Starting phenix.real_space_refine on Sun Dec 29 05:23:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bwo_16292/12_2024/8bwo_16292.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bwo_16292/12_2024/8bwo_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_16292/12_2024/8bwo_16292.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bwo_16292/12_2024/8bwo_16292.map" model { file = "/net/cci-nas-00/data/ceres_data/8bwo_16292/12_2024/8bwo_16292.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bwo_16292/12_2024/8bwo_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 6.28, per 1000 atoms: 0.65 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: 2.38 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: 1.11 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: 3.72 Time building geometry restraints manager: 2.73 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: 3.200 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 24.990 Find NCS groups from input model: 0.120 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.760 ------------------------------------------------------------------------------- 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 : 1.087 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: 0.3000 time to fit residues: 87.9467 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 : 1.202 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 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 : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7440 (pt0) cc_final: 0.6625 (pm20) REVERT: A 76 GLN cc_start: 0.5264 (pt0) cc_final: 0.4987 (mt0) REVERT: A 77 LYS cc_start: 0.7883 (pptt) cc_final: 0.7538 (mmmt) REVERT: A 89 TRP cc_start: 0.8341 (p-90) cc_final: 0.7987 (p-90) REVERT: A 165 ARG cc_start: 0.6841 (mtt90) cc_final: 0.6391 (mtm180) REVERT: A 176 ARG cc_start: 0.7014 (ttm170) cc_final: 0.6637 (ttt180) REVERT: A 264 LYS cc_start: 0.7324 (mttp) cc_final: 0.7074 (mttt) REVERT: A 293 LYS cc_start: 0.7167 (mttt) cc_final: 0.6911 (mmmt) REVERT: A 312 ARG cc_start: 0.7072 (mtm-85) cc_final: 0.6828 (mtt180) REVERT: A 326 SER cc_start: 0.8281 (p) cc_final: 0.8074 (p) REVERT: A 413 GLN cc_start: 0.7849 (tt0) cc_final: 0.7371 (tp40) REVERT: A 509 LYS cc_start: 0.8298 (ttmt) cc_final: 0.7799 (tttp) REVERT: A 571 ARG cc_start: 0.7130 (ttt180) cc_final: 0.6853 (tmm160) REVERT: A 607 LYS cc_start: 0.6366 (mttt) cc_final: 0.6147 (pptt) REVERT: A 611 MET cc_start: 0.8320 (ttp) cc_final: 0.8034 (ttp) REVERT: A 695 LYS cc_start: 0.7356 (ptpt) cc_final: 0.6313 (tttp) REVERT: A 706 ARG cc_start: 0.7588 (mmm-85) cc_final: 0.6544 (tpt90) REVERT: A 744 MET cc_start: 0.4725 (OUTLIER) cc_final: 0.3810 (pp-130) REVERT: A 800 LYS cc_start: 0.6766 (mtmt) cc_final: 0.6387 (mmtp) REVERT: A 1020 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7454 (pm20) REVERT: A 1021 LYS cc_start: 0.8248 (mtpt) cc_final: 0.7937 (mmtm) REVERT: A 1066 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.7939 (mtmm) REVERT: A 1140 GLU cc_start: 0.7988 (tt0) cc_final: 0.7636 (mt-10) REVERT: A 1169 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7501 (mm-30) REVERT: A 1176 ASN cc_start: 0.7596 (t0) cc_final: 0.7188 (t0) REVERT: A 1210 ARG cc_start: 0.7831 (mtp85) cc_final: 0.7292 (mtt90) REVERT: A 1274 GLN cc_start: 0.8388 (mm-40) cc_final: 0.7881 (tt0) outliers start: 19 outliers final: 10 residues processed: 184 average time/residue: 0.2733 time to fit residues: 67.2774 Evaluate side-chains 164 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 1.035 ------------------------------------------------------------------------------- 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 61 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 110 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 37 optimal weight: 0.5980 chunk 88 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9916 Z= 0.223 Angle : 0.556 7.262 13450 Z= 0.295 Chirality : 0.041 0.151 1562 Planarity : 0.004 0.037 1660 Dihedral : 8.016 75.912 1373 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.80 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: 0.69 (0.24), residues: 1203 helix: 0.81 (0.18), residues: 775 sheet: -1.11 (0.56), residues: 75 loop : 0.34 (0.35), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 763 HIS 0.004 0.001 HIS A 152 PHE 0.017 0.002 PHE A 698 TYR 0.009 0.001 TYR A 737 ARG 0.003 0.000 ARG A 998 *********************** 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 184 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 1.155 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7425 (pt0) cc_final: 0.6665 (pm20) REVERT: A 77 LYS cc_start: 0.7854 (pptt) cc_final: 0.7516 (mmmt) REVERT: A 89 TRP cc_start: 0.8382 (p-90) cc_final: 0.8029 (p-90) REVERT: A 176 ARG cc_start: 0.7007 (ttm170) cc_final: 0.6565 (ttt180) REVERT: A 264 LYS cc_start: 0.7323 (mttp) cc_final: 0.7071 (mttt) REVERT: A 276 MET cc_start: 0.8210 (tpp) cc_final: 0.7858 (mmm) REVERT: A 293 LYS cc_start: 0.7095 (mttt) cc_final: 0.6861 (mmmt) REVERT: A 312 ARG cc_start: 0.7096 (mtm-85) cc_final: 0.6820 (mtt-85) REVERT: A 338 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7620 (p) REVERT: A 413 GLN cc_start: 0.7903 (tt0) cc_final: 0.7404 (tp40) REVERT: A 481 GLN cc_start: 0.8295 (mm-40) cc_final: 0.8066 (mm-40) REVERT: A 509 LYS cc_start: 0.8343 (ttmt) cc_final: 0.7847 (tttm) REVERT: A 571 ARG cc_start: 0.7153 (ttt180) cc_final: 0.6818 (tmm160) REVERT: A 611 MET cc_start: 0.8277 (ttp) cc_final: 0.7964 (ttp) REVERT: A 695 LYS cc_start: 0.7448 (ptpt) cc_final: 0.6334 (tttp) REVERT: A 744 MET cc_start: 0.4745 (OUTLIER) cc_final: 0.3813 (pp-130) REVERT: A 800 LYS cc_start: 0.6722 (mtmt) cc_final: 0.6335 (mmtm) REVERT: A 1020 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7489 (pm20) REVERT: A 1021 LYS cc_start: 0.8253 (mtpt) cc_final: 0.7923 (mmtm) REVERT: A 1030 ARG cc_start: 0.7826 (mtp180) cc_final: 0.7218 (mtp180) REVERT: A 1140 GLU cc_start: 0.7997 (tt0) cc_final: 0.7691 (mt-10) REVERT: A 1169 GLU cc_start: 0.7920 (mm-30) cc_final: 0.7588 (mm-30) REVERT: A 1176 ASN cc_start: 0.7750 (t0) cc_final: 0.7329 (t0) REVERT: A 1210 ARG cc_start: 0.7881 (mtp85) cc_final: 0.7343 (mtt90) REVERT: A 1253 LYS cc_start: 0.8305 (ptmt) cc_final: 0.7963 (ptmm) REVERT: A 1274 GLN cc_start: 0.8396 (mm-40) cc_final: 0.7863 (tt0) outliers start: 23 outliers final: 13 residues processed: 175 average time/residue: 0.2625 time to fit residues: 62.3631 Evaluate side-chains 160 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 145 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ASP Chi-restraints excluded: chain A residue 56 LEU 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 1011 GLU Chi-restraints excluded: chain A residue 1061 LEU Chi-restraints excluded: chain A residue 1108 ILE 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 108 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 73 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 116 optimal weight: 1.9990 chunk 104 optimal weight: 0.0470 chunk 31 optimal weight: 0.9990 chunk 97 optimal weight: 0.0980 