Starting phenix.real_space_refine on Fri Feb 14 06:54:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bwo_16292/02_2025/8bwo_16292.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bwo_16292/02_2025/8bwo_16292.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8bwo_16292/02_2025/8bwo_16292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bwo_16292/02_2025/8bwo_16292.map" model { file = "/net/cci-nas-00/data/ceres_data/8bwo_16292/02_2025/8bwo_16292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bwo_16292/02_2025/8bwo_16292.cif" } resolution = 3.2 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= 0.054 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 42 5.16 5 C 6279 2.51 5 N 1636 2.21 5 O 1747 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 9712 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 9648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1211, 9648 Classifications: {'peptide': 1211} Link IDs: {'PTRANS': 36, 'TRANS': 1174} 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: 6.74, per 1000 atoms: 0.69 Number of scatterers: 9712 At special positions: 0 Unit cell: (75.712, 90.688, 148.928, 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 42 16.00 P 6 15.00 Mg 2 11.99 O 1747 8.00 N 1636 7.00 C 6279 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.1 seconds 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 6 sheets defined 70.0% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 Processing helix chain 'A' and resid 17 through 23 Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 27 through 35 removed outlier: 3.776A pdb=" N PHE A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A 33 " --> pdb=" O PRO A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 51 Processing helix chain 'A' and resid 52 through 69 Processing helix chain 'A' and resid 79 through 120 removed outlier: 5.630A pdb=" N LYS A 90 " --> pdb=" O LYS A 86 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N SER A 91 " --> pdb=" O CYS A 87 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL A 94 " --> pdb=" O LYS A 90 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LEU A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE A 98 " --> pdb=" O VAL A 94 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 133 through 150 removed outlier: 4.104A pdb=" N TYR A 137 " --> pdb=" O THR A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 181 removed outlier: 4.015A pdb=" N LEU A 154 " --> pdb=" O ILE A 150 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG A 180 " --> pdb=" O ARG A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 200 Processing helix chain 'A' and resid 203 through 212 removed outlier: 4.084A pdb=" N GLN A 207 " --> pdb=" O ASN A 203 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR A 209 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL A 210 " --> pdb=" O ASP A 206 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE A 211 " --> pdb=" O GLN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 231 Proline residue: A 219 - end of helix Processing helix chain 'A' and resid 236 through 290 removed outlier: 3.884A pdb=" N GLY A 240 " --> pdb=" O SER A 236 " (cutoff:3.500A) Proline residue: A 249 - end of helix removed outlier: 3.667A pdb=" N GLY A 255 " --> pdb=" O GLN A 251 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N LYS A 256 " --> pdb=" O SER A 252 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU A 257 " --> pdb=" O CYS A 253 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N ARG A 284 " --> pdb=" O ILE A 280 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N ILE A 285 " --> pdb=" O THR A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 341 removed outlier: 3.690A pdb=" N LYS A 309 " --> pdb=" O LYS A 305 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N SER A 328 " --> pdb=" O PHE A 324 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LYS A 329 " --> pdb=" O PHE A 325 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 348 through 367 removed outlier: 4.928A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N THR A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 391 removed outlier: 3.677A pdb=" N VAL A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 459 Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 500 through 511 Processing helix chain 'A' and resid 529 through 533 Processing helix chain 'A' and resid 536 through 552 removed outlier: 3.664A pdb=" N ARG A 542 " --> pdb=" O GLY A 538 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 548 " --> pdb=" O ASN A 544 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP A 552 " --> pdb=" O ALA A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 566 through 577 Processing helix chain 'A' and resid 593 through 598 removed outlier: 3.624A pdb=" N LEU A 597 " --> pdb=" O GLN A 593 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 593 through 598' Processing helix chain 'A' and resid 616 through 621 Processing helix chain 'A' and resid 697 through 709 Processing helix chain 'A' and resid 710 through 743 removed outlier: 3.573A pdb=" N PHE A 714 " --> pdb=" O HIS A 710 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASP A 732 " --> pdb=" O TYR A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 756 removed outlier: 3.685A pdb=" N GLY A 753 " --> pdb=" O ASN A 750 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ASN A 754 " --> pdb=" O GLY A 751 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL A 755 " --> pdb=" O GLY A 752 " (cutoff:3.500A) Processing helix chain 'A' and resid 760 through 807 Processing helix chain 'A' and resid 809 through 816 removed outlier: 3.767A pdb=" N PHE A 813 " --> pdb=" O PRO A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 834 removed outlier: 3.964A pdb=" N ARG A 824 " --> pdb=" O ARG A 820 