Starting phenix.real_space_refine on Sun May 18 09:36:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ki7_37253/05_2025/8ki7_37253.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ki7_37253/05_2025/8ki7_37253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ki7_37253/05_2025/8ki7_37253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ki7_37253/05_2025/8ki7_37253.map" model { file = "/net/cci-nas-00/data/ceres_data/8ki7_37253/05_2025/8ki7_37253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ki7_37253/05_2025/8ki7_37253.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.064 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: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 105 5.16 5 C 10557 2.51 5 N 2801 2.21 5 O 3289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16784 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 16102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2003, 16102 Classifications: {'peptide': 2003} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 53, 'TRANS': 1949} Chain breaks: 6 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 217 Classifications: {'RNA': 10} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 7} Chain: "B" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna3p': 8} Chain: "F" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 270 Classifications: {'RNA': 13} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 4, 'rna3p_pyr': 7} Link IDs: {'rna2p': 1, 'rna3p': 11} Time building chain proxies: 8.69, per 1000 atoms: 0.52 Number of scatterers: 16784 At special positions: 0 Unit cell: (116.48, 110.24, 143.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 105 16.00 P 32 15.00 O 3289 8.00 N 2801 7.00 C 10557 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 1.9 seconds 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3848 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 9 sheets defined 58.7% alpha, 5.4% beta 11 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 5.23 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 4.136A pdb=" N ILE A 10 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU A 11 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A 12 " --> pdb=" O LYS A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.861A pdb=" N ARG A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 69 removed outlier: 4.414A pdb=" N VAL A 46 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 111 Processing helix chain 'A' and resid 125 through 140 Processing helix chain 'A' and resid 147 through 158 removed outlier: 4.173A pdb=" N GLU A 152 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG A 153 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 210 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 251 through 258 Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 259 through 268 Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 285 through 307 removed outlier: 3.671A pdb=" N ILE A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLU A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 352 through 363 Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.629A pdb=" N THR A 370 " --> pdb=" O HIS A 367 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET A 371 " --> pdb=" O ILE A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 371' Processing helix chain 'A' and resid 374 through 390 Processing helix chain 'A' and resid 397 through 413 Processing helix chain 'A' and resid 415 through 432 removed outlier: 3.673A pdb=" N LYS A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 455 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.606A pdb=" N THR A 466 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 502 Processing helix chain 'A' and resid 521 through 536 Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.943A pdb=" N GLU A 570 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TRP A 571 " --> pdb=" O SER A 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 571' Processing helix chain 'A' and resid 591 through 606 Processing helix chain 'A' and resid 610 through 626 removed outlier: 3.762A pdb=" N LYS A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 682 removed outlier: 3.661A pdb=" N ASN A 682 " --> pdb=" O PHE A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 700 removed outlier: 3.558A pdb=" N VAL A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 removed outlier: 3.837A pdb=" N CYS A 704 " --> pdb=" O ASN A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 729 Processing helix chain 'A' and resid 730 through 748 Processing helix chain 'A' and resid 796 through 804 Processing helix chain 'A' and resid 828 through 837 Processing helix chain 'A' and resid 837 through 853 Proline residue: A 843 - end of helix Processing helix chain 'A' and resid 853 through 863 Processing helix chain 'A' and resid 874 through 893 Processing helix chain 'A' and resid 896 through 908 removed outlier: 3.887A pdb=" N MET A 900 " --> pdb=" O LYS A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 927 Processing helix chain 'A' and resid 937 through 953 Processing helix chain 'A' and resid 991 through 1005 removed outlier: 3.668A pdb=" N LEU A 995 " --> pdb=" O THR A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1036 Proline residue: A1024 - end of helix removed outlier: 4.114A pdb=" N PHE A1031 " --> pdb=" O TRP A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1075 Processing helix chain 'A' and resid 1077 through 1089 Processing helix chain 'A' and resid 1094 through 1097 Processing helix chain 'A' and resid 1098 through 1103 Processing helix chain 'A' and resid 1114 through 1124 Processing helix chain 'A' and resid 1126 through 1130 removed outlier: 3.714A pdb=" N ILE A1130 " --> pdb=" O ILE A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1151 Processing helix chain 'A' and resid 1151 through 1163 removed outlier: 3.956A pdb=" N LEU A1155 " --> pdb=" O GLU A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1178 removed outlier: 3.838A pdb=" N LEU A1169 " --> pdb=" O ASN A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1195 removed outlier: 3.736A pdb=" N ILE A1193 " --> pdb=" O THR A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1209 removed outlier: 3.968A pdb=" N VAL A1201 " --> pdb=" O HIS A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1235 Processing helix chain 'A' and resid 1241 through 1247 removed outlier: 3.662A pdb=" N VAL A1245 " --> pdb=" O ASP A1241 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET A1246 " --> pdb=" O LEU A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1271 Processing helix chain 'A' and resid 1300 through 1313 Processing helix chain 'A' and resid 1314 through 1320 Processing helix chain 'A' and resid 1331 through 1353 removed outlier: 4.148A pdb=" N ARG A1335 " --> pdb=" O ASP A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1385 removed outlier: 3.771A pdb=" N VAL A1381 " --> pdb=" O THR A1377 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE A1385 " --> pdb=" O VAL A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1408 Processing helix chain 'A' and resid 1414 through 1428 Processing helix chain 'A' and resid 1434 through 1439 Processing helix chain 'A' and resid 1460 through 1478 Processing helix chain 'A' and resid 1505 through 1513 Processing helix chain 'A' and resid 1517 through 1532 Processing helix chain 'A' and resid 1565 through 1572 Processing helix chain 'A' and resid 1580 through 1598 removed outlier: 3.617A pdb=" N HIS A1591 " --> pdb=" O SER A1587 " (cutoff:3.500A) Processing helix chain 'A' and resid 1604 through 1620 Processing helix chain 'A' and resid 1630 through 1638 Processing helix chain 'A' and resid 1647 through 1651 Processing helix chain 'A' and resid 1657 through 1664 Processing helix chain 'A' and resid 1667 through 1682 Processing helix chain 'A' and resid 1686 through 1696 removed outlier: 4.033A pdb=" N SER A1696 " --> pdb=" O ASP