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9916 Z= 0.179 Angle : 0.526 6.806 13450 Z= 0.277 Chirality : 0.040 0.150 1562 Planarity : 0.003 0.037 1660 Dihedral : 7.635 79.329 1373 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.90 % Allowed : 11.97 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.24), residues: 1203 helix: 1.16 (0.19), residues: 773 sheet: -0.97 (0.55), residues: 75 loop : 0.39 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 763 HIS 0.002 0.001 HIS A 934 PHE 0.019 0.001 PHE A 352 TYR 0.012 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 179 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 159 time to evaluate : 1.147 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7389 (pt0) cc_final: 0.6631 (pm20) REVERT: A 77 LYS cc_start: 0.7846 (pptt) cc_final: 0.7507 (mmmt) REVERT: A 89 TRP cc_start: 0.8346 (p-90) cc_final: 0.8032 (p-90) REVERT: A 176 ARG cc_start: 0.6889 (ttm170) cc_final: 0.6480 (ttt180) REVERT: A 264 LYS cc_start: 0.7350 (mttp) cc_final: 0.7083 (mttt) REVERT: A 276 MET cc_start: 0.8117 (tpp) cc_final: 0.7794 (mmm) REVERT: A 312 ARG cc_start: 0.6992 (mtm-85) cc_final: 0.6738 (mtt-85) REVERT: A 338 THR cc_start: 0.7935 (OUTLIER) cc_final: 0.7506 (p) REVERT: A 413 GLN cc_start: 0.7966 (tt0) cc_final: 0.7589 (tp40) REVERT: A 509 LYS cc_start: 0.8352 (ttmt) cc_final: 0.7851 (tttp) REVERT: A 571 ARG cc_start: 0.7126 (ttt180) cc_final: 0.6791 (tmm160) REVERT: A 611 MET cc_start: 0.8172 (ttp) cc_final: 0.7839 (ttp) REVERT: A 695 LYS cc_start: 0.7396 (ptpt) cc_final: 0.6234 (tttp) REVERT: A 744 MET cc_start: 0.4650 (OUTLIER) cc_final: 0.3734 (pp-130) REVERT: A 800 LYS cc_start: 0.6652 (mtmt) cc_final: 0.6335 (mmtm) REVERT: A 1020 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7475 (pm20) REVERT: A 1021 LYS cc_start: 0.8213 (mtpt) cc_final: 0.7880 (mmtm) REVERT: A 1140 GLU cc_start: 0.7975 (tt0) cc_final: 0.7573 (mt-10) REVERT: A 1169 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7590 (mm-30) REVERT: A 1176 ASN cc_start: 0.7783 (t0) cc_final: 0.7382 (t0) REVERT: A 1194 LYS cc_start: 0.7077 (mtmm) cc_final: 0.6871 (ptpt) REVERT: A 1210 ARG cc_start: 0.7841 (mtp85) cc_final: 0.7166 (mpt180) REVERT: A 1272 MET cc_start: 0.7233 (mtp) cc_final: 0.6954 (mtt) REVERT: A 1274 GLN cc_start: 0.8348 (mm-40) cc_final: 0.7857 (tt0) outliers start: 20 outliers final: 12 residues processed: 169 average time/residue: 0.2671 time to fit residues: 61.2075 Evaluate side-chains 161 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 THR 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 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 1238 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 48 optimal weight: 0.0070 chunk 99 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 overall best weight: 0.7200 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3286 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= 0.223 Angle : 0.546 7.041 13450 Z= 0.288 Chirality : 0.041 0.148 1562 Planarity : 0.003 0.040 1660 Dihedral : 7.573 82.084 1371 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.18 % Allowed : 13.49 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.24), residues: 1203 helix: 1.17 (0.19), residues: 775 sheet: -0.84 (0.55), residues: 75 loop : 0.32 (0.34), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 230 HIS 0.004 0.001 HIS A 152 PHE 0.017 0.001 PHE A 698 TYR 0.017 0.001 TYR A 737 ARG 0.006 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 171 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7481 (pt0) cc_final: 0.6653 (pm20) REVERT: A 77 LYS cc_start: 0.7800 (pptt) cc_final: 0.7480 (mmmt) REVERT: A 89 TRP cc_start: 0.8366 (p-90) cc_final: 0.8045 (p-90) REVERT: A 264 LYS cc_start: 0.7374 (mttp) cc_final: 0.7113 (mttt) REVERT: A 312 ARG cc_start: 0.7018 (mtm-85) cc_final: 0.6760 (mtt-85) REVERT: A 338 THR cc_start: 0.8034 (OUTLIER) cc_final: 0.7559 (p) REVERT: A 413 GLN cc_start: 0.7928 (tt0) cc_final: 0.7420 (tp40) REVERT: A 509 LYS cc_start: 0.8398 (ttmt) cc_final: 0.7896 (tttp) REVERT: A 571 ARG cc_start: 0.7149 (ttt180) cc_final: 0.6776 (tmm160) REVERT: A 744 MET cc_start: 0.4684 (OUTLIER) cc_final: 0.3784 (pp-130) REVERT: A 800 LYS cc_start: 0.6712 (mtmt) cc_final: 0.6327 (mmtm) REVERT: A 1020 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7477 (pm20) REVERT: A 1021 LYS cc_start: 0.8282 (mtpt) cc_final: 0.7881 (mmtm) REVERT: A 1140 GLU cc_start: 0.7848 (tt0) cc_final: 0.7644 (mt-10) REVERT: A 1176 ASN cc_start: 0.7854 (t0) cc_final: 0.7466 (t0) REVERT: A 1194 LYS cc_start: 0.7155 (mtmm) cc_final: 0.6939 (ptpt) REVERT: A 1210 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7195 (mpt180) REVERT: A 1274 GLN cc_start: 0.8357 (mm-40) cc_final: 0.7886 (tt0) outliers start: 23 outliers final: 18 residues processed: 161 average time/residue: 0.2523 time to fit residues: 55.9471 Evaluate side-chains 158 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 1.171 ------------------------------------------------------------------------------- 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 346 ILE 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 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 1125 VAL 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 105 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 112 optimal weight: 0.0670 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 183 ASN A 845 GLN A1151 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9916 Z= 0.200 Angle : 0.526 6.810 13450 Z= 0.278 Chirality : 0.040 0.150 1562 Planarity : 0.003 0.040 1660 Dihedral : 7.548 86.150 1371 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.99 % Allowed : 14.91 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.24), residues: 1203 helix: 1.30 (0.19), residues: 770 sheet: -0.61 (0.60), residues: 70 loop : 0.28 (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 0.020 0.001 PHE A 352 TYR 0.016 0.001 TYR A1259 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 169 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7500 (pt0) cc_final: 0.6705 (pm20) REVERT: A 77 LYS cc_start: 0.7794 (pptt) cc_final: 0.7465 (mmmt) REVERT: A 89 TRP cc_start: 0.8351 (p-90) cc_final: 0.8037 (p-90) REVERT: A 264 LYS cc_start: 0.7359 (mttp) cc_final: 0.7093 (mttt) REVERT: A 276 MET cc_start: 0.8154 (tpp) cc_final: 0.7804 (mmm) REVERT: A 312 ARG cc_start: 0.7001 (mtm-85) cc_final: 0.6744 (mtt-85) REVERT: A 338 THR cc_start: 0.7994 (OUTLIER) cc_final: 0.7557 (p) REVERT: A 384 ARG cc_start: 0.7155 (mtm110) cc_final: 0.6924 (mtm-85) REVERT: A 413 GLN cc_start: 0.7927 (tt0) cc_final: 0.7423 (tp40) REVERT: A 509 LYS cc_start: 0.8401 (ttmt) cc_final: 0.7897 (tttp) REVERT: A 571 ARG cc_start: 0.7151 (ttt180) cc_final: 0.6765 (tmm160) REVERT: A 715 ILE cc_start: 0.7948 (mp) cc_final: 0.7665 (tp) REVERT: A 744 MET cc_start: 0.4685 (OUTLIER) cc_final: 0.3753 (pp-130) REVERT: A 800 LYS cc_start: 0.6737 (mtmt) cc_final: 0.6361 (mmtm) REVERT: A 1021 LYS cc_start: 0.8287 (mtpt) cc_final: 0.7901 (mmtm) REVERT: A 1176 ASN cc_start: 0.7838 (t0) cc_final: 