Starting phenix.real_space_refine on Sun Aug 4 03:56:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kci_37105/08_2024/8kci_37105.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kci_37105/08_2024/8kci_37105.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kci_37105/08_2024/8kci_37105.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kci_37105/08_2024/8kci_37105.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kci_37105/08_2024/8kci_37105.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kci_37105/08_2024/8kci_37105.cif" } resolution = 3.94 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= 0.014 sd= 0.090 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 59 5.16 5 C 6101 2.51 5 N 1619 2.21 5 O 1728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 680": "OE1" <-> "OE2" Residue "A GLU 1072": "OE1" <-> "OE2" Residue "A TYR 1135": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 9515 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1203, 9451 Classifications: {'peptide': 1203} Link IDs: {'CIS': 1, 'PTRANS': 36, 'TRANS': 1165} Chain breaks: 3 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'ATP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.70, per 1000 atoms: 0.60 Number of scatterers: 9515 At special positions: 0 Unit cell: (88.58, 92.88, 144.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 59 16.00 P 6 15.00 Mg 2 11.99 O 1728 8.00 N 1619 7.00 C 6101 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 - 3.50 Amino acid : False - 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=6, symmetry=0 Number of additional bonds: simple=6, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.87 Conformation dependent library (CDL) restraints added in 1.6 seconds 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2262 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 6 sheets defined 59.4% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 99 through 103 removed outlier: 3.521A pdb=" N ASP A 102 " --> pdb=" O HIS A 99 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN A 103 " --> pdb=" O PRO A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 103' Processing helix chain 'A' and resid 115 through 125 removed outlier: 3.946A pdb=" N ARG A 120 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 125 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 133 removed outlier: 3.869A pdb=" N ASP A 132 " --> pdb=" O SER A 129 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL A 133 " --> pdb=" O MET A 130 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 129 through 133' Processing helix chain 'A' and resid 144 through 160 removed outlier: 4.711A pdb=" N VAL A 160 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 210 removed outlier: 4.049A pdb=" N LEU A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET A 187 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLY A 196 " --> pdb=" O ALA A 192 " (cutoff:3.500A) Proline residue: A 197 - end of helix removed outlier: 3.690A pdb=" N LYS A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 247 removed outlier: 4.392A pdb=" N LEU A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 263 removed outlier: 3.906A pdb=" N THR A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 293 removed outlier: 3.676A pdb=" N ILE A 277 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASP A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY A 284 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE A 288 " --> pdb=" O GLY A 284 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 290 " --> pdb=" O ARG A 286 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA A 291 " --> pdb=" O MET A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 299 Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.948A pdb=" N LEU A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 328 removed outlier: 3.540A pdb=" N LEU A 328 " --> pdb=" O ALA A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 363 removed outlier: 4.269A pdb=" N MET A 333 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N MET A 334 " --> pdb=" O TYR A 330 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR A 342 " --> pdb=" O ARG A 338 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 343 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU A 353 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ARG A 354 " --> pdb=" O ALA A 350 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN A 359 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU A 360 " --> pdb=" O GLN A 356 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N VAL A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU A 362 " --> pdb=" O MET A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 401 removed outlier: 4.192A pdb=" N PHE A 398 " --> pdb=" O LYS A 394 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN A 399 " --> pdb=" O ALA A 395 