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ASP A 828 " --> pdb=" O ARG A 824 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE A 829 " --> pdb=" O PHE A 825 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 860 removed outlier: 3.872A pdb=" N LEU A 838 " --> pdb=" O ASP A 834 " (cutoff:3.500A) Processing helix chain 'A' and resid 861 through 863 No H-bonds generated for 'chain 'A' and resid 861 through 863' Processing helix chain 'A' and resid 864 through 910 Proline residue: A 870 - end of helix removed outlier: 3.549A pdb=" N ILE A 873 " --> pdb=" O VAL A 869 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N THR A 885 " --> pdb=" O TYR A 881 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASP A 888 " --> pdb=" O GLU A 884 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER A 898 " --> pdb=" O SER A 894 " (cutoff:3.500A) Proline residue: A 899 - end of helix Processing helix chain 'A' and resid 910 through 918 Processing helix chain 'A' and resid 919 through 966 Processing helix chain 'A' and resid 967 through 975 removed outlier: 6.236A pdb=" N ALA A 971 " --> pdb=" O LEU A 968 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N LYS A 972 " --> pdb=" O ILE A 969 " (cutoff:3.500A) Processing helix chain 'A' and resid 976 through 981 removed outlier: 3.672A pdb=" N GLY A 980 " --> pdb=" O ALA A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 1007 removed outlier: 4.724A pdb=" N GLY A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N GLN A 994 " --> pdb=" O MET A 990 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU A1004 " --> pdb=" O SER A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1018 removed outlier: 3.698A pdb=" N TYR A1016 " --> pdb=" O ARG A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1089 removed outlier: 4.003A pdb=" N ILE A1085 " --> pdb=" O LYS A1081 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A1086 " --> pdb=" O SER A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1106 through 1108 No H-bonds generated for 'chain 'A' and resid 1106 through 1108' Processing helix chain 'A' and resid 1109 through 1116 removed outlier: 4.073A pdb=" N LYS A1116 " --> pdb=" O ASP A1112 " (cutoff:3.500A) Processing helix chain 'A' and resid 1130 through 1136 Processing helix chain 'A' and resid 1142 through 1153 Processing helix chain 'A' and resid 1155 through 1162 removed outlier: 3.573A pdb=" N ASP A1161 " --> pdb=" O GLU A1157 " (cutoff:3.500A) Processing helix chain 'A' and resid 1164 through 1168 Processing helix chain 'A' and resid 1171 through 1175 Processing helix chain 'A' and resid 1178 through 1194 removed outlier: 3.597A pdb=" N CYS A1186 " --> pdb=" O ARG A1182 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS A1194 " --> pdb=" O ALA A1190 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1223 removed outlier: 3.964A pdb=" N LEU A1214 " --> pdb=" O ARG A1210 " (cutoff:3.500A) Processing helix chain 'A' and resid 1234 through 1239 Processing helix chain 'A' and resid 1257 through 1263 Processing helix chain 'A' and resid 1267 through 1276 Processing helix chain 'A' and resid 1277 through 1293 Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 431 removed outlier: 5.761A pdb=" N GLN A 429 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA A 417 " --> pdb=" O GLN A 429 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 428 through 431 removed outlier: 5.761A pdb=" N GLN A 429 " --> pdb=" O ALA A 417 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ALA A 417 " --> pdb=" O GLN A 429 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE A 415 " --> pdb=" O HIS A 466 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N HIS A 466 " --> pdb=" O PHE A 415 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.497A pdb=" N GLU A 439 " --> pdb=" O THR A 587 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU A 589 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU A 441 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A 613 " --> pdb=" O ILE A 605 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LYS A 607 " --> pdb=" O MET A 611 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N MET A 611 " --> pdb=" O LYS A 607 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 487 through 488 Processing sheet with id=AA5, first strand: chain 'A' and resid 1058 through 1065 removed outlier: 5.708A pdb=" N LYS A1059 " --> pdb=" O PHE A1048 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N PHE A1048 " --> pdb=" O LYS A1059 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N ALA A1063 " --> pdb=" O ASP A1044 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASP A1044 " --> pdb=" O ALA A1063 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N ILE A1065 " --> pdb=" O ILE A1042 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ILE A1042 " --> pdb=" O ILE A1065 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1117 through 1120 removed outlier: 7.283A pdb=" N LEU A1198 " --> pdb=" O LEU A1229 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N ILE A1231 " --> pdb=" O LEU A1198 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE A1200 " --> pdb=" O ILE A1231 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LYS A1070 " --> pdb=" O LYS A1243 " (cutoff:3.500A) removed outlier: 7.775A pdb=" N MET A1245 " --> pdb=" O LYS A1070 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLY A1072 " --> pdb=" O MET A1245 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N LEU A1247 " --> pdb=" O GLY A1072 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL A1074 " --> pdb=" O LEU A1247 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP A1256 " --> pdb=" O ILE A1244 " (cutoff:3.500A) 617 hydrogen bonds defined for protein. 