0.7459 (t0) REVERT: A 1195 ASN cc_start: 0.8235 (m-40) cc_final: 0.7551 (m-40) REVERT: A 1210 ARG cc_start: 0.7863 (mtp85) cc_final: 0.7190 (mpt180) REVERT: A 1259 TYR cc_start: 0.7851 (t80) cc_final: 0.7544 (t80) REVERT: A 1274 GLN cc_start: 0.8374 (mm-40) cc_final: 0.7932 (tt0) outliers start: 21 outliers final: 14 residues processed: 160 average time/residue: 0.2534 time to fit residues: 55.5694 Evaluate side-chains 152 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 338 THR 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 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 1125 VAL Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1238 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 183 ASN A1151 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9916 Z= 0.238 Angle : 0.547 6.805 13450 Z= 0.287 Chirality : 0.040 0.148 1562 Planarity : 0.003 0.041 1660 Dihedral : 7.702 89.820 1371 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.18 % Allowed : 15.00 % Favored : 82.81 % 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: 1.16 (0.24), residues: 1203 helix: 1.24 (0.18), residues: 771 sheet: -0.63 (0.62), residues: 65 loop : 0.26 (0.34), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 763 HIS 0.004 0.001 HIS A 934 PHE 0.019 0.001 PHE A 698 TYR 0.016 0.001 TYR A 737 ARG 0.005 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 162 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 139 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7492 (pt0) cc_final: 0.6697 (pm20) REVERT: A 77 LYS cc_start: 0.7792 (pptt) cc_final: 0.7458 (mmmt) REVERT: A 89 TRP cc_start: 0.8367 (p-90) cc_final: 0.8039 (p-90) REVERT: A 264 LYS cc_start: 0.7378 (mttp) cc_final: 0.7125 (mttt) REVERT: A 276 MET cc_start: 0.8162 (tpp) cc_final: 0.7883 (mmm) REVERT: A 312 ARG cc_start: 0.7057 (mtm-85) cc_final: 0.6802 (mtt-85) REVERT: A 338 THR cc_start: 0.8045 (OUTLIER) cc_final: 0.7578 (p) REVERT: A 413 GLN cc_start: 0.7911 (tt0) cc_final: 0.7544 (tp40) REVERT: A 509 LYS cc_start: 0.8407 (ttmt) cc_final: 0.7909 (tttp) REVERT: A 571 ARG cc_start: 0.7172 (ttt180) cc_final: 0.6766 (tmm160) REVERT: A 744 MET cc_start: 0.4618 (OUTLIER) cc_final: 0.3737 (pp-130) REVERT: A 800 LYS cc_start: 0.6733 (mtmt) cc_final: 0.6327 (mmtm) REVERT: A 1021 LYS cc_start: 0.8321 (mtpt) cc_final: 0.7910 (mmtm) REVERT: A 1176 ASN cc_start: 0.7871 (t0) cc_final: 0.7484 (t0) REVERT: A 1195 ASN cc_start: 0.8220 (m-40) cc_final: 0.7493 (m-40) REVERT: A 1210 ARG cc_start: 0.7891 (mtp85) cc_final: 0.7182 (mpt180) REVERT: A 1274 GLN cc_start: 0.8358 (mm-40) cc_final: 0.7873 (tt0) outliers start: 23 outliers final: 19 residues processed: 153 average time/residue: 0.2562 time to fit residues: 53.3853 Evaluate side-chains 156 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 108 optimal weight: 0.0870 overall best weight: 0.7158 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9916 Z= 0.226 Angle : 0.541 6.992 13450 Z= 0.286 Chirality : 0.040 0.146 1562 Planarity : 0.003 0.042 1660 Dihedral : 7.617 80.014 1371 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.09 % Allowed : 15.10 % Favored : 82.81 % 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: 1.16 (0.24), residues: 1203 helix: 1.25 (0.18), residues: 771 sheet: -0.62 (0.62), residues: 65 loop : 0.21 (0.33), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 763 HIS 0.003 0.001 HIS A 934 PHE 0.018 0.001 PHE A 698 TYR 0.015 0.001 TYR A 737 ARG 0.007 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 158 