Starting phenix.real_space_refine on Sun Aug 24 10:03:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kdc_37131/08_2025/8kdc_37131.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kdc_37131/08_2025/8kdc_37131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8kdc_37131/08_2025/8kdc_37131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kdc_37131/08_2025/8kdc_37131.map" model { file = "/net/cci-nas-00/data/ceres_data/8kdc_37131/08_2025/8kdc_37131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kdc_37131/08_2025/8kdc_37131.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.001 sd= 0.085 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 Zn 2 6.06 5 Mg 1 5.21 5 S 97 5.16 5 C 11999 2.51 5 N 3174 2.21 5 O 3535 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18808 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 17067 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2114, 17047 Classifications: {'peptide': 2114} Link IDs: {'PTRANS': 73, 'TRANS': 2040} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 2114, 17047 Classifications: {'peptide': 2114} Link IDs: {'PTRANS': 73, 'TRANS': 2040} Chain breaks: 5 bond proxies already assigned to first conformer: 17372 Chain: "B" Number of atoms: 510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 510 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 1, 'TRANS': 63} Chain: "C" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 305 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "D" Number of atoms: 335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 335 Classifications: {'peptide': 41} Link IDs: {'TRANS': 40} Chain: "E" Number of atoms: 309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 309 Classifications: {'peptide': 38} Link IDs: {'TRANS': 37} Chain: "F" Number of atoms: 279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 279 Classifications: {'peptide': 34} Link IDs: {'TRANS': 33} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9243 SG CYS A1177 71.681 111.770 64.772 1.00 88.89 S ATOM 9266 SG CYS A1180 73.631 109.989 62.572 1.00 86.70 S ATOM 8907 SG CYS A1132 84.963 107.508 80.610 1.00 82.90 S ATOM 10714 SG CYS A1371 84.136 109.336 76.945 1.00110.51 S ATOM 10720 SG CYS A1372 82.652 106.601 78.646 1.00101.40 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AMET A 472 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 472 " occ=0.50 residue: pdb=" N ATYR A 649 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 649 " occ=0.50 Time building chain proxies: 8.45, per 1000 atoms: 0.45 Number of scatterers: 18808 At special positions: 0 Unit cell: (115.222, 144.571, 150.006, 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) Zn 2 29.99 S 97 16.00 Mg 1 11.99 O 3535 8.00 N 3174 7.00 C 11999 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: 2.09 Conformation dependent library (CDL) restraints added in 1.7 seconds Enol-peptide restraints added in 476.8 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A3002 " pdb="ZN ZN A3002 " - pdb=" ND1 HIS A1364 " pdb="ZN ZN A3002 " - pdb=" NE2 HIS A1366 " pdb="ZN ZN A3002 " - pdb=" SG CYS A1180 " pdb="ZN ZN A3002 " - pdb=" SG CYS A1177 " pdb=" ZN A3003 " pdb="ZN ZN A3003 " - pdb=" SG CYS A1372 " pdb="ZN ZN A3003 " - pdb=" SG CYS A1132 " pdb="ZN ZN A3003 " - pdb=" SG CYS A1371 " Number of angles added : 2 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4448 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 11 sheets defined 58.4% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.09 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 48 through 60 Processing helix chain 'A' and resid 63 through 71 Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 109 through 123 removed outlier: 3.939A pdb=" N LEU A 113 " --> pdb=" O LYS A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 140 Processing helix chain 'A' and resid 151 through 166 removed outlier: 3.644A pdb=" N ILE A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER A 158 " --> pdb=" O ILE A 154 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LYS A 159 " --> pdb=" O ASN A 155 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL A 160 " --> pdb=" O ASN A 156 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N HIS A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N THR A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 193 Processing helix chain 'A' and resid 232 through 256 removed outlier: 3.557A pdb=" N ASP A 256 " --> pdb=" O CYS A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 280 removed outlier: 3.760A pdb=" N GLN A 264 " --> pdb=" O GLN A 260 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A 275 " --> pdb=" O GLU A 271 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU A 276 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N PHE A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Proline residue: A 278 - end of helix Processing helix chain 'A' and resid 283 through 301 removed outlier: 3.711A pdb=" N VAL A 287 " --> pdb=" O LYS A 283 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N GLU A 292 " --> pdb=" O ILE A 288 " (cutoff:3.500A) Proline residue: A 293 - end of helix Processing helix chain 'A' and resid 312 through 325 Processing helix chain 'A' and resid 327 through 334 Processing helix chain 'A' and resid 337 through 344 Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 357 through 360 Processing helix chain 'A' and resid 370 through 382 removed outlier: 3.850A pdb=" N LYS A 377 " --> pdb=" O ILE A 373 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 378 " --> pdb=" O ALA A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 412 Processing helix chain 'A' and resid 426 through 436 Processing helix chain 'A' and resid 440 through 447 Processing helix chain 'A' and resid 448 through 451 Processing helix chain 'A' and resid 467 through 471 removed outlier: 3.688A pdb=" N ILE A 470 " --> pdb=" O ASP A 467 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TYR A 471 " --> pdb=" O LEU A 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 467 through 471' Processing