A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1714 Processing helix chain 'A' and resid 1717 through 1732 Processing helix chain 'A' and resid 1763 through 1770 removed outlier: 3.671A pdb=" N LEU A1767 " --> pdb=" O ASN A1763 " (cutoff:3.500A) Processing helix chain 'A' and resid 1770 through 1780 Processing helix chain 'A' and resid 1814 through 1829 removed outlier: 3.679A pdb=" N ASN A1829 " --> pdb=" O ILE A1825 " (cutoff:3.500A) Processing helix chain 'A' and resid 1830 through 1835 removed outlier: 3.839A pdb=" N ILE A1835 " --> pdb=" O GLU A1831 " (cutoff:3.500A) Processing helix chain 'A' and resid 1843 through 1850 Processing helix chain 'A' and resid 1867 through 1877 removed outlier: 3.950A pdb=" N ASP A1871 " --> pdb=" O LYS A1867 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS A1877 " --> pdb=" O VAL A1873 " (cutoff:3.500A) Processing helix chain 'A' and resid 1891 through 1904 Processing helix chain 'A' and resid 1910 through 1923 Processing helix chain 'A' and resid 1924 through 1936 Proline residue: A1932 - end of helix Processing helix chain 'A' and resid 1951 through 1965 removed outlier: 4.670A pdb=" N LYS A1957 " --> pdb=" O PHE A1953 " (cutoff:3.500A) Proline residue: A1960 - end of helix Processing helix chain 'A' and resid 1986 through 2008 Processing helix chain 'A' and resid 2018 through 2030 removed outlier: 3.980A pdb=" N ASN A2030 " --> pdb=" O PHE A2026 " (cutoff:3.500A) Processing helix chain 'A' and resid 2031 through 2043 Processing helix chain 'A' and resid 2052 through 2058 removed outlier: 3.775A pdb=" N ARG A2058 " --> pdb=" O THR A2054 " (cutoff:3.500A) Processing helix chain 'A' and resid 2059 through 2066 Processing helix chain 'A' and resid 2067 through 2069 No H-bonds generated for 'chain 'A' and resid 2067 through 2069' Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 172 removed outlier: 3.587A pdb=" N CYS A 180 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N PHE A 227 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 181 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N SER A 229 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILE A 183 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL A 231 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASP A 185 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N LEU A 233 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 214 through 215 Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 509 removed outlier: 6.914A pdb=" N ILE A 821 " --> pdb=" O TYR A 809 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR A 811 " --> pdb=" O ILE A 819 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 819 " --> pdb=" O TYR A 811 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARG A 813 " --> pdb=" O ASN A 817 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASN A 817 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ALA A 788 " --> pdb=" O MET A 822 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 768 " --> pdb=" O LEU A 789 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1109 through 1110 removed outlier: 3.629A pdb=" N GLN A1109 " --> pdb=" O LYS A1219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1295 through 1299 removed outlier: 6.765A pdb=" N VAL A1281 " --> pdb=" O CYS A1412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1484 through 1486 Processing sheet with id=AA7, first strand: chain 'A' and resid 1484 through 1486 Processing sheet with id=AA8, first strand: chain 'A' and resid 1548 through 1549 Processing sheet with id=AA9, first strand: chain 'A' and resid 1974 through 1975 removed outlier: 6.882A pdb=" N VAL A1974 " --> pdb=" O THR A2083 " (cutoff:3.500A) 832 hydrogen bonds defined for protein. 2433 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 7.33 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4123 1.33 - 1.46: 3648 1.46 - 1.58: 9142 1.58 - 1.70: 61 1.70 - 1.82: 173 Bond restraints: 17147 Sorted by residual: bond pdb=" C LEU A 912 " pdb=" N PRO A 913 " ideal model delta sigma weight residual 1.337 1.380 -0.044 9.80e-03 1.04e+04 1.98e+01 bond pdb=" C SER A1965 " pdb=" N PRO A1966 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.20e+00 bond pdb=" CB ILE A1724 " pdb=" CG2 ILE A1724 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.57e+00 bond pdb=" CB GLU A 715 " pdb=" CG GLU A 715 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.28e+00 bond pdb=" CB PHE A2026 " pdb=" CG PHE A2026 " ideal model delta sigma weight residual 1.502 1.542 -0.040 2.30e-02 1.89e+03 2.99e+00 ... (remaining 17142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 22882 3.59 - 7.19: 294 7.19 - 10.78: 56 10.78 - 14.38: 9 14.38 - 17.97: 3 Bond angle restraints: 23244 Sorted by residual: angle pdb=" N ILE A 299 " pdb=" CA ILE A 299 " pdb=" C ILE A 299 " ideal model delta sigma weight residual 113.71 106.69 7.02 9.50e-01 1.11e+00 5.46e+01 angle pdb=" CB MET A2042 " pdb=" CG MET A2042 " pdb=" SD MET A2042 " ideal model delta sigma weight residual 112.70 130.67 -17.97 3.00e+00 1.11e-01 3.59e+01 angle pdb=" CG1 ILE A 791 " pdb=" CB ILE A 791 " pdb=" CG2 ILE A 791 " ideal model delta sigma weight residual 110.70 93.94 16.76 3.00e+00 1.11e-01 3.12e+01 angle pdb=" N ILE A 555 " pdb=" CA ILE A 555 " pdb=" C ILE A 555 " ideal model delta sigma weight residual 111.48 106.39 5.09 9.40e-01 1.13e+00 2.94e+01 angle pdb=" C PRO A 456 " pdb=" N ASN A 457 " pdb=" CA ASN A 457 " ideal model delta sigma weight residual 122.46 129.73 -7.27 1.41e+00 5.03e-01 2.66e+01 ... (remaining 23239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.40: 9601 26.40 - 52.80: 854 52.80 - 79.20: 88 79.20 - 105.59: 7 105.59 - 131.99: 1 Dihedral angle restraints: 10551 sinusoidal: 4626 harmonic: 5925 Sorted by residual: dihedral pdb=" O4' C F 12 " pdb=" C1' C F 12 " pdb=" N1 C F 12 " pdb=" C2 C F 12 " ideal model delta sinusoidal sigma weight residual 200.00 68.01 131.99 1 1.50e+01 4.44e-03 7.12e+01 dihedral pdb=" CA TYR A1044 " pdb=" C TYR A1044 " pdb=" N PRO A1045 " pdb=" CA PRO A1045 " ideal model delta harmonic sigma weight residual -180.00 -153.31 -26.69 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA GLY A1393 " pdb=" C GLY A1393 " pdb=" N GLU A1394 " pdb=" CA GLU A1394 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 10548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2390 0.088 - 0.177: 249 0.177 - 0.265: 18 0.265 - 0.353: 3 0.353 - 0.441: 2 Chirality restraints: 2662 Sorted by residual: chirality pdb=" CG LEU A1510 " pdb=" CB LEU A1510 " pdb=" CD1 LEU A1510 " pdb=" CD2 LEU A1510 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CB ILE A 791 " pdb=" CA ILE A 791 " pdb=" CG1 ILE A 791 " pdb=" CG2 ILE A 791 " both_signs ideal model delta sigma weight residual False 2.64 3.00 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CB ILE A 188 " pdb=" CA ILE A 188 " pdb=" CG1 ILE A 188 " pdb=" CG2 ILE A 188 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 2659 not shown) Planarity restraints: 2811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 737 " 0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" CG ASP A 737 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASP A 737 " 0.026 2.00e-02 2.50e+03 pdb=" OD2 ASP A 737 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 363 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ASN A 363 " -0.055 2.00e-02 2.50e+03 pdb=" O ASN A 363 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE A 364 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1738 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C ASP A1738 " 0.052 2.00e-02 2.50e+03 pdb=" O ASP A1738 " -0.020 2.00e-02 2.50e+03 pdb=" N SER A1739 " -0.017 2.00e-02 2.50e+03 ... (remaining 2808 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2098 2.76 - 3.29: 16478 3.29 - 3.83: 29477 3.83 - 4.36: 33137 4.36 - 4.90: 56789 Nonbonded interactions: 137979 Sorted by model distance: nonbonded pdb=" O PHE A2061 " pdb=" OG SER A2065 " model vdw 2.221 3.040 nonbonded pdb=" O MET A 472 " pdb=" OH