Starting phenix.real_space_refine on Sun Nov 17 13:58:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izm_35865/11_2024/8izm_35865.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izm_35865/11_2024/8izm_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izm_35865/11_2024/8izm_35865.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izm_35865/11_2024/8izm_35865.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izm_35865/11_2024/8izm_35865.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8izm_35865/11_2024/8izm_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 8.36, per 1000 atoms: 0.66 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: 3.06 Conformation dependent library (CDL) restraints added in 1.6 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: 1.38 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: 3.84 Time building geometry restraints manager: 3.58 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: 3.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.340 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.900 ------------------------------------------------------------------------------- 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 12977 Z= 0.441 Angle : 1.069 11.939 17591 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 *********************** 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 : 1.522 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: 0.2996 time to fit residues: 206.3000 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 : 1.494 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 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 12977 Z= 0.246 Angle : 0.654 11.609 17591 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 *********************** 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 : 1.438 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 275 ILE cc_start: 0.7522 (OUTLIER) cc_final: 0.7053 (mp) REVERT: C 248 MET cc_start: 0.6017 (mmt) cc_final: 0.5635 (mmt) REVERT: E 222 MET cc_start: 0.8553 (mmm) cc_final: 0.7979 (mpp) REVERT: A 15 ASN cc_start: 0.7892 (m-40) cc_final: 0.7565 (m-40) REVERT: A 50 LYS cc_start: 0.8407 (tttm) cc_final: 0.8101 (ttmm) REVERT: A 66 ILE cc_start: 0.8509 (tt) cc_final: 0.8199 (pt) REVERT: A 76 SER cc_start: 0.8164 (p) cc_final: 0.7690 (p) REVERT: A 77 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8430 (mm) REVERT: A 94 ILE cc_start: 0.7901 (tt) cc_final: 0.7505 (tp) REVERT: A 97 ILE cc_start: 0.8197 (mt) cc_final: 0.7984 (mt) REVERT: A 107 MET cc_start: 0.6356 (ttp) cc_final: 0.5620 (ttp) REVERT: A 129 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7224 (mt-10) REVERT: A 137 ASN cc_start: 0.7948 (t0) cc_final: 0.7648 (t0) REVERT: A 138 GLN cc_start: 0.8199 (tm-30) cc_final: 0.7501 (tm-30) REVERT: A 184 MET cc_start: 0.7200 (tmm) cc_final: 0.6865 (ttt) REVERT: A 207 ILE cc_start: 0.8135 (OUTLIER) cc_final: 0.7768 (mt) REVERT: A 313 LYS cc_start: 0.8304 (tttp) cc_final: 0.7937 (ttmm) REVERT: A 322 ASN cc_start: 0.7450 (t0) cc_final: 0.7220 (m-40) REVERT: A 398 MET cc_start: 0.7815 (mmm) cc_final: 0.7574 (mmt) REVERT: A 420 TRP cc_start: 0.6974 (m-10) cc_final: 0.6293 (m100) REVERT: A 428 ASN cc_start: 0.7375 (p0) cc_final: 0.7065 (p0) REVERT: A 442 GLU cc_start: 0.7122 (tt0) cc_final: 0.6825 (tt0) REVERT: A 444 LYS cc_start: 0.7933 (mttt) cc_final: 0.7661 (mtpp) REVERT: A 457 MET cc_start: 0.7379 (mpp) cc_final: 0.6889 (mtm) REVERT: A 494 ARG cc_start: 0.6990 (ttt180) cc_final: 0.6722 (mtt180) REVERT: A 539 GLU cc_start: 0.7334 (tp30) cc_final: 0.6924 (tp30) REVERT: A 553 LYS cc_start: 0.8304 (tttp) cc_final: 0.8039 (tttp) REVERT: A 576 VAL cc_start: 0.7804 (p) cc_final: 0.7467 (m) REVERT: A 579 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6858 (mm-30) REVERT: A 661 ILE cc_start: 0.5726 (OUTLIER) cc_final: 0.5511 (tt) REVERT: A 674 CYS cc_start: 0.7808 (p) cc_final: 0.7602 (m) REVERT: A 675 LEU cc_start: 0.8672 (mt) cc_final: 0.8420 (mt) REVERT: A 692 MET cc_start: 0.8236 (mtm) cc_final: 0.7975 (mtp) REVERT: A 801 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7963 (tp40) REVERT: A 840 LYS cc_start: 0.8373 (mtpt) cc_final: 0.8163 (mtpt) REVERT: A 965 SER cc_start: 0.8462 (t) cc_final: 0.8245 (m) REVERT: A 972 ARG cc_start: 0.7767 (mtt180) cc_final: 0.7457 (mtt180) REVERT: A 982 TRP cc_start: 0.7773 (p-90) cc_final: 0.7344 (p-90) REVERT: A 998 SER cc_start: 0.8357 (t) cc_final: 0.8146 (p) REVERT: A 1006 THR cc_start: 0.8000 (m) cc_final: 0.7476 (p) REVERT: A 1020 LYS cc_start: 0.8221 (mttt) cc_final: 0.7915 (mttm) REVERT: A 1021 LYS cc_start: 0.7992 (mmtp) cc_final: 0.7752 (mptt) REVERT: A 1104 LYS cc_start: 0.8298 (mttt) cc_final: 0.7998 (mttt) REVERT: A 1112 TYR cc_start: 0.8101 (t80) cc_final: 0.7852 (t80) REVERT: A 1176 VAL cc_start: 0.7942 (m) cc_final: 0.7327 (m) REVERT: A 1249 LEU cc_start: 0.8090 (mt) cc_final: 0.7752 (mm) REVERT: A 1282 GLU cc_start: 0.7567 (mp0) cc_final: 0.7033 (mp0) REVERT: A 1403 GLN cc_start: 0.8452 (mm-40) cc_final: 0.8242 (mm110) REVERT: A 1410 ASP cc_start: 0.7881 (p0) cc_final: 0.7379 (p0) outliers start: 53 outliers final: 14 residues processed: 475 average time/residue: 0.3007 time to fit residues: 198.1207 Evaluate side-chains 429 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 411 time to evaluate : 1.813 ------------------------------------------------------------------------------- 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 80 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 chunk 128 optimal weight: 0.8980 chunk 143 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12977 Z= 0.217 Angle : 0.608 10.499 17591 Z= 0.313 Chirality : 0.044 0.318 2061 Planarity : 0.005 0.057 2226 Dihedral : 4.227 32.781 1737 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.06 % Allowed : 23.17 % Favored : 73.76 % 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: 1.01 (0.21), residues: 1588 helix: 1.54 (0.17), residues: 884 sheet: -0.31 (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 0.007 0.001 ARG A 485 *********************** 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 488 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 444 time to evaluate : 1.260 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: 0.5856 (tpp) cc_final: 0.5617 (tpp) REVERT: B 274 LYS cc_start: 0.8021 (OUTLIER) cc_final: 0.7781 (mmtp) REVERT: C 248 MET cc_start: 0.6069 (mmt) cc_final: 0.5864 (mmt) REVERT: A 15 ASN cc_start: 0.7932 (m-40) cc_final: 0.7531 (m-40) REVERT: A 50 LYS cc_start: 0.8455 (tttm) cc_final: 0.8141 (ttmm) REVERT: A 66 ILE cc_start: 0.8530 (tt) cc_final: 0.8228 (pt) REVERT: A 69 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7428 (mm-30) REVERT: A 107 MET cc_start: 0.6444 (ttp) cc_final: 0.5639 (ttp) REVERT: A 137 ASN cc_start: 0.7982 (t0) cc_final: 0.7721 (t0) REVERT: A 138 GLN cc_start: 0.8173 (tm-30) cc_final: 0.7821 (tm-30) REVERT: A 184 MET cc_start: 0.7170 (tmm) cc_final: 0.6884 (ttt) REVERT: A 207 ILE cc_start: 0.8170 (mt) cc_final: 0.7871 (mt) REVERT: A 279 ASP cc_start: 0.7848 (m-30) cc_final: 0.7560 (m-30) REVERT: A 313 LYS cc_start: 0.8395 (tttp) cc_final: 0.8178 (tttm) REVERT: A 360 GLU cc_start: 0.7317 (mm-30) cc_final: 0.6971 (mm-30) REVERT: A 366 ARG cc_start: 0.7877 (mmt90) cc_final: 0.7517 (mmt90) REVERT: A 394 PHE cc_start: 0.7589 (t80) cc_final: 0.7131 (t80) REVERT: A 428 ASN cc_start: 0.7864 (p0) cc_final: 0.7575 (p0) REVERT: A 437 ARG cc_start: 0.7689 (ttp80) cc_final: 0.7163 (ttt180) REVERT: A 442 GLU cc_start: 0.7611 (tt0) cc_final: 0.7263 (tt0) REVERT: A 444 LYS cc_start: 0.7971 (mttt) cc_final: 0.7720 (mmmt) REVERT: A 457 MET cc_start: 0.7664 (mpp) cc_final: 0.7418 (mtm) REVERT: A 494 ARG cc_start: 0.7053 (ttt180) cc_final: 0.6709 (mtt180) REVERT: A 503 ASP cc_start: 0.7528 (m-30) cc_final: 0.7196 (m-30) REVERT: A 539 GLU cc_start: 0.7350 (tp30) cc_final: 0.6962 (tp30) REVERT: A 550 TYR cc_start: 0.8521 (m-80) cc_final: 0.8255 (m-80) REVERT: A 553 LYS cc_start: 0.8334 (tttp) cc_final: 0.8053 (tttm) REVERT: A 555 LYS cc_start: 0.8125 (mttp) cc_final: 0.7511 (mttt) REVERT: A 579 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6858 (mm-30) REVERT: A 704 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8446 (mp) REVERT: A 801 GLN cc_start: 0.8188 (mm-40) cc_final: 0.7832 (tp40) REVERT: A 840 LYS cc_start: 0.8415 (mtpt) cc_final: 0.8172 (mtpt) REVERT: A 883 ARG cc_start: 0.7639 (mpt180) cc_final: 0.7172 (mpt180) REVERT: A 886 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7825 (mt-10) REVERT: A 933 ILE cc_start: 0.8432 (mt) cc_final: 0.8204 (mp) REVERT: A 965 SER cc_start: 0.8522 (t) cc_final: 0.8230 (m) REVERT: A 996 LYS cc_start: 0.8131 (mttm) cc_final: 0.7781 (mtmm) REVERT: A 1006 THR cc_start: 0.8294 (m) cc_final: 0.7730 (p) REVERT: A 1020 LYS cc_start: 0.8251 (mttt) cc_final: 0.7881 (mttp) REVERT: A 1021 LYS cc_start: 0.8091 (mmtp) cc_final: 0.7800 (mmtm) REVERT: A 1112 TYR cc_start: 0.8205 (t80) cc_final: 0.7893 (t80) REVERT: A 1174 GLU cc_start: 0.8038 (tt0) cc_final: 0.7619 (tt0) REVERT: A 1249 LEU cc_start: 0.8078 (mt) cc_final: 0.7862 (mt) REVERT: A 1282 GLU cc_start: 0.7467 (mp0) cc_final: 0.6949 (mp0) REVERT: A 1403 GLN cc_start: 0.8442 (mm110) cc_final: 0.8195 (mm110) REVERT: A 1410 ASP cc_start: 0.7662 (p0) cc_final: 0.7403 (p0) outliers start: 44 outliers final: 15 residues processed: 462 average time/residue: 0.2459 time to fit residues: 159.6713 Evaluate side-chains 418 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 401 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 228 MET Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 262 THR 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 704 LEU 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 1396 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 142 optimal weight: 0.0170 chunk 108 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 153 optimal weight: 0.0970 chunk 137 optimal weight: 0.0570 chunk 41 optimal weight: 0.8980 chunk 127 optimal weight: 0.5980 overall best weight: 0.3134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 GLN D 245 GLN A 105 GLN A 122 ASN A 172 ASN 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12977 Z= 0.164 Angle : 0.598 11.758 17591 Z= 0.301 Chirality : 0.041 0.189 2061 Planarity : 0.004 0.053 2226 Dihedral : 4.019 23.653 1733 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.78 % Allowed : 25.89 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.21), residues: 1588 helix: 1.67 (0.18), residues: 882 sheet: -0.22 (0.54), residues: 89 loop : -0.29 (0.25), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 982 HIS 0.012 0.001 HIS B 234 PHE 0.021 0.001 PHE A 319 TYR 0.015 0.001 TYR A 679 ARG 0.005 0.000 ARG A 788 *********************** 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 447 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 407 time to evaluate : 1.642 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: 0.5715 (tpp) cc_final: 0.5492 (tpp) REVERT: B 274 LYS cc_start: 0.7960 (OUTLIER) cc_final: 0.7713 (mmtp) REVERT: D 221 ILE cc_start: 0.8266 (tp) cc_final: 0.7952 (tp) REVERT: E 222 MET cc_start: 0.8380 (mmm) cc_final: 0.7841 (mpp) REVERT: A 12 VAL cc_start: 0.8542 (t) cc_final: 0.8334 (p) REVERT: A 50 LYS cc_start: 0.8456 (tttm) cc_final: 0.8123 (ttmm) REVERT: A 64 LYS cc_start: 0.8216 (ttpp) cc_final: 0.7960 (ttpp) REVERT: A 66 ILE cc_start: 0.8453 (tt) cc_final: 0.8185 (pt) REVERT: A 69 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7403 (mm-30) REVERT: A 94 ILE cc_start: 0.7796 (tt) cc_final: 0.7407 (tp) REVERT: A 137 ASN cc_start: 0.7987 (t0) cc_final: 0.7749 (t0) REVERT: A 138 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7686 (tm-30) REVERT: A 207 ILE cc_start: 0.8101 (OUTLIER) cc_final: 0.7807 (mt) REVERT: A 278 ASP cc_start: 0.7534 (m-30) cc_final: 0.7255 (m-30) REVERT: A 279 ASP cc_start: 0.7841 (m-30) cc_final: 0.7533 (m-30) REVERT: A 313 LYS cc_start: 0.8356 (tttp) cc_final: 0.8085 (tttm) REVERT: A 360 GLU cc_start: 0.7312 (mm-30) cc_final: 0.6931 (mm-30) REVERT: A 366 ARG cc_start: 0.7845 (mmt90) cc_final: 0.7477 (mmt90) REVERT: A 386 MET cc_start: 0.7829 (mtm) cc_final: 0.7155 (mtm) REVERT: A 394 PHE cc_start: 0.7783 (t80) cc_final: 0.7470 (t80) REVERT: A 428 ASN cc_start: 0.7807 (p0) cc_final: 0.7467 (p0) REVERT: A 437 ARG cc_start: 0.7750 (ttp80) cc_final: 0.7273 (ttt180) REVERT: A 442 GLU cc_start: 0.7666 (tt0) cc_final: 0.7290 (tt0) REVERT: A 444 LYS cc_start: 0.7986 (mttt) cc_final: 0.7738 (mmmt) REVERT: A 457 MET cc_start: 0.7447 (mpp) cc_final: 0.7245 (mtm) REVERT: A 499 GLN cc_start: 0.8143 (tp40) cc_final: 0.7543 (tp40) REVERT: A 503 ASP cc_start: 0.7531 (m-30) cc_final: 0.7041 (m-30) REVERT: A 527 ASP cc_start: 0.7453 (t0) cc_final: 0.7214 (t0) REVERT: A 539 GLU cc_start: 0.7335 (tp30) cc_final: 0.6947 (tp30) REVERT: A 553 LYS cc_start: 0.8320 (tttp) cc_final: 0.8027 (tttm) REVERT: A 556 GLU cc_start: 0.7355 (tp30) cc_final: 0.7101 (tp30) REVERT: A 579 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6862 (mm-30) REVERT: A 704 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8341 (mp) REVERT: A 746 GLU cc_start: 0.7308 (mp0) cc_final: 0.7045 (mp0) REVERT: A 801 GLN cc_start: 0.8157 (mm-40) cc_final: 0.7861 (tp40) REVERT: A 840 LYS cc_start: 0.8435 (mtpt) cc_final: 0.8188 (mtpt) REVERT: A 883 ARG cc_start: 0.7651 (mpt180) cc_final: 0.7179 (mpt180) REVERT: A 886 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7674 (mt-10) REVERT: A 933 ILE cc_start: 0.8485 (mt) cc_final: 0.8223 (mp) REVERT: A 965 SER cc_start: 0.8515 (t) cc_final: 0.8220 (m) REVERT: A 996 LYS cc_start: 0.8101 (mttm) cc_final: 0.7529 (mtmm) REVERT: A 1006 THR cc_start: 0.8231 (m) cc_final: 0.7698 (p) REVERT: A 1020 LYS cc_start: 0.8239 (mttt) cc_final: 0.8004 (mttm) REVERT: A 1021 LYS cc_start: 0.8066 (mmtp) cc_final: 0.7767 (mmtm) REVERT: A 1030 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8315 (mtp85) REVERT: A 1041 SER cc_start: 0.8231 (t) cc_final: 0.7976 (t) REVERT: A 1049 GLU cc_start: 0.7960 (tp30) cc_final: 0.7589 (tp30) REVERT: A 1112 TYR cc_start: 0.8107 (t80) cc_final: 0.7846 (t80) REVERT: A 1141 THR cc_start: 0.8452 (m) cc_final: 0.7735 (p) REVERT: A 1174 GLU cc_start: 0.8028 (tt0) cc_final: 0.7461 (tt0) REVERT: A 1249 LEU cc_start: 0.8035 (mt) cc_final: 0.7828 (mt) REVERT: A 1282 GLU cc_start: 0.7464 (mp0) cc_final: 0.6960 (mp0) REVERT: A 1393 LEU cc_start: 0.8103 (tp) cc_final: 0.7886 (tt) REVERT: A 1403 GLN cc_start: 0.8453 (mm110) cc_final: 0.8216 (mm110) REVERT: A 1410 ASP cc_start: 0.7657 (p0) cc_final: 0.7342 (p0) outliers start: 40 outliers final: 19 residues processed: 426 average time/residue: 0.2909 time to fit residues: 171.4092 Evaluate side-chains 412 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 389 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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 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 296 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 385 SER Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 704 LEU 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 1055 LEU Chi-restraints excluded: chain A residue 1234 SER Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1342 ILE 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 87 optimal weight: 0.4980 chunk 2 optimal weight: 0.5980 chunk 114 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 137 optimal weight: 0.2980 chunk 38 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 438 HIS A 451 ASN ** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1322 HIS ** A1328 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12977 Z= 0.196 Angle : 0.607 10.697 17591 Z= 0.308 Chirality : 0.043 0.246 2061 Planarity : 0.005 0.053 2226 Dihedral : 4.027 23.914 1733 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 3.41 % Allowed : 25.40 % 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: 1.15 (0.21), residues: 1588 helix: 1.59 (0.18), residues: 893 sheet: 0.02 (0.59), residues: 81 loop : -0.30 (0.25), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 982 HIS 0.020 0.001 HIS B 234 PHE 0.022 0.002 PHE A1197 TYR 0.012 0.001 TYR A 289 ARG 0.010 0.000 ARG A 742 *********************** 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 461 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 412 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 MET cc_start: 0.5682 (tpp) cc_final: 0.5431 (tpp) REVERT: B 274 LYS cc_start: 0.7969 (OUTLIER) cc_final: 0.7701 (mmtp) REVERT: D 245 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8223 (pm20) REVERT: E 222 MET cc_start: 0.8415 (mmm) cc_final: 0.7881 (mpp) REVERT: A 64 LYS cc_start: 0.8215 (ttpp) cc_final: 0.7960 (ttpp) REVERT: A 66 ILE cc_start: 0.8465 (tt) cc_final: 0.8182 (pt) REVERT: A 69 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7376 (mm-30) REVERT: A 94 ILE cc_start: 0.7799 (tt) cc_final: 0.7387 (tp) REVERT: A 104 ARG cc_start: 0.7028 (OUTLIER) cc_final: 0.6702 (ttm110) REVERT: A 137 ASN cc_start: 0.8016 (t0) cc_final: 0.7792 (t0) REVERT: A 138 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7877 (tm-30) REVERT: A 142 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7952 (mttp) REVERT: A 165 GLU cc_start: 0.7592 (mp0) cc_final: 0.6682 (mp0) REVERT: A 184 MET cc_start: 0.6828 (OUTLIER) cc_final: 0.6234 (tmm) REVERT: A 207 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7943 (mt) REVERT: A 279 ASP cc_start: 0.7888 (m-30) cc_final: 0.7582 (m-30) REVERT: A 286 ASP cc_start: 0.7407 (p0) cc_final: 0.7180 (p0) REVERT: A 313 LYS cc_start: 0.8409 (tttp) cc_final: 0.8067 (tttm) REVERT: A 337 GLU cc_start: 0.7194 (mt-10) cc_final: 0.6950 (mt-10) REVERT: A 360 GLU cc_start: 0.7362 (mm-30) cc_final: 0.6926 (mm-30) REVERT: A 366 ARG cc_start: 0.7847 (mmt90) cc_final: 0.7444 (mmt90) REVERT: A 394 PHE cc_start: 0.7918 (t80) cc_final: 0.7706 (t80) REVERT: A 428 ASN cc_start: 0.7960 (p0) cc_final: 0.7725 (p0) REVERT: A 437 ARG cc_start: 0.7864 (ttp80) cc_final: 0.7390 (ttt180) REVERT: A 442 GLU cc_start: 0.7715 (tt0) cc_final: 0.7383 (tt0) REVERT: A 444 LYS cc_start: 0.7993 (mttt) cc_final: 0.7759 (mmmt) REVERT: A 457 MET cc_start: 0.7691 (mpp) cc_final: 0.7426 (mtm) REVERT: A 489 MET cc_start: 0.7949 (mtp) cc_final: 0.7620 (ttm) REVERT: A 499 GLN cc_start: 0.8226 (tp40) cc_final: 0.7555 (tp40) REVERT: A 503 ASP cc_start: 0.7514 (m-30) cc_final: 0.7033 (m-30) REVERT: A 527 ASP cc_start: 0.7472 (t0) cc_final: 0.7242 (t0) REVERT: A 539 GLU cc_start: 0.7360 (tp30) cc_final: 0.6976 (tp30) REVERT: A 553 LYS cc_start: 0.8339 (tttp) cc_final: 0.8079 (tttm) REVERT: A 579 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6908 (mm-30) REVERT: A 601 LYS cc_start: 0.7058 (mtmt) cc_final: 0.6737 (mtmt) REVERT: A 704 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8320 (mp) REVERT: A 710 THR cc_start: 0.8521 (m) cc_final: 0.7940 (p) REVERT: A 738 ILE cc_start: 0.7701 (OUTLIER) cc_final: 0.7442 (mt) REVERT: A 746 GLU cc_start: 0.7317 (mp0) cc_final: 0.7077 (mp0) REVERT: A 797 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7430 (mm-30) REVERT: A 801 GLN cc_start: 0.8143 (mm-40) cc_final: 0.7829 (tp40) REVERT: A 840 LYS cc_start: 0.8470 (mtpt) cc_final: 0.8182 (mtpt) REVERT: A 854 LYS cc_start: 0.8220 (ttmm) cc_final: 0.7963 (ttmt) REVERT: A 883 ARG cc_start: 0.7640 (mpt180) cc_final: 0.7209 (mpt180) REVERT: A 886 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7730 (mt-10) REVERT: A 933 ILE cc_start: 0.8499 (mt) cc_final: 0.8253 (mp) REVERT: A 965 SER cc_start: 0.8518 (t) cc_final: 0.8223 (m) REVERT: A 982 TRP cc_start: 0.8177 (p-90) cc_final: 0.7872 (p-90) REVERT: A 996 LYS cc_start: 0.8021 (mttm) cc_final: 0.7630 (mtmm) REVERT: A 1006 THR cc_start: 0.8322 (m) cc_final: 0.7778 (p) REVERT: A 1020 LYS cc_start: 0.8261 (mttt) cc_final: 0.8038 (mttm) REVERT: A 1021 LYS cc_start: 0.8098 (mmtp) cc_final: 