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 401 " --> pdb=" O TYR A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 422 Processing helix chain 'A' and resid 432 through 448 removed outlier: 3.840A pdb=" N VAL A 436 " --> pdb=" O GLN A 432 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N PHE A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ALA A 446 " --> pdb=" O SER A 442 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LEU A 447 " --> pdb=" O MET A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 449 through 471 removed outlier: 3.629A pdb=" N VAL A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 610 removed outlier: 4.067A pdb=" N ILE A 608 " --> pdb=" O LEU A 604 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU A 609 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY A 610 " --> pdb=" O SER A 606 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 645 Processing helix chain 'A' and resid 651 through 661 Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 686 through 702 removed outlier: 3.974A pdb=" N ASP A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 727 Processing helix chain 'A' and resid 768 through 770 No H-bonds generated for 'chain 'A' and resid 768 through 770' Processing helix chain 'A' and resid 777 through 783 removed outlier: 4.257A pdb=" N ASN A 783 " --> pdb=" O THR A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 843 through 851 Processing helix chain 'A' and resid 854 through 885 removed outlier: 3.650A pdb=" N ALA A 858 " --> pdb=" O GLY A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 910 through 957 removed outlier: 3.847A pdb=" N ARG A 953 " --> pdb=" O ASP A 949 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG A 954 " --> pdb=" O GLU A 950 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 966 removed outlier: 3.654A pdb=" N PHE A 963 " --> pdb=" O PRO A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 973 removed outlier: 3.911A pdb=" N ASN A 973 " --> pdb=" O GLY A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 974 through 976 No H-bonds generated for 'chain 'A' and resid 974 through 976' Processing helix chain 'A' and resid 977 through 983 removed outlier: 3.521A pdb=" N GLU A 981 " --> pdb=" O LYS A 977 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP A 983 " --> pdb=" O MET A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1010 removed outlier: 3.612A pdb=" N GLN A 989 " --> pdb=" O ARG A 985 " (cutoff:3.500A) Processing helix chain 'A' and resid 1017 through 1046 removed outlier: 4.324A pdb=" N VAL A1034 " --> pdb=" O ILE A1030 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N LEU A1035 " --> pdb=" O VAL A1031 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR A1046 " --> pdb=" O LEU A1042 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1057 removed outlier: 3.813A pdb=" N LEU A1051 " --> pdb=" O GLN A1047 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1068 Processing helix chain 'A' and resid 1069 through 1086 removed outlier: 4.157A pdb=" N PHE A1073 " --> pdb=" O LYS A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1120 removed outlier: 3.812A pdb=" N THR A1092 " --> pdb=" O PHE A1088 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET A1095 " --> pdb=" O PHE A1091 " (cutoff:3.500A) Processing helix chain 'A' and resid 1131 through 1157 removed outlier: 3.502A pdb=" N GLN A1138 " --> pdb=" O SER A1134 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A1148 " --> pdb=" O GLN A1144 " (cutoff:3.500A) Processing helix chain 'A' and resid 1158 through 1165 Processing helix chain 'A' and resid 1262 through 1268 removed outlier: 3.833A pdb=" N LEU A1266 " --> pdb=" O GLY A1262 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER A1268 " --> pdb=" O ALA A1264 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1289 removed outlier: 3.871A pdb=" N ASN A1287 " --> pdb=" O THR A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1296 through 1306 removed outlier: 3.753A pdb=" N TRP A1300 " --> pdb=" O GLU A1296 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR A1306 " --> pdb=" O ALA A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1309 through 1314 removed outlier: 4.039A pdb=" N ALA A1313 " --> pdb=" O LYS A1309 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN A1314 " --> pdb=" O GLU A1310 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1309 through 1314' Processing helix chain 'A' and resid 1331 through 1347 removed outlier: 4.334A pdb=" N LEU A1337 " --> pdb=" O GLY A1333 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A1345 " --> pdb=" O ALA A1341 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG A1346 " --> pdb=" O ARG A1342 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N HIS A1347 " --> pdb=" O ALA A1343 " (cutoff:3.500A) Processing helix chain 'A' and resid 1362 through 1376 removed outlier: 4.110A pdb=" N LEU A1366 " --> pdb=" O THR A1362 