TYR A 786 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR A1773 " pdb=" O LYS A1785 " model vdw 2.278 3.040 nonbonded pdb=" O GLY A1251 " pdb=" ND2 ASN A1839 " model vdw 2.288 3.120 nonbonded pdb=" OG SER A 477 " pdb=" O LEU A 680 " model vdw 2.291 3.040 ... (remaining 137974 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.460 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: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 40.200 Find NCS groups from input model: 0.150 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17147 Z= 0.232 Angle : 1.069 17.974 23244 Z= 0.557 Chirality : 0.056 0.441 2662 Planarity : 0.006 0.075 2811 Dihedral : 18.157 131.992 6703 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.34 % Favored : 92.46 % Rotamer: Outliers : 3.86 % Allowed : 23.19 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.17), residues: 1989 helix: -0.89 (0.14), residues: 1050 sheet: 0.55 (0.54), residues: 100 loop : -2.22 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 474 HIS 0.014 0.002 HIS A1529 PHE 0.051 0.003 PHE A1234 TYR 0.025 0.002 TYR A1938 ARG 0.015 0.001 ARG A1679 Details of bonding type rmsd hydrogen bonds : bond 0.07230 ( 856) hydrogen bonds : angle 5.80709 ( 2485) covalent geometry : bond 0.00480 (17147) covalent geometry : angle 1.06859 (23244) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 541 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ASP cc_start: 0.6885 (m-30) cc_final: 0.6534 (m-30) REVERT: A 822 MET cc_start: 0.8598 (mmt) cc_final: 0.8391 (mmm) REVERT: A 833 LEU cc_start: 0.8900 (tp) cc_final: 0.8627 (tt) REVERT: A 1028 GLU cc_start: 0.6857 (tm-30) cc_final: 0.6653 (tm-30) REVERT: A 1084 GLU cc_start: 0.7024 (pt0) cc_final: 0.6307 (pt0) REVERT: A 1376 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7873 (mt) REVERT: A 1534 CYS cc_start: 0.7585 (t) cc_final: 0.7242 (t) REVERT: A 1728 ASN cc_start: 0.7363 (t0) cc_final: 0.5486 (t0) REVERT: A 1747 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.6856 (pttt) REVERT: A 1992 ASP cc_start: 0.7181 (m-30) cc_final: 0.6886 (m-30) REVERT: A 2063 PHE cc_start: 0.5673 (t80) cc_final: 0.5101 (t80) outliers start: 71 outliers final: 28 residues processed: 581 average time/residue: 0.2865 time to fit residues: 249.8297 Evaluate side-chains 362 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 332 time to evaluate : 1.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 1661 LEU Chi-restraints excluded: chain A residue 1747 LYS Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1822 VAL Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2061 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 103 HIS A 358 HIS A 404 HIS A 697 ASN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 ASN A1312 HIS A1457 ASN A1683 ASN A1749 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.120681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.093118 restraints weight = 44665.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.096292 restraints weight = 23355.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.098390 restraints weight = 15111.878| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 17147 Z= 0.210 Angle : 0.770 12.390 23244 Z= 0.397 Chirality : 0.047 0.257 2662 Planarity : 0.005 0.062 2811 Dihedral : 12.521 138.829 2678 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.29 % Favored : 92.51 % Rotamer: Outliers : 6.04 % Allowed : 23.95 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.18), residues: 1989 helix: 0.06 (0.15), residues: 1069 sheet: 1.03 (0.58), residues: 76 loop : -2.19 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1958 HIS 0.005 0.001 HIS A 404 PHE 0.035 0.002 PHE A 741 TYR 0.027 0.002 TYR A1465 ARG 0.006 0.001 ARG A1294 Details of bonding type rmsd hydrogen bonds : bond 0.04191 ( 856) hydrogen bonds : angle 4.79050 ( 2485) covalent geometry : bond 0.00470 (17147) covalent geometry : angle 0.76974 (23244) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 349 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.9256 (tp) cc_final: 0.8994 (mp) REVERT: A 199 MET cc_start: 0.9312 (tpp) cc_final: 0.8757 (ttt) REVERT: A 378 ASP cc_start: 0.7857 (t0) cc_final: 0.7289 (t70) REVERT: A 402 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8172 (tptm) REVERT: A 472 MET cc_start: 0.7163 (mpp) cc_final: 0.6704 (mpp) REVERT: A 480 LYS cc_start: 0.7187 (tmtt) cc_final: 0.6756 (tmtt) REVERT: A 684 ASP cc_start: 0.6660 (OUTLIER) cc_final: 0.6433 (m-30) REVERT: A 768 MET cc_start: 0.7907 (ptm) cc_final: 0.7549 (ttp) REVERT: A 809 TYR cc_start: 0.6809 (OUTLIER) cc_final: 0.6388 (m-80) REVERT: A 822 MET cc_start: 0.9064 (mmt) cc_final: 0.8325 (mmm) REVERT: A 833 LEU cc_start: 0.9191 (tp) cc_final: 0.8989 (tt) REVERT: A 882 ILE cc_start: 0.9327 (mt) cc_final: 0.9097 (mt) REVERT: A 904 ASP cc_start: 0.7966 (m-30) cc_final: 0.7617 (m-30) REVERT: A 982 CYS cc_start: 0.8125 (m) cc_final: 0.7657 (m) REVERT: A 1267 MET cc_start: 0.8903 (mmm) cc_final: 0.8664 (mmt) REVERT: A 1376 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7979 (mt) REVERT: A 1398 MET cc_start: 0.7728 (tpp) cc_final: 0.7123 (mtt) REVERT: A 1431 ASN cc_start: 0.6302 (t0) cc_final: 0.5949 (m-40) REVERT: A 1475 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.7843 (ttmm) REVERT: A 1534 CYS cc_start: 0.8012 (t) cc_final: 0.7608 (t) REVERT: A 1554 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6414 (mt-10) REVERT: A 1598 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7701 (mmmt) REVERT: A 1622 MET cc_start: 0.8060 (mmm) cc_final: 0.6625 (mmp) REVERT: A 1691 LYS cc_start: 0.9322 (ptmt) cc_final: 0.9008 (ptpp) REVERT: A 1747 LYS cc_start: 0.8764 (OUTLIER) cc_final: 0.8483 (pttt) REVERT: A 1749 GLN cc_start: 0.8287 (mm-40) cc_final: 0.7379 (mm-40) REVERT: A 1779 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8569 (pt) REVERT: A 1903 MET cc_start: 0.8303 (mmp) cc_final: 0.8066 (tpp) REVERT: A 1929 MET cc_start: 0.8837 (mtp) cc_final: 0.7799 (ptt) outliers start: 111 outliers final: 56 residues processed: 430 average time/residue: 0.2466 time to fit residues: 167.1165 Evaluate side-chains 364 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 300 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 402 LYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 670 CYS Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1348 TYR Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1475 LYS Chi-restraints excluded: chain A residue 1580 SER Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1598 LYS Chi-restraints excluded: chain A residue 1663 ILE Chi-restraints excluded: chain A residue 1747 LYS Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1931 ILE Chi-restraints excluded: chain A residue 1955 THR Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2061 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 55 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 148 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 25 optimal weight: 0.0570 chunk 147 optimal weight: 0.9990 chunk 201 optimal weight: 20.0000 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 overall best weight: 0.7700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 103 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 ASN A1074 ASN A1728 ASN ** A2030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.122720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.095882 restraints weight = 44008.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.099098 restraints weight = 22633.