1794 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: 3.57 Time building geometry restraints manager: 2.96 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: 3058 1.34 - 1.46: 1356 1.46 - 1.57: 5430 1.57 - 1.69: 4 1.69 - 1.81: 68 Bond restraints: 9916 Sorted by residual: bond pdb=" C5' ATP A1401 " pdb=" O5' ATP A1401 " ideal model delta sigma weight residual 1.443 1.221 0.222 1.00e-02 1.00e+04 4.95e+02 bond pdb=" C5' ATP A1402 " pdb=" O5' ATP A1402 " ideal model delta sigma weight residual 1.443 1.221 0.222 1.00e-02 1.00e+04 4.92e+02 bond pdb=" C4' ATP A1401 " pdb=" O4' ATP A1401 " ideal model delta sigma weight residual 1.444 1.397 0.047 1.10e-02 8.26e+03 1.80e+01 bond pdb=" C1' ATP A1402 " pdb=" O4' ATP A1402 " ideal model delta sigma weight residual 1.416 1.364 0.052 1.30e-02 5.92e+03 1.59e+01 bond pdb=" C4' ATP A1402 " pdb=" O4' ATP A1402 " ideal model delta sigma weight residual 1.444 1.401 0.043 1.10e-02 8.26e+03 1.54e+01 ... (remaining 9911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.43: 13428 7.43 - 14.85: 13 14.85 - 22.27: 1 22.27 - 29.70: 4 29.70 - 37.12: 4 Bond angle restraints: 13450 Sorted by residual: angle pdb=" C5' ATP A1402 " pdb=" O5' ATP A1402 " pdb=" PA ATP A1402 " ideal model delta sigma weight residual 121.27 158.39 -37.12 1.00e+00 1.00e+00 1.38e+03 angle pdb=" C5' ATP A1401 " pdb=" O5' ATP A1401 " pdb=" PA ATP A1401 " ideal model delta sigma weight residual 121.27 157.40 -36.13 1.00e+00 1.00e+00 1.31e+03 angle pdb=" C3' ATP A1402 " pdb=" C4' ATP A1402 " pdb=" C5' ATP A1402 " ideal model delta sigma weight residual 115.19 83.42 31.77 1.76e+00 3.23e-01 3.26e+02 angle pdb=" C3' ATP A1401 " pdb=" C4' ATP A1401 " pdb=" C5' ATP A1401 " ideal model delta sigma weight residual 115.19 85.14 30.05 1.76e+00 3.23e-01 2.92e+02 angle pdb=" C4' ATP A1402 " pdb=" C5' ATP A1402 " pdb=" O5' ATP A1402 " ideal model delta sigma weight residual 108.83 137.57 -28.74 2.33e+00 1.85e-01 1.52e+02 ... (remaining 13445 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 5481 17.98 - 35.96: 371 35.96 - 53.95: 66 53.95 - 71.93: 19 71.93 - 89.91: 12 Dihedral angle restraints: 5949 sinusoidal: 2418 harmonic: 3531 Sorted by residual: dihedral pdb=" CA CYS A1226 " pdb=" C CYS A1226 " pdb=" N THR A1227 " pdb=" CA THR A1227 " ideal model delta harmonic sigma weight residual 180.00 151.93 28.07 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA MET A 409 " pdb=" C MET A 409 " pdb=" N VAL A 410 " pdb=" CA VAL A 410 " ideal model delta harmonic sigma weight residual 180.00 152.03 27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA LEU A 513 " pdb=" C LEU A 513 " pdb=" N LYS A 514 " pdb=" CA LYS A 514 " ideal model delta harmonic sigma weight residual 180.00 154.37 25.63 0 5.00e+00 4.00e-02 2.63e+01 ... (remaining 5946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.090: 1472 0.090 - 0.180: 83 0.180 - 0.270: 4 0.270 - 0.360: 1 0.360 - 0.450: 2 Chirality restraints: 1562 Sorted by residual: chirality pdb=" C4' ATP A1402 " pdb=" C3' ATP A1402 " pdb=" C5' ATP A1402 " pdb=" O4' ATP A1402 " both_signs ideal model delta sigma weight residual False -2.49 -2.94 0.45 2.00e-01 2.50e+01 5.07e+00 chirality pdb=" C4' ATP A1401 " pdb=" C3' ATP A1401 " pdb=" C5' ATP A1401 " pdb=" O4' ATP A1401 " both_signs ideal model delta sigma weight residual False -2.49 -2.94 0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" C3' ATP A1402 " pdb=" C2' ATP A1402 " pdb=" C4' ATP A1402 " pdb=" O3' ATP A1402 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 1559 not shown) Planarity restraints: 1660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 157 " 0.002 2.00e-02 2.50e+03 1.72e-02 5.93e+00 pdb=" CG TYR A 157 " 0.001 2.00e-02 2.50e+03 pdb=" CD1 TYR A 157 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TYR A 157 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 157 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 157 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 157 " -0.024 2.00e-02 2.50e+03 pdb=" OH TYR A 157 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 37 " -0.174 9.50e-02 1.11e+02 7.87e-02 4.98e+00 pdb=" NE ARG A 37 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 37 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG A 37 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 37 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 998 " -0.170 9.50e-02 1.11e+02 7.67e-02 4.89e+00 pdb=" NE ARG A 998 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG A 998 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG A 998 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 998 " 0.000 2.00e-02 2.50e+03 ... (remaining 1657 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 44 2.50 - 3.10: 7428 3.10 - 3.70: 14881 3.70 - 4.30: 22729 4.30 - 4.90: 37486 Nonbonded interactions: 82568 Sorted by model distance: nonbonded pdb=" O3G ATP A1402 " pdb="MG MG A1403 " model vdw 1.900 2.170 nonbonded pdb=" O1B ATP A1402 " pdb="MG MG A1403 " model vdw 1.940 2.170 nonbonded pdb=" OG SER A1082 " pdb="MG MG A1404 " model vdw 1.945 2.170 nonbonded pdb=" OE1 GLN A1122 " pdb="MG MG A1404 " model vdw 2.004 2.170 nonbonded pdb=" OH TYR A 92 " pdb=" O THR A 209 " model vdw 2.251 3.040 ... (remaining 82563 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=0.00 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: 3.670 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: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.140 Find NCS groups from input model: 0.100 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 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 : 0.005 0.222 9916 Z= 0.371 Angle : 1.109 37.125 13450 Z= 0.718 Chirality : 0.050 0.450 1562 Planarity : 0.008 0.079 1660 Dihedral : 13.918 89.908 3661 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 0.47 % Allowed : 2.47 % Favored : 97.06 % 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: -1.54 (0.22), residues: 