Starting phenix.real_space_refine on Fri Jul 3 23:10:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ki7_37253/07_2026/8ki7_37253.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ki7_37253/07_2026/8ki7_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_37253/07_2026/8ki7_37253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ki7_37253/07_2026/8ki7_37253.map" model { file = "/net/cci-nas-00/data/ceres_data/8ki7_37253/07_2026/8ki7_37253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ki7_37253/07_2026/8ki7_37253.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 'GLN:plan1': 1, 'ARG:plan': 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: 3.55, per 1000 atoms: 0.21 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: 1.40 Conformation dependent library (CDL) restraints added in 715.2 milliseconds 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: 2.17 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: 4.05 Time building geometry restraints manager: 1.89 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=" N1 U F 7 " pdb=" C2 U F 7 " ideal model delta sigma weight residual 1.381 1.398 -0.017 9.00e-03 1.23e+04 3.62e+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 ... (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=" C1' C F 12 " pdb=" N1 C F 12 " pdb=" C2 C F 12 " ideal model delta sigma weight residual 118.80 127.19 -8.39 1.10e+00 8.26e-01 5.82e+01 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=" N1 C E 9 " pdb=" C2 C E 9 " pdb=" O2 C E 9 " ideal model delta sigma weight residual 118.90 123.29 -4.39 6.00e-01 2.78e+00 5.36e+01 angle pdb=" N1 C F 12 " pdb=" C2 C F 12 " pdb=" O2 C F 12 " ideal model delta sigma weight residual 118.90 123.17 -4.27 6.00e-01 2.78e+00 5.06e+01 angle pdb=" O2 C E 9 " pdb=" C2 C E 9 " pdb=" N3 C E 9 " ideal model delta sigma weight residual 121.90 116.97 4.93 7.00e-01 2.04e+00 4.95e+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: 0.750 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.380 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 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= 0.238 Angle : 1.069 17.974 23244 Z= 0.596 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 : 8.03 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.015 0.001 ARG A1679 TYR 0.025 0.002 TYR A1938 PHE 0.051 0.003 PHE A1234 TRP 0.025 0.002 TRP A 474 HIS 0.014 0.002 HIS A1529 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.24 (17147) covalent geometry : angle 1.06863 / 0.60 (23244) hydrogen bonds : bond 0.07230 / 4.45 ( 856) hydrogen bonds : angle 5.80709 / 4.06 ( 2485) *********************** 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 : 0.650 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: 0.7180 (m-30) cc_final: 0.6886 (m-30) REVERT: A 2063 PHE cc_start: 0.5672 (t80) cc_final: 0.5101 (t80) outliers start: 71 outliers final: 28 residues processed: 581 average time/residue: 0.1303 time to fit residues: 114.7915 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 : 0.620 ------------------------------------------------------------------------------- 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 98 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 0.8980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 ** A1954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.118762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.092213 restraints weight = 43872.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.095285 restraints weight = 22608.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.097363 restraints weight = 14483.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.098762 restraints weight = 10709.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.099465 restraints weight = 8733.878| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.2635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 17147 Z= 0.281 Angle : 0.840 12.490 23244 Z= 0.439 Chirality : 0.049 0.223 2662 Planarity : 0.005 0.077 2811 Dihedral : 12.668 142.911 2678 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.44 % Favored : 92.36 % Rotamer: Outliers : 6.04 % Allowed : 24.33 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.43 (0.18), residues: 1989 helix: -0.13 (0.15), residues: 1072 sheet: 0.58 (0.53), residues: 96 loop : -2.26 (0.20), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1289 TYR 0.023 0.002 TYR A1465 PHE 0.038 0.003 PHE A 741 TRP 0.023 0.002 TRP A 474 HIS 0.008 0.001 HIS A 419 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.28 (17147) covalent geometry : angle 0.84002 / 0.44 (23244) hydrogen bonds : bond 0.04732 / 3.10 ( 856) hydrogen bonds : angle 4.95283 / 3.42 ( 2485) *********************** 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 452 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 341 time to evaluate : 0.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.9164 (tp) cc_final: 0.8947 (mp) REVERT: A 140 LYS cc_start: 0.8784 (mttt) cc_final: 0.8300 (ttpp) REVERT: A 199 MET cc_start: 0.9311 (tpp) cc_final: 0.8787 (ttt) REVERT: A 363 ASN cc_start: 0.8503 (p0) cc_final: 0.8299 (p0) REVERT: A 378 ASP cc_start: 0.7765 (t0) cc_final: 0.7295 (t70) REVERT: A 480 LYS cc_start: 0.6965 (tmtt) cc_final: 0.6710 (tmtt) REVERT: A 584 GLU cc_start: 0.8118 (tt0) cc_final: 0.7892 (pt0) REVERT: A 684 ASP cc_start: 0.6738 (OUTLIER) cc_final: 0.6135 (m-30) REVERT: A 809 TYR cc_start: 0.6934 (OUTLIER) cc_final: 0.6442 (m-80) REVERT: A 822 MET cc_start: 0.9108 (mmt) cc_final: 0.8380 (mmm) REVERT: A 882 ILE cc_start: 0.9402 (mt) cc_final: 0.9191 (mt) REVERT: A 906 MET cc_start: 0.8781 (ttm) cc_final: 0.8573 (ttm) REVERT: A 982 CYS cc_start: 0.8042 (m) cc_final: 0.7466 (m) REVERT: A 1267 MET cc_start: 0.8865 (mmm) cc_final: 0.8652 (mmt) REVERT: A 1372 SER cc_start: 0.8983 (p) cc_final: 0.8636 (p) REVERT: A 1376 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7938 (mm) REVERT: A 1398 MET cc_start: 0.7785 (tpp) cc_final: 0.7251 (mtt) REVERT: A 1475 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.7839 (ttmm) REVERT: A 1554 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6476 (mt-10) REVERT: A 1598 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7592 (mmmt) REVERT: A 1691 LYS cc_start: 0.9294 (ptmt) cc_final: 0.9008 (ptpp) REVERT: A 1747 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8170 (pttt) REVERT: A 1749 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7453 (mm-40) REVERT: A 1850 MET cc_start: 0.8283 (ttp) cc_final: 0.8075 (ttp) REVERT: A 1903 MET cc_start: 0.8295 (mmp) cc_final: 0.8057 (tpp) REVERT: A 1992 ASP cc_start: 0.8602 (m-30) cc_final: 0.7981 (m-30) outliers start: 111 outliers final: 58 residues processed: 417 average time/residue: 0.1115 time to fit residues: 74.9046 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 : 0.533 ------------------------------------------------------------------------------- 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 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 411 ILE Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 587 MET 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 756 SER 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 1017 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1038 ASN Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1268 SER 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 1444 THR 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 1534 CYS 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 1917 CYS 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 74 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 145 optimal weight: 4.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 ASN A 103 HIS A 260 HIS A 358 HIS ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 ASN A1628 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.120496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.094272 restraints weight = 44038.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.097416 restraints weight = 22387.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.099495 restraints weight = 14234.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.100687 restraints weight = 10504.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.101739 restraints weight = 8717.639| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2967 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= 0.163 Angle : 0.740 11.259 23244 Z= 0.381 Chirality : 0.046 0.226 2662 Planarity : 0.004 0.049 2811 Dihedral : 12.419 140.914 2659 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.44 % Favored : 92.36 % Rotamer: Outliers : 5.33 % Allowed : 25.31 % Favored : 69.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.18), residues: 1989 helix: 0.18 (0.15), residues: 1077 sheet: 0.74 (0.54), residues: 96 loop : -2.23 (0.20), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 268 TYR 0.016 0.001 TYR A1465 PHE 0.032 0.002 PHE A1950 TRP 0.027 0.002 TRP A1958 HIS 0.005 0.001 HIS A1578 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (17147) covalent geometry : angle 0.73972 / 0.38 (23244) hydrogen bonds : bond 0.04230 / 2.76 ( 856) hydrogen bonds : angle 4.78307 / 3.31 ( 2485) *********************** 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 425 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 327 time to evaluate : 0.610 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 30 LEU cc_start: 0.9251 (tp) cc_final: 0.8922 (mp) REVERT: A 140 LYS cc_start: 0.8748 (mttt) cc_final: 0.8284 (ttpp) REVERT: A 150 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8117 (mt-10) REVERT: A 199 MET cc_start: 0.9317 (tpp) cc_final: 0.8557 (ttt) REVERT: A 298 LYS cc_start: 0.9317 (mttt) cc_final: 0.8759 (pttp) REVERT: A 378 ASP cc_start: 0.7774 (t0) cc_final: 0.7265 (t70) REVERT: A 472 MET cc_start: 0.6537 (mpp) cc_final: 0.6067 (tpp) REVERT: A 480 LYS cc_start: 0.7127 (tmtt) cc_final: 0.6662 (tmtt) REVERT: A 677 LEU cc_start: 0.9284 (tp) cc_final: 0.9067 (tt) REVERT: A 684 ASP cc_start: 0.6549 (OUTLIER) cc_final: 0.6264 (m-30) REVERT: A 882 ILE cc_start: 0.9394 (mt) cc_final: 0.9177 (mt) REVERT: A 890 MET cc_start: 0.8542 (tpp) cc_final: 0.8011 (tpp) REVERT: A 900 MET cc_start: 0.7573 (mpp) cc_final: 0.7351 (mpp) REVERT: A 982 CYS cc_start: 0.7990 (m) cc_final: 0.7507 (m) REVERT: A 1267 MET cc_start: 0.8823 (mmm) cc_final: 0.8620 (mmp) REVERT: A 1376 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7855 (mt) REVERT: A 1398 MET cc_start: 0.7743 (tpp) cc_final: 0.7291 (mtp) REVERT: A 1470 MET cc_start: 0.8748 (tpp) cc_final: 0.8427 (tpp) REVERT: A 1534 CYS cc_start: 0.7942 (t) cc_final: 0.7570 (t) REVERT: A 1691 LYS cc_start: 0.9271 (ptmt) cc_final: 0.9042 (ptpp) REVERT: A 1747 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8279 (pttt) REVERT: A 1749 GLN cc_start: 0.8333 (mm-40) cc_final: 0.7428 (mm-40) REVERT: A 1929 MET cc_start: 0.8686 (mtm) cc_final: 0.7647 (ptt) REVERT: A 1958 TRP cc_start: 0.5896 (m-90) cc_final: 0.5618 (m-90) outliers start: 98 outliers final: 61 residues processed: 390 average time/residue: 0.1054 time to fit residues: 66.1730 Evaluate side-chains 367 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 302 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 150 GLU Chi-restraints excluded: chain A residue 239 MET 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 371 MET Chi-restraints excluded: chain A residue 374 GLN 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 566 LYS Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 756 SER Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 792 VAL 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 937 ASP Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1215 VAL 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 1391 THR Chi-restraints excluded: chain A residue 1411 VAL 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 1589 SER Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1603 GLU 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 1917 CYS Chi-restraints excluded: chain A residue 1931 ILE Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2061 PHE Chi-restraints excluded: chain A residue 2084 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 134 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 117 optimal weight: 6.9990 chunk 33 optimal weight: 0.1980 chunk 146 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 187 optimal weight: 0.0000 chunk 77 optimal weight: 10.0000 overall best weight: 0.