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU A1367 " --> pdb=" O GLU A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1410 through 1416 removed outlier: 3.681A pdb=" N SER A1416 " --> pdb=" O SER A1412 " (cutoff:3.500A) Processing helix chain 'A' and resid 1420 through 1429 Processing sheet with id=AA1, first strand: chain 'A' and resid 584 through 586 removed outlier: 3.699A pdb=" N ILE A 585 " --> pdb=" O ILE A 490 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE A 490 " --> pdb=" O ILE A 585 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 625 through 627 removed outlier: 3.948A pdb=" N ILE A 707 " --> pdb=" O ALA A 626 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR A 706 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 5.543A pdb=" N VAL A 591 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU A 590 " --> pdb=" O GLU A 752 " (cutoff:3.500A) removed outlier: 7.913A pdb=" N ILE A 754 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLY A 592 " --> pdb=" O ILE A 754 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N MET A 756 " --> pdb=" O GLY A 592 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL A 753 " --> pdb=" O ARG A 764 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ARG A 764 " --> pdb=" O VAL A 753 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N PHE A 755 " --> pdb=" O THR A 762 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1193 through 1194 Processing sheet with id=AA4, first strand: chain 'A' and resid 1381 through 1384 removed outlier: 3.880A pdb=" N ILE A1223 " --> pdb=" O MET A1381 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS A1222 " --> pdb=" O ARG A1396 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N MET A1398 " --> pdb=" O LYS A1222 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N GLY A1224 " --> pdb=" O MET A1398 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1252 through 1253 Processing sheet with id=AA6, first strand: chain 'A' and resid 1270 through 1273 462 hydrogen bonds defined for protein. 1371 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: 3.07 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3037 1.34 - 1.46: 1837 1.46 - 1.58: 4720 1.58 - 1.70: 8 1.70 - 1.82: 98 Bond restraints: 9700 Sorted by residual: bond pdb=" CA ARG A1177 " pdb=" C ARG A1177 " ideal model delta sigma weight residual 1.523 1.459 0.064 1.34e-02 5.57e+03 2.32e+01 bond pdb=" CG1 ILE A 408 " pdb=" CD1 ILE A 408 " ideal model delta sigma weight residual 1.513 1.374 0.139 3.90e-02 6.57e+02 1.27e+01 bond pdb=" CA LEU A1172 " pdb=" C LEU A1172 " ideal model delta sigma weight residual 1.522 1.484 0.039 1.20e-02 6.94e+03 1.04e+01 bond pdb=" CA ALA A1174 " pdb=" CB ALA A1174 " ideal model delta sigma weight residual 1.534 1.498 0.035 1.30e-02 5.92e+03 7.26e+00 bond pdb=" CA PRO A1175 " pdb=" C PRO A1175 " ideal model delta sigma weight residual 1.520 1.482 0.037 1.42e-02 4.96e+03 6.84e+00 ... (remaining 9695 not shown) Histogram of bond angle deviations from ideal: 94.92 - 103.90: 120 103.90 - 112.89: 5381 112.89 - 121.87: 5726 121.87 - 130.85: 1866 130.85 - 139.83: 49 Bond angle restraints: 13142 Sorted by residual: angle pdb=" C LYS A1233 " pdb=" N SER A1234 " pdb=" CA SER A1234 " ideal model delta sigma weight residual 121.70 131.92 -10.22 1.80e+00 3.09e-01 3.22e+01 angle pdb=" CA ILE A 479 " pdb=" CB ILE A 479 " pdb=" CG1 ILE A 479 " ideal model delta sigma weight residual 110.40 118.27 -7.87 1.70e+00 3.46e-01 2.14e+01 angle pdb=" O SER A1171 " pdb=" C SER A1171 " pdb=" N LEU A1172 " ideal model delta sigma weight residual 122.79 118.17 4.62 1.14e+00 7.69e-01 1.64e+01 angle pdb=" CA ILE A 408 " pdb=" CB ILE A 408 " pdb=" CG1 ILE A 408 " ideal model delta sigma weight residual 110.40 103.69 6.71 1.70e+00 3.46e-01 1.56e+01 angle pdb=" CB ILE A 479 " pdb=" CG1 ILE A 479 " pdb=" CD1 ILE A 479 " ideal model delta sigma weight residual 113.80 121.70 -7.90 2.10e+00 2.27e-01 1.42e+01 ... (remaining 13137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 4857 17.76 - 35.51: 727 35.51 - 53.27: 217 53.27 - 71.03: 38 71.03 - 88.79: 14 Dihedral angle restraints: 5853 sinusoidal: 2362 harmonic: 3491 Sorted by residual: dihedral pdb=" CA GLY A1232 " pdb=" C GLY A1232 " pdb=" N LYS A1233 " pdb=" CA LYS A1233 " ideal model delta harmonic sigma weight residual 180.00 157.86 22.14 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA PHE A1241 " pdb=" C PHE A1241 " pdb=" N ARG A1242 " pdb=" CA ARG A1242 " ideal model delta harmonic sigma weight residual 180.00 -158.01 -21.99 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA LEU A1240 " pdb=" C LEU A1240 " pdb=" N PHE A1241 " pdb=" CA PHE A1241 " ideal model delta harmonic sigma weight residual -180.00 -160.54 -19.46 0 5.00e+00 4.00e-02 1.52e+01 ... (remaining 5850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1146 0.042 - 0.084: 308 0.084 - 0.126: 74 0.126 - 0.169: 5 0.169 - 0.211: 1 