helix chain 'A' and resid 489 through 493 removed outlier: 3.630A pdb=" N LEU A 493 " --> pdb=" O ALA A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 512 removed outlier: 3.514A pdb=" N VAL A 509 " --> pdb=" O ARG A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 527 removed outlier: 4.083A pdb=" N ILE A 521 " --> pdb=" O ASP A 517 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU A 522 " --> pdb=" O PRO A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 574 Processing helix chain 'A' and resid 576 through 580 Processing helix chain 'A' and resid 588 through 602 Processing helix chain 'A' and resid 672 through 688 removed outlier: 3.697A pdb=" N THR A 676 " --> pdb=" O ARG A 672 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N LEU A 678 " --> pdb=" O GLU A 674 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N PHE A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 701 Processing helix chain 'A' and resid 721 through 724 Processing helix chain 'A' and resid 744 through 763 removed outlier: 4.157A pdb=" N ILE A 762 " --> pdb=" O ALA A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 815 removed outlier: 3.633A pdb=" N LYS A 798 " --> pdb=" O GLU A 794 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP A 799 " --> pdb=" O ILE A 795 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP A 805 " --> pdb=" O VAL A 801 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N SER A 806 " --> pdb=" O ARG A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 851 removed outlier: 3.575A pdb=" N LEU A 850 " --> pdb=" O ALA A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 864 through 881 Processing helix chain 'A' and resid 884 through 906 Processing helix chain 'A' and resid 914 through 923 removed outlier: 3.640A pdb=" N LYS A 922 " --> pdb=" O ASP A 918 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 933 Processing helix chain 'A' and resid 944 through 949 Processing helix chain 'A' and resid 956 through 970 Processing helix chain 'A' and resid 975 through 983 Processing helix chain 'A' and resid 990 through 997 Processing helix chain 'A' and resid 1008 through 1020 Processing helix chain 'A' and resid 1027 through 1034 Processing helix chain 'A' and resid 1037 through 1051 removed outlier: 3.596A pdb=" N GLU A1041 " --> pdb=" O THR A1037 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1067 Processing helix chain 'A' and resid 1068 through 1077 Processing helix chain 'A' and resid 1081 through 1093 Processing helix chain 'A' and resid 1096 through 1105 removed outlier: 5.187A pdb=" N LYS A1102 " --> pdb=" O SER A1098 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N ILE A1103 " --> pdb=" O LEU A1099 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER A1104 " --> pdb=" O LEU A1100 " (cutoff:3.500A) Processing helix chain 'A' and resid 1105 through 1119 Processing helix chain 'A' and resid 1132 through 1145 Processing helix chain 'A' and resid 1145 through 1150 Processing helix chain 'A' and resid 1161 through 1165 Processing helix chain 'A' and resid 1177 through 1184 Processing helix chain 'A' and resid 1234 through 1251 Processing helix chain 'A' and resid 1254 through 1266 Processing helix chain 'A' and resid 1272 through 1280 Processing helix chain 'A' and resid 1331 through 1350 Processing helix chain 'A' and resid 1410 through 1424 Processing helix chain 'A' and resid 1430 through 1456 removed outlier: 3.974A pdb=" N ARG A1455 " --> pdb=" O SER A1451 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ASP A1456 " --> pdb=" O GLN A1452 " (cutoff:3.500A) Processing helix chain 'A' and resid 1458 through 1463 Processing helix chain 'A' and resid 1473 through 1480 Processing helix chain 'A' and resid 1481 through 1504 removed outlier: 5.114A pdb=" N TYR A1499 " --> pdb=" O ASN A1495 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N THR A1500 " --> pdb=" O GLN A1496 " (cutoff:3.500A) Processing helix chain 'A' and resid 1508 through 1523 removed outlier: 4.118A pdb=" N TRP A1513 " --> pdb=" O ARG A1509 " (cutoff:3.500A) Processing helix chain 'A' and resid 1528 through 1535 Processing helix chain 'A' and resid 1538 through 1546 Processing helix chain 'A' and resid 1562 through 1585 Processing helix chain 'A' and resid 1596 through 1619 Processing helix chain 'A' and resid 1632 through 1651 Processing helix chain 'A' and resid 1670 through 1686 Processing helix chain 'A' and resid 1708 through 1724 removed outlier: 3.716A pdb=" N ASP A1714 " --> pdb=" O LYS A1710 " (cutoff:3.500A) Processing helix chain 'A' and resid 1769 through 1775 removed outlier: 3.608A pdb=" N GLN A1773 " --> pdb=" O LEU A1770 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU A1774 " --> pdb=" O SER A1771 " (cutoff:3.500A) Processing helix chain 'A' and resid 1785 through 1798 removed outlier: 4.435A pdb=" N GLN A1792 " --> pdb=" O LEU A1788 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N ILE A1793 " --> pdb=" O GLU A1789 " (cutoff:3.500A) Processing helix chain 'A' and resid 1812 through 1822 Processing helix chain 'A' and resid 1834 through 1838 Processing helix chain 'A' and resid 1848 through 1859 Processing helix chain 'A' and resid 1863 through 1866 Processing helix chain 'A' and resid 1875 through 1879 Processing helix chain 'A' and resid 1884 through 1895 Processing helix chain 'A' and resid 1913 through 1931 Processing helix chain 'A' and resid 1951 through 1961 Processing helix chain 'A' and resid 1994 through 2001 Processing helix chain 'A' and resid 2005 through 2037 Processing helix chain 'A' and resid 2042 through 2052 Processing helix chain 'A' and resid 2056 through 2065 Processing helix chain 'A' and resid 2073 through 2094 Processing helix chain 'A' and resid 2115 through 2140 Processing helix chain 'A' and resid 2147 through 2155 Processing helix chain 'A' and resid 2161 through 2166 Processing helix chain 'A' and resid 2172 through 2181 removed outlier: 3.632A pdb=" N CYS A2181 " --> pdb=" O ASN A2177 " (cutoff:3.500A) Processing helix chain 'A' and resid 2190 through 2207 Processing