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN A 103 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 ASN A1074 ASN A1863 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.121956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.095785 restraints weight = 43996.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.099041 restraints weight = 22301.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.101195 restraints weight = 14051.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.102426 restraints weight = 10294.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.103416 restraints weight = 8492.822| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 17147 Z= 0.137 Angle : 0.709 10.954 23244 Z= 0.363 Chirality : 0.045 0.314 2662 Planarity : 0.004 0.041 2811 Dihedral : 12.290 140.868 2659 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.64 % Favored : 92.16 % Rotamer: Outliers : 5.39 % Allowed : 25.37 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.18), residues: 1989 helix: 0.33 (0.15), residues: 1076 sheet: 0.69 (0.53), residues: 98 loop : -2.16 (0.20), residues: 815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 580 TYR 0.016 0.001 TYR A1447 PHE 0.028 0.002 PHE A1950 TRP 0.018 0.001 TRP A 474 HIS 0.005 0.001 HIS A1578 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (17147) covalent geometry : angle 0.70908 / 0.36 (23244) hydrogen bonds : bond 0.03916 / 2.57 ( 856) hydrogen bonds : angle 4.69200 / 3.25 ( 2485) *********************** 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 438 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 339 time to evaluate : 0.630 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 87 MET cc_start: 0.8175 (mtp) cc_final: 0.7974 (ptm) REVERT: A 114 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8140 (mm) REVERT: A 140 LYS cc_start: 0.8764 (mttt) cc_final: 0.8219 (tmtt) REVERT: A 150 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8131 (mt-10) REVERT: A 199 MET cc_start: 0.9274 (tpp) cc_final: 0.8736 (ttt) REVERT: A 378 ASP cc_start: 0.7721 (t0) cc_final: 0.7320 (t70) REVERT: A 480 LYS cc_start: 0.7040 (tmtt) cc_final: 0.6582 (tmtt) REVERT: A 684 ASP cc_start: 0.6331 (OUTLIER) cc_final: 0.5991 (m-30) REVERT: A 750 ARG cc_start: 0.8649 (tpp80) cc_final: 0.8444 (tpp80) REVERT: A 822 MET cc_start: 0.8992 (mmt) cc_final: 0.8322 (mmm) REVERT: A 882 ILE cc_start: 0.9388 (mt) cc_final: 0.9170 (mt) REVERT: A 890 MET cc_start: 0.8541 (tpp) cc_final: 0.8274 (tpp) REVERT: A 900 MET cc_start: 0.7349 (mpp) cc_final: 0.6742 (mpp) REVERT: A 904 ASP cc_start: 0.7999 (m-30) cc_final: 0.7551 (m-30) REVERT: A 1267 MET cc_start: 0.8821 (mmm) cc_final: 0.8547 (mmp) REVERT: A 1361 LEU cc_start: 0.8908 (tp) cc_final: 0.8693 (tp) REVERT: A 1376 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7778 (tt) REVERT: A 1398 MET cc_start: 0.7801 (tpp) cc_final: 0.7329 (mtp) REVERT: A 1403 LEU cc_start: 0.8457 (mm) cc_final: 0.8006 (tp) REVERT: A 1470 MET cc_start: 0.8788 (tpp) cc_final: 0.8406 (tpp) REVERT: A 1475 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8237 (mtpp) REVERT: A 1534 CYS cc_start: 0.7934 (t) cc_final: 0.7686 (t) REVERT: A 1598 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7724 (mmmt) REVERT: A 1691 LYS cc_start: 0.9291 (ptmt) cc_final: 0.9061 (ptpp) REVERT: A 1728 ASN cc_start: 0.8800 (t0) cc_final: 0.8466 (t0) REVERT: A 1747 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8319 (pttp) REVERT: A 1748 PHE cc_start: 0.7523 (m-10) cc_final: 0.7232 (m-10) REVERT: A 1779 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8444 (pt) REVERT: A 1841 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.7654 (tmm-80) REVERT: A 1903 MET cc_start: 0.8501 (tpp) cc_final: 0.8034 (tpp) REVERT: A 1929 MET cc_start: 0.8622 (mtm) cc_final: 0.7628 (ptt) REVERT: A 1953 PHE cc_start: 0.6848 (m-80) cc_final: 0.6237 (m-80) outliers start: 99 outliers final: 50 residues processed: 404 average time/residue: 0.1115 time to fit residues: 71.2611 Evaluate side-chains 366 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 307 time to evaluate : 0.595 ------------------------------------------------------------------------------- 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 150 GLU 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 365 CYS Chi-restraints excluded: chain A residue 374 GLN 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 566 LYS 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 681 HIS Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 712 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 789 LEU 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 912 LEU Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1023 VAL 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 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 1376 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1390 LEU Chi-restraints excluded: chain A residue 1391 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 1596 LEU Chi-restraints excluded: chain A residue 1598 LYS 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 1917 CYS Chi-restraints excluded: chain A residue 1931 ILE Chi-restraints excluded: chain A residue 1948 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 71 optimal weight: 3.9990 chunk 93 optimal weight: 0.2980 chunk 37 optimal weight: 0.6980 chunk 123 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 113 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 61 optimal weight: 8.9990 chunk 54 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** A1063 ASN ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1749 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.121850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.094425 restraints weight = 44710.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.097624 restraints weight = 23291.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.099773 restraints weight = 15105.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.101219 restraints weight = 11250.