Chirality restraints: 1534 Sorted by residual: chirality pdb=" CA ILE A 408 " pdb=" N ILE A 408 " pdb=" C ILE A 408 " pdb=" CB ILE A 408 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE A 927 " pdb=" N ILE A 927 " pdb=" C ILE A 927 " pdb=" CB ILE A 927 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CB ILE A 479 " pdb=" CA ILE A 479 " pdb=" CG1 ILE A 479 " pdb=" CG2 ILE A 479 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 1531 not shown) Planarity restraints: 1633 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ATP A1601 " -0.016 2.00e-02 2.50e+03 2.44e-02 1.63e+01 pdb=" C2 ATP A1601 " 0.020 2.00e-02 2.50e+03 pdb=" C4 ATP A1601 " -0.061 2.00e-02 2.50e+03 pdb=" C5 ATP A1601 " -0.008 2.00e-02 2.50e+03 pdb=" C6 ATP A1601 " 0.009 2.00e-02 2.50e+03 pdb=" C8 ATP A1601 " 0.008 2.00e-02 2.50e+03 pdb=" N1 ATP A1601 " -0.005 2.00e-02 2.50e+03 pdb=" N3 ATP A1601 " 0.013 2.00e-02 2.50e+03 pdb=" N6 ATP A1601 " -0.007 2.00e-02 2.50e+03 pdb=" N7 ATP A1601 " 0.007 2.00e-02 2.50e+03 pdb=" N9 ATP A1601 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 479 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.29e+00 pdb=" C ILE A 479 " -0.047 2.00e-02 2.50e+03 pdb=" O ILE A 479 " 0.018 2.00e-02 2.50e+03 pdb=" N LYS A 480 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A1048 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.57e+00 pdb=" N PRO A1049 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A1049 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A1049 " -0.030 5.00e-02 4.00e+02 ... (remaining 1630 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 74 2.58 - 3.16: 7934 3.16 - 3.74: 14393 3.74 - 4.32: 17427 4.32 - 4.90: 29164 Nonbonded interactions: 68992 Sorted by model distance: nonbonded pdb=" OE1 GLN A 630 " pdb="MG MG A1603 " model vdw 2.001 2.170 nonbonded pdb=" NE1 TRP A 499 " pdb=" C5 ATP A1601 " model vdw 2.159 2.672 nonbonded pdb=" CG TRP A 499 " pdb=" N3 ATP A1601 " model vdw 2.238 2.672 nonbonded pdb=" O SER A1057 " pdb=" OG SER A1057 " model vdw 2.244 3.040 nonbonded pdb=" OD1 ASN A 996 " pdb=" OG1 THR A1146 " model vdw 2.247 3.040 ... (remaining 68987 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 28.400 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6764 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 : 0.004 0.139 9700 Z= 0.276 Angle : 0.666 10.220 13142 Z= 0.360 Chirality : 0.039 0.211 1534 Planarity : 0.004 0.053 1633 Dihedral : 18.605 88.785 3591 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.25 % Allowed : 9.96 % Favored : 89.79 % Rotamer: Outliers : 1.35 % Allowed : 31.04 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.20 (0.25), residues: 1195 helix: 1.41 (0.21), residues: 661 sheet: 0.10 (0.90), residues: 42 loop : -2.45 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 499 HIS 0.003 0.001 HIS A 767 PHE 0.030 0.001 PHE A1241 TYR 0.011 0.001 TYR A1077 ARG 0.002 0.000 ARG A1267 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 72 time to evaluate : 1.075 Fit side-chains REVERT: A 399 GLN cc_start: 0.6918 (tp-100) cc_final: 0.6512 (tp-100) outliers start: 14 outliers final: 2 residues processed: 80 average time/residue: 0.1913 time to fit residues: 23.0773 Evaluate side-chains 73 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 1331 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 101 optimal weight: 0.6980 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 0.0270 chunk 70 optimal weight: 2.9990 chunk 108 optimal weight: 0.0670 overall best weight: 1.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.0836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9700 Z= 0.187 Angle : 0.574 7.702 13142 Z= 0.291 Chirality : 0.039 0.152 1534 Planarity : 0.004 0.047 1633 Dihedral : 8.023 76.028 1368 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 1.74 % Allowed : 31.62 % Favored : 66.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.05 (0.25), residues: 1195 helix: 1.56 (0.21), residues: 678 sheet: 0.16 (0.89), residues: 42 loop : -2.59 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 499 HIS 0.004 0.001 HIS A1121 PHE 0.015 0.001 PHE A1241 TYR 0.011 0.001 TYR A1135 ARG 0.009 0.000 ARG A1177 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 1.302 Fit side-chains REVERT: A 399 GLN cc_start: 0.7166 (tp-100) cc_final: 0.6656 (tp-100) REVERT: A 1398 MET cc_start: 0.5591 (OUTLIER) cc_final: 0.5115 (ppp) REVERT: A 1414 LEU cc_start: 0.8191 (mt) cc_final: 0.7988 (mp) outliers start: 18 outliers final: 9 residues processed: 95 average time/residue: 0.2151 time to fit residues: 31.0697 Evaluate side-chains 86 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 1.