0.7783 (mmtm) REVERT: A 1028 MET cc_start: 0.8704 (mmm) cc_final: 0.8480 (tpp) REVERT: A 1030 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7729 (ttm110) REVERT: A 1048 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7411 (tm-30) REVERT: A 1112 TYR cc_start: 0.8221 (t80) cc_final: 0.7914 (t80) REVERT: A 1141 THR cc_start: 0.8521 (m) cc_final: 0.7818 (p) REVERT: A 1174 GLU cc_start: 0.8087 (tt0) cc_final: 0.7799 (tt0) REVERT: A 1196 LYS cc_start: 0.7660 (mmmt) cc_final: 0.7302 (mmmt) REVERT: A 1282 GLU cc_start: 0.7550 (mp0) cc_final: 0.6919 (mp0) REVERT: A 1393 LEU cc_start: 0.8219 (tp) cc_final: 0.7989 (tt) REVERT: A 1403 GLN cc_start: 0.8466 (mm110) cc_final: 0.8173 (mm110) REVERT: A 1410 ASP cc_start: 0.7590 (p0) cc_final: 0.7315 (p0) outliers start: 49 outliers final: 25 residues processed: 429 average time/residue: 0.2829 time to fit residues: 168.9126 Evaluate side-chains 436 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 402 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 228 MET Chi-restraints excluded: chain B residue 274 LYS Chi-restraints excluded: chain C 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 A residue 104 ARG Chi-restraints excluded: chain A residue 142 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 230 LYS Chi-restraints excluded: chain A residue 296 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 725 GLN Chi-restraints excluded: chain A residue 738 ILE 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 978 CYS 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 1106 LEU Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1354 ILE Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1389 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 138 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 37 optimal weight: 0.0270 chunk 153 optimal weight: 0.0170 chunk 127 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 148 optimal weight: 0.0270 overall best weight: 0.3936 ------------------------------------------------------------------------------- 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 E 245 GLN A 395 GLN A 451 ASN ** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 HIS A1120 ASN A1322 HIS A1328 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12977 Z= 0.166 Angle : 0.605 10.934 17591 Z= 0.304 Chirality : 0.042 0.246 2061 Planarity : 0.004 0.050 2226 Dihedral : 3.955 23.805 1733 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.34 % Allowed : 26.17 % Favored : 70.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.24 (0.21), residues: 1588 helix: 1.67 (0.18), residues: 891 sheet: 0.12 (0.60), residues: 81 loop : -0.27 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 982 HIS 0.013 0.001 HIS B 234 PHE 0.021 0.001 PHE A1197 TYR 0.012 0.001 TYR A 289 ARG 0.009 0.000 ARG A 742 *********************** 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 459 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 411 time to evaluate : 1.400 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: 0.5684 (tpp) cc_final: 0.5426 (tpp) REVERT: B 275 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7119 (mp) REVERT: E 222 MET cc_start: 0.8289 (mmm) cc_final: 0.7768 (mpp) REVERT: A 64 LYS cc_start: 0.8179 (ttpp) cc_final: 0.7796 (ttpp) REVERT: A 66 ILE cc_start: 0.8433 (tt) cc_final: 0.8169 (pt) REVERT: A 68 VAL cc_start: 0.8760 (t) cc_final: 0.8419 (m) REVERT: A 69 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7324 (mm-30) REVERT: A 77 LEU cc_start: 0.8653 (mt) cc_final: 0.8431 (mm) REVERT: A 94 ILE cc_start: 0.7754 (tt) cc_final: 0.7339 (tp) REVERT: A 104 ARG cc_start: 0.6918 (OUTLIER) cc_final: 0.6591 (ttm110) REVERT: A 137 ASN cc_start: 0.8027 (t0) cc_final: 0.7806 (t0) REVERT: A 138 GLN cc_start: 0.8193 (tm-30) cc_final: 0.7910 (tm-30) REVERT: A 142 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7947 (mttp) REVERT: A 165 GLU cc_start: 0.7644 (mp0) cc_final: 0.6726 (mp0) REVERT: A 172 ASN cc_start: 0.7956 (m-40) cc_final: 0.7620 (m-40) REVERT: A 179 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7897 (p) REVERT: A 207 ILE cc_start: 0.8113 (OUTLIER) cc_final: 0.7849 (mt) REVERT: A 279 ASP cc_start: 0.7883 (m-30) cc_final: 0.7590 (m-30) REVERT: A 313 LYS cc_start: 0.8373 (tttp) cc_final: 0.8050 (tttm) REVERT: A 360 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6918 (mm-30) REVERT: A 366 ARG cc_start: 0.7826 (mmt90) cc_final: 0.7426 (mmt90) REVERT: A 428 ASN cc_start: 0.8023 (p0) cc_final: 0.7751 (p0) REVERT: A 431 LYS cc_start: 0.7729 (mppt) cc_final: 0.7509 (mtmm) REVERT: A 437 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7482 (ttt180) REVERT: A 442 GLU cc_start: 0.7735 (tt0) cc_final: 0.7410 (tt0) REVERT: A 444 LYS cc_start: 0.7993 (mttt) cc_final: 0.7752 (mmmt) REVERT: A 457 MET cc_start: 0.7645 (mpp) cc_final: 0.7428 (mtm) REVERT: A 499 GLN cc_start: 0.8179 (tp40) cc_final: 0.7509 (tp40) REVERT: A 503 ASP cc_start: 0.7482 (m-30) cc_final: 0.6996 (m-30) REVERT: A 527 ASP cc_start: 0.7463 (t0) cc_final: 0.7234 (t0) REVERT: A 539 GLU cc_start: 0.7351 (tp30) cc_final: 0.6964 (tp30) REVERT: A 553 LYS cc_start: 0.8344 (tttp) cc_final: 0.8021 (tttm) REVERT: A 556 GLU cc_start: 0.7378 (tp30) cc_final: 0.7079 (tp30) REVERT: A 579 GLU cc_start: 0.7174 (mm-30) cc_final: 0.6892 (mm-30) REVERT: A 601 LYS cc_start: 0.7076 (mtmt) cc_final: 0.6750 (mtmt) REVERT: A 704 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8307 (mp) REVERT: A 710 THR cc_start: 0.8515 (m) cc_final: 0.7930 (p) REVERT: A 730 THR cc_start: 0.8438 (m) cc_final: 0.7987 (p) REVERT: A 746 GLU cc_start: 0.7286 (mp0) cc_final: 0.7074 (mp0) REVERT: A 797 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7427 (mm-30) REVERT: A 826 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7516 (mp0) REVERT: A 840 LYS cc_start: 0.8476 (mtpt) cc_final: 0.8155 (mtpt) REVERT: A 854 LYS cc_start: 0.8223 (ttmm) cc_final: 0.7977 (ttmt) REVERT: A 883 ARG cc_start: 0.7615 (mpt180) cc_final: 0.7168 (mpt180) REVERT: A 886 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7685 (mt-10) REVERT: A 933 ILE cc_start: 0.8506 (mt) cc_final: 0.8252 (mp) REVERT: A 965 SER cc_start: 0.8482 (t) cc_final: 0.8196 (m) REVERT: A 996 LYS cc_start: 0.7926 (mttm) cc_final: 0.7601 (mtmm) REVERT: A 1006 THR cc_start: 0.8307 (m) cc_final: 0.7786 (p) REVERT: A 1020 LYS cc_start: 0.8260 (mttt) cc_final: 0.8027 (mttm) REVERT: A 1021 LYS cc_start: 0.8094 (mmtp) cc_final: 0.7768 (mmtm) REVERT: A 1028 MET cc_start: 0.8670 (mmm) cc_final: 0.8449 (tpp) REVERT: A 1030 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.7747 (ttm110) REVERT: A 1112 TYR cc_start: 0.8197 (t80) cc_final: 0.7916 (t80) REVERT: A 1141 THR cc_start: 0.8498 (m) cc_final: 0.8144 (t) REVERT: A 1174 GLU cc_start: 0.8087 (tt0) cc_final: 0.7802 (tt0) REVERT: A 1196 LYS cc_start: 0.7635 (mmmt) cc_final: 0.7279 (mmmt) REVERT: A 1249 LEU cc_start: 0.8063 (mt) cc_final: 0.7773 (mm) REVERT: A 1267 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7742 (mm-40) REVERT: A 1282 GLU cc_start: 0.7569 (mp0) cc_final: 0.6905 (mp0) REVERT: A 1393 LEU cc_start: 0.8309 (tp) cc_final: 0.8094 (tt) REVERT: A 1403 GLN cc_start: 0.8461 (mm110) cc_final: 0.8178 (mm110) REVERT: A 1410 ASP cc_start: 0.7501 (p0) cc_final: 0.7232 (p0) outliers start: 48 outliers final: 27 residues processed: 431 average time/residue: 0.2897 time to fit residues: 173.5937 Evaluate side-chains 428 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 394 time to evaluate : 1.