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.101264 restraints weight = 14568.134| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17147 Z= 0.136 Angle : 0.702 13.286 23244 Z= 0.357 Chirality : 0.044 0.194 2662 Planarity : 0.004 0.051 2811 Dihedral : 12.214 135.541 2659 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.09 % Favored : 92.71 % Rotamer: Outliers : 4.35 % Allowed : 25.53 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.18), residues: 1989 helix: 0.30 (0.15), residues: 1082 sheet: 1.05 (0.53), residues: 93 loop : -2.23 (0.20), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A1958 HIS 0.004 0.001 HIS A1529 PHE 0.032 0.002 PHE A1950 TYR 0.015 0.001 TYR A1620 ARG 0.006 0.001 ARG A 899 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 856) hydrogen bonds : angle 4.62837 ( 2485) covalent geometry : bond 0.00303 (17147) covalent geometry : angle 0.70203 (23244) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 430 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 350 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 MET cc_start: 0.9287 (tpp) cc_final: 0.8629 (ttt) REVERT: A 298 LYS cc_start: 0.9343 (mttt) cc_final: 0.8760 (pttp) REVERT: A 378 ASP cc_start: 0.7819 (t0) cc_final: 0.7398 (t70) REVERT: A 472 MET cc_start: 0.7142 (mpp) cc_final: 0.6846 (mpp) REVERT: A 480 LYS cc_start: 0.7024 (tmtt) cc_final: 0.6573 (tmtt) REVERT: A 536 GLU cc_start: 0.8251 (mt-10) cc_final: 0.8030 (tm-30) REVERT: A 552 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7888 (pm20) REVERT: A 684 ASP cc_start: 0.6445 (OUTLIER) cc_final: 0.6154 (m-30) REVERT: A 882 ILE cc_start: 0.9364 (mt) cc_final: 0.9141 (mt) REVERT: A 890 MET cc_start: 0.8515 (tpp) cc_final: 0.7724 (tpp) REVERT: A 900 MET cc_start: 0.7193 (mpp) cc_final: 0.6597 (mpp) REVERT: A 904 ASP cc_start: 0.7942 (m-30) cc_final: 0.7556 (m-30) REVERT: A 982 CYS cc_start: 0.8106 (m) cc_final: 0.7888 (m) REVERT: A 985 THR cc_start: 0.8644 (m) cc_final: 0.8396 (p) REVERT: A 1004 TYR cc_start: 0.7603 (m-80) cc_final: 0.7247 (m-80) REVERT: A 1086 GLU cc_start: 0.6148 (mt-10) cc_final: 0.5754 (mt-10) REVERT: A 1345 ILE cc_start: 0.9443 (mm) cc_final: 0.8481 (mm) REVERT: A 1361 LEU cc_start: 0.8945 (tp) cc_final: 0.8731 (tp) REVERT: A 1376 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7829 (mt) REVERT: A 1398 MET cc_start: 0.7887 (tpp) cc_final: 0.7363 (mtp) REVERT: A 1403 LEU cc_start: 0.8385 (mm) cc_final: 0.7938 (tp) REVERT: A 1470 MET cc_start: 0.8663 (tpp) cc_final: 0.8364 (tpp) REVERT: A 1475 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8219 (mtpp) REVERT: A 1534 CYS cc_start: 0.7929 (t) cc_final: 0.7576 (t) REVERT: A 1691 LYS cc_start: 0.9300 (ptmt) cc_final: 0.9037 (ptpp) REVERT: A 1747 LYS cc_start: 0.8708 (OUTLIER) cc_final: 0.8374 (pttp) REVERT: A 1749 GLN cc_start: 0.8313 (mm-40) cc_final: 0.7441 (mm-40) REVERT: A 1779 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8441 (pt) REVERT: A 1841 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7553 (tmm-80) REVERT: A 1929 MET cc_start: 0.8694 (mtp) cc_final: 0.7821 (ptt) REVERT: A 1958 TRP cc_start: 0.5834 (m-90) cc_final: 0.5463 (m-90) REVERT: A 1998 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8108 (tp) outliers start: 80 outliers final: 43 residues processed: 407 average time/residue: 0.2564 time to fit residues: 164.0143 Evaluate side-chains 362 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 311 time to evaluate : 1.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 670 CYS Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1348 TYR Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1475 LYS Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1747 LYS Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1822 VAL Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1841 ARG Chi-restraints excluded: chain A residue 1912 CYS Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1920 LEU Chi-restraints excluded: chain A residue 1931 ILE Chi-restraints excluded: chain A residue 1948 TYR Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2061 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 33 optimal weight: 0.0980 chunk 9 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 73 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 121 optimal weight: 3.9990 chunk 57 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS A 260 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1022 ASN A1063 ASN A1074 ASN A1863 GLN ** A2030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.121323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.095059 restraints weight = 43455.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.098257 restraints weight = 22157.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.100388 restraints weight = 14076.426| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17147 Z= 0.144 Angle : 0.693 10.160 23244 Z= 0.352 Chirality : 0.044 0.276 2662 Planarity : 0.004 0.057 2811 Dihedral : 12.157 137.310 2657 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.54 % Favored : 92.26 % Rotamer: Outliers : 5.44 % Allowed : 24.28 % Favored : 70.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.19), residues: 1989 helix: 0.62 (0.16), residues: 1080 sheet: 0.50 (0.47), residues: 119 loop : -2.08 (0.21), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1958 HIS 0.004 0.001 HIS A1529 PHE 0.027 0.002 PHE A1950 TYR 0.020 0.001 TYR A1675 ARG 0.004 0.001 ARG A 823 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 856) hydrogen bonds : angle 4.51058 ( 2485) covalent geometry : bond 0.00320 (17147) covalent geometry : angle 0.69253 (23244) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 334 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.9274 (tp) cc_final: 0.9041 (pp) REVERT: A 114 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7982 (mm) REVERT: A 140 LYS cc_start: 0.8707 (mttt) cc_final: 0.8310 (ttpp) REVERT: A 199 MET cc_start: 0.9253 (tpp) cc_final: 0.8740 (ttt) REVERT: A 200 GLU cc_start: 0.8977 (tt0) cc_final: 0.8502 (tt0) REVERT: A 378 ASP cc_start: 0.7866 (t0) cc_final: 0.7466 (t70) REVERT: A 472 MET cc_start: 0.7111 (mpp) cc_final: 0.6859 (mpp) REVERT: A 480 LYS cc_start: 0.6987 (tmtt) cc_final: 0.6534 (tmtt) REVERT: A 536 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8018 (tm-30) REVERT: A 684 ASP cc_start: 0.6574 (OUTLIER) cc_final: 0.6360 (m-30) REVERT: A 809 TYR cc_start: 0.6450 (OUTLIER) cc_final: 0.6207 (m-80) REVERT: A 878 LYS cc_start: 0.9338 (tttt) cc_final: 0.9105 (ttpp) REVERT: A 882 ILE cc_start: 0.9391 (mt) cc_final: 0.9160 (mt) REVERT: A 890 MET cc_start: 0.8467 (tpp) cc_final: 0.8221 (tpp) REVERT: A 900 MET cc_start: 0.7363 (mpp) cc_final: 0.7146 (mpp) REVERT: A 1335 ARG cc_start: 0.7520 (mpt180) cc_final: 0.7137 (mmt-90) REVERT: A 1361 LEU cc_start: 0.8945 (tp) cc_final: 0.8738 (tp) REVERT: A 1376 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7743 (tt) REVERT: A 1398 MET cc_start: 0.7815 (tpp) cc_final: 0.7127 (mtp) REVERT: A 1403 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8029 (tp) REVERT: A 1470 MET cc_start: 0.8682 (tpp) cc_final: 0.8311 (tpp) REVERT: A 1598 LYS cc_start: 0.7997 (OUTLIER) cc_final: 0.7702 (mmmt) REVERT: A 1675 TYR cc_start: 0.8885 (t80) cc_final: 0.8555 (t80) REVERT: A 1691 LYS cc_start: 0.9316 (ptmt) cc_final: 0.9092 (ptpp) REVERT: A 1748 PHE cc_start: 0.7500 (m-10) cc_final: 0.7190 (m-10) REVERT: A 1779 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8523 (pt) REVERT: A 1929 MET cc_start: 0.8531 (mtp) cc_final: 0.7796 (ptt) REVERT: A 1953 PHE cc_start: 0.6996 (m-80) cc_final: 0.6592 (m-80) REVERT: A 1998 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8369 (tp) outliers start: 100 outliers final: 58 residues processed: 405 average time/residue: 0.2473 time to fit residues: 158.6363 Evaluate side-chains 373 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 307 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 670 CYS Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1110 SER Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1450 SER Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1475 LYS Chi-restraints excluded: chain A residue 1580 SER Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1598 LYS Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1822 VAL Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1920 LEU Chi-restraints excluded: chain A residue 1931 ILE Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2043 ILE Chi-restraints excluded: chain A residue 2061 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 63 optimal weight: 10.0000 chunk 180 optimal weight: 0.2980 chunk 46 optimal weight: 0.4980 chunk 39 optimal weight: 8.9990 chunk 174 optimal weight: 10.0000 chunk 143 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 166 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 195 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS A 167 ASN ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 491 ASN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 ASN ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1628 ASN ** A2030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.119522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.093267 restraints weight = 44041.