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7519 (pt0) cc_final: 0.6723 (pm20) REVERT: A 77 LYS cc_start: 0.7797 (pptt) cc_final: 0.7462 (mmmt) REVERT: A 89 TRP cc_start: 0.8357 (p-90) cc_final: 0.8026 (p-90) REVERT: A 264 LYS cc_start: 0.7344 (mttp) cc_final: 0.7092 (mttt) REVERT: A 276 MET cc_start: 0.8162 (tpp) cc_final: 0.7880 (mmm) REVERT: A 312 ARG cc_start: 0.7043 (mtm-85) cc_final: 0.6774 (mtt-85) REVERT: A 338 THR cc_start: 0.8037 (OUTLIER) cc_final: 0.7582 (p) REVERT: A 413 GLN cc_start: 0.7909 (tt0) cc_final: 0.7537 (tp40) REVERT: A 509 LYS cc_start: 0.8406 (ttmt) cc_final: 0.7908 (tttp) REVERT: A 571 ARG cc_start: 0.7172 (ttt180) cc_final: 0.6761 (tmm160) REVERT: A 744 MET cc_start: 0.4547 (OUTLIER) cc_final: 0.3643 (pp-130) REVERT: A 800 LYS cc_start: 0.6726 (mtmt) cc_final: 0.6319 (mmtm) REVERT: A 931 GLN cc_start: 0.7552 (mm-40) cc_final: 0.6947 (mt0) REVERT: A 1021 LYS cc_start: 0.8299 (mtpt) cc_final: 0.7879 (mmtm) REVERT: A 1176 ASN cc_start: 0.7844 (t0) cc_final: 0.7465 (t0) REVERT: A 1195 ASN cc_start: 0.8126 (m-40) cc_final: 0.7421 (m110) REVERT: A 1210 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7178 (mpt180) REVERT: A 1259 TYR cc_start: 0.7707 (t80) cc_final: 0.7440 (t80) REVERT: A 1274 GLN cc_start: 0.8301 (mm-40) cc_final: 0.7886 (tt0) outliers start: 22 outliers final: 20 residues processed: 149 average time/residue: 0.2558 time to fit residues: 52.5025 Evaluate side-chains 158 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 111 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 114 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9916 Z= 0.291 Angle : 0.574 7.292 13450 Z= 0.302 Chirality : 0.041 0.147 1562 Planarity : 0.004 0.042 1660 Dihedral : 7.724 87.510 1371 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.47 % Allowed : 15.19 % 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: 0.99 (0.24), residues: 1203 helix: 1.14 (0.18), residues: 766 sheet: -0.67 (0.61), residues: 65 loop : 0.10 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 230 HIS 0.004 0.001 HIS A 152 PHE 0.019 0.002 PHE A 698 TYR 0.016 0.002 TYR A 737 ARG 0.007 0.001 ARG A 384 *********************** 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 156 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 130 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7576 (pt0) cc_final: 0.6813 (pm20) REVERT: A 77 LYS cc_start: 0.7813 (pptt) cc_final: 0.7462 (mmmt) REVERT: A 89 TRP cc_start: 0.8349 (p-90) cc_final: 0.8028 (p-90) REVERT: A 230 TRP cc_start: 0.7005 (t60) cc_final: 0.6278 (t60) REVERT: A 264 LYS cc_start: 0.7374 (mttp) cc_final: 0.7132 (mttt) REVERT: A 276 MET cc_start: 0.8181 (tpp) cc_final: 0.7902 (mmm) REVERT: A 312 ARG cc_start: 0.7028 (mtm-85) cc_final: 0.6756 (mtt-85) REVERT: A 413 GLN cc_start: 0.7910 (tt0) cc_final: 0.7527 (tp40) REVERT: A 509 LYS cc_start: 0.8428 (ttmt) cc_final: 0.7929 (tttp) REVERT: A 744 MET cc_start: 0.4586 (OUTLIER) cc_final: 0.3663 (pp-130) REVERT: A 800 LYS cc_start: 0.6701 (mtmt) cc_final: 0.6285 (mmtm) REVERT: A 931 GLN cc_start: 0.7570 (mm-40) cc_final: 0.6932 (mt0) REVERT: A 1176 ASN cc_start: 0.7841 (t0) cc_final: 0.7454 (t0) REVERT: A 1195 ASN cc_start: 0.8212 (m-40) cc_final: 0.7505 (m110) REVERT: A 1210 ARG cc_start: 0.7884 (mtp85) cc_final: 0.7161 (mpt180) REVERT: A 1274 GLN cc_start: 0.8363 (mm-40) cc_final: 0.7891 (tt0) outliers start: 26 outliers final: 21 residues processed: 147 average time/residue: 0.2574 time to fit residues: 51.9299 Evaluate side-chains 150 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 