1203 helix: -1.22 (0.16), residues: 761 sheet: -0.58 (0.59), residues: 68 loop : -0.16 (0.34), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 711 HIS 0.004 0.001 HIS A 172 PHE 0.020 0.002 PHE A 948 TYR 0.026 0.005 TYR A 157 ARG 0.021 0.004 ARG A 782 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 224 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7466 (pt0) cc_final: 0.6664 (pm20) REVERT: A 76 GLN cc_start: 0.5073 (pt0) cc_final: 0.4846 (mt0) REVERT: A 176 ARG cc_start: 0.7245 (ttm170) cc_final: 0.7028 (ttt-90) REVERT: A 264 LYS cc_start: 0.7508 (mttp) cc_final: 0.7197 (mttp) REVERT: A 293 LYS cc_start: 0.7341 (mttt) cc_final: 0.7083 (mmmt) REVERT: A 413 GLN cc_start: 0.7676 (tt0) cc_final: 0.7243 (tp40) REVERT: A 509 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7650 (tttp) REVERT: A 571 ARG cc_start: 0.7027 (ttt180) cc_final: 0.6808 (tmm160) REVERT: A 695 LYS cc_start: 0.7108 (ptpt) cc_final: 0.6088 (tptt) REVERT: A 706 ARG cc_start: 0.7723 (mmm-85) cc_final: 0.6696 (tpt90) REVERT: A 715 ILE cc_start: 0.8179 (mm) cc_final: 0.7977 (mp) REVERT: A 835 LEU cc_start: 0.8349 (tp) cc_final: 0.8111 (tt) REVERT: A 925 GLU cc_start: 0.7874 (tt0) cc_final: 0.7594 (tt0) REVERT: A 1020 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7303 (pm20) REVERT: A 1021 LYS cc_start: 0.8392 (mtpt) cc_final: 0.7960 (mmtm) REVERT: A 1077 THR cc_start: 0.8683 (p) cc_final: 0.8479 (p) REVERT: A 1152 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7748 (mt-10) REVERT: A 1169 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7614 (mm-30) REVERT: A 1201 ASP cc_start: 0.8160 (t0) cc_final: 0.7841 (t0) REVERT: A 1210 ARG cc_start: 0.7879 (mtp85) cc_final: 0.7353 (mtt90) outliers start: 5 outliers final: 1 residues processed: 226 average time/residue: 0.3012 time to fit residues: 88.5623 Evaluate side-chains 142 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 0.3980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 4.9990 chunk 70 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 153 HIS A 183 ASN A 703 ASN A1047 ASN A1225 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.149046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121225 restraints weight = 12022.721| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.18 r_work: 0.3235 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9916 Z= 0.296 Angle : 0.641 7.822 13450 Z= 0.341 Chirality : 0.044 0.154 1562 Planarity : 0.004 0.054 1660 Dihedral : 8.519 74.875 1373 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.80 % Allowed : 7.31 % Favored : 90.88 % 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: 0.15 (0.23), residues: 1203 helix: 0.35 (0.18), residues: 772 sheet: -0.79 (0.59), residues: 68 loop : 0.07 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 763 HIS 0.005 0.001 HIS A 153 PHE 0.016 0.002 PHE A 336 TYR 0.013 0.002 TYR A 737 ARG 0.005 0.001 ARG A1193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7991 (pt0) cc_final: 0.7370 (pm20) REVERT: A 76 GLN cc_start: 0.5616 (pt0) cc_final: 0.5125 (mt0) REVERT: A 77 LYS cc_start: 0.8228 (pptt) cc_final: 0.7951 (mmmt) REVERT: A 89 TRP cc_start: 0.8655 (p-90) cc_final: 0.8417 (p-90) REVERT: A 165 ARG cc_start: 0.8336 (mtt90) cc_final: 0.7949 (mtm180) REVERT: A 176 ARG cc_start: 0.8256 (ttm170) cc_final: 0.8017 (ttt180) REVERT: A 264 LYS cc_start: 0.8637 (mttp) cc_final: 0.8396 (mttt) REVERT: A 312 ARG cc_start: 0.8228 (mtm-85) cc_final: 0.8027 (mtt180) REVERT: A 413 GLN cc_start: 0.8365 (tt0) cc_final: 0.7876 (tp40) REVERT: A 509 LYS cc_start: 0.8841 (ttmt) cc_final: 0.8434 (tttp) REVERT: A 571 ARG cc_start: 0.7972 (ttt180) cc_final: 0.7511 (tmm160) REVERT: A 607 LYS cc_start: 0.7213 (mttt) cc_final: 0.6929 (pptt) REVERT: A 611 MET cc_start: 0.8746 (ttp) cc_final: 0.8498 (ttp) REVERT: A 695 LYS cc_start: 0.7604 (ptpt) cc_final: 0.6644 (tttp) REVERT: A 706 ARG cc_start: 0.8119 (mmm-85) cc_final: 0.6955 (tpt90) REVERT: A 744 MET cc_start: 0.5090 (OUTLIER) cc_final: 0.4155 (pp-130) REVERT: A 800 LYS cc_start: 0.7827 (mtmt) cc_final: 0.7570 (mmtp) REVERT: A 1020 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7753 (pm20) REVERT: A 1021 LYS cc_start: 0.8517 (mtpt) cc_final: 0.8297 (mmtm) REVERT: A 1066 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8308 (mtmm) REVERT: A 1140 GLU cc_start: 0.8463 (tt0) cc_final: 0.8174 (mt-10) REVERT: A 1169 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7565 (mm-30) REVERT: A 1176 ASN cc_start: 0.8322 (t0) cc_final: 0.7980 (t0) REVERT: A 1210 ARG cc_start: 0.8420 (mtp85) cc_final: 0.7762 (mtt90) REVERT: A 1274 GLN cc_start: 0.8513 (mm-40) cc_final: 0.7934 (tt0) outliers start: 19 outliers final: 10 residues processed: 184 average time/residue: 0.2771 time to fit residues: 68.0226 Evaluate side-chains 163 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1066 LYS Chi-restraints excluded: chain A residue 1108 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 41 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 87 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 60 optimal weight: 9.9990 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1216 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.150215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.122908 restraints weight = 12119.055| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.12 r_work: 0.3238 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9916 Z= 0.213 Angle : 0.551 7.228 13450 Z= 0.292 Chirality : 0.041 0.156 1562 Planarity : 0.004 0.037 1660 Dihedral : 7.991 76.168 1373 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.18 % Allowed : 10.35 % Favored : 87.46 % 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: 0.74 (0.24), residues: 1203 helix: 0.85 (0.18), residues: 773 sheet: -1.10 (0.56), residues: 75 loop : 0.37 