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.096406 restraints weight = 22274.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.098507 restraints weight = 14138.277| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17147 Z= 0.166 Angle : 0.703 11.479 23244 Z= 0.356 Chirality : 0.045 0.259 2662 Planarity : 0.004 0.043 2811 Dihedral : 12.165 138.449 2653 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.64 % Favored : 92.16 % Rotamer: Outliers : 5.33 % Allowed : 24.99 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.19), residues: 1989 helix: 0.72 (0.16), residues: 1084 sheet: 0.50 (0.49), residues: 112 loop : -1.99 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A1958 HIS 0.004 0.001 HIS A1492 PHE 0.028 0.002 PHE A 741 TYR 0.015 0.001 TYR A 95 ARG 0.003 0.000 ARG A 899 Details of bonding type rmsd hydrogen bonds : bond 0.03782 ( 856) hydrogen bonds : angle 4.44754 ( 2485) covalent geometry : bond 0.00371 (17147) covalent geometry : angle 0.70337 (23244) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 319 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8259 (OUTLIER) cc_final: 0.7956 (mm) REVERT: A 140 LYS cc_start: 0.8669 (mttt) cc_final: 0.8263 (ttpp) REVERT: A 199 MET cc_start: 0.9249 (tpp) cc_final: 0.8736 (ttt) REVERT: A 200 GLU cc_start: 0.8971 (tt0) cc_final: 0.8697 (tt0) REVERT: A 298 LYS cc_start: 0.9368 (mttt) cc_final: 0.8864 (pttp) REVERT: A 378 ASP cc_start: 0.7990 (t0) cc_final: 0.7480 (t0) REVERT: A 450 GLU cc_start: 0.8860 (tt0) cc_final: 0.8469 (tp30) REVERT: A 472 MET cc_start: 0.7324 (mpp) cc_final: 0.7014 (mpp) REVERT: A 480 LYS cc_start: 0.7092 (tmtt) cc_final: 0.6582 (tmtt) REVERT: A 536 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8014 (tm-30) REVERT: A 584 GLU cc_start: 0.8087 (pt0) cc_final: 0.7882 (pt0) REVERT: A 688 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7749 (mm-30) REVERT: A 767 MET cc_start: 0.6473 (mmt) cc_final: 0.5999 (mmt) REVERT: A 809 TYR cc_start: 0.6431 (OUTLIER) cc_final: 0.6152 (m-80) REVERT: A 878 LYS cc_start: 0.9347 (tttt) cc_final: 0.9108 (ttpp) REVERT: A 890 MET cc_start: 0.8587 (tpp) cc_final: 0.8283 (tpp) REVERT: A 900 MET cc_start: 0.7486 (mpp) cc_final: 0.6799 (mpp) REVERT: A 985 THR cc_start: 0.8571 (m) cc_final: 0.8284 (p) REVERT: A 994 ASP cc_start: 0.8741 (m-30) cc_final: 0.8390 (m-30) REVERT: A 1171 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8284 (pp20) REVERT: A 1319 GLN cc_start: 0.8602 (mt0) cc_final: 0.8037 (tm-30) REVERT: A 1335 ARG cc_start: 0.7579 (mpt180) cc_final: 0.7158 (mmt-90) REVERT: A 1361 LEU cc_start: 0.8932 (tp) cc_final: 0.8722 (tp) REVERT: A 1376 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7737 (mt) REVERT: A 1403 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8148 (tp) REVERT: A 1431 ASN cc_start: 0.6491 (t0) cc_final: 0.6034 (m-40) REVERT: A 1470 MET cc_start: 0.8602 (tpp) cc_final: 0.8217 (tpp) REVERT: A 1688 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8831 (tm-30) REVERT: A 1691 LYS cc_start: 0.9296 (ptmt) cc_final: 0.9092 (ptpp) REVERT: A 1819 MET cc_start: 0.9255 (tpp) cc_final: 0.9043 (tpp) REVERT: A 1841 ARG cc_start: 0.7933 (OUTLIER) cc_final: 0.7610 (tmm-80) REVERT: A 1929 MET cc_start: 0.8533 (mtp) cc_final: 0.7669 (ptt) REVERT: A 1958 TRP cc_start: 0.6035 (m-90) cc_final: 0.5616 (m-90) REVERT: A 1983 LEU cc_start: 0.6638 (OUTLIER) cc_final: 0.6190 (tt) REVERT: A 1998 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8444 (tp) outliers start: 98 outliers final: 59 residues processed: 387 average time/residue: 0.2417 time to fit residues: 147.9002 Evaluate side-chains 361 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 293 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 670 CYS Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1110 SER Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1475 LYS Chi-restraints excluded: chain A residue 1580 SER Chi-restraints excluded: chain A residue 1589 SER Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1672 ILE Chi-restraints excluded: chain A residue 1688 GLU Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1841 ARG Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1920 LEU Chi-restraints excluded: chain A residue 1931 ILE Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1983 LEU Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2061 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 73 optimal weight: 0.6980 chunk 114 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 192 optimal weight: 0.3980 chunk 112 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 196 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 103 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1863 GLN ** A2030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.120773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.093989 restraints weight = 44294.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.097162 restraints weight = 22580.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.099261 restraints weight = 14449.741| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.4044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17147 Z= 0.138 Angle : 0.703 13.856 23244 Z= 0.351 Chirality : 0.044 0.241 2662 Planarity : 0.004 0.044 2811 Dihedral : 12.113 137.197 2653 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.34 % Favored : 92.46 % Rotamer: Outliers : 5.33 % Allowed : 25.86 % Favored : 68.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.19), residues: 1989 helix: 0.76 (0.16), residues: 1088 sheet: 0.67 (0.47), residues: 119 loop : -1.98 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1958 HIS 0.004 0.001 HIS A1529 PHE 0.025 0.001 PHE A 741 TYR 0.021 0.001 TYR A 133 ARG 0.005 0.000 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.03630 ( 856) hydrogen bonds : angle 4.45248 ( 2485) covalent geometry : bond 0.00309 (17147) covalent geometry : angle 0.70294 (23244) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 319 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7998 (mm) REVERT: A 140 LYS cc_start: 0.8660 (mttt) cc_final: 0.8332 (ttpp) REVERT: A 199 MET cc_start: 0.9242 (tpp) cc_final: 0.8781 (ttt) REVERT: A 200 GLU cc_start: 0.9028 (tt0) cc_final: 0.8731 (tt0) REVERT: A 368 ILE cc_start: 0.9019 (tp) cc_final: 0.8789 (tp) REVERT: A 378 ASP cc_start: 0.8041 (t0) cc_final: 0.7532 (t0) REVERT: A 408 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7484 (mmpt) REVERT: A 450 GLU cc_start: 0.8889 (tt0) cc_final: 0.8520 (tp30) REVERT: A 472 MET cc_start: 0.7248 (mpp) cc_final: 0.7011 (mpp) REVERT: A 480 LYS cc_start: 0.7024 (tmtt) cc_final: 0.6546 (tmtt) REVERT: A 536 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7983 (tm-30) REVERT: A 767 MET cc_start: 0.6235 (mmt) cc_final: 0.5849 (mmt) REVERT: A 890 MET cc_start: 0.8542 (tpp) cc_final: 0.8223 (tpp) REVERT: A 900 MET cc_start: 0.7478 (mpp) cc_final: 0.6843 (mpp) REVERT: A 985 THR cc_start: 0.8386 (m) cc_final: 0.8183 (p) REVERT: A 1005 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.7510 (ttt) REVERT: A 1171 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8295 (pp20) REVERT: A 1264 GLU