helix chain 'B' and resid 551 through 564 Processing helix chain 'B' and resid 568 through 581 removed outlier: 3.601A pdb=" N HIS B 581 " --> pdb=" O ASN B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 584 through 602 removed outlier: 3.605A pdb=" N VAL B 588 " --> pdb=" O ASN B 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 469 removed outlier: 3.714A pdb=" N ILE C 447 " --> pdb=" O HIS C 443 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU C 448 " --> pdb=" O ARG C 444 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN C 449 " --> pdb=" O ARG C 445 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 463 Processing helix chain 'E' and resid 435 through 469 Processing helix chain 'F' and resid 435 through 463 Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 6.420A pdb=" N THR A 87 " --> pdb=" O GLY A 228 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N LEU A 230 " --> pdb=" O THR A 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 387 through 389 Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 420 Processing sheet with id=AA4, first strand: chain 'A' and resid 553 through 557 removed outlier: 4.812A pdb=" N ILE A 538 " --> pdb=" O THR A 704 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N TYR A 706 " --> pdb=" O ILE A 538 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 641 through 644 Processing sheet with id=AA6, first strand: chain 'A' and resid 765 through 771 removed outlier: 4.137A pdb=" N ARG A 765 " --> pdb=" O THR A 780 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 829 through 832 Processing sheet with id=AA8, first strand: chain 'A' and resid 1054 through 1055 Processing sheet with id=AA9, first strand: chain 'A' and resid 1166 through 1171 removed outlier: 4.063A pdb=" N VAL A1362 " --> pdb=" O ILE A1171 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1588 through 1593 Processing sheet with id=AB2, first strand: chain 'A' and resid 1738 through 1740 removed outlier: 3.635A pdb=" N LYS A1941 " --> pdb=" O CYS A1904 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N ASP A1803 " --> pdb=" O ILE A1899 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N LEU A1901 " --> pdb=" O ASP A1803 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ARG A1804 " --> pdb=" O TYR A1828 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N ASN A1830 " --> pdb=" O ARG A1804 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N PHE A1806 " --> pdb=" O ASN A1830 " (cutoff:3.500A) 1020 hydrogen bonds defined for protein. 2973 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.75 Time building geometry restraints manager: 2.64 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: 6082 1.34 - 1.46: 2975 1.46 - 1.58: 9942 1.58 - 1.69: 0 1.69 - 1.81: 160 Bond restraints: 19159 Sorted by residual: bond pdb=" CB PRO A1993 " pdb=" CG PRO A1993 " ideal model delta sigma weight residual 1.492 1.575 -0.083 5.00e-02 4.00e+02 2.74e+00 bond pdb=" CB PRO A2068 " pdb=" CG PRO A2068 " ideal model delta sigma weight residual 1.492 1.572 -0.080 5.00e-02 4.00e+02 2.54e+00 bond pdb=" CA GLN A 123 " pdb=" C GLN A 123 " ideal model delta sigma weight residual 1.518 1.572 -0.054 4.01e-02 6.22e+02 1.81e+00 bond pdb=" CB PRO A2144 " pdb=" CG PRO A2144 " ideal model delta sigma weight residual 1.492 1.558 -0.066 5.00e-02 4.00e+02 1.73e+00 bond pdb=" C LEU A1763 " pdb=" N PRO A1764 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.06e+00 ... (remaining 19154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 25245 1.30 - 2.61: 508 2.61 - 3.91: 100 3.91 - 5.22: 26 5.22 - 6.52: 12 Bond angle restraints: 25891 Sorted by residual: angle pdb=" CA PRO A1993 " pdb=" N PRO A1993 " pdb=" CD PRO A1993 " ideal model delta sigma weight residual 112.00 107.53 4.47 1.40e+00 5.10e-01 1.02e+01 angle pdb=" CA PRO A2068 " pdb=" N PRO A2068 " pdb=" CD PRO A2068 " ideal model delta sigma weight residual 112.00 107.65 4.35 1.40e+00 5.10e-01 9.64e+00 angle pdb=" CA PRO A2144 " pdb=" N PRO A2144 " pdb=" CD PRO A2144 " ideal model delta sigma weight residual 112.00 107.82 4.18 1.40e+00 5.10e-01 8.90e+00 angle pdb=" CA MET A1517 " pdb=" CB MET A1517 " pdb=" CG MET A1517 " ideal model delta sigma weight residual 114.10 108.53 5.57 2.00e+00 2.50e-01 7.76e+00 angle pdb=" N ASP A 651 " pdb=" CA ASP A 651 " pdb=" C ASP A 651 " ideal model delta sigma weight residual 113.28 108.92 4.36 1.57e+00 4.06e-01 7.71e+00 ... (remaining 25886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 10459 17.90 - 35.79: 1018 35.79 - 53.69: 166 53.69 - 71.58: 30 71.58 - 89.48: 9 Dihedral angle restraints: 11682 sinusoidal: 4815 harmonic: 6867 Sorted by residual: dihedral pdb=" CA TYR A 42 " pdb=" C TYR A 42 " pdb=" N ASP A 43 " pdb=" CA ASP A 43 " ideal model delta harmonic sigma weight residual 180.00 163.09 16.91 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CB GLU A 535 " pdb=" CG GLU A 535 " pdb=" CD GLU A 535 " pdb=" OE1 GLU A 535 " ideal model delta sinusoidal sigma weight residual 0.00 -89.48 89.48 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CA ASP A 126 " pdb=" CB ASP A 126 " pdb=" CG ASP A 126 " pdb=" OD1 ASP A 126 " ideal model delta sinusoidal sigma weight residual -30.00 -85.53 55.53 1 2.00e+01 2.50e-03 1.04e+01 ... (remaining 11679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2319 0.046 - 0.092: 522 0.092 - 0.138: 100 0.138 - 0.185: 5 0.185 - 0.231: 1 Chirality restraints: 2947 Sorted by residual: chirality pdb=" CB ILE A1307 " pdb=" CA ILE A1307 " pdb=" CG1 ILE A1307 " pdb=" CG2 ILE A1307 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.33e+00 chirality pdb=" CA GLU A2063 " pdb=" N GLU A2063 " pdb=" C GLU A2063 " pdb=" CB GLU A2063 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.60e-01 chirality pdb=" CB VAL A1798 " pdb=" CA VAL A1798 " pdb=" CG1 VAL A1798 " pdb=" CG2 VAL A1798 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.57e-01 ... (remaining 2944 not shown) Planarity restraints: 3270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A2067 " 0.073 5.00e-02 4.00e+02 1.08e-01 1.87e+01 pdb=" N