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 763 HIS 0.004 0.001 HIS A 152 PHE 0.016 0.001 PHE A 698 TYR 0.010 0.001 TYR A 737 ARG 0.003 0.000 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7930 (pt0) cc_final: 0.7374 (pm20) REVERT: A 76 GLN cc_start: 0.5527 (pt0) cc_final: 0.5195 (mt0) REVERT: A 77 LYS cc_start: 0.8198 (pptt) cc_final: 0.7946 (mmmt) REVERT: A 89 TRP cc_start: 0.8667 (p-90) cc_final: 0.8416 (p-90) REVERT: A 176 ARG cc_start: 0.8227 (ttm170) cc_final: 0.7954 (ttt180) REVERT: A 264 LYS cc_start: 0.8611 (mttp) cc_final: 0.8374 (mttt) REVERT: A 276 MET cc_start: 0.8949 (tpp) cc_final: 0.8503 (mmm) REVERT: A 312 ARG cc_start: 0.8200 (mtm-85) cc_final: 0.7999 (mtt-85) REVERT: A 413 GLN cc_start: 0.8401 (tt0) cc_final: 0.7889 (tp40) REVERT: A 481 GLN cc_start: 0.8673 (mm-40) cc_final: 0.8423 (mm-40) REVERT: A 509 LYS cc_start: 0.8856 (ttmt) cc_final: 0.8458 (tttm) REVERT: A 571 ARG cc_start: 0.8000 (ttt180) cc_final: 0.7487 (tmm160) REVERT: A 607 LYS cc_start: 0.7190 (mttt) cc_final: 0.6971 (pptt) REVERT: A 611 MET cc_start: 0.8637 (ttp) cc_final: 0.8378 (ttp) REVERT: A 695 LYS cc_start: 0.7653 (ptpt) cc_final: 0.6671 (tttp) REVERT: A 744 MET cc_start: 0.5176 (OUTLIER) cc_final: 0.4174 (pp-130) REVERT: A 800 LYS cc_start: 0.7776 (mtmt) cc_final: 0.7524 (mmtm) REVERT: A 1020 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7777 (pm20) REVERT: A 1021 LYS cc_start: 0.8561 (mtpt) cc_final: 0.8287 (mmtm) REVERT: A 1030 ARG cc_start: 0.7946 (mtp180) cc_final: 0.7340 (mtp180) REVERT: A 1140 GLU cc_start: 0.8474 (tt0) cc_final: 0.8224 (mt-10) REVERT: A 1169 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7653 (mm-30) REVERT: A 1176 ASN cc_start: 0.8386 (t0) cc_final: 0.8046 (t0) REVERT: A 1210 ARG cc_start: 0.8446 (mtp85) cc_final: 0.7799 (mtt90) REVERT: A 1253 LYS cc_start: 0.8597 (ptmt) cc_final: 0.8290 (ptmm) REVERT: A 1274 GLN cc_start: 0.8520 (mm-40) cc_final: 0.7900 (tt0) outliers start: 23 outliers final: 12 residues processed: 176 average time/residue: 0.2588 time to fit residues: 61.4555 Evaluate side-chains 164 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1236 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 86 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 544 ASN A 602 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.147496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.119891 restraints weight = 12079.826| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 1.99 r_work: 0.3272 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9916 Z= 0.236 Angle : 0.552 6.768 13450 Z= 0.290 Chirality : 0.041 0.149 1562 Planarity : 0.004 0.038 1660 Dihedral : 7.795 78.693 1373 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 1.99 % Allowed : 12.35 % Favored : 85.66 % 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: 0.92 (0.24), residues: 1203 helix: 1.01 (0.18), residues: 773 sheet: -1.01 (0.55), residues: 75 loop : 0.36 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 763 HIS 0.004 0.001 HIS A 152 PHE 0.017 0.002 PHE A 698 TYR 0.011 0.001 TYR A1259 ARG 0.005 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 154 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8004 (pt0) cc_final: 0.7387 (pm20) REVERT: A 76 GLN cc_start: 0.5563 (pt0) cc_final: 0.5208 (mt0) REVERT: A 77 LYS cc_start: 0.8202 (pptt) cc_final: 0.7944 (mmmt) REVERT: A 89 TRP cc_start: 0.8673 (p-90) cc_final: 0.8452 (p-90) REVERT: A 264 LYS cc_start: 0.8629 (mttp) cc_final: 0.8379 (mttt) REVERT: A 276 MET cc_start: 0.8924 (tpp) cc_final: 0.8493 (mmm) REVERT: A 338 THR cc_start: 0.8437 (OUTLIER) cc_final: 0.7951 (p) REVERT: A 413 GLN cc_start: 0.8428 (tt0) cc_final: 0.8035 (tp40) REVERT: A 509 LYS cc_start: 0.8881 (ttmt) cc_final: 0.8474 (tttp) REVERT: A 571 ARG cc_start: 0.8040 (ttt180) cc_final: 0.7496 (tmm160) REVERT: A 611 MET cc_start: 0.8662 (ttp) cc_final: 0.8396 (ttp) REVERT: A 695 LYS cc_start: 0.7644 (ptpt) cc_final: 0.6602 (tttp) REVERT: A 744 MET cc_start: 0.5145 (OUTLIER) cc_final: 0.4153 (pp-130) REVERT: A 800 LYS cc_start: 0.7792 (mtmt) cc_final: 0.7552 (mmtm) REVERT: A 1020 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7800 (pm20) REVERT: A 1021 LYS cc_start: 0.8576 (mtpt) cc_final: 0.8308 (mmtm) REVERT: A 1140 GLU cc_start: 0.8424 (tt0) cc_final: 0.8204 (mt-10) REVERT: A 1169 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7653 (mm-30) REVERT: A 1176 ASN cc_start: 0.8429 (t0) cc_final: 0.8107 (t0) REVERT: A 1194 LYS cc_start: 0.7544 (mtmm) cc_final: 0.7279 (ptpt) REVERT: A 1210 ARG cc_start: 0.8449 (mtp85) cc_final: 0.7616 (mpt180) REVERT: A 1274 GLN cc_start: 0.8484 (mm-40) cc_final: 0.7919 (tt0) outliers start: 21 outliers final: 17 residues processed: 165 average time/residue: 0.2703 time to fit residues: 60.3011 Evaluate side-chains 162 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 143 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 285 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 346 ILE Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1238 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 57 optimal weight: 0.4980 chunk 92 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.150153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.121730 restraints weight = 12039.087| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.24 r_work: 0.3252 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 0.3243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9916 Z= 0.222 Angle : 0.543 7.023 13450 Z= 0.286 Chirality : 0.040 0.148 1562 Planarity : 0.003 0.040 1660 Dihedral : 7.732 82.503 1373 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.28 % Allowed : 13.58 % Favored : 84.14 % 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: 0.98 (0.24), residues: 1203 helix: 1.10 (0.18), residues: 775 sheet: -0.92 (0.55), residues: 75 loop : 0.26 