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.101972 restraints weight = 9258.205| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3460 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= 0.149 Angle : 0.711 12.843 23244 Z= 0.362 Chirality : 0.045 0.327 2662 Planarity : 0.004 0.040 2811 Dihedral : 12.189 142.198 2657 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.59 % Favored : 92.21 % Rotamer: Outliers : 4.84 % Allowed : 25.64 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.18), residues: 1989 helix: 0.49 (0.15), residues: 1082 sheet: 0.70 (0.53), residues: 98 loop : -2.13 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1555 TYR 0.023 0.001 TYR A1465 PHE 0.030 0.001 PHE A1950 TRP 0.049 0.002 TRP A1958 HIS 0.004 0.001 HIS A1578 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (17147) covalent geometry : angle 0.71142 / 0.36 (23244) hydrogen bonds : bond 0.03855 / 2.53 ( 856) hydrogen bonds : angle 4.60020 / 3.18 ( 2485) *********************** 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 408 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 319 time to evaluate : 0.671 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 30 LEU cc_start: 0.9186 (tp) cc_final: 0.8956 (mt) REVERT: A 114 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8177 (mm) REVERT: A 140 LYS cc_start: 0.8767 (mttt) cc_final: 0.8345 (ttpp) REVERT: A 199 MET cc_start: 0.9237 (tpp) cc_final: 0.8701 (ttt) REVERT: A 378 ASP cc_start: 0.7817 (t0) cc_final: 0.7327 (t70) REVERT: A 472 MET cc_start: 0.6536 (mpp) cc_final: 0.5628 (tpp) REVERT: A 480 LYS cc_start: 0.7071 (tmtt) cc_final: 0.6585 (tmtt) REVERT: A 495 ASN cc_start: 0.9061 (OUTLIER) cc_final: 0.8837 (p0) REVERT: A 684 ASP cc_start: 0.6273 (OUTLIER) cc_final: 0.5663 (m-30) REVERT: A 882 ILE cc_start: 0.9387 (mt) cc_final: 0.9171 (mt) REVERT: A 890 MET cc_start: 0.8513 (tpp) cc_final: 0.8269 (tpp) REVERT: A 900 MET cc_start: 0.7385 (mpp) cc_final: 0.7105 (mpp) REVERT: A 1267 MET cc_start: 0.8845 (mmm) cc_final: 0.8606 (mmp) REVERT: A 1361 LEU cc_start: 0.8934 (tp) cc_final: 0.8706 (tp) REVERT: A 1376 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7803 (tt) REVERT: A 1398 MET cc_start: 0.7833 (tpp) cc_final: 0.7156 (mtp) REVERT: A 1403 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7986 (tp) REVERT: A 1431 ASN cc_start: 0.6330 (t0) cc_final: 0.5942 (m-40) REVERT: A 1470 MET cc_start: 0.8664 (tpp) cc_final: 0.8230 (tpp) REVERT: A 1534 CYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7726 (t) REVERT: A 1691 LYS cc_start: 0.9298 (ptmt) cc_final: 0.9052 (ptpp) REVERT: A 1748 PHE cc_start: 0.7526 (m-10) cc_final: 0.7229 (m-10) REVERT: A 1779 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8509 (pt) REVERT: A 1903 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8193 (tpp) REVERT: A 1929 MET cc_start: 0.8655 (mtm) cc_final: 0.7677 (ptt) REVERT: A 1958 TRP cc_start: 0.5842 (m-90) cc_final: 0.5628 (m-90) outliers start: 89 outliers final: 60 residues processed: 373 average time/residue: 0.1023 time to fit residues: 61.3846 Evaluate side-chains 360 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 292 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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 119 LYS Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 223 ASP 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 374 GLN Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 495 ASN Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 585 PHE 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 712 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 789 LEU 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 912 LEU Chi-restraints excluded: chain A residue 985 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1023 VAL 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 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 1365 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 1403 LEU 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 1534 CYS Chi-restraints excluded: chain A residue 1589 SER Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1661 LEU 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 1903 MET 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 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 112 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 152 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 168 optimal weight: 0.0000 chunk 158 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 156 optimal weight: 0.9980 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 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** A1749 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.121584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.095533 restraints weight = 43531.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.098742 restraints weight = 22121.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.100887 restraints weight = 14030.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.102299 restraints weight = 10255.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.103097 restraints weight = 8343.720| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3645 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= 0.137 Angle : 0.724 11.741 23244 Z= 0.364 Chirality : 0.045 0.354 2662 Planarity : 0.004 0.038 2811 Dihedral : 12.173 141.995 2653 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.34 % Favored : 92.46 % Rotamer: Outliers : 4.95 % Allowed : 25.42 % Favored : 69.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.19), residues: 1989 helix: 0.54 (0.15), residues: 1092 sheet: 1.20 (0.56), residues: 84 loop : -2.13 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1488 TYR 0.026 0.001 TYR A1465 PHE 0.027 0.001 PHE A1950 TRP 0.027 0.001 TRP A1958 HIS 0.004 0.001 HIS A1529 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (17147) covalent geometry : angle 0.72357 / 0.36 (23244) hydrogen bonds : bond 0.03779 / 2.48 ( 856) hydrogen bonds : angle 4.56217 / 3.16 ( 2485) *********************** 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 416 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 325 time to evaluate : 0.647 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 114 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8122 (mm) REVERT: A 140 LYS cc_start: 0.8686 (mttt) cc_final: 0.8296 (ttpp) REVERT: A 199 MET cc_start: 0.9190 (tpp) cc_final: 0.8634 (ttt) REVERT: A 298 LYS cc_start: 0.9352 (mttt) cc_final: 0.8850 (pttp) REVERT: A 480 LYS cc_start: 0.7056 (tmtt) cc_final: 