PRO A2068 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO A2068 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO A2068 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A1992 " 0.067 5.00e-02 4.00e+02 9.94e-02 1.58e+01 pdb=" N PRO A1993 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO A1993 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO A1993 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A2143 " -0.040 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO A2144 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO A2144 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A2144 " -0.032 5.00e-02 4.00e+02 ... (remaining 3267 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 115 2.58 - 3.16: 15273 3.16 - 3.74: 28142 3.74 - 4.32: 37550 4.32 - 4.90: 66755 Nonbonded interactions: 147835 Sorted by model distance: nonbonded pdb=" OE2 GLU A1164 " pdb="ZN ZN A3003 " model vdw 2.001 2.230 nonbonded pdb=" OD2 ASP A 773 " pdb="MG MG A3001 " model vdw 2.068 2.170 nonbonded pdb=" OE1 GLU A2033 " pdb=" NH2 ARG A2042 " model vdw 2.165 3.120 nonbonded pdb=" O SER A 857 " pdb=" ND2 ASN A 870 " model vdw 2.206 3.120 nonbonded pdb=" OD1 ASN B 542 " pdb=" OG1 THR B 544 " model vdw 2.240 3.040 ... (remaining 147830 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'C' and resid 435 through 467) selection = (chain 'D' and resid 435 through 467) selection = (chain 'E' and resid 435 through 467) selection = (chain 'F' and resid 435 through 467) } 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=0.50 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: 3.080 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: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 29.110 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.070 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:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 : 0.003 0.083 19166 Z= 0.117 Angle : 0.533 23.890 25893 Z= 0.266 Chirality : 0.039 0.231 2947 Planarity : 0.004 0.108 3270 Dihedral : 14.094 89.480 7234 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.05 % Allowed : 0.47 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.18), residues: 2313 helix: 2.11 (0.15), residues: 1286 sheet: -0.14 (0.40), residues: 177 loop : -1.16 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1127 TYR 0.027 0.001 TYR A 164 PHE 0.020 0.001 PHE A 99 TRP 0.032 0.001 TRP A2188 HIS 0.007 0.001 HIS A2059 Details of bonding type rmsd covalent geometry : bond 0.00275 (19159) covalent geometry : angle 0.49476 (25891) hydrogen bonds : bond 0.11708 ( 1020) hydrogen bonds : angle 4.43907 ( 2973) metal coordination : bond 0.03164 ( 7) metal coordination : angle 22.60989 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 264 time to evaluate : 0.795 Fit side-chains REVERT: A 523 ASP cc_start: 0.8092 (t0) cc_final: 0.7854 (t70) REVERT: A 1398 GLU cc_start: 0.8458 (pt0) cc_final: 0.8209 (pm20) REVERT: A 1770 LEU cc_start: 0.8442 (mp) cc_final: 0.7738 (tp) REVERT: A 1906 MET cc_start: 0.7701 (mtm) cc_final: 0.5414 (mtm) REVERT: A 1920 GLU cc_start: 0.7730 (mt-10) cc_final: 0.7195 (tt0) REVERT: A 2063 GLU cc_start: 0.7235 (mt-10) cc_final: 0.7025 (mt-10) REVERT: C 465 LYS cc_start: 0.7599 (ttmm) cc_final: 0.7195 (ttmm) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.1618 time to fit residues: 65.4934 Evaluate side-chains 212 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 212 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 2.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 200 optimal weight: 6.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1110 GLN ** A1773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 573 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.139483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.104223 restraints weight = 49389.788| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.44 r_work: 0.3191 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19166 Z= 0.121 Angle : 0.506 7.920 25893 Z= 0.263 Chirality : 0.040 0.186 2947 Planarity : 0.004 0.080 3270 Dihedral : 3.823 16.832 2531 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.61 % Allowed : 6.07 % Favored : 93.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.29 (0.18), residues: 2313 helix: 2.23 (0.15), residues: 1292 sheet: -0.10 (0.40), residues: 177 loop : -1.17 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 865 TYR 0.012 0.001 TYR A 942 PHE 0.018 0.001 PHE A1578 TRP 0.024 0.001 TRP A1880 HIS 0.003 0.001 HIS A 19 Details of bonding type rmsd covalent geometry : bond 0.00288 (19159) covalent geometry : angle 0.50285 (25891) hydrogen bonds : bond 0.04092 ( 1020) hydrogen bonds : angle 3.89835 ( 2973) metal coordination : bond 0.01600 ( 7) metal coordination : angle 6.50708 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 229 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 466 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7239 (mt-10) REVERT: A 523 ASP cc_start: 0.8381 (t0) cc_final: 0.7987 (t0) REVERT: A 1368 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7584 (mm-30) REVERT: A 1415 MET cc_start: 0.8003 (mmt) cc_final: 0.7787 (mmm) REVERT: A 1514 ASP cc_start: 0.8168 (t70) cc_final: 0.7832 (t0) REVERT: A 1770 LEU cc_start: 0.8567 (mp) cc_final: 0.7999 (tp) REVERT: A 1795 MET cc_start: 0.8250 (ptm) cc_final: 0.7801 (ptm) REVERT: A 1875 ASN cc_start: 0.8747 (t0) cc_final: 0.8467 (t0) REVERT: A 1906 MET cc_start: 0.7709 (mtm) cc_final: 0.6087 (mtm) REVERT: A 1920 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7544 (tt0) REVERT: A 2144 PRO cc_start: 0.7792 (Cg_endo) cc_final: 0.7550 (Cg_exo) outliers start: 12 outliers final: 4 residues processed: 237 average time/residue: 0.1583 time to fit residues: 57.0485 Evaluate side-chains 217 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 213 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1322 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 175 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 216 optimal weight: 5.9990 chunk 194 optimal weight: 0.9990 chunk 206 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1110 GLN ** A1147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1290 HIS ** A1773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.137578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.102250 restraints weight = 48297.623| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.29 r_work: 0.3133 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.0936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19166 Z= 0.145 Angle : 0.512 8.080 25893 Z= 0.266 Chirality : 0.040 0.160 2947 Planarity : 0.004 0.071 3270 Dihedral : 3.891 17.969 2531 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.89 % Allowed : 7.62 % Favored : 91.