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 232 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain E residue 248 MET 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 142 LYS 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 207 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 230 LYS 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 472 LEU Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 704 LEU 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 1046 GLU Chi-restraints excluded: chain A residue 1106 LEU Chi-restraints excluded: chain A residue 1263 GLU Chi-restraints excluded: chain A residue 1381 ILE Chi-restraints excluded: chain A residue 1389 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 17 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 129 optimal weight: 0.0870 chunk 85 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 70 optimal weight: 0.0000 chunk 94 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 overall best weight: 0.5562 ------------------------------------------------------------------------------- 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 451 ASN ** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1322 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12977 Z= 0.184 Angle : 0.603 10.552 17591 Z= 0.306 Chirality : 0.042 0.250 2061 Planarity : 0.004 0.051 2226 Dihedral : 3.929 23.461 1733 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.13 % Allowed : 26.24 % 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: 1.22 (0.21), residues: 1588 helix: 1.64 (0.18), residues: 892 sheet: 0.16 (0.60), residues: 81 loop : -0.26 (0.25), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 982 HIS 0.021 0.001 HIS B 234 PHE 0.021 0.001 PHE A1197 TYR 0.013 0.001 TYR A 225 ARG 0.010 0.000 ARG A 742 *********************** 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 448 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 403 time to evaluate : 1.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 MET cc_start: 0.5704 (tpp) cc_final: 0.5449 (tpp) REVERT: E 232 LEU cc_start: 0.9172 (pp) cc_final: 0.8904 (pp) REVERT: A 27 ILE cc_start: 0.8151 (pt) cc_final: 0.7841 (mt) REVERT: A 64 LYS cc_start: 0.8173 (ttpp) cc_final: 0.7785 (ttpp) REVERT: A 66 ILE cc_start: 0.8441 (tt) cc_final: 0.8027 (pt) REVERT: A 68 VAL cc_start: 0.8751 (t) cc_final: 0.8412 (m) REVERT: A 77 LEU cc_start: 0.8679 (mt) cc_final: 0.8460 (mm) REVERT: A 104 ARG cc_start: 0.6892 (OUTLIER) cc_final: 0.6568 (ttm110) REVERT: A 137 ASN cc_start: 0.8043 (t0) cc_final: 0.7826 (t0) REVERT: A 138 GLN cc_start: 0.8197 (tm-30) cc_final: 0.7927 (tm-30) REVERT: A 142 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7961 (mttp) REVERT: A 165 GLU cc_start: 0.7640 (mp0) cc_final: 0.7379 (mt-10) REVERT: A 172 ASN cc_start: 0.7944 (m-40) cc_final: 0.7598 (m-40) REVERT: A 179 VAL cc_start: 0.8161 (OUTLIER) cc_final: 0.7939 (p) REVERT: A 207 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7929 (mt) REVERT: A 279 ASP cc_start: 0.7911 (m-30) cc_final: 0.7604 (m-30) REVERT: A 313 LYS cc_start: 0.8380 (tttp) cc_final: 0.8137 (tttp) REVERT: A 337 GLU cc_start: 0.7283 (mt-10) cc_final: 0.7021 (mt-10) REVERT: A 360 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6878 (mm-30) REVERT: A 366 ARG cc_start: 0.7834 (mmt90) cc_final: 0.7421 (mmt90) REVERT: A 428 ASN cc_start: 0.8057 (p0) cc_final: 0.7852 (p0) REVERT: A 437 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7528 (ttt180) REVERT: A 444 LYS cc_start: 0.7987 (mttt) cc_final: 0.7725 (mmmt) REVERT: A 489 MET cc_start: 0.7935 (mtp) cc_final: 0.7720 (ttm) REVERT: A 499 GLN cc_start: 0.8206 (tp40) cc_final: 0.7542 (tp40) REVERT: A 503 ASP cc_start: 0.7480 (m-30) cc_final: 0.6991 (m-30) REVERT: A 531 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7183 (tp30) REVERT: A 539 GLU cc_start: 0.7369 (tp30) cc_final: 0.6969 (tp30) REVERT: A 553 LYS cc_start: 0.8350 (tttp) cc_final: 0.8024 (tttm) REVERT: A 556 GLU cc_start: 0.7375 (tp30) cc_final: 0.7066 (tp30) REVERT: A 579 GLU cc_start: 0.7167 (mm-30) cc_final: 0.6875 (mm-30) REVERT: A 601 LYS cc_start: 0.7120 (mtmt) cc_final: 0.6777 (mtmt) REVERT: A 661 ILE cc_start: 0.6692 (mt) cc_final: 0.6467 (tt) REVERT: A 695 ILE cc_start: 0.8813 (mt) cc_final: 0.8579 (pt) REVERT: A 704 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8292 (mp) REVERT: A 710 THR cc_start: 0.8537 (m) cc_final: 0.7971 (p) REVERT: A 730 THR cc_start: 0.8418 (m) cc_final: 0.7985 (p) REVERT: A 738 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7296 (mt) REVERT: A 797 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7523 (mp0) REVERT: A 840 LYS cc_start: 0.8494 (mtpt) cc_final: 0.8180 (mtpt) REVERT: A 854 LYS cc_start: 0.8202 (ttmm) cc_final: 0.7968 (ttmt) REVERT: A 883 ARG cc_start: 0.7644 (mpt180) cc_final: 0.7272 (mpt180) REVERT: A 933 ILE cc_start: 0.8529 (mt) cc_final: 0.8303 (mp) REVERT: A 965 SER cc_start: 0.8469 (t) cc_final: 0.8194 (m) REVERT: A 996 LYS cc_start: 0.7907 (mttm) cc_final: 0.7585 (mtmm) REVERT: A 1006 THR cc_start: 0.8338 (m) cc_final: 0.7810 (p) REVERT: A 1021 LYS cc_start: 0.8093 (mmtp) cc_final: 0.7762 (mmtm) REVERT: A 1050 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7343 (mt-10) REVERT: A 1112 TYR cc_start: 0.8242 (t80) cc_final: 0.7938 (t80) REVERT: A 1141 THR cc_start: 0.8488 (m) cc_final: 0.8211 (t) REVERT: A 1143 SER cc_start: 0.8290 (p) cc_final: 0.8033 (m) REVERT: A 1196 LYS cc_start: 0.7647 (mmmt) cc_final: 0.7313 (mmmt) REVERT: A 1249 LEU cc_start: 0.8075 (mt) cc_final: 0.7774 (mm) REVERT: A 1265 SER cc_start: 0.8369 (m) cc_final: 0.7828 (p) REVERT: A 1267 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7755 (mm-40) REVERT: A 1282 GLU cc_start: 0.7568 (mp0) cc_final: 