0.6536 (tmtt) REVERT: A 495 ASN cc_start: 0.9056 (OUTLIER) cc_final: 0.8838 (p0) REVERT: A 684 ASP cc_start: 0.6150 (OUTLIER) cc_final: 0.5618 (m-30) REVERT: A 822 MET cc_start: 0.8931 (mmt) cc_final: 0.8400 (mmm) REVERT: A 878 LYS cc_start: 0.9308 (tttt) cc_final: 0.9100 (ttpp) REVERT: A 882 ILE cc_start: 0.9411 (mt) cc_final: 0.9197 (mt) REVERT: A 890 MET cc_start: 0.8528 (tpp) cc_final: 0.8252 (tpp) REVERT: A 900 MET cc_start: 0.7404 (mpp) cc_final: 0.6782 (mpp) REVERT: A 1022 ASN cc_start: 0.8088 (m-40) cc_final: 0.7871 (m-40) REVERT: A 1089 GLU cc_start: 0.9057 (mm-30) cc_final: 0.8822 (mm-30) REVERT: A 1361 LEU cc_start: 0.8873 (tp) cc_final: 0.8656 (tp) REVERT: A 1376 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7766 (tt) REVERT: A 1403 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7943 (tp) REVERT: A 1431 ASN cc_start: 0.6323 (t0) cc_final: 0.5929 (m-40) REVERT: A 1470 MET cc_start: 0.8679 (tpp) cc_final: 0.8250 (tpp) REVERT: A 1534 CYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7698 (t) REVERT: A 1598 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7711 (mmmt) REVERT: A 1723 MET cc_start: 0.8717 (tpp) cc_final: 0.8372 (tpp) REVERT: A 1819 MET cc_start: 0.9302 (tpp) cc_final: 0.9072 (tpp) REVERT: A 1841 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7595 (tmm-80) REVERT: A 1903 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.8190 (tpp) REVERT: A 1929 MET cc_start: 0.8637 (mtm) cc_final: 0.7695 (ptt) REVERT: A 1958 TRP cc_start: 0.5657 (m-90) cc_final: 0.5136 (m-90) REVERT: A 1983 LEU cc_start: 0.5959 (OUTLIER) cc_final: 0.5456 (tt) outliers start: 91 outliers final: 57 residues processed: 384 average time/residue: 0.1028 time to fit residues: 63.4862 Evaluate side-chains 361 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 294 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 150 GLU 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 365 CYS Chi-restraints excluded: chain A residue 374 GLN 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 495 ASN 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 585 PHE 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 712 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 789 LEU 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 912 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 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 1391 THR 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 1534 CYS 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 1661 LEU 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 1903 MET 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 2061 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 193 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 180 optimal weight: 4.9990 chunk 160 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 178 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 HIS ** 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** ** 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 = 0.3858 r_free = 0.3858 target = 0.117563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.091358 restraints weight = 43802.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.094468 restraints weight = 22243.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.096513 restraints weight = 14121.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.097703 restraints weight = 10420.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.098728 restraints weight = 8643.495| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.4008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 17147 Z= 0.212 Angle : 0.758 11.757 23244 Z= 0.385 Chirality : 0.046 0.314 2662 Planarity : 0.004 0.042 2811 Dihedral : 12.257 144.659 2649 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.94 % Favored : 91.86 % Rotamer: Outliers : 5.17 % Allowed : 25.97 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.19), residues: 1989 helix: 0.64 (0.16), residues: 1094 sheet: 0.65 (0.49), residues: 112 loop : -2.15 (0.21), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 247 TYR 0.031 0.002 TYR A1465 PHE 0.035 0.002 PHE A2067 TRP 0.027 0.002 TRP A1958 HIS 0.005 0.001 HIS A1578 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 (17147) covalent geometry : angle 0.75819 / 0.39 (23244) hydrogen bonds : bond 0.03999 / 2.62 ( 856) hydrogen bonds : angle 4.58315 / 3.17 ( 2485) *********************** 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 395 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 300 time to evaluate : 0.626 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: 0.9265 (tp) cc_final: 0.9019 (pp) REVERT: A 114 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7970 (mm) REVERT: A 140 LYS cc_start: 0.8671 (mttt) cc_final: 0.8332 (ttpp) REVERT: A 199 MET cc_start: 0.9211 (tpp) cc_final: 0.8648 (ttt) REVERT: A 298 LYS cc_start: 0.9357 (mttt) cc_final: 0.8866 (pttp) REVERT: A 378 ASP cc_start: 0.7958 (t0) cc_final: 0.7483 (t0) REVERT: A 408 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7569 (mmpt) REVERT: A 450 GLU cc_start: 0.8786 (tt0) cc_final: 0.8418 (tp30) REVERT: A 480 LYS cc_start: 0.7126 (tmtt) cc_final: 0.6794 (tmtt) REVERT: A 587 MET cc_start: 0.7896 (pmm) cc_final: 0.7670 (pmm) REVERT: A 684 ASP cc_start: 0.6680 (OUTLIER) cc_final: 0.6050 (m-30) REVERT: A 878 LYS cc_start: 0.9329 (tttt) cc_final: 0.9120 (ttpp) REVERT: A 890 MET cc_start: 0.8620 (tpp) cc_final: 0.8308 (tpp) REVERT: A 900 MET cc_start: 0.7656 (mpp) cc_final: 0.6910 (mpp) REVERT: A 1005 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7798 (ttt) REVERT: A 1319 GLN cc_start: 0.8566 (mt0) cc_final: 0.8081 (tm-30) REVERT: A 1403 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8205 (tp) REVERT: A 1451 MET cc_start: 0.8049 (mtm) cc_final: 0.7704 (mtm) REVERT: A 1470 MET cc_start: 0.8643 (tpp) cc_final: 0.8180 (tpp) REVERT: A 1534 CYS cc_start: 0.8016 (OUTLIER) cc_final: 0.7759 (t) REVERT: A 1728 ASN cc_start: 0.8883 (t0) cc_final: 0.8574 (m-40) REVERT: A 1779 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8607 (pt) REVERT: A 1858 ASN cc_start: 0.8059 (p0) cc_final: 0.7659 (p0) REVERT: A 1903 MET cc_start: 0.8572 (tpp) cc_final: 0.8210 (tpp) REVERT: A 1929 MET cc_start: 0.8435 (mtm) cc_final: 0.7742 (ptt) REVERT: A 2063 PHE cc_start: 0.8085 (t80) cc_final: 0.7368 (t80) outliers start: 95 outliers final: 65 residues processed: 359 average time/residue: 0.0989 time to fit residues: 57.7657 Evaluate side-chains 355 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 283 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 150 GLU Chi-restraints excluded: chain A residue 223 ASP 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 365 CYS Chi-restraints excluded: chain A residue 374 GLN 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 562 VAL Chi-restraints excluded: chain A residue 566 LYS 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 712 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 767 MET 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 1005 MET Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1220 SER 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 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 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 1534 CYS 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 1596 LEU Chi-restraints excluded: chain A residue 1661 LEU Chi-restraints excluded: chain A residue 1663 ILE Chi-restraints excluded: chain A residue 1720 ASP 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 1909 ASP 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 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 84 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 chunk 183 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 176 optimal weight: 0.9990 chunk 130 optimal weight: 8.9990 chunk 160 optimal weight: 2.9990 chunk 29 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 HIS A 167 ASN ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 ASN A1312 HIS ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1749 GLN ** A1954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1982 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 = 0.3872 r_free = 0.3872 target = 0.118240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.091434 restraints weight = 44476.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.094548 restraints weight = 22815.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.096625 restraints weight = 14664.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.098014 restraints weight = 10882.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.098635 restraints weight = 8924.907| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 17147 Z= 0.179 Angle : 0.752 12.806 23244 Z= 0.380 Chirality : 0.046 0.291 2662 Planarity : 0.004 0.042 2811 Dihedral : 12.269 143.460 2646 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.89 % Favored : 91.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.19), residues: 1989 helix: 0.62 (0.16), residues: 1088 sheet: 0.59 (0.48), residues: 112 loop : -2.06 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 247 TYR 0.027 0.002 TYR A1465 PHE 0.030 0.002 PHE A1748 TRP 0.021 0.001 TRP A 474 HIS 0.005 0.001 HIS A1578 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (17147) covalent geometry : angle 0.75199 / 0.38 (23244) hydrogen bonds : bond 0.03933 / 2.58 ( 856) hydrogen bonds : angle 4.58021 / 3.17 ( 2485) *********************** 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 385 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 297 time to evaluate : 0.502 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: 0.8354 (OUTLIER) cc_final: 0.8001 (mm) REVERT: A 140 LYS cc_start: 0.8733 (mttt) cc_final: 0.8426 (ttpp) REVERT: A 199 MET cc_start: 0.9148 (tpp) cc_final: 0.8638 (ttt) REVERT: A 200 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8774 (pp20) REVERT: A 378 ASP cc_start: 0.7990 (t0) cc_final: 0.7506 (t0) REVERT: A 408 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7532 (mmpt) REVERT: A 450 GLU cc_start: 0.8818 (tt0) cc_final: 0.8466 (tp30) REVERT: A 480 LYS cc_start: 0.7103 (tmtt) cc_final: 0.6535 (tmtt) REVERT: A 495 ASN cc_start: 0.9079 (OUTLIER) cc_final: 0.8845 (p0) REVERT: A 587 MET cc_start: 0.7944 (pmm) cc_final: 0.7736 (pmm) REVERT: A 684 ASP cc_start: 0.6737 (OUTLIER) cc_final: 0.6495 (m-30) REVERT: A 890 MET cc_start: 0.8575 (tpp) cc_final: 0.8257 (tpp) REVERT: A 900 MET cc_start: 0.7599 (mpp) cc_final: 0.6902 (mpp) REVERT: A 1005 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.7656 (ttt) REVERT: A 1319 GLN cc_start: 0.8582 (mt0) cc_final: 0.8061 (tm-30) REVERT: A 1431 ASN cc_start: 0.6547 (t0) cc_final: 0.6140 (m-40) REVERT: A 1470 MET cc_start: 0.8684 (tpp) cc_final: 0.8256 (tpp) REVERT: A 1534 CYS cc_start: 0.8014 (OUTLIER) cc_final: 0.7732 (t) REVERT: A 1819 MET cc_start: 0.9210 (tpp) cc_final: 0.8994 (tpp) REVERT: A 1858 ASN cc_start: 0.8139 (p0) cc_final: 0.7722 (p0) REVERT: A 1903 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8203 (tpp) REVERT: A 1929 MET cc_start: 0.8459 (mtm) cc_final: 0.7770 (ptt) REVERT: A 1958 TRP cc_start: 0.6065 (m-90) cc_final: 0.5750 (m-90) REVERT: A 2063 PHE cc_start: 0.8073 (t80) cc_final: 0.7200 (t80) outliers start: 88 outliers final: 62 residues processed: 353 average time/residue: 0.1002 time to fit residues: 56.9456 Evaluate side-chains 354 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 284 time to evaluate : 0.545 ------------------------------------------------------------------------------- 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 150 GLU Chi-restraints excluded: chain A residue 200 GLU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 495 ASN 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 585 PHE Chi-restraints excluded: chain A residue 604 VAL 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 745 LEU 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 995 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 1220 SER 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 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 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 1534 CYS Chi-restraints excluded: chain A residue 1583 ASP Chi-restraints excluded: chain A residue 1589 SER Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 1663 ILE Chi-restraints excluded: chain A residue 1691 LYS 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 1903 MET 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 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 127 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 175 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 105 optimal weight: 9.9990 chunk 24 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 137 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1749 GLN A1982 ASN ** 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 = 0.3873 r_free = 0.3873 target = 0.118623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.092139 restraints weight = 43853.