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.18), residues: 2313 helix: 2.22 (0.15), residues: 1291 sheet: -0.13 (0.40), residues: 177 loop : -1.19 (0.20), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A2082 TYR 0.013 0.001 TYR A2044 PHE 0.017 0.002 PHE A1578 TRP 0.025 0.001 TRP A1880 HIS 0.003 0.001 HIS A2059 Details of bonding type rmsd covalent geometry : bond 0.00353 (19159) covalent geometry : angle 0.50922 (25891) hydrogen bonds : bond 0.04203 ( 1020) hydrogen bonds : angle 3.83038 ( 2973) metal coordination : bond 0.01569 ( 7) metal coordination : angle 5.65170 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 219 time to evaluate : 0.763 Fit side-chains revert: symmetry clash REVERT: A 466 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7337 (mt-10) REVERT: A 523 ASP cc_start: 0.8493 (t0) cc_final: 0.8038 (t0) REVERT: A 1368 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7735 (mm-30) REVERT: A 1415 MET cc_start: 0.8059 (mmt) cc_final: 0.7796 (mmm) REVERT: A 1514 ASP cc_start: 0.8194 (t70) cc_final: 0.7844 (t0) REVERT: A 1770 LEU cc_start: 0.8595 (mp) cc_final: 0.8016 (tp) REVERT: A 1795 MET cc_start: 0.8236 (ptm) cc_final: 0.7759 (ptm) REVERT: A 1875 ASN cc_start: 0.8777 (t0) cc_final: 0.8499 (t0) REVERT: A 1906 MET cc_start: 0.7753 (mtm) cc_final: 0.6176 (mtm) REVERT: A 1920 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7533 (tt0) outliers start: 18 outliers final: 13 residues processed: 234 average time/residue: 0.1607 time to fit residues: 57.4216 Evaluate side-chains 220 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 207 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 521 ILE Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1784 CYS Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain E residue 462 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 13 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 229 optimal weight: 0.7980 chunk 167 optimal weight: 0.0030 chunk 134 optimal weight: 1.9990 chunk 182 optimal weight: 0.9990 chunk 178 optimal weight: 2.9990 chunk 158 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.139073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.103620 restraints weight = 48174.420| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 3.29 r_work: 0.3170 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 19166 Z= 0.115 Angle : 0.482 7.772 25893 Z= 0.251 Chirality : 0.039 0.174 2947 Planarity : 0.004 0.065 3270 Dihedral : 3.814 17.772 2531 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.75 % Allowed : 8.98 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.18), residues: 2313 helix: 2.32 (0.15), residues: 1285 sheet: -0.10 (0.40), residues: 177 loop : -1.19 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 362 TYR 0.011 0.001 TYR A 942 PHE 0.018 0.001 PHE A1578 TRP 0.026 0.001 TRP A1880 HIS 0.004 0.001 HIS A2059 Details of bonding type rmsd covalent geometry : bond 0.00274 (19159) covalent geometry : angle 0.47997 (25891) hydrogen bonds : bond 0.03743 ( 1020) hydrogen bonds : angle 3.70281 ( 2973) metal coordination : bond 0.01677 ( 7) metal coordination : angle 5.32701 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 224 time to evaluate : 0.775 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 466 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7307 (mt-10) REVERT: A 523 ASP cc_start: 0.8471 (t0) cc_final: 0.8002 (t0) REVERT: A 689 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.7994 (pp) REVERT: A 1368 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7779 (mm-30) REVERT: A 1415 MET cc_start: 0.8021 (mmt) cc_final: 0.7754 (mmm) REVERT: A 1514 ASP cc_start: 0.8147 (t70) cc_final: 0.7795 (t0) REVERT: A 1770 LEU cc_start: 0.8558 (mp) cc_final: 0.7960 (tp) REVERT: A 1795 MET cc_start: 0.8196 (ptm) cc_final: 0.7805 (ptm) REVERT: A 1875 ASN cc_start: 0.8762 (t0) cc_final: 0.8468 (t0) REVERT: A 1906 MET cc_start: 0.7774 (mtm) cc_final: 0.6326 (mtm) REVERT: A 1920 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7510 (tt0) REVERT: A 2033 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7312 (tm-30) outliers start: 15 outliers final: 10 residues processed: 232 average time/residue: 0.1639 time to fit residues: 58.1838 Evaluate side-chains 219 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 208 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 945 MET Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1784 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 188 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 220 optimal weight: 7.9990 chunk 175 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1110 GLN A1147 HIS ** A1773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.135619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.100023 restraints weight = 45450.501| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 3.22 r_work: 0.3121 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 19166 Z= 0.181 Angle : 0.533 7.591 25893 Z= 0.278 Chirality : 0.041 0.160 2947 Planarity : 0.004 0.061 3270 Dihedral : 3.963 18.607 2531 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.46 % Allowed : 9.03 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.18), residues: 2313 helix: 2.16 (0.15), residues: 1285 sheet: -0.21 (0.40), residues: 177 loop : -1.23 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 