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 499 TRP Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1398 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 60 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 90 optimal weight: 30.0000 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 117 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9700 Z= 0.231 Angle : 0.602 7.049 13142 Z= 0.312 Chirality : 0.040 0.132 1534 Planarity : 0.004 0.044 1633 Dihedral : 7.914 64.056 1367 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 4.74 % Allowed : 30.08 % Favored : 65.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.10 (0.25), residues: 1195 helix: 1.55 (0.21), residues: 678 sheet: 0.08 (0.87), residues: 42 loop : -2.64 (0.26), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 499 HIS 0.005 0.001 HIS A 767 PHE 0.019 0.001 PHE A1088 TYR 0.013 0.001 TYR A 918 ARG 0.003 0.000 ARG A 681 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 96 time to evaluate : 1.023 Fit side-chains REVERT: A 114 TRP cc_start: 0.7999 (OUTLIER) cc_final: 0.7799 (p90) REVERT: A 212 GLU cc_start: 0.6126 (mp0) cc_final: 0.5575 (pp20) REVERT: A 257 MET cc_start: 0.8228 (tpp) cc_final: 0.7893 (ttm) REVERT: A 478 MET cc_start: 0.4185 (tpt) cc_final: 0.3966 (tpp) REVERT: A 574 LEU cc_start: 0.4775 (tt) cc_final: 0.4554 (tt) REVERT: A 1241 PHE cc_start: 0.8510 (p90) cc_final: 0.8149 (p90) REVERT: A 1243 LEU cc_start: 0.5139 (pt) cc_final: 0.3989 (pp) REVERT: A 1308 MET cc_start: 0.6724 (mpp) cc_final: 0.6417 (mpp) REVERT: A 1398 MET cc_start: 0.5782 (OUTLIER) cc_final: 0.5126 (ppp) outliers start: 49 outliers final: 32 residues processed: 137 average time/residue: 0.1941 time to fit residues: 39.7088 Evaluate side-chains 124 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 90 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 114 TRP Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 499 TRP Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 772 ASN Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1184 SER Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1406 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 107 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 103 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6878 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9700 Z= 0.180 Angle : 0.559 7.486 13142 Z= 0.286 Chirality : 0.039 0.149 1534 Planarity : 0.003 0.039 1633 Dihedral : 7.628 65.783 1367 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 4.64 % Allowed : 31.24 % Favored : 64.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: 0.07 (0.26), residues: 1195 helix: 1.71 (0.21), residues: 673 sheet: 0.02 (0.85), residues: 42 loop : -2.55 (0.26), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 499 HIS 0.003 0.001 HIS A 948 PHE 0.017 0.001 PHE A 377 TYR 0.012 0.001 TYR A1135 ARG 0.003 0.000 ARG A1267 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 89 time to evaluate : 1.160 Fit side-chains REVERT: A 212 GLU cc_start: 0.6235 (mp0) cc_final: 0.5718 (pp20) REVERT: A 369 LYS cc_start: 0.6723 (OUTLIER) cc_final: 0.6491 (tptp) REVERT: A 1241 PHE cc_start: 0.8484 (p90) cc_final: 0.8273 (p90) REVERT: A 1398 MET cc_start: 0.5778 (OUTLIER) cc_final: 0.5089 (ppp) outliers start: 48 outliers final: 35 residues processed: 128 average time/residue: 0.1858 time to fit residues: 35.4674 Evaluate side-chains 121 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 84 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 499 TRP Chi-restraints excluded: chain A residue 576 ARG Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 772 ASN Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1184 SER Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1312 ILE Chi-restraints excluded: chain A residue 1398 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 96 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 86 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 HIS A1138 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 9700 Z= 0.291 Angle : 0.658 7.908 13142 Z= 0.340 Chirality : 0.042 0.163 1534 Planarity : 0.004 0.040 1633 Dihedral : 7.843 58.332 1367 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 6.29 % Allowed : 30.27 % Favored : 63.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.28 (0.25), residues: 1195 helix: 1.39 (0.21), residues: 661 sheet: -0.25 (0.85), residues: 42 loop : -2.54 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 499 HIS 0.004 0.001 HIS A1065 PHE 0.017 0.002 PHE A 377 TYR 0.015 0.002 TYR A1077 ARG 0.006 0.000 ARG A 942 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 93 time to evaluate : 1.280 Fit side-chains revert: symmetry clash REVERT: A 212 GLU cc_start: 0.6198 (mp0) cc_final: 0.5604 (pp20) REVERT: A 257 MET cc_start: 0.8251 (tpp) cc_final: 0.7943 (ttm) REVERT: A 478 MET cc_start: 0.3714 (OUTLIER) cc_final: 0.3390 (tpp) REVERT: A 601 LYS cc_start: 0.6120 (OUTLIER) cc_final: 0.5858 (pttm) REVERT: A 614 LEU cc_start: 0.6557 (pt) cc_final: 0.6001 (tp) REVERT: A 1308 MET cc_start: 0.7149 (mpp) cc_final: 0.6907 (mpp) REVERT: A 1398 MET cc_start: 0.5880 (OUTLIER) cc_final: 0.5152 (ppp) outliers start: 