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 230 HIS 0.003 0.001 HIS A 152 PHE 0.017 0.001 PHE A 698 TYR 0.014 0.001 TYR A1259 ARG 0.005 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8020 (pt0) cc_final: 0.7397 (pm20) REVERT: A 76 GLN cc_start: 0.5643 (pt0) cc_final: 0.5296 (mt0) REVERT: A 77 LYS cc_start: 0.8162 (pptt) cc_final: 0.7905 (mmmt) REVERT: A 89 TRP cc_start: 0.8661 (p-90) cc_final: 0.8433 (p-90) REVERT: A 264 LYS cc_start: 0.8642 (mttp) cc_final: 0.8395 (mttt) REVERT: A 338 THR cc_start: 0.8456 (OUTLIER) cc_final: 0.7988 (p) REVERT: A 413 GLN cc_start: 0.8436 (tt0) cc_final: 0.7872 (tp40) REVERT: A 509 LYS cc_start: 0.8868 (ttmt) cc_final: 0.8442 (tttp) REVERT: A 571 ARG cc_start: 0.7994 (ttt180) cc_final: 0.7422 (tmm160) REVERT: A 744 MET cc_start: 0.5097 (OUTLIER) cc_final: 0.4156 (pp-130) REVERT: A 800 LYS cc_start: 0.7781 (mtmt) cc_final: 0.7516 (mmtm) REVERT: A 1020 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7768 (pm20) REVERT: A 1021 LYS cc_start: 0.8612 (mtpt) cc_final: 0.8299 (mmtm) REVERT: A 1140 GLU cc_start: 0.8405 (tt0) cc_final: 0.8153 (mt-10) REVERT: A 1176 ASN cc_start: 0.8370 (t0) cc_final: 0.8060 (t0) REVERT: A 1194 LYS cc_start: 0.7522 (mtmm) cc_final: 0.7290 (ptpt) REVERT: A 1210 ARG cc_start: 0.8447 (mtp85) cc_final: 0.7601 (mpt180) REVERT: A 1274 GLN cc_start: 0.8502 (mm-40) cc_final: 0.7919 (tt0) outliers start: 24 outliers final: 17 residues processed: 165 average time/residue: 0.2572 time to fit residues: 57.6430 Evaluate side-chains 167 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 854 VAL Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1253 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 59 optimal weight: 7.9990 chunk 3 optimal weight: 0.8980 chunk 38 optimal weight: 0.0970 chunk 87 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 71 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.150208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.122216 restraints weight = 12073.443| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.22 r_work: 0.3238 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9916 Z= 0.213 Angle : 0.537 6.891 13450 Z= 0.284 Chirality : 0.040 0.175 1562 Planarity : 0.003 0.040 1660 Dihedral : 7.665 87.225 1373 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.18 % Allowed : 14.34 % Favored : 83.48 % 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: 1.12 (0.24), residues: 1203 helix: 1.23 (0.19), residues: 770 sheet: -0.78 (0.59), residues: 70 loop : 0.25 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 763 HIS 0.003 0.001 HIS A 934 PHE 0.019 0.001 PHE A 352 TYR 0.011 0.001 TYR A 737 ARG 0.006 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8055 (pt0) cc_final: 0.7446 (pm20) REVERT: A 76 GLN cc_start: 0.5603 (pt0) cc_final: 0.5267 (mt0) REVERT: A 77 LYS cc_start: 0.8180 (pptt) cc_final: 0.7887 (mmmt) REVERT: A 89 TRP cc_start: 0.8659 (p-90) cc_final: 0.8439 (p-90) REVERT: A 264 LYS cc_start: 0.8639 (mttp) cc_final: 0.8388 (mttt) REVERT: A 276 MET cc_start: 0.8919 (tpp) cc_final: 0.8450 (mmm) REVERT: A 338 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.7928 (p) REVERT: A 413 GLN cc_start: 0.8436 (tt0) cc_final: 0.7882 (tp40) REVERT: A 509 LYS cc_start: 0.8906 (ttmt) cc_final: 0.8489 (tttp) REVERT: A 571 ARG cc_start: 0.7999 (ttt180) cc_final: 0.7429 (tmm160) REVERT: A 715 ILE cc_start: 0.8192 (mp) cc_final: 0.7919 (tp) REVERT: A 744 MET cc_start: 0.5067 (OUTLIER) cc_final: 0.4088 (pp-130) REVERT: A 800 LYS cc_start: 0.7775 (mtmt) cc_final: 0.7541 (mmtm) REVERT: A 845 GLN cc_start: 0.7584 (pt0) cc_final: 0.7353 (mt0) REVERT: A 1020 GLU cc_start: 0.8221 (mm-30) cc_final: 0.7759 (pm20) REVERT: A 1021 LYS cc_start: 0.8624 (mtpt) cc_final: 0.8303 (mmtm) REVERT: A 1176 ASN cc_start: 0.8394 (t0) cc_final: 0.8094 (t0) REVERT: A 1194 LYS cc_start: 0.7553 (mtmm) cc_final: 0.7315 (ptpt) REVERT: A 1195 ASN cc_start: 0.8444 (m-40) cc_final: 0.7881 (m-40) REVERT: A 1210 ARG cc_start: 0.8453 (mtp85) cc_final: 0.7601 (mpt180) REVERT: A 1274 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8004 (tt0) outliers start: 23 outliers final: 18 residues processed: 171 average time/residue: 0.2598 time to fit residues: 60.5630 Evaluate side-chains 164 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1111 HIS Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1253 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 44 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 110 optimal weight: 0.5980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A1151 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.149755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.121964 restraints weight = 12088.511| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.22 r_work: 0.3237 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9916 Z= 0.220 Angle : 0.543 7.070 13450 Z= 0.286 Chirality : 0.040 0.148 1562 Planarity : 0.003 0.041 1660 Dihedral : 7.646 86.587 1373 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.37 % Allowed : 14.62 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.24), residues: 1203 helix: 1.29 (0.19), residues: 770 sheet: -0.77 (0.60), residues: 70 loop : 0.25 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 230 HIS 0.003 0.001 HIS A 934 PHE 0.018 0.001 PHE A 698 TYR 0.015 0.001 TYR A1259 ARG 0.006 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 144 time to evaluate : 1.159 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8089 (pt0) cc_final: 0.7456 (pm20) REVERT: A 76 GLN cc_start: 0.5578 (pt0) cc_final: 0.5268 (mt0) REVERT: A 77 LYS cc_start: 0.8170 (pptt) cc_final: 0.7895 (mmmt) REVERT: A 89 TRP cc_start: 0.8674 (p-90) cc_final: 0.8452 (p-90) REVERT: A 264 LYS cc_start: 0.8609 (mttp) cc_final: 0.8373 (mttt) REVERT: A 276 MET cc_start: 0.8910 (tpp) cc_final: 0.8496 (mmm) REVERT: A 338 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.7952 (p) REVERT: A 384 ARG cc_start: 0.8101 (mtm110) cc_final: 0.7830 (mtm-85) REVERT: A 413 GLN cc_start: 0.8396 (tt0) cc_final: 0.7952 (tp40) REVERT: A 509 LYS cc_start: 0.8860 (ttmt) cc_final: 0.8450 (tttp) REVERT: A 571 ARG cc_start: 0.7939 (ttt180) cc_final: 0.7385 (tmm160) REVERT: A 744 MET cc_start: 0.4973 (OUTLIER) cc_final: 0.4042 (pp-130) REVERT: A 800 LYS cc_start: 0.7773 (mtmt) cc_final: 0.7472 (mmtm) REVERT: A 1016 TYR cc_start: 0.8520 (m-10) cc_final: 0.8309 (m-10) REVERT: A 1020 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7727 (pm20) REVERT: A 1021 LYS cc_start: 0.8659 (mtpt) cc_final: 0.8284 (mmtm) REVERT: A 1176 ASN cc_start: 0.8373 (t0) cc_final: 0.8061 (t0) REVERT: A 1194 LYS cc_start: 0.7554 (mtmm) cc_final: 0.7325 (ptpt) REVERT: A 1195 ASN cc_start: 0.8524 (m-40) cc_final: 0.7958 (m-40) REVERT: A 1210 ARG cc_start: 0.8426 (mtp85) cc_final: 0.7584 (mpt180) REVERT: A 1259 TYR cc_start: 0.8122 (t80) cc_final: 0.7869 (t80) REVERT: A 1274 GLN cc_start: 0.8535 (mm-40) cc_final: 0.7904 (tt0) outliers start: 25 outliers final: 21 residues processed: 159 average time/residue: 0.2573 time to fit residues: 56.5007 Evaluate side-chains 166 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 143 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1111 HIS Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1253 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 4 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 89 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 70 optimal weight: 0.5980 chunk 66 optimal weight: 7.9990 chunk 96 optimal weight: 0.0970 chunk 8 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 183 ASN A1151 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.151054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.124697 restraints weight = 12082.656| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.94 r_work: 0.3259 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9916 Z= 0.213 Angle : 0.535 6.994 13450 Z= 0.283 Chirality : 0.040 0.146 1562 Planarity : 0.003 0.041 1660 Dihedral : 7.566 81.143 1371 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.56 % Allowed : 14.43 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.24), residues: 1203 helix: 1.30 (0.19), residues: 771 sheet: -0.71 (0.61), residues: 70 loop : 0.27 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 230 HIS 0.003 0.001 HIS A 934 PHE 0.019 0.001 PHE A 698 TYR 0.011 0.001 TYR A 737 ARG 0.006 0.000 ARG A 384 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 146 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8065 (pt0) cc_final: 0.7437 (pm20) REVERT: A 76 GLN cc_start: 0.5547 (pt0) cc_final: 0.5256 (mt0) REVERT: A 77 LYS cc_start: 0.8159 (pptt) cc_final: 0.7884 (mmmt) REVERT: A 89 TRP cc_start: 0.8654 (p-90) cc_final: 0.8425 (p-90) REVERT: A 264 LYS cc_start: 0.8582 (mttp) cc_final: 0.8345 (mttt) REVERT: A 276 MET cc_start: 0.8871 (tpp) cc_final: 0.8464 (mmm) REVERT: A 338 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.7959 (p) REVERT: A 384 ARG cc_start: 0.8056 (mtm110) cc_final: 0.7785 (mtm-85) REVERT: A 413 GLN cc_start: 0.8341 (tt0) cc_final: 0.7925 (tp40) REVERT: A 509 LYS cc_start: 0.8839 (ttmt) cc_final: 0.8429 (tttp) REVERT: A 571 ARG cc_start: 0.7918 (ttt180) cc_final: 0.7368 (tmm160) REVERT: A 744 MET cc_start: 0.4939 (OUTLIER) cc_final: 0.3969 (pp-130) REVERT: A 800 LYS cc_start: 0.7750 (mtmt) cc_final: 0.7466 (mmtm) REVERT: A 1016 TYR cc_start: 0.8525 (m-10) cc_final: 0.8299 (m-10) REVERT: A 1020 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7687 (pm20) REVERT: A 1021 LYS cc_start: 0.8683 (mtpt) cc_final: 0.8318 (mmtm) REVERT: A 1176 ASN cc_start: 0.8353 (t0) cc_final: 0.8047 (t0) REVERT: A 1195 ASN cc_start: 0.8481 (m-40) cc_final: 0.7877 (m110) REVERT: A 1210 ARG cc_start: 0.8408 (mtp85) cc_final: 0.7560 (mpt180) REVERT: A 1274 GLN cc_start: 0.8455 (mm-40) cc_final: 0.7912 (tt0) outliers start: 27 outliers final: 23 residues processed: 163 average time/residue: 0.2504 time to fit residues: 56.3060 Evaluate side-chains 166 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1111 HIS Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1253 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 50 optimal weight: 0.0020 chunk 55 optimal weight: 0.9980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 849 GLN A1151 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.150307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.122933 restraints weight = 12087.617| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.23 r_work: 0.3255 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9916 Z= 0.213 Angle : 0.537 6.915 13450 Z= 0.283 Chirality : 0.040 0.146 1562 Planarity : 0.003 0.042 1660 Dihedral : 7.350 82.387 1371 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.56 % Allowed : 14.53 % Favored : 82.91 % 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 (0.24), residues: 1203 helix: 1.31 (0.19), residues: 771 sheet: -0.72 (0.61), residues: 70 loop : 0.25 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 230 HIS 0.004 0.001 HIS A 710 PHE 0.018 0.001 PHE A 698 TYR 0.011 0.001 TYR A1259 ARG 0.006 0.000 ARG A 782 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 143 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8111 (pt0) cc_final: 0.7477 (pm20) REVERT: A 76 GLN cc_start: 0.5541 (pt0) cc_final: 0.5156 (mt0) REVERT: A 77 LYS cc_start: 0.8167 (pptt) cc_final: 0.7881 (mmmt) REVERT: A 89 TRP cc_start: 0.8647 (p-90) cc_final: 0.8426 (p-90) REVERT: A 264 LYS cc_start: 0.8620 (mttp) cc_final: 0.8378 (mttt) REVERT: A 276 MET cc_start: 0.8918 (tpp) cc_final: 0.8528 (mmm) REVERT: A 338 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.7966 (p) REVERT: A 413 GLN cc_start: 