cc_start: 0.8524 (mt-10) cc_final: 0.8195 (mt-10) REVERT: A 1319 GLN cc_start: 0.8575 (mt0) cc_final: 0.8015 (tm-30) REVERT: A 1431 ASN cc_start: 0.6673 (t0) cc_final: 0.6158 (m-40) REVERT: A 1470 MET cc_start: 0.8571 (tpp) cc_final: 0.8144 (tpp) REVERT: A 1580 SER cc_start: 0.8850 (OUTLIER) cc_final: 0.8590 (p) REVERT: A 1598 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7709 (mmmt) REVERT: A 1841 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7534 (tmm-80) REVERT: A 1929 MET cc_start: 0.8564 (mtp) cc_final: 0.7742 (ptt) REVERT: A 1983 LEU cc_start: 0.6554 (OUTLIER) cc_final: 0.6166 (tt) REVERT: A 1998 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8412 (tp) outliers start: 98 outliers final: 66 residues processed: 385 average time/residue: 0.2416 time to fit residues: 147.7954 Evaluate side-chains 373 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 298 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 670 CYS Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1005 MET Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1110 SER Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1475 LYS Chi-restraints excluded: chain A residue 1487 THR Chi-restraints excluded: chain A residue 1580 SER Chi-restraints excluded: chain A residue 1583 ASP Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1598 LYS Chi-restraints excluded: chain A residue 1672 ILE Chi-restraints excluded: chain A residue 1724 ILE Chi-restraints excluded: chain A residue 1749 GLN Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1822 VAL Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1841 ARG Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1920 LEU Chi-restraints excluded: chain A residue 1931 ILE Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1983 LEU Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2043 ILE Chi-restraints excluded: chain A residue 2061 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 88 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 143 optimal weight: 1.9990 chunk 188 optimal weight: 1.9990 chunk 182 optimal weight: 9.9990 chunk 4 optimal weight: 8.9990 chunk 98 optimal weight: 0.4980 chunk 16 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 186 optimal weight: 0.7980 chunk 148 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 ASN ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2030 ASN ** 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 = 0.3908 r_free = 0.3908 target = 0.120686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.094648 restraints weight = 43636.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.097806 restraints weight = 22009.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.099890 restraints weight = 13966.861| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17147 Z= 0.141 Angle : 0.716 12.925 23244 Z= 0.356 Chirality : 0.044 0.215 2662 Planarity : 0.004 0.047 2811 Dihedral : 12.057 137.334 2650 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.54 % Favored : 92.26 % Rotamer: Outliers : 4.79 % Allowed : 26.84 % Favored : 68.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.19), residues: 1989 helix: 0.77 (0.16), residues: 1095 sheet: 0.84 (0.48), residues: 117 loop : -1.99 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 412 HIS 0.007 0.001 HIS A1578 PHE 0.032 0.002 PHE A2067 TYR 0.015 0.001 TYR A 95 ARG 0.005 0.000 ARG A 328 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 856) hydrogen bonds : angle 4.39918 ( 2485) covalent geometry : bond 0.00314 (17147) covalent geometry : angle 0.71623 (23244) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 314 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7450 (mt) REVERT: A 199 MET cc_start: 0.9221 (tpp) cc_final: 0.8818 (ttt) REVERT: A 200 GLU cc_start: 0.9062 (tt0) cc_final: 0.8667 (tt0) REVERT: A 368 ILE cc_start: 0.9017 (tp) cc_final: 0.8737 (tp) REVERT: A 378 ASP cc_start: 0.7987 (t0) cc_final: 0.7494 (t0) REVERT: A 408 LYS cc_start: 0.7643 (OUTLIER) cc_final: 0.7428 (mmpt) REVERT: A 450 GLU cc_start: 0.8847 (tt0) cc_final: 0.8511 (tp30) REVERT: A 472 MET cc_start: 0.7130 (mpp) cc_final: 0.6698 (mpp) REVERT: A 480 LYS cc_start: 0.7040 (tmtt) cc_final: 0.6561 (tmtt) REVERT: A 536 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7970 (tm-30) REVERT: A 809 TYR cc_start: 0.6493 (OUTLIER) cc_final: 0.6210 (m-80) REVERT: A 825 GLN cc_start: 0.7420 (mm-40) cc_final: 0.6923 (mm-40) REVERT: A 882 ILE cc_start: 0.9339 (mt) cc_final: 0.9065 (mt) REVERT: A 890 MET cc_start: 0.8526 (tpp) cc_final: 0.8192 (tpp) REVERT: A 900 MET cc_start: 0.7418 (mpp) cc_final: 0.6799 (mpp) REVERT: A 1005 MET cc_start: 0.7715 (OUTLIER) cc_final: 0.7472 (ttt) REVERT: A 1264 GLU cc_start: 0.8500 (mt-10) cc_final: 0.8134 (mt-10) REVERT: A 1301 MET cc_start: 0.9032 (tpt) cc_final: 0.8795 (tpp) REVERT: A 1319 GLN cc_start: 0.8506 (mt0) cc_final: 0.7984 (tm-30) REVERT: A 1431 ASN cc_start: 0.6764 (t0) cc_final: 0.6192 (m-40) REVERT: A 1470 MET cc_start: 0.8486 (tpp) cc_final: 0.8169 (tpp) REVERT: A 1475 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8122 (mtpp) REVERT: A 1478 GLU cc_start: 0.8764 (pt0) cc_final: 0.8257 (pt0) REVERT: A 1580 SER cc_start: 0.8823 (OUTLIER) cc_final: 0.8557 (p) REVERT: A 1598 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7659 (mmmt) REVERT: A 1819 MET cc_start: 0.9280 (tpp) cc_final: 0.9019 (tpp) REVERT: A 1841 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7536 (tmm-80) REVERT: A 1929 MET cc_start: 0.8527 (mtp) cc_final: 0.7730 (ptt) REVERT: A 1954 GLN cc_start: 0.7464 (tp40) cc_final: 0.5747 (tp40) REVERT: A 1958 TRP cc_start: 0.6401 (m-90) cc_final: 0.5351 (m-90) REVERT: A 1983 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.6104 (tt) REVERT: A 1998 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8452 (tp) REVERT: A 2063 PHE cc_start: 0.7970 (t80) cc_final: 0.6956 (t80) outliers start: 88 outliers final: 64 residues processed: 373 average time/residue: 0.2601 time to fit residues: 153.3935 Evaluate side-chains 372 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 298 time to evaluate : 2.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 670 CYS Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 1005 MET Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1110 SER Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1311 GLU Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1403 LEU Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1475 LYS Chi-restraints excluded: chain A residue 1487 THR Chi-restraints excluded: chain A residue 1580 SER Chi-restraints excluded: chain A residue 1583 ASP Chi-restraints excluded: chain A residue 1589 SER Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1598 LYS Chi-restraints excluded: chain A residue 1672 ILE Chi-restraints excluded: chain A residue 1724 ILE Chi-restraints excluded: chain A residue 1749 GLN Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1822 VAL Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1841 ARG Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1920 LEU Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1983 LEU Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2043 ILE Chi-restraints excluded: chain A residue 2061 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 163 optimal weight: 9.9990 chunk 185 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 40 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 168 optimal weight: 0.5980 chunk 143 optimal weight: 2.9990 chunk 186 optimal weight: 7.9990 chunk 173 optimal weight: 5.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 ASN A1074 ASN ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1863 GLN ** A1954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.118936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.092428 restraints weight = 43670.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.095492 restraints weight = 22230.