362 TYR 0.034 0.002 TYR A 942 PHE 0.017 0.002 PHE A 400 TRP 0.055 0.002 TRP A2188 HIS 0.004 0.001 HIS A2059 Details of bonding type rmsd covalent geometry : bond 0.00448 (19159) covalent geometry : angle 0.53101 (25891) hydrogen bonds : bond 0.04516 ( 1020) hydrogen bonds : angle 3.85734 ( 2973) metal coordination : bond 0.01495 ( 7) metal coordination : angle 5.62002 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 0.798 Fit side-chains REVERT: A 466 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7356 (mt-10) REVERT: A 523 ASP cc_start: 0.8500 (t0) cc_final: 0.7998 (t0) REVERT: A 689 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8078 (pp) REVERT: A 1368 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7825 (mm-30) REVERT: A 1415 MET cc_start: 0.8092 (mmt) cc_final: 0.7798 (mmm) REVERT: A 1514 ASP cc_start: 0.8180 (t70) cc_final: 0.7822 (t0) REVERT: A 1770 LEU cc_start: 0.8613 (mp) cc_final: 0.8020 (tp) REVERT: A 1795 MET cc_start: 0.8248 (ptm) cc_final: 0.7853 (ptm) REVERT: A 1875 ASN cc_start: 0.8793 (t0) cc_final: 0.8443 (t0) REVERT: A 1906 MET cc_start: 0.7819 (mtm) cc_final: 0.6361 (mtm) REVERT: A 1920 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7523 (tt0) REVERT: A 2033 GLU cc_start: 0.7589 (tm-30) cc_final: 0.7237 (tm-30) REVERT: A 2198 MET cc_start: 0.8069 (mmm) cc_final: 0.7651 (mmm) outliers start: 30 outliers final: 20 residues processed: 231 average time/residue: 0.1648 time to fit residues: 57.5966 Evaluate side-chains 229 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 208 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 945 MET Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1117 THR Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1423 THR Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1784 CYS Chi-restraints excluded: chain A residue 1798 VAL Chi-restraints excluded: chain A residue 1914 GLU Chi-restraints excluded: chain A residue 2018 LEU Chi-restraints excluded: chain B residue 565 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 14 optimal weight: 0.0770 chunk 197 optimal weight: 0.6980 chunk 224 optimal weight: 8.9990 chunk 162 optimal weight: 1.9990 chunk 181 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 167 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 57 optimal weight: 0.0980 chunk 118 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1110 GLN ** A1773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 HIS ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 443 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.139241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.103589 restraints weight = 44325.597| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.16 r_work: 0.3194 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.1181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.082 19166 Z= 0.103 Angle : 0.475 7.322 25893 Z= 0.248 Chirality : 0.038 0.152 2947 Planarity : 0.003 0.058 3270 Dihedral : 3.789 18.068 2531 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.85 % Allowed : 10.40 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.38 (0.18), residues: 2313 helix: 2.36 (0.15), residues: 1286 sheet: -0.17 (0.40), residues: 177 loop : -1.20 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 362 TYR 0.021 0.001 TYR A 942 PHE 0.018 0.001 PHE A1578 TRP 0.036 0.001 TRP A2188 HIS 0.003 0.001 HIS A2059 Details of bonding type rmsd covalent geometry : bond 0.00243 (19159) covalent geometry : angle 0.47244 (25891) hydrogen bonds : bond 0.03562 ( 1020) hydrogen bonds : angle 3.63759 ( 2973) metal coordination : bond 0.01749 ( 7) metal coordination : angle 5.22191 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 0.808 Fit side-chains REVERT: A 523 ASP cc_start: 0.8406 (t0) cc_final: 0.7983 (t0) REVERT: A 689 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7991 (pp) REVERT: A 1415 MET cc_start: 0.8044 (mmt) cc_final: 0.7789 (mmm) REVERT: A 1514 ASP cc_start: 0.8162 (t70) cc_final: 0.7827 (t0) REVERT: A 1770 LEU cc_start: 0.8566 (mp) cc_final: 0.7998 (tp) REVERT: A 1795 MET cc_start: 0.8170 (ptm) cc_final: 0.7818 (ptm) REVERT: A 1875 ASN cc_start: 0.8736 (t0) cc_final: 0.8354 (t0) REVERT: A 1906 MET cc_start: 0.7704 (mtm) cc_final: 0.6220 (mtm) REVERT: A 1920 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7562 (tt0) REVERT: A 2033 GLU cc_start: 0.7691 (tm-30) cc_final: 0.7406 (tm-30) REVERT: B 577 ASN cc_start: 0.8109 (m110) cc_final: 0.7828 (m110) REVERT: D 469 GLU cc_start: 0.8774 (pm20) cc_final: 0.8504 (pm20) outliers start: 17 outliers final: 14 residues processed: 233 average time/residue: 0.1629 time to fit residues: 57.5396 Evaluate side-chains 227 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 212 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1784 CYS Chi-restraints excluded: chain A residue 1798 VAL Chi-restraints excluded: chain A residue 1914 GLU Chi-restraints excluded: chain B residue 565 SER Chi-restraints excluded: chain E residue 462 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 175 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 198 optimal weight: 3.9990 chunk 168 optimal weight: 0.1980 chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 35 optimal weight: 0.3980 chunk 166 optimal weight: 7.9990 chunk 176 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 200 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 HIS ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.137855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.102362 restraints weight = 40050.164| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.94 r_work: 0.3184 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 19166 Z= 0.134 Angle : 0.496 7.434 25893 Z= 0.259 Chirality : 0.039 0.153 2947 Planarity : 0.004 0.057 3270 Dihedral : 3.795 17.942 2531 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.03 % Allowed : 10.54 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.18), residues: 2313 helix: 2.33 (0.15), residues: 1286 sheet: -0.17 (0.40), residues: 177 loop : -1.19 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 362 TYR 0.019 0.001 TYR A1422 PHE 0.017 0.001 PHE A1578 TRP 0.034 0.001 TRP A2188 HIS 0.004 0.001 HIS A2059 Details of bonding type rmsd covalent geometry : bond 0.00329 (19159) covalent geometry : angle 0.49400 (25891) hydrogen bonds : bond 0.03869 ( 1020) hydrogen bonds : angle 3.66904 ( 2973) metal coordination : bond 0.01672 ( 7) metal coordination : angle 4.96920 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 0.884 Fit side-chains REVERT: A 523 ASP cc_start: 0.8390 (t0) cc_final: 0.7973 (t0) REVERT: A 689 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8094 (pp) REVERT: A 1415 MET cc_start: 0.8057 (mmt) cc_final: 0.7800 (mmm) REVERT: A 1514 ASP cc_start: 0.8174 (t70) cc_final: 0.7839 (t0) REVERT: A 1770 LEU cc_start: 0.8541 (mp) cc_final: 0.8020 (tp) REVERT: A 1795 MET cc_start: 0.8205 (ptm) cc_final: 0.7845 (ptm) REVERT: A 1875 ASN cc_start: 0.8724 (t0) cc_final: 0.8490 (t0) REVERT: A 1906 MET cc_start: 0.7656 (mtm) cc_final: 0.6170 (mtm) REVERT: A 1920 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7537 (tt0) REVERT: A 2063 GLU cc_start: 0.8346 (pt0) cc_final: 0.8090 (mt-10) REVERT: A 2198 MET cc_start: 0.8207 (mmm) cc_final: 0.7838 (mmm) REVERT: B 577 ASN cc_start: 0.8186 (m110) cc_final: 0.7895 (m110) outliers start: 21 outliers final: 18 residues processed: 223 average time/residue: 0.1649 time to fit residues: 55.9876 Evaluate side-chains 227 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 208 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 945 MET Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1784 CYS Chi-restraints excluded: chain A residue 1798 VAL Chi-restraints excluded: chain A residue 1914 GLU Chi-restraints excluded: chain A residue 2018 LEU Chi-restraints excluded: chain B residue 565 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 44 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 128 optimal weight: 0.0670 chunk 125 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 156 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 120 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.138078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.102777 restraints weight = 50588.998| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 3.64 r_work: 0.3154 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19166 Z= 0.130 Angle : 0.498 7.447 25893 Z= 0.260 Chirality : 0.039 0.153 2947 Planarity : 0.004 0.056 3270 Dihedral : 3.790 17.903 2531 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.08 % Allowed : 10.63 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.18), residues: 2313 helix: 2.34 (0.15), residues: 1285 sheet: -0.17 (0.40), residues: 177 loop : -1.19 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 362 TYR 0.013 0.001 TYR A2044 PHE 0.016 0.001 PHE A1578 TRP 0.033 0.001 TRP A2188 HIS 0.004 0.001 HIS A2059 Details of bonding type rmsd covalent geometry : bond 0.00316 (19159) covalent geometry : angle 0.49625 (25891) hydrogen bonds : bond 0.03840 ( 1020) hydrogen bonds : angle 3.65386 ( 2973) metal coordination : bond 0.01514 ( 7) metal coordination : angle 4.92429 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 211 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 523 ASP cc_start: 0.8444 (t0) cc_final: 0.7988 (t0) REVERT: A 689 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7994 (pp) REVERT: A 997 ASP cc_start: 0.8304 (t70) cc_final: 0.8087 (t70) REVERT: A 1415 MET cc_start: 0.8038 (mmt) cc_final: 0.7749 (mmm) REVERT: A 1514 ASP cc_start: 0.8172 (t70) cc_final: 0.7832 (t0) REVERT: A 1770 LEU cc_start: 0.8507 (mp) cc_final: 0.7937 (tp) REVERT: A 1795 MET cc_start: 0.8169 (ptm) cc_final: 0.7803 (ptm) REVERT: A 1875 ASN cc_start: 0.8757 (t0) cc_final: 0.8516 (t0) REVERT: A 1906 MET cc_start: 0.7785 (mtm) cc_final: 0.6223 (mtm) REVERT: A 1920 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7535 (tt0) REVERT: A 2198 MET cc_start: 0.8158 (mmm) cc_final: 0.7853 (mmm) REVERT: B 577 ASN cc_start: 0.8096 (m110) cc_final: 0.7782 (m110) REVERT: D 469 GLU cc_start: 0.8748 (pm20) cc_final: 0.8547 (pm20) outliers start: 22 outliers final: 19 residues processed: 227 average time/residue: 0.1536 time to fit residues: 52.9016 Evaluate side-chains 228 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 208 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 557 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 945 MET Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1784 CYS Chi-restraints excluded: chain A residue 1798 VAL Chi-restraints excluded: chain A residue 1914 GLU Chi-restraints excluded: chain A residue 2018 LEU Chi-restraints excluded: chain B residue 565 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 20 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 226 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 155 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.136575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.101908 restraints weight = 39189.287| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 2.91 r_work: 0.3147 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3189 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 19166 Z= 0.170 Angle : 0.534 7.703 25893 Z= 0.279 Chirality : 0.040 0.156 2947 Planarity : 0.004 0.055 3270 Dihedral : 3.919 18.310 2531 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.08 % Allowed : 10.72 % Favored : 88.