001 HIS B 234 PHE 0.022 0.001 PHE A1197 TYR 0.016 0.001 TYR A 679 ARG 0.007 0.000 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 690) hydrogen bonds : angle 4.05740 ( 2001) metal coordination : bond 0.01755 ( 7) metal coordination : angle 0.18853 ( 1) covalent geometry : bond 0.00275 (12977) covalent geometry : angle 0.59745 (17591) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 417 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 MET cc_start: 0.6497 (tpp) cc_final: 0.6089 (tpp) REVERT: B 269 MET cc_start: 0.7091 (mmm) cc_final: 0.6613 (mmm) REVERT: C 276 MET cc_start: 0.7270 (ttp) cc_final: 0.6971 (ttp) REVERT: D 236 GLU cc_start: 0.6732 (mm-30) cc_final: 0.6460 (mp0) REVERT: E 222 MET cc_start: 0.8186 (mmm) cc_final: 0.7780 (mpp) REVERT: A 27 ILE cc_start: 0.8526 (pt) cc_final: 0.8158 (mt) REVERT: A 66 ILE cc_start: 0.8524 (tt) cc_final: 0.8264 (pt) REVERT: A 69 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7573 (mm-30) REVERT: A 94 ILE cc_start: 0.8093 (tt) cc_final: 0.7718 (tp) REVERT: A 104 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7325 (ttm110) REVERT: A 137 ASN cc_start: 0.8379 (t0) cc_final: 0.8155 (t0) REVERT: A 138 GLN cc_start: 0.8468 (tm-30) cc_final: 0.8238 (tm-30) REVERT: A 165 GLU cc_start: 0.7910 (mp0) cc_final: 0.7075 (mp0) REVERT: A 179 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8179 (p) REVERT: A 184 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7073 (tmm) REVERT: A 207 ILE cc_start: 0.8385 (OUTLIER) cc_final: 0.8139 (mt) REVERT: A 279 ASP cc_start: 0.8194 (m-30) cc_final: 0.7953 (m-30) REVERT: A 286 ASP cc_start: 0.7693 (p0) cc_final: 0.7481 (p0) REVERT: A 313 LYS cc_start: 0.8536 (tttp) cc_final: 0.8303 (tttm) REVERT: A 337 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7537 (mt-10) REVERT: A 360 GLU cc_start: 0.7539 (mm-30) cc_final: 0.7200 (mm-30) REVERT: A 366 ARG cc_start: 0.8425 (mmt90) cc_final: 0.8045 (mmt90) REVERT: A 428 ASN cc_start: 0.8232 (p0) cc_final: 0.8019 (p0) REVERT: A 437 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7887 (ttt180) REVERT: A 442 GLU cc_start: 0.7872 (tt0) cc_final: 0.7656 (tt0) REVERT: A 457 MET cc_start: 0.8330 (mpp) cc_final: 0.8025 (mtm) REVERT: A 489 MET cc_start: 0.8414 (mtp) cc_final: 0.8177 (ttm) REVERT: A 499 GLN cc_start: 0.8359 (tp40) cc_final: 0.7783 (tp40) REVERT: A 503 ASP cc_start: 0.7918 (m-30) cc_final: 0.7471 (m-30) REVERT: A 539 GLU cc_start: 0.7672 (tp30) cc_final: 0.7325 (tp30) REVERT: A 553 LYS cc_start: 0.8593 (tttp) cc_final: 0.8383 (tttm) REVERT: A 579 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7243 (mm-30) REVERT: A 601 LYS cc_start: 0.7265 (mtmt) cc_final: 0.6942 (mtmt) REVERT: A 659 PHE cc_start: 0.6336 (OUTLIER) cc_final: 0.5980 (m-10) REVERT: A 661 ILE cc_start: 0.7124 (mt) cc_final: 0.6803 (tt) REVERT: A 710 THR cc_start: 0.8696 (m) cc_final: 0.8185 (p) REVERT: A 730 THR cc_start: 0.8585 (m) cc_final: 0.8148 (p) REVERT: A 738 ILE cc_start: 0.8040 (OUTLIER) cc_final: 0.7605 (mt) REVERT: A 797 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7677 (mm-30) REVERT: A 826 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7914 (mp0) REVERT: A 883 ARG cc_start: 0.8158 (mpt180) cc_final: 0.7672 (mpt180) REVERT: A 886 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8176 (mt-10) REVERT: A 933 ILE cc_start: 0.8815 (mt) cc_final: 0.8590 (mp) REVERT: A 965 SER cc_start: 0.8748 (t) cc_final: 0.8448 (m) REVERT: A 996 LYS cc_start: 0.8332 (mttm) cc_final: 0.8066 (mtmm) REVERT: A 1006 THR cc_start: 0.8719 (m) cc_final: 0.8275 (p) REVERT: A 1021 LYS cc_start: 0.8442 (mmtp) cc_final: 0.8151 (mmtm) REVERT: A 1030 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8480 (mtp85) REVERT: A 1112 TYR cc_start: 0.8457 (t80) cc_final: 0.8185 (t80) REVERT: A 1141 THR