0.8408 (tt0) cc_final: 0.7983 (tp40) REVERT: A 509 LYS cc_start: 0.8859 (ttmt) cc_final: 0.8452 (tttp) REVERT: A 571 ARG cc_start: 0.7980 (ttt180) cc_final: 0.7407 (tmm160) REVERT: A 744 MET cc_start: 0.4894 (OUTLIER) cc_final: 0.3919 (pp-130) REVERT: A 800 LYS cc_start: 0.7788 (mtmt) cc_final: 0.7502 (mmtm) REVERT: A 1016 TYR cc_start: 0.8553 (m-10) cc_final: 0.8325 (m-10) REVERT: A 1020 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7684 (pm20) REVERT: A 1021 LYS cc_start: 0.8753 (mtpt) cc_final: 0.8345 (mmtm) REVERT: A 1176 ASN cc_start: 0.8372 (t0) cc_final: 0.8066 (t0) REVERT: A 1195 ASN cc_start: 0.8313 (m-40) cc_final: 0.7671 (m110) REVERT: A 1210 ARG cc_start: 0.8451 (mtp85) cc_final: 0.7596 (mpt180) REVERT: A 1259 TYR cc_start: 0.8006 (t80) cc_final: 0.7714 (t80) REVERT: A 1263 GLN cc_start: 0.7653 (pt0) cc_final: 0.7008 (pp30) REVERT: A 1274 GLN cc_start: 0.8451 (mm-40) cc_final: 0.7880 (tt0) outliers start: 27 outliers final: 23 residues processed: 160 average time/residue: 0.2490 time to fit residues: 54.5426 Evaluate side-chains 163 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1104 LEU Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1111 HIS Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1253 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 37 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.148054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.120700 restraints weight = 12134.157| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.11 r_work: 0.3196 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9916 Z= 0.273 Angle : 0.576 9.186 13450 Z= 0.303 Chirality : 0.041 0.147 1562 Planarity : 0.004 0.042 1660 Dihedral : 7.334 68.036 1371 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.37 % Allowed : 15.29 % Favored : 82.34 % 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: 1.05 (0.24), residues: 1203 helix: 1.20 (0.19), residues: 765 sheet: -0.68 (0.61), residues: 65 loop : 0.08 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 230 HIS 0.004 0.001 HIS A 710 PHE 0.019 0.001 PHE A 698 TYR 0.018 0.001 TYR A 737 ARG 0.008 0.000 ARG A 384 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2406 Ramachandran restraints generated. 1203 Oldfield, 0 Emsley, 1203 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 138 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8079 (pt0) cc_final: 0.7499 (pm20) REVERT: A 76 GLN cc_start: 0.5654 (pt0) cc_final: 0.5234 (mt0) REVERT: A 77 LYS cc_start: 0.8159 (pptt) cc_final: 0.7889 (mmmt) REVERT: A 89 TRP cc_start: 0.8663 (p-90) cc_final: 0.8432 (p-90) REVERT: A 264 LYS cc_start: 0.8670 (mttp) cc_final: 0.8440 (mttt) REVERT: A 276 MET cc_start: 0.8917 (tpp) cc_final: 0.8538 (mmm) REVERT: A 338 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8014 (p) REVERT: A 413 GLN cc_start: 0.8369 (tt0) cc_final: 0.7949 (tp40) REVERT: A 509 LYS cc_start: 0.8883 (ttmt) cc_final: 0.8475 (tttp) REVERT: A 744 MET cc_start: 0.5072 (OUTLIER) cc_final: 0.4150 (pp-130) REVERT: A 800 LYS cc_start: 0.7812 (mtmt) cc_final: 0.7497 (mmtm) REVERT: A 931 GLN cc_start: 0.8406 (mm-40) cc_final: 0.7987 (mt0) REVERT: A 1016 TYR cc_start: 0.8578 (m-10) cc_final: 0.8348 (m-10) REVERT: A 1020 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7672 (pm20) REVERT: A 1021 LYS cc_start: 0.8752 (mtpt) cc_final: 0.8345 (mmtm) REVERT: A 1176 ASN cc_start: 0.8349 (t0) cc_final: 0.8039 (t0) REVERT: A 1195 ASN cc_start: 0.8340 (m-40) cc_final: 0.7708 (m110) REVERT: A 1210 ARG cc_start: 0.8430 (mtp85) cc_final: 0.7606 (mpt180) REVERT: A 1259 TYR cc_start: 0.8141 (t80) cc_final: 0.7906 (t80) REVERT: A 1274 GLN cc_start: 0.8466 (mm-40) cc_final: 0.7921 (tt0) outliers start: 25 outliers final: 22 residues processed: 153 average time/residue: 0.2494 time to fit residues: 52.4370 Evaluate side-chains 160 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 351 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 434 THR Chi-restraints excluded: chain A residue 486 SER Chi-restraints excluded: chain A residue 744 MET Chi-restraints excluded: chain A residue 773 VAL Chi-restraints excluded: chain A residue 805 ILE Chi-restraints excluded: chain A residue 835 LEU Chi-restraints excluded: chain A residue 906 SER Chi-restraints excluded: chain A residue 1011 GLU Chi-restraints excluded: chain A residue 1046 VAL Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1108 ILE Chi-restraints excluded: chain A residue 1111 HIS Chi-restraints excluded: chain A residue 1125 VAL Chi-restraints excluded: chain A residue 1130 THR Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1253 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 49 optimal weight: 0.4980 chunk 50 optimal weight: 0.2980 chunk 8 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 94 optimal weight: 0.0020 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A1151 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.152239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.125666 restraints weight = 11964.812| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.08 r_work: 0.3275 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9916 Z= 0.175 Angle : 0.524 7.817 13450 Z= 0.277 Chirality : 0.039 0.144 1562 Planarity : 0.003 0.042 1660 Dihedral : 6.866 59.633 1371 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.18 % Allowed : 15.86 % Favored : 81.96 % 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: 1.34 (0.24), residues: 1203 helix: 1.46 (0.19), residues: 764 sheet: -0.63 (0.61), residues: 70 loop : 0.16 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 230 HIS 0.004 0.001 HIS A 710 PHE 0.018 0.001 PHE A 698 TYR 0.016 0.001 TYR A 737 ARG 0.007 0.000 ARG A 384 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5200.70 seconds wall clock time: 93 minutes 6.79 seconds (5586.79 seconds total)