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.18), residues: 2313 helix: 2.21 (0.15), residues: 1285 sheet: -0.20 (0.40), residues: 177 loop : -1.24 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 362 TYR 0.022 0.001 TYR A1422 PHE 0.016 0.002 PHE A 400 TRP 0.035 0.002 TRP A2188 HIS 0.003 0.001 HIS A1147 Details of bonding type rmsd covalent geometry : bond 0.00420 (19159) covalent geometry : angle 0.53220 (25891) hydrogen bonds : bond 0.04387 ( 1020) hydrogen bonds : angle 3.78499 ( 2973) metal coordination : bond 0.01398 ( 7) metal coordination : angle 5.00931 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 213 time to evaluate : 0.659 Fit side-chains revert: symmetry clash REVERT: A 523 ASP cc_start: 0.8466 (t0) cc_final: 0.8020 (t0) REVERT: A 689 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8107 (pp) REVERT: A 1415 MET cc_start: 0.8074 (mmt) cc_final: 0.7787 (mmm) REVERT: A 1770 LEU cc_start: 0.8582 (mp) cc_final: 0.7998 (tp) REVERT: A 1795 MET cc_start: 0.8265 (ptm) cc_final: 0.7875 (ptm) REVERT: A 1875 ASN cc_start: 0.8769 (t0) cc_final: 0.8483 (t0) REVERT: A 1906 MET cc_start: 0.7802 (mtm) cc_final: 0.6352 (mtm) REVERT: A 1920 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7466 (tt0) REVERT: A 2198 MET cc_start: 0.8162 (mmm) cc_final: 0.7809 (mmm) REVERT: B 577 ASN cc_start: 0.8117 (m110) cc_final: 0.7804 (m110) REVERT: D 469 GLU cc_start: 0.8768 (pm20) cc_final: 0.8563 (pm20) outliers start: 22 outliers final: 19 residues processed: 229 average time/residue: 0.1595 time to fit residues: 54.9179 Evaluate side-chains 230 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 210 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1784 CYS Chi-restraints excluded: chain A residue 1798 VAL Chi-restraints excluded: chain A residue 1914 GLU Chi-restraints excluded: chain A residue 2018 LEU Chi-restraints excluded: chain B residue 565 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 1 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 229 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 184 optimal weight: 0.8980 chunk 225 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 177 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.137025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.101999 restraints weight = 46863.630| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 3.15 r_work: 0.3152 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 19166 Z= 0.135 Angle : 0.512 7.527 25893 Z= 0.267 Chirality : 0.039 0.154 2947 Planarity : 0.004 0.055 3270 Dihedral : 3.878 18.251 2531 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.99 % Allowed : 10.96 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.18), residues: 2313 helix: 2.27 (0.15), residues: 1285 sheet: -0.21 (0.40), residues: 177 loop : -1.21 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 362 TYR 0.014 0.001 TYR A2156 PHE 0.017 0.001 PHE A1578 TRP 0.036 0.001 TRP A1880 HIS 0.002 0.001 HIS A1611 Details of bonding type rmsd covalent geometry : bond 0.00328 (19159) covalent geometry : angle 0.51035 (25891) hydrogen bonds : bond 0.04007 ( 1020) hydrogen bonds : angle 3.71049 ( 2973) metal coordination : bond 0.01504 ( 7) metal coordination : angle 5.00619 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4626 Ramachandran restraints generated. 2313 Oldfield, 0 Emsley, 2313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 212 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 ASP cc_start: 0.8473 (t0) cc_final: 0.7987 (t0) REVERT: A 689 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8031 (pp) REVERT: A 997 ASP cc_start: 0.8285 (t70) cc_final: 0.8062 (t70) REVERT: A 1415 MET cc_start: 0.8028 (mmt) cc_final: 0.7742 (mmm) REVERT: A 1514 ASP cc_start: 0.8189 (t70) cc_final: 0.7823 (t0) REVERT: A 1770 LEU cc_start: 0.8519 (mp) cc_final: 0.7939 (tp) REVERT: A 1795 MET cc_start: 0.8215 (ptm) cc_final: 0.7832 (ptm) REVERT: A 1875 ASN cc_start: 0.8760 (t0) cc_final: 0.8529 (t0) REVERT: A 2198 MET cc_start: 0.8139 (mmm) cc_final: 0.7788 (mmm) REVERT: B 577 ASN cc_start: 0.7917 (m110) cc_final: 0.7563 (m110) REVERT: D 469 GLU cc_start: 0.8745 (pm20) cc_final: 0.8537 (pm20) outliers start: 20 outliers final: 17 residues processed: 228 average time/residue: 0.1571 time to fit residues: 54.3366 Evaluate side-chains 227 residues out of total 2122 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 209 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 357 ILE Chi-restraints excluded: chain A residue 382 MET Chi-restraints excluded: chain A residue 515 LYS Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 689 LEU Chi-restraints excluded: chain A residue 800 VAL Chi-restraints excluded: chain A residue 1096 THR Chi-restraints excluded: chain A residue 1307 ILE Chi-restraints excluded: chain A residue 1322 ILE Chi-restraints excluded: chain A residue 1406 LEU Chi-restraints excluded: chain A residue 1624 PHE Chi-restraints excluded: chain A residue 1784 CYS Chi-restraints excluded: chain A residue 1798 VAL Chi-restraints excluded: chain A residue 1914 GLU Chi-restraints excluded: chain B residue 565 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 43 optimal weight: 2.9990 chunk 217 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 183 optimal weight: 0.0570 chunk 218 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 184 optimal weight: 2.9990 chunk 220 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2059 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.138022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.103280 restraints weight = 49696.360| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.66 r_work: 0.3159 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19166 Z= 0.122 Angle : 0.505 8.943 25893 Z= 0.263 Chirality : 0.039 0.153 2947 Planarity : 0.004 0.055 3270 Dihedral : 3.801 17.915 2531 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.03 % Allowed : 10.87 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.35 (0.18), residues: 2313 helix: 2.33 (0.15), residues: 1285 sheet: -0.19 (0.40), residues: 177 loop : -1.19 (0.20), residues: 851 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 362 TYR 0.023 0.001 TYR A1422 PHE 0.018 0.001 PHE A1578 TRP 0.036 0.001 TRP A1880 HIS 0.004 0.001 HIS A2059 Details of bonding type rmsd covalent geometry : bond 0.00293 (19159) covalent geometry : angle 0.50288 (25891) hydrogen bonds : bond 0.03783 ( 1020) hydrogen bonds : angle 3.65883 ( 2973) metal coordination : bond 0.01565 ( 7) metal coordination : angle 4.89797 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4799.69 seconds wall clock time: 83 minutes 18.17 seconds (4998.17 seconds total)