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.097542 restraints weight = 14261.860| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.4522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17147 Z= 0.163 Angle : 0.728 12.705 23244 Z= 0.365 Chirality : 0.044 0.186 2662 Planarity : 0.004 0.052 2811 Dihedral : 12.167 139.160 2650 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.89 % Favored : 91.91 % Rotamer: Outliers : 5.23 % Allowed : 27.05 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.19), residues: 1989 helix: 0.84 (0.16), residues: 1085 sheet: 0.86 (0.50), residues: 111 loop : -1.97 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 474 HIS 0.006 0.001 HIS A1578 PHE 0.030 0.002 PHE A 741 TYR 0.017 0.001 TYR A 706 ARG 0.004 0.000 ARG A1597 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 856) hydrogen bonds : angle 4.39192 ( 2485) covalent geometry : bond 0.00369 (17147) covalent geometry : angle 0.72833 (23244) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 300 time to evaluate : 2.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7579 (mm) REVERT: A 140 LYS cc_start: 0.8775 (mttt) cc_final: 0.8459 (ttpp) REVERT: A 199 MET cc_start: 0.9250 (tpp) cc_final: 0.8793 (ttt) REVERT: A 200 GLU cc_start: 0.9024 (tt0) cc_final: 0.8206 (tt0) REVERT: A 368 ILE cc_start: 0.9043 (tp) cc_final: 0.8759 (tp) REVERT: A 378 ASP cc_start: 0.8010 (t0) cc_final: 0.7541 (t0) REVERT: A 408 LYS cc_start: 0.7772 (OUTLIER) cc_final: 0.7508 (mmpt) REVERT: A 450 GLU cc_start: 0.8905 (tt0) cc_final: 0.8619 (tp30) REVERT: A 472 MET cc_start: 0.7270 (mpp) cc_final: 0.7030 (mpp) REVERT: A 480 LYS cc_start: 0.7121 (tmtt) cc_final: 0.6627 (tmtt) REVERT: A 536 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8037 (tm-30) REVERT: A 587 MET cc_start: 0.7912 (pmm) cc_final: 0.7557 (pmm) REVERT: A 882 ILE cc_start: 0.9374 (mt) cc_final: 0.9116 (mt) REVERT: A 900 MET cc_start: 0.7556 (mpp) cc_final: 0.6856 (mpp) REVERT: A 1171 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8347 (pp20) REVERT: A 1264 GLU cc_start: 0.8533 (mt-10) cc_final: 0.8326 (mt-10) REVERT: A 1319 GLN cc_start: 0.8559 (mt0) cc_final: 0.8018 (tm-30) REVERT: A 1348 TYR cc_start: 0.7855 (OUTLIER) cc_final: 0.7366 (m-80) REVERT: A 1431 ASN cc_start: 0.6831 (t0) cc_final: 0.6200 (m-40) REVERT: A 1475 LYS cc_start: 0.8702 (OUTLIER) cc_final: 0.8146 (mtpp) REVERT: A 1478 GLU cc_start: 0.8791 (pt0) cc_final: 0.8276 (pt0) REVERT: A 1580 SER cc_start: 0.8903 (OUTLIER) cc_final: 0.8681 (p) REVERT: A 1660 PRO cc_start: 0.9450 (Cg_exo) cc_final: 0.9175 (Cg_endo) REVERT: A 1691 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8527 (ptpp) REVERT: A 1841 ARG cc_start: 0.7942 (OUTLIER) cc_final: 0.7577 (tmm-80) REVERT: A 1929 MET cc_start: 0.8563 (mtp) cc_final: 0.7761 (ptt) REVERT: A 1954 GLN cc_start: 0.7374 (tp40) cc_final: 0.6718 (tp40) REVERT: A 1958 TRP cc_start: 0.6654 (m-90) cc_final: 0.6124 (m-90) REVERT: A 2063 PHE cc_start: 0.8046 (t80) cc_final: 0.7044 (t80) outliers start: 96 outliers final: 69 residues processed: 361 average time/residue: 0.2448 time to fit residues: 140.0982 Evaluate side-chains 362 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 285 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 670 CYS Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1110 SER Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1311 GLU Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1348 TYR Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1475 LYS Chi-restraints excluded: chain A residue 1487 THR Chi-restraints excluded: chain A residue 1498 THR Chi-restraints excluded: chain A residue 1580 SER Chi-restraints excluded: chain A residue 1583 ASP Chi-restraints excluded: chain A residue 1589 SER Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1658 ILE Chi-restraints excluded: chain A residue 1663 ILE Chi-restraints excluded: chain A residue 1672 ILE Chi-restraints excluded: chain A residue 1691 LYS Chi-restraints excluded: chain A residue 1720 ASP Chi-restraints excluded: chain A residue 1724 ILE Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1822 VAL Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1841 ARG Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1931 ILE Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1979 TYR Chi-restraints excluded: chain A residue 1983 LEU Chi-restraints excluded: chain A residue 2043 ILE Chi-restraints excluded: chain A residue 2061 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 39 optimal weight: 0.9980 chunk 131 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 135 optimal weight: 0.0010 chunk 6 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 157 optimal weight: 0.0070 chunk 67 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 overall best weight: 0.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1863 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2030 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.120845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.095164 restraints weight = 43684.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.098364 restraints weight = 21912.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.100478 restraints weight = 13756.171| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17147 Z= 0.135 Angle : 0.736 13.312 23244 Z= 0.365 Chirality : 0.044 0.261 2662 Planarity : 0.004 0.052 2811 Dihedral : 12.060 136.659 2646 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.64 % Favored : 92.21 % Rotamer: Outliers : 3.92 % Allowed : 28.36 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.19), residues: 1989 helix: 0.77 (0.16), residues: 1091 sheet: 0.83 (0.48), residues: 118 loop : -1.93 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 474 HIS 0.004 0.001 HIS A1529 PHE 0.032 0.002 PHE A 478 TYR 0.020 0.001 TYR A1675 ARG 0.006 0.000 ARG A2048 Details of bonding type rmsd hydrogen bonds : bond 0.03642 ( 856) hydrogen bonds : angle 4.41206 ( 2485) covalent geometry : bond 0.00302 (17147) covalent geometry : angle 0.73648 (23244) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 305 time to evaluate : 1.964 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7530 (mm) REVERT: A 140 LYS cc_start: 0.8735 (mttt) cc_final: 0.8415 (ttpp) REVERT: A 199 MET cc_start: 0.9214 (tpp) cc_final: 0.8841 (ttt) REVERT: A 200 GLU cc_start: 0.9015 (tt0) cc_final: 0.8354 (tt0) REVERT: A 368 ILE cc_start: 0.8967 (tp) cc_final: 0.8641 (tp) REVERT: A 378 ASP cc_start: 0.8020 (t0) cc_final: 0.7547 (t0) REVERT: A 450 GLU cc_start: 0.8892 (tt0) cc_final: 0.8453 (tp30) REVERT: A 472 MET cc_start: 0.7181 (mpp) cc_final: 0.6632 (mpp) REVERT: A 480 LYS cc_start: 0.7007 (tmtt) cc_final: 0.6529 (tmtt) REVERT: A 536 GLU cc_start: 0.8383 (mt-10) cc_final: 0.7964 (tm-30) REVERT: A 587 MET cc_start: 0.8009 (pmm) cc_final: 0.7733 (pmm) REVERT: A 825 GLN cc_start: 0.7580 (mm-40) cc_final: 0.6818 (mm-40) REVERT: A 882 ILE cc_start: 0.9364 (mt) cc_final: 0.9082 (mt) REVERT: A 890 MET cc_start: 0.8398 (tpp) cc_final: 0.7970 (tpp) REVERT: A 900 MET cc_start: 0.7318 (mpp) cc_final: 0.6817 (mpp) REVERT: A 1171 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8327 (pp20) REVERT: A 1264 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8054 (mt-10) REVERT: A 1348 TYR cc_start: 0.7808 (OUTLIER) cc_final: 0.7323 (m-80) REVERT: A 1431 ASN cc_start: 0.6721 (t0) cc_final: 0.6150 (m-40) REVERT: A 1478 GLU cc_start: 0.8748 (pt0) cc_final: 0.8225 (pt0) REVERT: A 1566 CYS cc_start: 0.9001 (p) cc_final: 0.8771 (p) REVERT: A 1660 PRO cc_start: 0.9441 (Cg_exo) cc_final: 0.9136 (Cg_endo) REVERT: A 1749 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7958 (mm-40) REVERT: A 1841 ARG cc_start: 0.7995 (OUTLIER) cc_final: 0.7660 (tmm-80) REVERT: A 1929 MET cc_start: 0.8492 (mtp) cc_final: 0.7718 (ptt) REVERT: A 1954 GLN cc_start: 0.7237 (tp40) cc_final: 0.5465 (tp40) REVERT: A 1958 TRP cc_start: 0.6603 (m-90) cc_final: 0.5641 (m-90) REVERT: A 2063 PHE cc_start: 0.7973 (t80) cc_final: 0.7066 (t80) outliers start: 72 outliers final: 63 residues processed: 351 average time/residue: 0.2497 time to fit residues: 140.0980 Evaluate side-chains 352 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 285 time to evaluate : 1.