cc_start: 0.8768 (m) cc_final: 0.8494 (t) REVERT: A 1174 GLU cc_start: 0.8344 (tt0) cc_final: 0.8045 (tt0) REVERT: A 1196 LYS cc_start: 0.7707 (mmmt) cc_final: 0.7397 (mmmt) REVERT: A 1249 LEU cc_start: 0.8570 (mt) cc_final: 0.8309 (mm) REVERT: A 1267 GLN cc_start: 0.8247 (mm-40) cc_final: 0.7989 (mm-40) REVERT: A 1282 GLU cc_start: 0.7950 (mp0) cc_final: 0.7333 (mp0) REVERT: A 1373 LEU cc_start: 0.7526 (tp) cc_final: 0.7318 (mp) REVERT: A 1403 GLN cc_start: 0.8551 (mm110) cc_final: 0.8291 (mm110) outliers start: 55 outliers final: 31 residues processed: 440 average time/residue: 0.2808 time to fit residues: 173.1566 Evaluate side-chains 446 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 408 time to evaluate : 1.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 420 TRP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 755 MET Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 978 CYS Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1030 ARG Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain A residue 1234 SER Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1354 ILE Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1396 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 58 optimal weight: 1.9990 chunk 118 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 98 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 142 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 245 GLN A 395 GLN A 451 ASN ** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1120 ASN A1322 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.137673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.119005 restraints weight = 21678.289| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 2.82 r_work: 0.3465 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.5982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 12984 Z= 0.187 Angle : 0.656 11.139 17592 Z= 0.334 Chirality : 0.045 0.233 2061 Planarity : 0.005 0.059 2226 Dihedral : 4.251 26.075 1733 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.34 % Allowed : 26.03 % Favored : 70.63 % 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: 1.00 (0.21), residues: 1588 helix: 1.45 (0.17), residues: 894 sheet: 0.01 (0.59), residues: 81 loop : -0.35 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 79 HIS 0.006 0.001 HIS B 234 PHE 0.022 0.002 PHE A1197 TYR 0.030 0.002 TYR A 225 ARG 0.005 0.001 ARG A 742 Details of bonding type rmsd hydrogen bonds : bond 0.04588 ( 690) hydrogen bonds : angle 4.18237 ( 2001) metal coordination : bond 0.02891 ( 7) metal coordination : angle 0.27667 ( 1) covalent geometry : bond 0.00422 (12977) covalent geometry : angle 0.65641 (17591) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 485 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 437 time to evaluate : 1.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 MET cc_start: 0.6774 (tpp) cc_final: 0.6335 (tpp) REVERT: B 269 MET cc_start: 0.7143 (mmm) cc_final: 0.6765 (mmm) REVERT: C 276 MET cc_start: 0.7249 (ttp) cc_final: 0.6905 (ttp) REVERT: E 232 LEU cc_start: 0.9157 (pp) cc_final: 0.8921 (pp) REVERT: A 27 ILE cc_start: 0.8647 (pt) cc_final: 0.8353 (mt) REVERT: A 62 ARG cc_start: 0.8670 (mtm-85) cc_final: 0.8424 (mtt180) REVERT: A 69 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7640 (mm-30) REVERT: A 94 ILE cc_start: 0.8178 (tt) cc_final: 0.7786 (tp) REVERT: A 137 ASN cc_start: 0.8398 (t0) cc_final: 0.8184 (t0) REVERT: A 138 GLN cc_start: 0.8444 (tm-30) cc_final: 0.8189 (tm-30) REVERT: A 172 ASN cc_start: 0.8368 (m-40) cc_final: 0.8108 (m-40) REVERT: A 184 MET cc_start: 0.7770 (OUTLIER) cc_final: 0.7101 (tmm) REVERT: A 207 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8367 (mt) REVERT: A 279 ASP cc_start: 0.8276 (m-30) cc_final: 0.8076 (m-30) REVERT: A 337 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7696 (mt-10) REVERT: A 360 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7185 (mm-30) REVERT: A 366 ARG cc_start: 0.8364 (mmt90) cc_final: 0.7983 (mmt90) REVERT: A 436 MET cc_start: 0.8711 (mmm) cc_final: 0.8415 (mtp) REVERT: A 437 ARG cc_start: 0.8308 (ttp80) cc_final: 0.7978 (ttt180) REVERT: A 442 GLU cc_start: 0.7947 (tt0) cc_final: 0.7690 (tt0) REVERT: A 524 ASP cc_start: 0.8084 (t0) cc_final: 0.7797 (t0) REVERT: A 539 GLU cc_start: 0.7700 (tp30) cc_final: 0.7356 (tp30) REVERT: A 550 TYR cc_start: 0.8735 (m-80) cc_final: 0.8255 (m-80) REVERT: A 555 LYS cc_start: 0.8430 (mttp) cc_final: 0.7771 (mttt) REVERT: A 579 GLU cc_start: 0.7555 (mm-30) cc_final: 0.7262 (mm-30) REVERT: A 601 LYS cc_start: 0.7424 (mtmt) cc_final: 0.7058 (mtmt) REVERT: A 659 PHE cc_start: 0.6655 (OUTLIER) cc_final: 0.6109 (m-10) REVERT: A 661 ILE cc_start: 0.7514 (mt) cc_final: 0.7251 (tt) REVERT: A 674 CYS cc_start: 0.8408 (p) cc_final: 0.7940 (m) REVERT: A 710 THR cc_start: 0.8752 (m) cc_final: 0.8280 (p) REVERT: A 730 THR cc_start: 0.8603 (m) cc_final: 0.8178 (p) REVERT: A 738 ILE cc_start: 0.8056 (OUTLIER) cc_final: 0.7747 (mt) REVERT: A 764 SER cc_start: 0.8674 (m) cc_final: 0.8351 (p) REVERT: A 790 VAL cc_start: 0.8983 (t) cc_final: 0.8747 (p) REVERT: A 793 LEU cc_start: 0.8496 (mp) cc_final: 0.8233 (mp) REVERT: A 797 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7718 (mm-30) REVERT: A 883 ARG cc_start: 0.8135 (mpt180) cc_final: 0.7813 (mpt180) REVERT: A 886 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8116 (mt-10) REVERT: A 898 ASN cc_start: 0.8537 (t0) cc_final: 0.8330 (t0) REVERT: A 965 SER cc_start: 0.8776 (t) cc_final: 0.8490 (m) REVERT: A 996 LYS cc_start: 0.8294 (mttm) cc_final: 0.7955 (mtmm) REVERT: A 1021 LYS cc_start: 0.8482 (mmtp) cc_final: 0.8208 (mmtm) REVERT: A 1030 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7972 (ttm110) REVERT: A 1105 LYS cc_start: 0.8509 (mmtm) cc_final: 0.8086 (mmmm) REVERT: A 1141 THR cc_start: 0.8757 (m) cc_final: 0.8178 (p) REVERT: A 1143 SER cc_start: 0.8500 (p) cc_final: 0.8278 (m) REVERT: A 1174 GLU cc_start: 0.8408 (tt0) cc_final: 0.8045 (tt0) REVERT: A 1196 LYS cc_start: 0.7738 (mmmt) cc_final: 0.7417 (mmmt) REVERT: A 1249 LEU cc_start: 0.8603 (mt) cc_final: 0.8330 (mm) REVERT: A 1265 SER cc_start: 0.8592 (m) cc_final: 0.8177 (p) REVERT: A 1267 GLN cc_start: 0.8285 (mm-40) cc_final: 0.8064 (mm-40) REVERT: A 1282 GLU cc_start: 0.7892 (mp0) cc_final: 0.7314 (mp0) outliers start: 48 outliers final: 33 residues processed: 456 average time/residue: 0.2835 time to fit residues: 180.7968 Evaluate side-chains 461 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 423 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain A residue 50 LYS Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 420 TRP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 495 SER Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 725 GLN Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 876 ASN Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1030 ARG Chi-restraints excluded: chain A residue 1118 SER Chi-restraints excluded: chain A residue 1169 THR Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain A residue 1234 SER Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1354 ILE Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1396 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 53 optimal weight: 0.7980 chunk 77 optimal weight: 0.0770 chunk 3 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 127 optimal weight: 3.9990 chunk 156 optimal weight: 0.0030 chunk 92 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 121 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 overall best weight: 