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.095274 restraints weight = 22461.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.097347 restraints weight = 14380.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.098527 restraints weight = 10677.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.099452 restraints weight = 8889.179| |-----------------------------------------------------------------------------| r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.4316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17147 Z= 0.165 Angle : 0.769 17.502 23244 Z= 0.382 Chirality : 0.046 0.326 2662 Planarity : 0.004 0.045 2811 Dihedral : 12.240 143.166 2644 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.20 % Favored : 91.60 % Rotamer: Outliers : 4.08 % Allowed : 27.98 % Favored : 67.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.19), residues: 1989 helix: 0.60 (0.16), residues: 1089 sheet: 0.63 (0.49), residues: 112 loop : -2.07 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 121 TYR 0.047 0.002 TYR A1465 PHE 0.035 0.002 PHE A1748 TRP 0.015 0.001 TRP A 474 HIS 0.004 0.001 HIS A1578 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (17147) covalent geometry : angle 0.76922 / 0.38 (23244) hydrogen bonds : bond 0.03912 / 2.56 ( 856) hydrogen bonds : angle 4.56378 / 3.17 ( 2485) *********************** 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 371 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 296 time to evaluate : 0.545 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: 0.8337 (OUTLIER) cc_final: 0.7984 (mm) REVERT: A 140 LYS cc_start: 0.8727 (mttt) cc_final: 0.8430 (ttpp) REVERT: A 199 MET cc_start: 0.9120 (tpp) cc_final: 0.8658 (ttt) REVERT: A 378 ASP cc_start: 0.7972 (t0) cc_final: 0.7500 (t0) REVERT: A 408 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7547 (mmpt) REVERT: A 450 GLU cc_start: 0.8793 (tt0) cc_final: 0.8444 (tp30) REVERT: A 480 LYS cc_start: 0.7122 (tmtt) cc_final: 0.6543 (tmtt) REVERT: A 495 ASN cc_start: 0.9090 (OUTLIER) cc_final: 0.8874 (p0) REVERT: A 684 ASP cc_start: 0.6666 (OUTLIER) cc_final: 0.6030 (m-30) REVERT: A 822 MET cc_start: 0.9091 (mmt) cc_final: 0.8522 (mmm) REVERT: A 882 ILE cc_start: 0.9415 (mt) cc_final: 0.9209 (mt) REVERT: A 890 MET cc_start: 0.8583 (tpp) cc_final: 0.8250 (tpp) REVERT: A 900 MET cc_start: 0.7597 (mpp) cc_final: 0.6942 (mpp) REVERT: A 1005 MET cc_start: 0.7849 (OUTLIER) cc_final: 0.7610 (ttt) REVERT: A 1068 SER cc_start: 0.9414 (t) cc_final: 0.9184 (m) REVERT: A 1319 GLN cc_start: 0.8556 (mt0) cc_final: 0.8040 (tm-30) REVERT: A 1431 ASN cc_start: 0.6558 (t0) cc_final: 0.6117 (m-40) REVERT: A 1451 MET cc_start: 0.7956 (mtm) cc_final: 0.7627 (mtm) REVERT: A 1534 CYS cc_start: 0.7953 (OUTLIER) cc_final: 0.7698 (t) REVERT: A 1675 TYR cc_start: 0.8716 (t80) cc_final: 0.8288 (t80) REVERT: A 1749 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7841 (tp-100) REVERT: A 1858 ASN cc_start: 0.8161 (p0) cc_final: 0.7748 (p0) REVERT: A 1903 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.7956 (tpp) REVERT: A 1929 MET cc_start: 0.8465 (mtm) cc_final: 0.7794 (ptt) REVERT: A 1958 TRP cc_start: 0.6106 (m-90) cc_final: 0.5712 (m-90) REVERT: A 2063 PHE cc_start: 0.8063 (t80) cc_final: 0.7089 (t80) outliers start: 75 outliers final: 57 residues processed: 344 average time/residue: 0.0975 time to fit residues: 54.5765 Evaluate side-chains 352 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 287 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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 150 GLU Chi-restraints excluded: chain A residue 223 ASP 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 365 CYS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 495 ASN 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 585 PHE Chi-restraints excluded: chain A residue 604 VAL 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 745 LEU 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 995 LEU Chi-restraints excluded: chain A residue 1005 MET Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1031 PHE 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 1245 VAL Chi-restraints excluded: chain A residue 1307 LEU 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 1444 THR Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1475 LYS Chi-restraints excluded: chain A residue 1487 THR Chi-restraints excluded: chain A residue 1534 CYS 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 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 1903 MET 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 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 187 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 174 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 94 optimal weight: 0.7980 chunk 7 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1982 ASN ** 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 = 0.3862 r_free = 0.3862 target = 0.117705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.091441 restraints weight = 43973.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.094551 restraints weight = 22375.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.096649 restraints weight = 14268.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.097925 restraints weight = 10518.