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 670 CYS Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1110 SER Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1311 GLU Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1348 TYR Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1475 LYS Chi-restraints excluded: chain A residue 1487 THR Chi-restraints excluded: chain A residue 1498 THR Chi-restraints excluded: chain A residue 1589 SER Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 1663 ILE Chi-restraints excluded: chain A residue 1672 ILE Chi-restraints excluded: chain A residue 1724 ILE Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1822 VAL Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1841 ARG Chi-restraints excluded: chain A residue 1865 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1979 TYR Chi-restraints excluded: chain A residue 1983 LEU Chi-restraints excluded: chain A residue 2043 ILE Chi-restraints excluded: chain A residue 2061 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 191 optimal weight: 4.9990 chunk 21 optimal weight: 0.0770 chunk 193 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 102 optimal weight: 0.5980 chunk 110 optimal weight: 0.8980 chunk 134 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.5142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1011 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1863 GLN ** A1954 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 = 0.3901 r_free = 0.3901 target = 0.120230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.092944 restraints weight = 44801.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.096039 restraints weight = 23239.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.098138 restraints weight = 15088.204| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.4817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17147 Z= 0.156 Angle : 0.759 15.516 23244 Z= 0.376 Chirality : 0.045 0.259 2662 Planarity : 0.004 0.055 2811 Dihedral : 12.094 138.229 2646 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.89 % Favored : 91.96 % Rotamer: Outliers : 3.76 % Allowed : 29.45 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.19), residues: 1989 helix: 0.72 (0.16), residues: 1098 sheet: 0.64 (0.48), residues: 120 loop : -1.98 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 412 HIS 0.004 0.001 HIS A1578 PHE 0.027 0.002 PHE A 741 TYR 0.027 0.001 TYR A1465 ARG 0.012 0.001 ARG A1335 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 856) hydrogen bonds : angle 4.44706 ( 2485) covalent geometry : bond 0.00355 (17147) covalent geometry : angle 0.75864 (23244) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 297 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7519 (mm) REVERT: A 199 MET cc_start: 0.9214 (tpp) cc_final: 0.8909 (ttt) REVERT: A 200 GLU cc_start: 0.8954 (tt0) cc_final: 0.8480 (tt0) REVERT: A 378 ASP cc_start: 0.8028 (t0) cc_final: 0.7584 (t0) REVERT: A 450 GLU cc_start: 0.8942 (tt0) cc_final: 0.8504 (tp30) REVERT: A 472 MET cc_start: 0.7107 (mpp) cc_final: 0.6663 (mpp) REVERT: A 480 LYS cc_start: 0.7065 (tmtt) cc_final: 0.6583 (tmtt) REVERT: A 536 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8037 (tm-30) REVERT: A 587 MET cc_start: 0.8045 (pmm) cc_final: 0.7767 (pmm) REVERT: A 688 GLU cc_start: 0.8162 (tp30) cc_final: 0.7941 (tp30) REVERT: A 825 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7253 (mm-40) REVERT: A 882 ILE cc_start: 0.9349 (mt) cc_final: 0.9070 (mt) REVERT: A 900 MET cc_start: 0.7374 (mpp) cc_final: 0.6854 (mpp) REVERT: A 1171 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8325 (pp20) REVERT: A 1178 ASN cc_start: 0.8722 (m-40) cc_final: 0.8440 (m-40) REVERT: A 1264 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8278 (mt-10) REVERT: A 1284 PHE cc_start: 0.7820 (m-80) cc_final: 0.7542 (m-80) REVERT: A 1319 GLN cc_start: 0.8542 (mt0) cc_final: 0.8237 (mm-40) REVERT: A 1348 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.7355 (m-80) REVERT: A 1416 ASP cc_start: 0.8525 (p0) cc_final: 0.8205 (p0) REVERT: A 1431 ASN cc_start: 0.6865 (t0) cc_final: 0.6245 (m-40) REVERT: A 1478 GLU cc_start: 0.8755 (pt0) cc_final: 0.8237 (pt0) REVERT: A 1566 CYS cc_start: 0.9010 (p) cc_final: 0.8781 (p) REVERT: A 1660 PRO cc_start: 0.9455 (Cg_exo) cc_final: 0.9179 (Cg_endo) REVERT: A 1749 GLN cc_start: 0.8272 (mm-40) cc_final: 0.7771 (mt0) REVERT: A 1819 MET cc_start: 0.9202 (tpp) cc_final: 0.8990 (tpp) REVERT: A 1826 MET cc_start: 0.8457 (mmt) cc_final: 0.7768 (mmm) REVERT: A 1841 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7615 (tmm-80) REVERT: A 1929 MET cc_start: 0.8492 (mtp) cc_final: 0.7738 (ptt) REVERT: A 1954 GLN cc_start: 0.7228 (tp40) cc_final: 0.5678 (tp40) REVERT: A 1958 TRP cc_start: 0.6692 (m-90) cc_final: 0.5887 (m-90) outliers start: 69 outliers final: 63 residues processed: 341 average time/residue: 0.2445 time to fit residues: 132.8748 Evaluate side-chains 354 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 287 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 670 CYS Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 992 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1110 SER Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1171 GLU Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1311 GLU Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1348 TYR Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1475 LYS Chi-restraints excluded: chain A residue 1487 THR Chi-restraints excluded: chain A residue 1498 THR Chi-restraints excluded: chain A residue 1589 SER Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 1663 ILE Chi-restraints excluded: chain A residue 1672 ILE Chi-restraints excluded: chain A residue 1724 ILE Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1822 VAL Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1841 ARG Chi-restraints excluded: chain A residue 1865 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1979 TYR Chi-restraints excluded: chain A residue 1983 LEU Chi-restraints excluded: chain A residue 2043 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 10 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 chunk 201 optimal weight: 20.0000 chunk 196 optimal weight: 0.9980 chunk 184 optimal weight: 0.0070 chunk 6 optimal weight: 6.9990 chunk 189 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 overall best weight: 1.7802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1954 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 = 0.3876 r_free = 0.3876 target = 0.118691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.092712 restraints weight = 43718.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.095785 restraints weight = 22068.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.097851 restraints weight = 14053.376| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 17147 Z= 0.164 Angle : 0.764 14.785 23244 Z= 0.378 Chirality : 0.045 0.257 2662 Planarity : 0.004 0.055 2811 Dihedral : 12.124 138.406 2644 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.99 % Favored : 91.86 % Rotamer: Outliers : 4.25 % Allowed : 28.80 % Favored : 66.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.19), residues: 1989 helix: 0.73 (0.16), residues: 1097 sheet: 0.55 (0.48), residues: 121 loop : -2.01 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1027 HIS 0.005 0.001 HIS A1529 PHE 0.030 0.002 PHE A 741 TYR 0.018 0.001 TYR A 706 ARG 0.004 0.000 ARG A 899 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 856) hydrogen bonds : angle 4.44770 ( 2485) covalent geometry : bond 0.00374 (17147) covalent geometry : angle 0.76363 (23244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5524.47 seconds wall clock time: 98 minutes 1.91 seconds (5881.91 seconds total)