0.6912 (mp0) REVERT: A 1393 LEU cc_start: 0.8355 (tp) cc_final: 0.8139 (tt) REVERT: A 1403 GLN cc_start: 0.8463 (mm110) cc_final: 0.8141 (mm110) REVERT: A 1410 ASP cc_start: 0.7496 (p0) cc_final: 0.7236 (p0) outliers start: 45 outliers final: 22 residues processed: 418 average time/residue: 0.2938 time to fit residues: 171.1644 Evaluate side-chains 427 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 399 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 266 ILE 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 142 LYS Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 230 LYS 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 609 MET Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 738 ILE 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 1106 LEU Chi-restraints excluded: chain A residue 1234 SER 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 91 optimal weight: 0.0050 chunk 46 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 14 optimal weight: 9.9990 chunk 120 optimal weight: 2.9990 chunk 139 optimal weight: 0.5980 chunk 146 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- 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 122 ASN A 395 GLN ** A 428 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 822 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1322 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12977 Z= 0.192 Angle : 0.629 11.887 17591 Z= 0.317 Chirality : 0.043 0.271 2061 Planarity : 0.005 0.051 2226 Dihedral : 3.964 23.832 1733 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 3.13 % Allowed : 26.51 % Favored : 70.35 % 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: 1.21 (0.21), residues: 1588 helix: 1.63 (0.18), residues: 894 sheet: 0.11 (0.59), residues: 81 loop : -0.28 (0.25), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 982 HIS 0.014 0.001 HIS B 234 PHE 0.021 0.001 PHE A1197 TYR 0.012 0.001 TYR A 445 ARG 0.013 0.001 ARG A 78 *********************** 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 447 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 402 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 MET cc_start: 0.5724 (tpp) cc_final: 0.5466 (tpp) REVERT: B 275 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7102 (mp) REVERT: E 232 LEU cc_start: 0.9128 (pp) cc_final: 0.8555 (pp) REVERT: A 27 ILE cc_start: 0.8195 (pt) cc_final: 0.7892 (mt) REVERT: A 64 LYS cc_start: 0.8139 (ttpp) cc_final: 0.7728 (ttpp) REVERT: A 68 VAL cc_start: 0.8721 (t) cc_final: 0.8373 (m) REVERT: A 104 ARG cc_start: 0.6847 (OUTLIER) cc_final: 0.6526 (ttm110) REVERT: A 137 ASN cc_start: 0.8053 (t0) cc_final: 0.7834 (t0) REVERT: A 138 GLN cc_start: 0.8187 (tm-30) cc_final: 0.7928 (tm-30) REVERT: A 142 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7974 (mttp) REVERT: A 165 GLU cc_start: 0.7656 (mp0) cc_final: 0.7422 (mt-10) REVERT: A 172 ASN cc_start: 0.7954 (m-40) cc_final: 0.7618 (m-40) REVERT: A 179 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7946 (p) REVERT: A 207 ILE cc_start: 0.8366 (mt) cc_final: 0.8002 (mt) REVERT: A 279 ASP cc_start: 0.7920 (m-30) cc_final: 0.7622 (m-30) REVERT: A 313 LYS cc_start: 0.8382 (tttp) cc_final: 0.8129 (tttp) REVERT: A 337 GLU cc_start: 0.7309 (mt-10) cc_final: 0.7040 (mt-10) REVERT: A 360 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6853 (mm-30) REVERT: A 366 ARG cc_start: 0.7847 (mmt90) cc_final: 0.7433 (mmt90) REVERT: A 437 ARG cc_start: 0.7901 (ttp80) cc_final: 0.7559 (ttt180) REVERT: A 444 LYS cc_start: 0.8016 (mttt) cc_final: 0.7778 (mmmt) REVERT: A 489 MET cc_start: 0.7914 (mtp) cc_final: 0.7590 (ttm) REVERT: A 531 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7204 (tp30) REVERT: A 539 GLU cc_start: 0.7367 (tp30) cc_final: 0.6969 (tp30) REVERT: A 553 LYS cc_start: 0.8341 (tttp) cc_final: 0.8085 (tttm) REVERT: A 579 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6894 (mm-30) REVERT: A 601 LYS cc_start: 0.7156 (mtmt) cc_final: 0.6805 (mtmt) REVERT: A 617 GLU cc_start: 0.7182 (tm-30) cc_final: 0.6956 (tm-30) REVERT: A 661 ILE cc_start: 0.6810 (mt) cc_final: 0.6591 (tt) REVERT: A 695 ILE cc_start: 0.8802 (mt) cc_final: 0.8565 (pt) REVERT: A 704 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8311 (mp) REVERT: A 710 THR cc_start: 0.8548 (m) cc_final: 0.7985 (p) REVERT: A 730 THR cc_start: 0.8422 (OUTLIER) cc_final: 0.7981 (p) REVERT: A 738 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7242 (mt) REVERT: A 797 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7533 (mp0) REVERT: A 840 LYS cc_start: 0.8515 (mtpt) cc_final: 0.8207 (mtpt) REVERT: A 854 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7994 (ttmt) REVERT: A 883 ARG cc_start: 0.7576 (mpt180) cc_final: 0.7140 (mpt180) REVERT: A 933 ILE cc_start: 0.8534 (mt) cc_final: 0.8304 (mp) REVERT: A 965 SER cc_start: 0.8447 (t) cc_final: 0.8171 (m) REVERT: A 996 LYS cc_start: 0.7893 (mttm) cc_final: 0.7462 (mtmm) REVERT: A 1006 THR cc_start: 0.8379 (m) cc_final: 0.7842 (p) REVERT: A 1021 LYS cc_start: 0.8102 (mmtp) cc_final: 0.7759 (mmtm) REVERT: A 1048 GLU cc_start: 0.7669 (tt0) cc_final: 0.7416 (tt0) REVERT: A 1141 THR cc_start: 0.8450 (m) cc_final: 0.8107 (t) REVERT: A 1143 SER cc_start: 0.8274 (p) cc_final: 0.8019 (m) REVERT: A 1168 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.5979 (mm-30) REVERT: A 1196 LYS cc_start: 0.7662 (mmmt) cc_final: 0.7326 (mmmt) REVERT: A 1249 LEU cc_start: 0.8072 (mt) cc_final: 0.7764 (mm) REVERT: A 1265 SER cc_start: 0.8368 (m) cc_final: 0.7843 (p) REVERT: A 1267 GLN cc_start: 0.8075 (mm-40) cc_final: 0.7745 (mm-40) REVERT: A 1282 GLU cc_start: 0.7568 (mp0) cc_final: 0.6918 (mp0) REVERT: A 1393 LEU cc_start: 0.8410 (tp) cc_final: 0.8183 (tt) REVERT: A 1403 GLN cc_start: 0.8453 (mm110) cc_final: 0.8139 (mm110) outliers start: 45 outliers final: 27 residues processed: 422 average time/residue: 0.2948 time to fit residues: 173.3866 Evaluate side-chains 431 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 396 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 ILE Chi-restraints excluded: chain C residue 266 ILE 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 70 LEU Chi-restraints excluded: chain A residue 71 ILE Chi-restraints excluded: chain A residue 104 ARG Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 230 LYS 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 420 TRP Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 457 MET Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 667 THR Chi-restraints excluded: chain A residue 704 LEU 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 