54 optimal weight: 0.8980 chunk 79 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 110 optimal weight: 0.0870 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 102 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9916 Z= 0.233 Angle : 0.549 7.141 13450 Z= 0.289 Chirality : 0.040 0.146 1562 Planarity : 0.004 0.043 1660 Dihedral : 7.289 70.469 1371 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.28 % Allowed : 15.48 % Favored : 82.24 % 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: 1.11 (0.24), residues: 1203 helix: 1.26 (0.19), residues: 764 sheet: -0.64 (0.62), residues: 65 loop : 0.08 (0.33), residues: 374 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 0.015 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 156 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7553 (pt0) cc_final: 0.6780 (pm20) REVERT: A 77 LYS cc_start: 0.7784 (pptt) cc_final: 0.7435 (mmmt) REVERT: A 89 TRP cc_start: 0.8346 (p-90) cc_final: 0.8032 (p-90) REVERT: A 230 TRP cc_start: 0.7013 (t60) cc_final: 0.6240 (t60) REVERT: A 264 LYS cc_start: 0.7368 (mttp) cc_final: 0.7110 (mttt) REVERT: A 276 MET cc_start: 0.8166 (tpp) cc_final: 0.7887 (mmm) REVERT: A 312 ARG cc_start: 0.7053 (mtm-85) cc_final: 0.6792 (mtt-85) REVERT: A 338 THR cc_start: 0.8073 (OUTLIER) cc_final: 0.7596 (p) REVERT: A 413 GLN cc_start: 0.7895 (tt0) cc_final: 0.7518 (tp40) REVERT: A 509 LYS cc_start: 0.8400 (ttmt) cc_final: 0.7908 (tttp) REVERT: A 744 MET cc_start: 0.4585 (OUTLIER) cc_final: 0.3723 (pp-130) REVERT: A 800 LYS cc_start: 0.6725 (mtmt) cc_final: 0.6310 (mmtm) REVERT: A 931 GLN cc_start: 0.7539 (mm-40) cc_final: 0.6942 (mt0) REVERT: A 1176 ASN cc_start: 0.7767 (t0) cc_final: 0.7386 (t0) REVERT: A 1195 ASN cc_start: 0.8107 (m-40) cc_final: 0.7407 (m110) REVERT: A 1210 ARG cc_start: 0.7872 (mtp85) cc_final: 0.7151 (mpt180) REVERT: A 1259 TYR cc_start: 0.7755 (t80) cc_final: 0.7525 (t80) REVERT: A 1274 GLN cc_start: 0.8297 (mm-40) cc_final: 0.7837 (tt0) outliers start: 24 outliers final: 21 residues processed: 147 average time/residue: 0.2548 time to fit residues: 51.2552 Evaluate side-chains 154 residues out of total 1053 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 1215 ILE 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 88 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 96 optimal weight: 0.0070 chunk 40 optimal weight: 0.9980 chunk 98 optimal weight: 0.8980 chunk 12 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- 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 = 0.3694 r_free = 0.3694 target = 0.146235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.120527 restraints weight = 12087.328| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.81 r_work: 0.3221 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3696 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= 0.320 Angle : 0.594 9.346 13450 Z= 0.311 Chirality : 0.042 0.147 1562 Planarity : 0.004 0.043 1660 Dihedral : 7.364 58.874 1371 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.18 % Allowed : 16.14 % Favored : 81.67 % 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: 0.90 (0.24), residues: 1203 helix: 1.08 (0.19), residues: 765 sheet: -0.67 (0.61), residues: 65 loop : 0.02 (0.33), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 230 HIS 0.005 0.001 HIS A 934 PHE 0.018 0.002 PHE A 698 TYR 0.016 0.002 TYR A 737 ARG 0.008 0.001 ARG A 384 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2454.42 seconds wall clock time: 45 minutes 30.06 seconds (2730.06 seconds total)