0.3748 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 245 GLN A 395 GLN A 416 HIS ** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1120 ASN A1322 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.141138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.122682 restraints weight = 21803.511| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.82 r_work: 0.3516 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.6140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12984 Z= 0.120 Angle : 0.626 11.774 17592 Z= 0.316 Chirality : 0.043 0.243 2061 Planarity : 0.005 0.050 2226 Dihedral : 4.078 24.867 1733 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.51 % Allowed : 27.70 % Favored : 69.80 % 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: 1.06 (0.21), residues: 1588 helix: 1.52 (0.18), residues: 900 sheet: 0.05 (0.59), residues: 81 loop : -0.39 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 982 HIS 0.007 0.001 HIS B 234 PHE 0.022 0.001 PHE A1197 TYR 0.029 0.001 TYR A 225 ARG 0.010 0.001 ARG A 742 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 690) hydrogen bonds : angle 4.02793 ( 2001) metal coordination : bond 0.01145 ( 7) metal coordination : angle 0.25463 ( 1) covalent geometry : bond 0.00262 (12977) covalent geometry : angle 0.62590 (17591) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 421 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 MET cc_start: 0.6681 (tpp) cc_final: 0.6251 (tpp) REVERT: B 269 MET cc_start: 0.7117 (mmm) cc_final: 0.6715 (mmm) REVERT: C 276 MET cc_start: 0.7100 (ttp) cc_final: 0.6799 (ttp) REVERT: E 232 LEU cc_start: 0.9104 (pp) cc_final: 0.8593 (pp) REVERT: A 27 ILE cc_start: 0.8598 (pt) cc_final: 0.8271 (mt) REVERT: A 68 VAL cc_start: 0.9002 (t) cc_final: 0.8728 (m) REVERT: A 69 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7544 (mm-30) REVERT: A 94 ILE cc_start: 0.8126 (tt) cc_final: 0.7735 (tp) REVERT: A 137 ASN cc_start: 0.8390 (t0) cc_final: 0.8171 (t0) REVERT: A 138 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8246 (tm-30) REVERT: A 165 GLU cc_start: 0.8030 (mp0) cc_final: 0.7157 (mp0) REVERT: A 172 ASN cc_start: 0.8295 (m-40) cc_final: 0.8036 (m-40) REVERT: A 184 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7090 (tmm) REVERT: A 207 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.8199 (mt) REVERT: A 279 ASP cc_start: 0.8251 (m-30) cc_final: 0.8037 (m-30) REVERT: A 337 GLU cc_start: 0.7953 (mt-10) cc_final: 0.7676 (mt-10) REVERT: A 360 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7158 (mm-30) REVERT: A 366 ARG cc_start: 0.8323 (mmt90) cc_final: 0.7930 (mmt90) REVERT: A 431 LYS cc_start: 0.7898 (mtmm) cc_final: 0.6917 (mtmm) REVERT: A 435 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7112 (mp0) REVERT: A 437 ARG cc_start: 0.8268 (ttp80) cc_final: 0.7995 (ttt180) REVERT: A 442 GLU cc_start: 0.7857 (tt0) cc_final: 0.7610 (tt0) REVERT: A 489 MET cc_start: 0.8414 (mtp) cc_final: 0.8164 (ttm) REVERT: A 524 ASP cc_start: 0.8064 (t0) cc_final: 0.7773 (t0) REVERT: A 539 GLU cc_start: 0.7687 (tp30) cc_final: 0.7342 (tp30) REVERT: A 550 TYR cc_start: 0.8674 (m-80) cc_final: 0.8216 (m-80) REVERT: A 555 LYS cc_start: 0.8375 (mttp) cc_final: 0.7726 (mttt) REVERT: A 556 GLU cc_start: 0.7678 (tp30) cc_final: 0.7458 (tp30) REVERT: A 579 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7236 (mm-30) REVERT: A 601 LYS cc_start: 0.7396 (mtmt) cc_final: 0.7065 (mtmt) REVERT: A 659 PHE cc_start: 0.6574 (OUTLIER) cc_final: 0.5924 (m-10) REVERT: A 661 ILE cc_start: 0.7432 (mt) cc_final: 0.7114 (tt) REVERT: A 695 ILE cc_start: 0.8923 (mt) cc_final: 0.8705 (pt) REVERT: A 710 THR cc_start: 0.8691 (m) cc_final: 0.8223 (p) REVERT: A 730 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.8174 (p) REVERT: A 738 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7649 (mt) REVERT: A 764 SER cc_start: 0.8620 (m) cc_final: 0.8364 (p) REVERT: A 797 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7699 (mm-30) REVERT: A 883 ARG cc_start: 0.8128 (mpt180) cc_final: 0.7607 (mpt180) REVERT: A 886 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8125 (mt-10) REVERT: A 965 SER cc_start: 0.8749 (t) cc_final: 0.8472 (m) REVERT: A 996 LYS cc_start: 0.8230 (mttm) cc_final: 0.7921 (mtmm) REVERT: A 1006 THR cc_start: 0.8767 (m) cc_final: 0.8369 (p) REVERT: A 1021 LYS cc_start: 0.8390 (mmtp) cc_final: 0.8127 (mmtm) REVERT: A 1118 SER cc_start: 0.8842 (t) cc_final: 0.8574 (p) REVERT: A 1141 THR cc_start: 0.8724 (m) cc_final: 0.8473 (t) REVERT: A 1143 SER cc_start: 0.8485 (p) cc_final: 0.8257 (m) REVERT: A 1174 GLU cc_start: 0.8376 (tt0) cc_final: 0.8030 (tt0) REVERT: A 1196 LYS cc_start: 0.7736 (mmmt) cc_final: 0.7468 (mmmt) REVERT: A 1249 LEU cc_start: 0.8544 (mt) cc_final: 0.8281 (mm) REVERT: A 1265 SER cc_start: 0.8523 (m) cc_final: 0.8145 (p) REVERT: A 1267 GLN cc_start: 0.8247 (mm-40) cc_final: 0.8024 (mm-40) REVERT: A 1282 GLU cc_start: 0.7863 (mp0) cc_final: 0.7292 (mp0) REVERT: A 1393 LEU cc_start: 0.8590 (tp) cc_final: 0.8348 (tt) outliers start: 36 outliers final: 19 residues processed: 437 average time/residue: 0.2704 time to fit residues: 166.1965 Evaluate side-chains 434 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 409 time to evaluate : 1.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 420 TRP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 435 GLU Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1389 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 68 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 chunk 123 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 121 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 34 optimal weight: 0.1980 chunk 99 optimal weight: 0.8980 chunk 107 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 ASN ** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1120 ASN A1322 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.142301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.123304 restraints weight = 21457.419| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 2.85 r_work: 0.3496 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.6261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12984 Z= 0.131 Angle : 0.645 12.297 17592 Z= 0.327 Chirality : 0.043 0.242 2061 Planarity : 0.005 0.050 2226 Dihedral : 4.037 24.377 1733 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.02 % Allowed : 28.04 % Favored : 69.94 % 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: 1.06 (0.21), residues: 1588 helix: 1.51 (0.17), residues: 900 sheet: -0.05 (0.59), residues: 81 loop : -0.35 (0.25), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 982 HIS 0.013 0.001 HIS A 229 PHE 0.021 0.001 PHE A1197 TYR 0.030 0.002 TYR A 225 ARG 0.010 0.001 ARG A 742 Details of bonding type rmsd hydrogen bonds : bond 0.04052 ( 690) hydrogen bonds : angle 4.06730 ( 2001) metal coordination : bond 0.01524 ( 7) metal coordination : angle 0.00923 ( 1) covalent geometry : bond 0.00292 (12977) covalent geometry : angle 0.64537 (17591) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 416 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 MET cc_start: 0.6691 (tpp) cc_final: 0.6255 (tpp) REVERT: B 269 MET cc_start: 0.7163 (mmm) cc_final: 0.6783 (mmm) REVERT: C 276 MET cc_start: 0.7099 (ttp) cc_final: 0.6788 (ttp) REVERT: E 222 MET cc_start: 0.8119 (mmm) cc_final: 0.7496 (mpp) REVERT: A 27 ILE cc_start: 0.8609 (pt) cc_final: 0.8281 (mt) REVERT: A 68 VAL cc_start: 0.9025 (t) cc_final: 0.8764 (m) REVERT: A 69 GLU cc_start: 0.7907 (mm-30) cc_final: 0.7519 (mm-30) REVERT: A 94 ILE cc_start: 0.8111 (tt) cc_final: 0.7714 (tp) REVERT: A 137 ASN cc_start: 0.8425 (t0) cc_final: 0.8208 (t0) REVERT: A 138 GLN cc_start: 0.8455 (tm-30) cc_final: 0.8222 (tm-30) REVERT: A 165 GLU cc_start: 0.8048 (mp0) cc_final: 0.7178 (mp0) REVERT: A 172 ASN cc_start: 0.8328 (m-40) cc_final: 0.8105 (m-40) REVERT: A 184 MET cc_start: 0.7557 (OUTLIER) cc_final: 0.7153 (tmm) REVERT: A 207 ILE cc_start: 0.8511 (mt) cc_final: 0.8259 (mt) REVERT: A 279 ASP cc_start: 0.8257 (m-30) cc_final: 0.8041 (m-30) REVERT: A 337 GLU cc_start: 0.7995 (mt-10) cc_final: 0.7710 (mt-10) REVERT: A 360 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7140 (mm-30) REVERT: A 366 ARG cc_start: 0.8300 (mmt90) cc_final: 0.7899 (mmt90) REVERT: A 431 LYS cc_start: 0.7964 (mtmm) cc_final: 0.7494 (mtmm) REVERT: A 437 ARG cc_start: 0.8277 (ttp80) cc_final: 0.8019 (ttt180) REVERT: A 524 ASP cc_start: 0.8105 (t0) cc_final: 0.7874 (t0) REVERT: A 539 GLU cc_start: 0.7683 (tp30) cc_final: 0.7335 (tp30) REVERT: A 550 TYR cc_start: 0.8681 (m-80) cc_final: 0.8210 (m-80) REVERT: A 555 LYS cc_start: 0.8358 (mttp) cc_final: 0.7698 (mttt) REVERT: A 556 GLU cc_start: 0.7701 (tp30) cc_final: 0.7487 (tp30) REVERT: A 579 GLU cc_start: 0.7546 (mm-30) cc_final: 0.7244 (mm-30) REVERT: A 601 LYS cc_start: 0.7448 (mtmt) cc_final: 0.7092 (mtmt) REVERT: A 659 PHE cc_start: 0.6660 (OUTLIER) cc_final: 0.5995 (m-10) REVERT: A 661 ILE cc_start: 0.7490 (mt) cc_final: 0.7163 (tt) REVERT: A 695 ILE cc_start: 0.8895 (mt) cc_final: 0.8683 (pt) REVERT: A 710 THR cc_start: 0.8710 (m) cc_final: 0.8233 (p) REVERT: A 730 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8135 (p) REVERT: A 738 ILE cc_start: 0.8001 (OUTLIER) cc_final: 0.7632 (mt) REVERT: A 764 SER cc_start: 0.8662 (m) cc_final: 0.8375 (p) REVERT: A 797 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7694 (mm-30) REVERT: A 883 ARG cc_start: 0.8178 (mpt180) cc_final: 0.7634 (mpt180) REVERT: A 886 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8156 (mt-10) REVERT: A 920 GLN cc_start: 0.8301 (mt0) cc_final: 0.8078 (mt0) REVERT: A 965 SER cc_start: 0.8772 (t) cc_final: 0.8480 (m) REVERT: A 996 LYS cc_start: 0.8253 (mttm) cc_final: 0.7923 (mtmm) REVERT: A 1006 THR cc_start: 0.8784 (m) cc_final: 0.8357 (p) REVERT: A 1021 LYS cc_start: 0.8408 (mmtp) cc_final: 0.8146 (mmtm) REVERT: A 1105 LYS cc_start: 0.8511 (mmtm) cc_final: 0.8083 (mmmm) REVERT: A 1118 SER cc_start: 0.8847 (t) cc_final: 0.8583 (p) REVERT: A 1141 THR cc_start: 0.8729 (m) cc_final: 0.8476 (t) REVERT: A 1143 SER cc_start: 0.8507 (p) cc_final: 0.8261 (m) REVERT: A 1174 GLU cc_start: 0.8421 (tt0) cc_final: 0.7702 (tt0) REVERT: A 1196 LYS cc_start: 0.7753 (mmmt) cc_final: 0.7481 (mmmt) REVERT: A 1249 LEU cc_start: 0.8561 (mt) cc_final: 0.8294 (mm) REVERT: A 1265 SER cc_start: 0.8560 (m) cc_final: 0.8173 (p) REVERT: A 1267 GLN cc_start: 0.8237 (mm-40) cc_final: 0.8007 (mm-40) REVERT: A 1282 GLU cc_start: 0.7874 (mp0) cc_final: 0.7307 (mp0) REVERT: A 1393 LEU cc_start: 0.8610 (tp) cc_final: 0.8372 (tt) outliers start: 29 outliers final: 20 residues processed: 429 average time/residue: 0.2707 time to fit residues: 162.7207 Evaluate side-chains 427 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 403 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 174 GLU Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 420 TRP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain A residue 1389 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 65 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 78 optimal weight: 0.0670 chunk 12 optimal weight: 8.9990 chunk 33 optimal weight: 0.0980 chunk 144 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 152 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 143 optimal weight: 