65 outliers final: 45 residues processed: 147 average time/residue: 0.1879 time to fit residues: 41.4754 Evaluate side-chains 137 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 89 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 499 TRP Chi-restraints excluded: chain A residue 576 ARG Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 742 HIS Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 772 ASN Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1028 LEU Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1184 SER Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1405 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 39 optimal weight: 8.9990 chunk 104 optimal weight: 10.0000 chunk 22 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 116 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 9 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 399 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7221 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.107 9700 Z= 0.542 Angle : 0.899 10.690 13142 Z= 0.470 Chirality : 0.049 0.167 1534 Planarity : 0.005 0.047 1633 Dihedral : 8.676 55.852 1367 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 7.74 % Allowed : 29.79 % Favored : 62.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -1.55 (0.24), residues: 1195 helix: 0.25 (0.20), residues: 664 sheet: -0.79 (0.87), residues: 36 loop : -2.94 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 499 HIS 0.008 0.002 HIS A1065 PHE 0.030 0.003 PHE A 377 TYR 0.022 0.003 TYR A1077 ARG 0.006 0.001 ARG A1096 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 93 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: A 155 GLU cc_start: 0.7261 (tm-30) cc_final: 0.6989 (tm-30) REVERT: A 257 MET cc_start: 0.8290 (tpp) cc_final: 0.8016 (ttm) REVERT: A 478 MET cc_start: 0.3943 (OUTLIER) cc_final: 0.3536 (tpp) REVERT: A 601 LYS cc_start: 0.6231 (OUTLIER) cc_final: 0.5965 (pttm) REVERT: A 614 LEU cc_start: 0.7018 (pt) cc_final: 0.6571 (tp) REVERT: A 911 MET cc_start: 0.3308 (mtt) cc_final: 0.2809 (tpt) REVERT: A 1200 MET cc_start: 0.8120 (mmm) cc_final: 0.7767 (mmm) REVERT: A 1228 ARG cc_start: 0.6437 (OUTLIER) cc_final: 0.5156 (ttt-90) REVERT: A 1293 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6717 (pt0) REVERT: A 1398 MET cc_start: 0.5924 (OUTLIER) cc_final: 0.5177 (ppp) outliers start: 80 outliers final: 54 residues processed: 160 average time/residue: 0.1916 time to fit residues: 44.8325 Evaluate side-chains 145 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 86 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 279 ILE Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 313 ILE Chi-restraints excluded: chain A residue 337 SER Chi-restraints excluded: chain A residue 360 GLU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 405 VAL Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 454 VAL Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 499 TRP Chi-restraints excluded: chain A residue 576 ARG Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 608 ILE Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain A residue 663 LEU Chi-restraints excluded: chain A residue 670 LEU Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 772 ASN Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 910 HIS Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 937 VAL Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 968 THR Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 982 VAL Chi-restraints excluded: chain A residue 986 LEU Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1000 VAL Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1100 VAL Chi-restraints excluded: chain A residue 1146 THR Chi-restraints excluded: chain A residue 1147 VAL Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1293 GLN Chi-restraints excluded: chain A residue 1383 THR Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1405 VAL Chi-restraints excluded: chain A residue 1406 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 111 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 97 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 115 optimal weight: 0.0670 chunk 72 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.6720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 9700 Z= 0.187 Angle : 0.649 8.236 13142 Z= 0.328 Chirality : 0.041 0.222 1534 Planarity : 0.003 0.049 1633 Dihedral : 7.969 60.959 1367 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 3.68 % Allowed : 33.56 % Favored : 62.