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.098894 restraints weight = 8659.510| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.4451 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= 0.178 Angle : 0.791 14.572 23244 Z= 0.395 Chirality : 0.046 0.298 2662 Planarity : 0.004 0.047 2811 Dihedral : 12.271 143.604 2644 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.30 % Favored : 91.50 % Rotamer: Outliers : 3.97 % Allowed : 28.14 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.64 (0.19), residues: 1989 helix: 0.61 (0.16), residues: 1084 sheet: 0.58 (0.49), residues: 112 loop : -2.07 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 328 TYR 0.041 0.002 TYR A1465 PHE 0.047 0.002 PHE A1748 TRP 0.017 0.002 TRP A 474 HIS 0.004 0.001 HIS A1578 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.18 (17147) covalent geometry : angle 0.79130 / 0.39 (23244) hydrogen bonds : bond 0.03934 / 2.58 ( 856) hydrogen bonds : angle 4.57719 / 3.18 ( 2485) ********************** 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 361 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 288 time to evaluate : 0.620 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: 0.8362 (OUTLIER) cc_final: 0.8015 (mm) REVERT: A 140 LYS cc_start: 0.8741 (mttt) cc_final: 0.8447 (ttpp) REVERT: A 199 MET cc_start: 0.9291 (tpp) cc_final: 0.8732 (ttt) REVERT: A 200 GLU cc_start: 0.8806 (pp20) cc_final: 0.8285 (pp20) REVERT: A 378 ASP cc_start: 0.8002 (t0) cc_final: 0.7547 (t0) REVERT: A 408 LYS cc_start: 0.7738 (OUTLIER) cc_final: 0.7538 (mmpt) REVERT: A 450 GLU cc_start: 0.8779 (tt0) cc_final: 0.8482 (tp30) REVERT: A 480 LYS cc_start: 0.7147 (tmtt) cc_final: 0.6559 (tmtt) REVERT: A 495 ASN cc_start: 0.9088 (OUTLIER) cc_final: 0.8857 (p0) REVERT: A 587 MET cc_start: 0.8190 (pmm) cc_final: 0.7970 (pmm) REVERT: A 684 ASP cc_start: 0.6735 (OUTLIER) cc_final: 0.6063 (m-30) REVERT: A 822 MET cc_start: 0.9106 (mmt) cc_final: 0.8587 (mmm) REVERT: A 882 ILE cc_start: 0.9423 (mt) cc_final: 0.9219 (mt) REVERT: A 890 MET cc_start: 0.8639 (tpp) cc_final: 0.8288 (tpp) REVERT: A 900 MET cc_start: 0.7624 (mpp) cc_final: 0.6968 (mpp) REVERT: A 1319 GLN cc_start: 0.8539 (mt0) cc_final: 0.7994 (tm-30) REVERT: A 1431 ASN cc_start: 0.6708 (t0) cc_final: 0.6200 (m-40) REVERT: A 1451 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7711 (mtm) REVERT: A 1475 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8319 (mtpp) REVERT: A 1534 CYS cc_start: 0.7913 (OUTLIER) cc_final: 0.7665 (t) REVERT: A 1660 PRO cc_start: 0.9408 (Cg_exo) cc_final: 0.9107 (Cg_endo) REVERT: A 1675 TYR cc_start: 0.8715 (t80) cc_final: 0.8287 (t80) REVERT: A 1746 MET cc_start: 0.7226 (tmm) cc_final: 0.6550 (ppp) REVERT: A 1749 GLN cc_start: 0.8187 (tp40) cc_final: 0.7483 (tp40) REVERT: A 1819 MET cc_start: 0.9190 (tpp) cc_final: 0.8963 (tpp) REVERT: A 1826 MET cc_start: 0.8087 (mmp) cc_final: 0.7711 (mmm) REVERT: A 1858 ASN cc_start: 0.8199 (p0) cc_final: 0.7804 (p0) REVERT: A 1903 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8000 (tpp) REVERT: A 1929 MET cc_start: 0.8479 (mtm) cc_final: 0.7814 (ptt) REVERT: A 1958 TRP cc_start: 0.6048 (m-90) cc_final: 0.5682 (m-90) REVERT: A 2063 PHE cc_start: 0.8042 (t80) cc_final: 0.7101 (t80) outliers start: 73 outliers final: 59 residues processed: 335 average time/residue: 0.0956 time to fit residues: 52.3074 Evaluate side-chains 343 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 276 time to evaluate : 0.436 ------------------------------------------------------------------------------- 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 150 GLU 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 365 CYS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 495 ASN 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 585 PHE Chi-restraints excluded: chain A residue 604 VAL 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 745 LEU 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 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 1245 VAL Chi-restraints excluded: chain A residue 1307 LEU 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 1444 THR Chi-restraints excluded: chain A residue 1451 MET Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1475 LYS Chi-restraints excluded: chain A residue 1487 THR Chi-restraints excluded: chain A residue 1534 CYS Chi-restraints excluded: chain A residue 1589 SER Chi-restraints excluded: chain A residue 1590 ILE 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 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 1901 LEU Chi-restraints excluded: chain A residue 1903 MET 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 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 136 optimal weight: 0.3980 chunk 74 optimal weight: 8.9990 chunk 7 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 0 optimal weight: 20.0000 chunk 190 optimal weight: 0.9980 chunk 21 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 25 optimal weight: 5.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 HIS A 266 HIS ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2030 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.117400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.091290 restraints weight = 43803.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.094401 restraints weight = 22228.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.096408 restraints weight = 14108.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.097816 restraints weight = 10413.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.098534 restraints weight = 8519.093| |-----------------------------------------------------------------------------| r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4650 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= 0.178 Angle : 0.788 13.816 23244 Z= 0.393 Chirality : 0.046 0.262 2662 Planarity : 0.004 0.048 2811 Dihedral : 12.310 143.792 2644 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.25 % Favored : 91.55 % Rotamer: Outliers : 3.97 % Allowed : 28.25 % Favored : 67.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.19), residues: 1989 helix: 0.64 (0.16), residues: 1084 sheet: 0.69 (0.50), residues: 112 loop : -2.09 (0.22), residues: 793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1597 TYR 0.026 0.002 TYR A 706 PHE 0.038 0.002 PHE A1748 TRP 0.018 0.002 TRP A 474 HIS 0.005 0.001 HIS A1529 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (17147) covalent geometry : angle 0.78750 / 0.39 (23244) hydrogen bonds : bond 0.03945 / 2.60 ( 856) hydrogen bonds : angle 4.59908 / 3.21 ( 2485) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2741.88 seconds wall clock time: 48 minutes 36.28 seconds (2916.28 seconds total)