0.6980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN A 122 ASN ** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1120 ASN A1322 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.143512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.124414 restraints weight = 21432.105| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 2.87 r_work: 0.3492 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.6376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12984 Z= 0.129 Angle : 0.663 14.926 17592 Z= 0.337 Chirality : 0.044 0.247 2061 Planarity : 0.005 0.070 2226 Dihedral : 3.998 23.103 1733 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.95 % Allowed : 28.67 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.21), residues: 1588 helix: 1.52 (0.17), residues: 901 sheet: -0.09 (0.59), residues: 81 loop : -0.32 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 982 HIS 0.012 0.001 HIS A 229 PHE 0.020 0.001 PHE A1197 TYR 0.032 0.001 TYR A 225 ARG 0.011 0.001 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 690) hydrogen bonds : angle 4.08625 ( 2001) metal coordination : bond 0.01666 ( 7) metal coordination : angle 0.17920 ( 1) covalent geometry : bond 0.00285 (12977) covalent geometry : angle 0.66266 (17591) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3176 Ramachandran restraints generated. 1588 Oldfield, 0 Emsley, 1588 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 403 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 MET cc_start: 0.6711 (tpp) cc_final: 0.6261 (tpp) REVERT: B 269 MET cc_start: 0.7162 (mmm) cc_final: 0.6700 (mmm) REVERT: C 276 MET cc_start: 0.6980 (ttp) cc_final: 0.6677 (ttp) REVERT: E 222 MET cc_start: 0.8096 (mmm) cc_final: 0.7480 (mpp) REVERT: A 27 ILE cc_start: 0.8597 (pt) cc_final: 0.8289 (mt) REVERT: A 68 VAL cc_start: 0.9018 (t) cc_final: 0.8764 (m) REVERT: A 69 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7510 (mm-30) REVERT: A 137 ASN cc_start: 0.8421 (t0) cc_final: 0.8216 (t0) REVERT: A 138 GLN cc_start: 0.8448 (tm-30) cc_final: 0.8229 (tm-30) REVERT: A 165 GLU cc_start: 0.8040 (mp0) cc_final: 0.7741 (mt-10) REVERT: A 184 MET cc_start: 0.7596 (OUTLIER) cc_final: 0.7154 (tmm) REVERT: A 207 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8227 (mt) REVERT: A 279 ASP cc_start: 0.8258 (m-30) cc_final: 0.8039 (m-30) REVERT: A 332 ASN cc_start: 0.8837 (m-40) cc_final: 0.8583 (t0) REVERT: A 337 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7713 (mt-10) REVERT: A 360 GLU cc_start: 0.7603 (mm-30) cc_final: 0.7162 (mm-30) REVERT: A 366 ARG cc_start: 0.8318 (mmt90) cc_final: 0.7918 (mmt90) REVERT: A 437 ARG cc_start: 0.8289 (ttp80) cc_final: 0.8014 (ttt180) REVERT: A 446 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7976 (mp0) REVERT: A 489 MET cc_start: 0.8478 (ttm) cc_final: 0.8203 (mtp) REVERT: A 494 ARG cc_start: 0.7798 (mtp180) cc_final: 0.7389 (mmm-85) REVERT: A 501 TYR cc_start: 0.8459 (m-80) cc_final: 0.8048 (m-80) REVERT: A 531 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7319 (tp30) REVERT: A 539 GLU cc_start: 0.7670 (tp30) cc_final: 0.7321 (tp30) REVERT: A 550 TYR cc_start: 0.8684 (m-80) cc_final: 0.8224 (m-80) REVERT: A 555 LYS cc_start: 0.8360 (mttp) cc_final: 0.7708 (mttt) REVERT: A 556 GLU cc_start: 0.7716 (tp30) cc_final: 0.7509 (tp30) REVERT: A 579 GLU cc_start: 0.7541 (mm-30) cc_final: 0.7240 (mm-30) REVERT: A 601 LYS cc_start: 0.7470 (mtmt) cc_final: 0.7108 (mtmt) REVERT: A 659 PHE cc_start: 0.6679 (OUTLIER) cc_final: 0.6006 (m-10) REVERT: A 661 ILE cc_start: 0.7514 (mt) cc_final: 0.7188 (tt) REVERT: A 710 THR cc_start: 0.8703 (m) cc_final: 0.8204 (p) REVERT: A 730 THR cc_start: 0.8560 (OUTLIER) cc_final: 0.8141 (p) REVERT: A 738 ILE cc_start: 0.7948 (OUTLIER) cc_final: 0.7589 (mt) REVERT: A 764 