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 1106 LEU Chi-restraints excluded: chain A residue 1168 GLU Chi-restraints excluded: chain A residue 1354 ILE Chi-restraints excluded: chain A residue 1370 THR Chi-restraints excluded: chain A residue 1389 VAL Chi-restraints excluded: chain A residue 1396 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 133 optimal weight: 0.1980 chunk 142 optimal weight: 8.9990 chunk 146 optimal weight: 0.3980 chunk 85 optimal weight: 4.9990 chunk 62 optimal weight: 0.0370 chunk 112 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 129 optimal weight: 0.0980 chunk 135 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 overall best weight: 0.2658 ------------------------------------------------------------------------------- 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 822 HIS ** A 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1322 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.6107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12977 Z= 0.174 Angle : 0.649 12.424 17591 Z= 0.326 Chirality : 0.043 0.234 2061 Planarity : 0.005 0.049 2226 Dihedral : 3.925 22.952 1733 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.16 % Allowed : 28.04 % 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: 1.19 (0.21), residues: 1588 helix: 1.59 (0.18), residues: 899 sheet: 0.07 (0.55), residues: 91 loop : -0.27 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 982 HIS 0.020 0.001 HIS B 234 PHE 0.019 0.001 PHE A1197 TYR 0.011 0.001 TYR A 540 ARG 0.009 0.001 ARG A 742 *********************** 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 431 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 400 time to evaluate : 1.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 GLN cc_start: 0.6878 (pp30) cc_final: 0.6632 (pp30) REVERT: B 248 MET cc_start: 0.5579 (tpp) cc_final: 0.5345 (tpp) REVERT: B 253 LYS cc_start: 0.7802 (pttt) cc_final: 0.7421 (pttt) REVERT: D 221 ILE cc_start: 0.7506 (pt) cc_final: 0.7075 (mt) REVERT: D 222 MET cc_start: 0.6429 (pmm) cc_final: 0.6210 (pmm) REVERT: D 245 GLN cc_start: 0.7506 (pm20) cc_final: 0.7229 (pm20) REVERT: E 222 MET cc_start: 0.8103 (mmm) cc_final: 0.7542 (mpp) REVERT: A 27 ILE cc_start: 0.8135 (pt) cc_final: 0.7831 (mt) REVERT: A 64 LYS cc_start: 0.8094 (ttpp) cc_final: 0.7738 (ttpp) REVERT: A 104 ARG cc_start: 0.6830 (OUTLIER) cc_final: 0.6512 (ttm110) REVERT: A 137 ASN cc_start: 0.8091 (t0) cc_final: 0.7864 (t0) REVERT: A 138 GLN cc_start: 0.8256 (tm-30) cc_final: 0.7996 (tm-30) REVERT: A 142 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7961 (mttp) REVERT: A 165 GLU cc_start: 0.7617 (mp0) cc_final: 0.7402 (mt-10) REVERT: A 179 VAL cc_start: 0.8143 (OUTLIER) cc_final: 0.7921 (p) REVERT: A 207 ILE cc_start: 0.8349 (mt) cc_final: 0.7994 (mt) REVERT: A 279 ASP cc_start: 0.7917 (m-30) cc_final: 0.7628 (m-30) REVERT: A 337 GLU cc_start: 0.7317 (mt-10) cc_final: 0.7047 (mt-10) REVERT: A 360 GLU cc_start: 0.7334 (mm-30) cc_final: 0.6845 (mm-30) REVERT: A 366 ARG cc_start: 0.7839 (mmt90) cc_final: 0.7426 (mmt90) REVERT: A 428 ASN cc_start: 0.8267 (p0) cc_final: 0.8003 (p0) REVERT: A 437 ARG cc_start: 0.7892 (ttp80) cc_final: 0.7567 (ttt180) REVERT: A 444 LYS cc_start: 0.8032 (mttt) cc_final: 0.7780 (mmmt) REVERT: A 531 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7162 (tp30) REVERT: A 539 GLU cc_start: 0.7349 (tp30) cc_final: 0.6953 (tp30) REVERT: A 553 LYS cc_start: 0.8324 (tttp) cc_final: 0.8092 (tttm) REVERT: A 579 GLU cc_start: 0.7150 (mm-30) cc_final: 0.6845 (mm-30) REVERT: A 601 LYS cc_start: 0.7163 (mtmt) cc_final: 0.6812 (mtmt) REVERT: A 661 ILE cc_start: 0.6753 (mt) cc_final: 0.6549 (tt) REVERT: A 704 LEU cc_start: 0.8461 (OUTLIER) cc_final: 0.8258 (mp) REVERT: A 710 THR cc_start: 0.8524 (m) cc_final: 0.7940 (p) REVERT: A 730 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.7964 (p) REVERT: A 738 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7127 (mt) REVERT: A 764 SER cc_start: 0.8480 (m) cc_final: 0.8158 (p) REVERT: A 797 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7548 (mp0) REVERT: A 840 LYS cc_start: 0.8514 (mtpt) cc_final: 0.8205 (mtpt) REVERT: A 877 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.8156 (mm) REVERT: A 883 ARG cc_start: 0.7537 (mpt180) cc_final: 0.7214 (mpt180) REVERT: A 920 GLN cc_start: 0.7937 (mt0) cc_final: 0.7717 (mt0) REVERT: A 933 ILE cc_start: 0.8542 (mt) cc_final: 0.8299 (mp) REVERT: A 965 SER cc_start: 0.8452 (t) cc_final: 0.8209 (m) REVERT: A 996 LYS cc_start: 0.7868 (mttm) cc_final: 0.7463 (mtmm) REVERT: A 1006 THR cc_start: 0.8341 (m) cc_final: 0.7850 (p) REVERT: A 1021 LYS cc_start: 0.8066 (mmtp) cc_final: 0.7731 (mmtm) REVERT: A 1048 GLU cc_start: 0.7654 (tt0) cc_final: 0.7404 (tt0) REVERT: A 1112 TYR cc_start: 0.8232 (t80) cc_final: 0.7956 (t80) REVERT: A 1141 THR cc_start: 0.8375 (m) cc_final: 0.8036 (t) REVERT: A 1143 SER cc_start: 0.8241 (p) cc_final: 0.7990 (m) REVERT: A 1196 LYS cc_start: 0.7636 (mmmt) cc_final: 0.7295 (mmmt) REVERT: A 1249 LEU cc_start: 0.8065 (mt) cc_final: 0.7763 (mm) REVERT: A 1265 SER cc_start: 0.8356 (m) cc_final: 0.7827 (p) REVERT: A 1267 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7702 (mm-40) REVERT: A 1282 GLU cc_start: 0.7556 (mp0) cc_final: 0.6909 (mp0) REVERT: A 1393 LEU cc_start: 0.8439 (tp) cc_final: 0.8233 (tt) REVERT: A 1403 GLN cc_start: 0.8453 (mm110) cc_final: 0.8158 (mm110) outliers start: 31 outliers final: 17 residues processed: 417 average time/residue: 0.2902 time to fit residues: 170.1541 Evaluate side-chains 419 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 395 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 225 LEU 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 142 LYS Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 218 THR 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 667 THR Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 876 ASN Chi-restraints excluded: chain A residue 877 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 1106 LEU Chi-restraints excluded: chain A residue 1354 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 92 optimal weight: 0.4980 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 134 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 5 ASN ** A 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1322 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.6254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12977 Z= 0.219 Angle : 0.683 15.504 17591 Z= 0.345 Chirality : 0.044 0.236 2061 Planarity : 0.005 0.050 2226 Dihedral : 3.990 22.273 1733 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.88 % Allowed : 28.11 % Favored : 70.01 % 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: 1.49 (0.18), residues: 899 sheet: 0.02 (0.55), residues: 91 loop : -0.28 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 79 HIS 0.015 0.001 HIS B 234 PHE 0.020 0.002 PHE A1197 TYR 0.013 0.001 TYR A 540 ARG 0.014 0.001 ARG A 78 ********************** 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 437 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 410 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 248 MET cc_start: 0.5519 (tpp) cc_final: 0.5297 (tpp) REVERT: D 221 ILE cc_start: 0.7453 (pt) cc_final: 0.7073 (mt) REVERT: D 245 GLN cc_start: 0.7543 (pm20) cc_final: 0.7213 (pm20) REVERT: E 222 MET cc_start: 0.8164 (mmm) cc_final: 0.7613 (mpp) REVERT: A 27 ILE cc_start: 0.8239 (pt) cc_final: 0.7989 (mt) REVERT: A 64 LYS cc_start: 0.8193 (ttpp) cc_final: 0.7907 (ttpp) REVERT: A 94 ILE cc_start: 0.7742 (tt) cc_final: 0.7327 (tp) REVERT: A 137 ASN cc_start: 0.8097 (t0) cc_final: 0.7882 (t0) REVERT: A 138 GLN cc_start: 0.8231 (tm-30) cc_final: 0.7972 (tm-30) REVERT: A 142 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.7996 (mttp) REVERT: A 165 GLU cc_start: 0.7657 (mp0) cc_final: 0.7442 (mt-10) REVERT: A 179 VAL cc_start: 0.8212 (OUTLIER) cc_final: 0.7988 (p) REVERT: A 184 MET cc_start: 0.7218 (ttp) cc_final: 0.7006 (ttt) REVERT: A 207 ILE cc_start: 0.8438 (mt) cc_final: 0.8224 (mp) REVERT: A 313 LYS cc_start: 0.8339 (tttp) cc_final: 0.8110 (tttm) REVERT: A 337 GLU cc_start: 0.7368 (mt-10) cc_final: 0.7094 (mt-10) REVERT: A 360 GLU cc_start: 0.7378 (mm-30) cc_final: 0.6848 (mm-30) REVERT: A 366 ARG cc_start: 0.7856 (mmt90) cc_final: 0.7425 (mmt90) REVERT: A 428 ASN cc_start: 0.8328 (p0) cc_final: 0.8060 (p0) REVERT: A 437 ARG cc_start: 0.7927 (ttp80) cc_final: 0.7610 (ttt180) REVERT: A 444 LYS cc_start: 0.8020 (mttt) cc_final: 0.7765 (mmmt) REVERT: A 489 MET cc_start: 0.8041 (ttm) cc_final: 0.7624 (ttm) REVERT: A 501 TYR cc_start: 0.8407 (m-80) cc_final: 0.7772 (m-80) REVERT: A 531 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7191 (tp30) REVERT: A 539 GLU cc_start: 0.7349 (tp30) cc_final: 0.6948 (tp30) REVERT: A 553 LYS cc_start: 0.8342 (tttp) cc_final: 0.8080 (tttm) REVERT: A 555 LYS cc_start: 0.8134 (mttp) cc_final: 0.7220 (mttt) REVERT: A 579 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6862 (mm-30) REVERT: A 601 LYS cc_start: 0.7221 (mtmt) cc_final: 0.6845 (mtmt) REVERT: A 661 ILE cc_start: 0.6949 (mt) cc_final: 0.6735 (tt) REVERT: A 704 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8267 (mp) REVERT: A 710 THR cc_start: 0.8566 (m) cc_final: 0.8013 (p) REVERT: A 730 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.7944 (p) REVERT: A 738 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7199 (mt) REVERT: A 764 SER cc_start: 0.8482 (m) cc_final: 0.8170 (p) REVERT: A 797 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7564 (mp0) REVERT: A 798 LYS cc_start: 0.8323 (ttpt) cc_final: 0.8028 (mtmt) REVERT: A 840 LYS cc_start: 0.8531 (mtpt) cc_final: 0.8232 (mtpt) REVERT: A 877 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8193 (mm) REVERT: A 883 ARG cc_start: 0.7481 (mpt180) cc_final: 0.7071 (mpt180) REVERT: A 920 GLN cc_start: 0.7957 (mt0) cc_final: 0.7735 (mt0) REVERT: A 965 SER cc_start: 0.8459 (t) cc_final: 0.8221 (m) REVERT: A 996 LYS cc_start: 0.7886 (mttm) cc_final: 0.7473 (mtmm) REVERT: A 1006 THR cc_start: 0.8414 (m) cc_final: 0.7861 (p) REVERT: A 1021 LYS cc_start: 0.8091 (mmtp) cc_final: 0.7800 (mmtm) REVERT: A 1048 GLU cc_start: 0.7680 (tt0) cc_final: 0.7413 (tt0) REVERT: A 1050 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7355 (mt-10) REVERT: A 1141 THR cc_start: 0.8421 (m) cc_final: 0.8089 (t) REVERT: A 1143 SER cc_start: 0.8267 (p) cc_final: 0.8012 (m) REVERT: A 1196 LYS cc_start: 0.7663 (mmmt) cc_final: 0.7323 (mmmt) REVERT: A 1249 LEU cc_start: 0.8098 (mt) cc_final: 0.7796 (mm) REVERT: A 1265 SER cc_start: 0.8381 (m) cc_final: 0.7855 (p) REVERT: A 1267 GLN cc_start: 0.8021 (mm-40) cc_final: 0.7693 (mm-40) REVERT: A 1282 GLU cc_start: 0.7572 (mp0) cc_final: 0.6919 (mp0) REVERT: A 1393 LEU cc_start: 0.8493 (tp) cc_final: 0.8277 (tt) REVERT: A 1403 GLN cc_start: 0.8481 (mm110) cc_final: 0.8158 (mm110) outliers start: 27 outliers final: 19 residues processed: 423 average time/residue: 0.3124 time to fit residues: 188.6015 Evaluate side-chains 428 residues out of total 1441 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 403 time to evaluate : 1.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain E residue 249 VAL Chi-restraints excluded: chain A residue 142 LYS Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 296 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 667 THR Chi-restraints excluded: chain A residue 700 GLU Chi-restraints excluded: chain A residue 704 LEU Chi-restraints excluded: chain A residue 730 THR Chi-restraints excluded: chain A residue 738 ILE Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 877 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 1106 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 159 random chunks: chunk 38 optimal weight: 0.6980 chunk 116 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 129 optimal weight: 0.2980 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 110 optimal weight: 0.0070 chunk 7 optimal weight: 0.7980 overall best weight: 0.5398 ------------------------------------------------------------------------------- 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 898 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1322 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.141715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.122984 restraints weight = 21812.143| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.85 r_work: 0.3509 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.6371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12977 Z= 0.195 Angle : 0.675 15.534 17591 Z= 0.340 Chirality : 0.044 0.262 2061 Planarity : 0.005 0.082 2226 Dihedral : 3.968 24.606 1733 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.51 % Allowed : 28.39 % Favored : 69.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.09 (0.21), residues: 1588 helix: 1.54 (0.17), residues: 899 sheet: -0.00 (0.55), residues: 91 loop : -0.35 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 982 HIS 0.021 0.001 HIS B 234 PHE 0.020 0.001 PHE A1197 TYR 0.016 0.001 TYR A 447 ARG 0.014 0.001 ARG A 78 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4023.82 seconds wall clock time: 78 minutes 33.33 seconds (4713.33 seconds total)