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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 (0.25), residues: 1195 helix: 1.04 (0.21), residues: 655 sheet: -0.76 (0.86), residues: 36 loop : -2.63 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 499 HIS 0.005 0.001 HIS A 948 PHE 0.015 0.001 PHE A 259 TYR 0.023 0.001 TYR A1135 ARG 0.006 0.000 ARG A1285 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 89 time to evaluate : 1.257 Fit side-chains revert: symmetry clash REVERT: A 200 MET cc_start: 0.5598 (mmp) cc_final: 0.5309 (mmt) REVERT: A 257 MET cc_start: 0.8138 (OUTLIER) cc_final: 0.7693 (ttm) REVERT: A 369 LYS cc_start: 0.6872 (OUTLIER) cc_final: 0.6532 (tptp) REVERT: A 478 MET cc_start: 0.3906 (OUTLIER) cc_final: 0.3522 (tpp) REVERT: A 601 LYS cc_start: 0.6166 (OUTLIER) cc_final: 0.5872 (pttm) REVERT: A 614 LEU cc_start: 0.6781 (pt) cc_final: 0.6379 (tp) REVERT: A 911 MET cc_start: 0.3283 (mtt) cc_final: 0.2707 (tpt) REVERT: A 1398 MET cc_start: 0.5762 (OUTLIER) cc_final: 0.4913 (ppp) outliers start: 38 outliers final: 28 residues processed: 118 average time/residue: 0.2085 time to fit residues: 36.0997 Evaluate side-chains 117 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 84 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 MET Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 369 LYS Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 426 PHE Chi-restraints excluded: chain A residue 462 VAL Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 499 TRP Chi-restraints excluded: chain A residue 576 ARG Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 772 ASN Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 976 SER Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1405 VAL Chi-restraints excluded: chain A residue 1406 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 73 optimal weight: 2.9990 chunk 78 optimal weight: 0.0050 chunk 57 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 105 optimal weight: 0.8980 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9700 Z= 0.178 Angle : 0.623 8.529 13142 Z= 0.311 Chirality : 0.040 0.200 1534 Planarity : 0.003 0.045 1633 Dihedral : 7.516 59.283 1367 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer: Outliers : 3.38 % Allowed : 34.24 % Favored : 62.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.31 (0.25), residues: 1195 helix: 1.42 (0.21), residues: 662 sheet: -0.73 (0.84), residues: 36 loop : -2.59 (0.26), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 499 HIS 0.006 0.001 HIS A 421 PHE 0.018 0.001 PHE A 426 TYR 0.021 0.001 TYR A1135 ARG 0.006 0.000 ARG A1285 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 87 time to evaluate : 1.015 Fit side-chains REVERT: A 200 MET cc_start: 0.5469 (mmp) cc_final: 0.5220 (mmt) REVERT: A 478 MET cc_start: 0.3827 (OUTLIER) cc_final: 0.3481 (tpp) REVERT: A 601 LYS cc_start: 0.6179 (OUTLIER) cc_final: 0.5822 (pttm) REVERT: A 614 LEU cc_start: 0.6798 (pt) cc_final: 0.6322 (tp) REVERT: A 911 MET cc_start: 0.3337 (mtt) cc_final: 0.2821 (tpt) REVERT: A 1308 MET cc_start: 0.6594 (mpp) cc_final: 0.6250 (mpp) REVERT: A 1398 MET cc_start: 0.5776 (OUTLIER) cc_final: 0.4887 (ppp) outliers start: 35 outliers final: 23 residues processed: 112 average time/residue: 0.1915 time to fit residues: 31.8143 Evaluate side-chains 107 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 81 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 422 MET Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 499 TRP Chi-restraints excluded: chain A residue 576 ARG Chi-restraints excluded: chain A residue 597 VAL Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 772 ASN Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1117 ILE Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1405 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 110 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 46 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 33 optimal weight: 0.0270 chunk 97 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9700 Z= 0.172 Angle : 0.621 9.131 13142 Z= 0.309 Chirality : 0.040 0.187 1534 Planarity : 0.003 0.044 1633 Dihedral : 7.369 60.222 1367 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.46 % Favored : 90.54 % Rotamer: Outliers : 3.29 % Allowed : 34.43 % Favored : 62.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.13 (0.25), residues: 1195 helix: 1.59 (0.21), residues: 659 sheet: -0.72 (0.83), residues: 36 loop : -2.50 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 499 HIS 0.006 0.001 HIS A 477 PHE 0.014 0.001 PHE A 259 TYR 0.021 0.001 TYR A1135 ARG 0.005 0.000 ARG A1285 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 80 time to evaluate : 1.354 Fit side-chains REVERT: A 200 MET cc_start: 0.5475 (mmp) cc_final: 0.5244 (mmt) REVERT: A 478 MET cc_start: 0.3827 (OUTLIER) cc_final: 0.3450 (tpp) REVERT: A 601 LYS cc_start: 0.6201 (OUTLIER) cc_final: 0.5816 (pttm) REVERT: A 614 LEU cc_start: 0.6735 (pt) cc_final: 0.6282 (tp) REVERT: A 911 MET cc_start: 0.3191 (mtt) cc_final: 0.2712 (tpt) REVERT: A 1228 ARG cc_start: 0.6459 (OUTLIER) cc_final: 0.4935 (ttt-90) REVERT: A 1308 MET cc_start: 0.6509 (mpp) cc_final: 0.6210 (mpp) REVERT: A 1398 MET cc_start: 0.5713 (OUTLIER) cc_final: 0.4827 (ppp) outliers start: 34 outliers final: 22 