SER cc_start: 0.8647 (m) cc_final: 0.8362 (p) REVERT: A 883 ARG cc_start: 0.8084 (mpt180) cc_final: 0.7747 (mpt180) REVERT: A 920 GLN cc_start: 0.8334 (mt0) cc_final: 0.8102 (mt0) REVERT: A 965 SER cc_start: 0.8768 (t) cc_final: 0.8491 (m) REVERT: A 996 LYS cc_start: 0.8221 (mttm) cc_final: 0.7893 (mtmm) REVERT: A 1006 THR cc_start: 0.8752 (m) cc_final: 0.8344 (p) REVERT: A 1021 LYS cc_start: 0.8376 (mmtp) cc_final: 0.8116 (mmtm) REVERT: A 1050 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7929 (mt-10) REVERT: A 1118 SER cc_start: 0.8837 (t) cc_final: 0.8574 (p) REVERT: A 1143 SER cc_start: 0.8479 (p) cc_final: 0.8269 (m) REVERT: A 1196 LYS cc_start: 0.7730 (mmmt) cc_final: 0.7471 (mmmt) REVERT: A 1249 LEU cc_start: 0.8562 (mt) cc_final: 0.8292 (mm) REVERT: A 1265 SER cc_start: 0.8564 (m) cc_final: 0.8347 (t) REVERT: A 1267 GLN cc_start: 0.8226 (mm-40) cc_final: 0.8002 (mm-40) REVERT: A 1282 GLU cc_start: 0.7882 (mp0) cc_final: 0.7316 (mp0) REVERT: A 1393 LEU cc_start: 0.8619 (tp) cc_final: 0.8382 (tt) outliers start: 28 outliers final: 19 residues processed: 413 average time/residue: 0.2754 time to fit residues: 158.2886 Evaluate side-chains 421 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 397 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 184 MET Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 246 MET Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 420 TRP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 659 PHE Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 725 GLN Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 840 LYS Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 876 ASN Chi-restraints excluded: chain A residue 946 LEU Chi-restraints excluded: chain A residue 1029 GLU Chi-restraints excluded: chain A residue 1046 GLU Chi-restraints excluded: chain A residue 1218 ILE Chi-restraints excluded: chain A residue 1389 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 140 optimal weight: 0.0060 chunk 62 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 134 optimal weight: 0.9980 chunk 131 optimal weight: 0.0770 chunk 130 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 14 optimal weight: 0.2980 chunk 28 optimal weight: 0.9980 chunk 108 optimal weight: 0.4980 overall best weight: 0.2954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 822 HIS ** A 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 914 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1120 ASN A1322 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.146649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.127552 restraints weight = 21382.333| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.87 r_work: 0.3526 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.6511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12984 Z= 0.123 Angle : 0.663 15.145 17592 Z= 0.335 Chirality : 0.043 0.245 2061 Planarity : 0.005 0.096 2226 Dihedral : 3.956 23.730 1733 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.88 % Allowed : 28.60 % Favored : 69.52 % 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: 1.14 (0.21), residues: 1588 helix: 1.59 (0.17), residues: 899 sheet: -0.12 (0.59), residues: 81 loop : -0.31 (0.25), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 982 HIS 0.009 0.001 HIS B 234 PHE 0.020 0.001 PHE A1197 TYR 0.030 0.001 TYR A 225 ARG 0.017 0.001 ARG B 231 Details of bonding type rmsd hydrogen bonds : bond 0.03893 ( 690) hydrogen bonds : angle 4.06778 ( 2001) metal coordination : bond 0.01339 ( 7) metal coordination : angle 0.06518 ( 1) covalent geometry : bond 0.00268 (12977) covalent geometry : angle 0.66253 (17591) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7326.44 seconds wall clock time: 128 minutes 34.95 seconds (7714.95 seconds total)