residues processed: 107 average time/residue: 0.1988 time to fit residues: 31.6709 Evaluate side-chains 106 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 80 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 315 LEU Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 397 TYR Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 499 TRP Chi-restraints excluded: chain A residue 576 ARG Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 772 ASN Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1405 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 54 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 119 optimal weight: 10.0000 chunk 110 optimal weight: 0.9980 chunk 95 optimal weight: 0.0970 chunk 9 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.3572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 9700 Z= 0.271 Angle : 0.692 10.066 13142 Z= 0.349 Chirality : 0.042 0.180 1534 Planarity : 0.004 0.044 1633 Dihedral : 7.565 56.676 1367 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 3.00 % Allowed : 34.33 % Favored : 62.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.37 (0.25), residues: 1195 helix: 1.33 (0.21), residues: 659 sheet: -0.65 (0.93), residues: 30 loop : -2.50 (0.26), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 499 HIS 0.006 0.001 HIS A 477 PHE 0.014 0.001 PHE A 377 TYR 0.022 0.001 TYR A1135 ARG 0.005 0.000 ARG A1285 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2390 Ramachandran restraints generated. 1195 Oldfield, 0 Emsley, 1195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 83 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 257 MET cc_start: 0.8261 (OUTLIER) cc_final: 0.7956 (ttm) REVERT: A 478 MET cc_start: 0.3832 (OUTLIER) cc_final: 0.3427 (tpp) REVERT: A 601 LYS cc_start: 0.6139 (OUTLIER) cc_final: 0.5792 (pttm) REVERT: A 614 LEU cc_start: 0.6813 (pt) cc_final: 0.6344 (tp) REVERT: A 911 MET cc_start: 0.3061 (mtt) cc_final: 0.2560 (tpt) REVERT: A 1228 ARG cc_start: 0.6462 (OUTLIER) cc_final: 0.4937 (ttt-90) REVERT: A 1308 MET cc_start: 0.6721 (mpp) cc_final: 0.6354 (mpp) REVERT: A 1398 MET cc_start: 0.5861 (OUTLIER) cc_final: 0.4953 (ppp) outliers start: 31 outliers final: 23 residues processed: 107 average time/residue: 0.2068 time to fit residues: 32.4195 Evaluate side-chains 110 residues out of total 1034 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 82 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 257 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 381 VAL Chi-restraints excluded: chain A residue 418 PHE Chi-restraints excluded: chain A residue 478 MET Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 499 TRP Chi-restraints excluded: chain A residue 576 ARG Chi-restraints excluded: chain A residue 601 LYS Chi-restraints excluded: chain A residue 674 ASP Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 761 ILE Chi-restraints excluded: chain A residue 772 ASN Chi-restraints excluded: chain A residue 925 MET Chi-restraints excluded: chain A residue 955 ILE Chi-restraints excluded: chain A residue 1007 ILE Chi-restraints excluded: chain A residue 1032 SER Chi-restraints excluded: chain A residue 1064 ILE Chi-restraints excluded: chain A residue 1149 LEU Chi-restraints excluded: chain A residue 1228 ARG Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1278 VAL Chi-restraints excluded: chain A residue 1398 MET Chi-restraints excluded: chain A residue 1405 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 87 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 39 optimal weight: 6.9990 chunk 97 optimal weight: 0.0060 chunk 12 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 chunk 83 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 996 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1292 ASN A1307 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.141568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.114776 restraints weight = 21433.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.115362 restraints weight = 17457.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.115828 restraints weight = 13731.701| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9700 Z= 0.196 Angle : 0.637 10.105 13142 Z= 0.319 Chirality : 0.040 0.180 1534 Planarity : 0.003 0.046 1633 Dihedral : 7.422 59.963 1367 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 3.09 % Allowed : 34.43 % Favored : 62.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.09 % 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: -0.25 (0.25), residues: 1195 helix: 1.47 (0.21), residues: 658 sheet: -0.55 (0.93), residues: 30 loop : -2.50 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 499 HIS 0.007 0.001 HIS A 477 PHE 0.012 0.001 PHE A 259 TYR 0.021 0.001 TYR A1135 ARG 0.003 0.000 ARG A1285 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1752.26 seconds wall clock time: 32 minutes 25.56 seconds (1945.56 seconds total)