Starting phenix.real_space_refine on Thu Aug 6 18:54:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ki7_37253/08_2026/8ki7_37253.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ki7_37253/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8ki7_37253/08_2026/8ki7_37253.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ki7_37253/08_2026/8ki7_37253.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ki7_37253/08_2026/8ki7_37253.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ki7_37253/08_2026/8ki7_37253.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 2.41, per 1000 atoms: 0.14 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: 1.18 Conformation dependent library (CDL) restraints added in 586.6 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: 1.81 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: 3.48 Time building geometry restraints manager: 1.55 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: 2362 0.088 - 0.177: 277 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: 0.610 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: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.520 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.370 ------------------------------------------------------------------------------- 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= 0.239 Angle : 1.078 17.974 23244 Z= 0.608 Chirality : 0.058 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 1.07838 / 0.61 (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 : 0.437 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: 0.6533 (m-30) REVERT: A 822 MET cc_start: 0.8598 (mmt) cc_final: 0.8389 (mmm) REVERT: A 833 LEU cc_start: 0.8900 (tp) cc_final: 0.8626 (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: 0.6308 (pt0) REVERT: A 1376 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7872 (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: 0.6857 (pttt) REVERT: A 1992 ASP cc_start: 0.7180 (m-30) cc_final: 0.6887 (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: 0.1088 time to fit residues: 96.2883 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 : 0.470 ------------------------------------------------------------------------------- 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: 0.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 A1628 ASN A1683 ASN A1749 GLN ** A1954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.118304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.091701 restraints weight = 43956.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.094772 restraints weight = 22643.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.096811 restraints weight = 14510.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.098166 restraints weight = 10741.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.098969 restraints weight = 8809.456| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 17147 Z= 0.292 Angle : 0.859 12.639 23244 Z= 0.449 Chirality : 0.049 0.234 2662 Planarity : 0.005 0.070 2811 Dihedral : 12.658 145.492 2678 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.49 % Favored : 92.31 % Rotamer: Outliers : 6.04 % Allowed : 24.28 % Favored : 69.68 % 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: -1.45 (0.18), residues: 1989 helix: -0.13 (0.15), residues: 1071 sheet: 0.54 (0.53), residues: 91 loop : -2.27 (0.20), residues: 827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 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 0.002 HIS A 419 Details of bonding type rmsd/Z covalent geometry : bond 0.00656 / 0.29 (17147) covalent geometry : angle 0.85907 / 0.45 (23244) hydrogen bonds : bond 0.04786 / 3.14 ( 856) hydrogen bonds : angle 4.95903 / 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 455 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 344 time to evaluate : 0.597 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: 0.9178 (tp) cc_final: 0.8922 (mp) REVERT: A 140 LYS cc_start: 0.8755 (mttt) cc_final: 0.8282 (ttpp) REVERT: A 199 MET cc_start: 0.9307 (tpp) cc_final: 0.8809 (ttt) REVERT: A 298 LYS cc_start: 0.9321 (mttt) cc_final: 0.8936 (mmtm) REVERT: A 378 ASP cc_start: 0.7792 (t0) cc_final: 0.7335 (t70) REVERT: A 480 LYS cc_start: 0.7202 (tmtt) cc_final: 0.6824 (tmtt) REVERT: A 584 GLU cc_start: 0.8098 (tt0) cc_final: 0.7889 (pt0) REVERT: A 684 ASP cc_start: 0.6764 (OUTLIER) cc_final: 0.6155 (m-30) REVERT: A 809 TYR cc_start: 0.7006 (OUTLIER) cc_final: 0.6503 (m-80) REVERT: A 882 ILE cc_start: 0.9396 (mt) cc_final: 0.9183 (mt) REVERT: A 982 CYS cc_start: 0.7985 (m) cc_final: 0.7540 (m) REVERT: A 1372 SER cc_start: 0.9001 (p) cc_final: 0.8650 (p) REVERT: A 1376 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7903 (mm) REVERT: A 1398 MET cc_start: 0.7804 (tpp) cc_final: 0.7280 (mtt) REVERT: A 1475 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.7840 (ttmm) REVERT: A 1554 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6519 (mt-10) REVERT: A 1598 LYS cc_start: 0.8052 (OUTLIER) cc_final: 0.7738 (mmmt) REVERT: A 1620 TYR cc_start: 0.6390 (m-80) cc_final: 0.6165 (m-80) REVERT: A 1691 LYS cc_start: 0.9292 (ptmt) cc_final: 0.9006 (ptpp) REVERT: A 1747 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8295 (pttt) REVERT: A 1749 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7501 (mm-40) REVERT: A 1779 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8576 (pt) REVERT: A 1850 MET cc_start: 0.8221 (ttp) cc_final: 0.8019 (ttp) REVERT: A 1903 MET cc_start: 0.8371 (mmp) cc_final: 0.8127 (tpp) REVERT: A 1992 ASP cc_start: 0.8611 (m-30) cc_final: 0.7998 (m-30) outliers start: 111 outliers final: 57 residues processed: 419 average time/residue: 0.0967 time to fit residues: 65.5941 Evaluate side-chains 370 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 306 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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 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 1223 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 74 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 145 optimal weight: 0.0170 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 ASN A 103 HIS A 260 HIS A 358 HIS A 404 HIS ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1074 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.120290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.093887 restraints weight = 44039.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.097027 restraints weight = 22341.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.099120 restraints weight = 14229.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.100294 restraints weight = 10482.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.101378 restraints weight = 8722.594| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 17147 Z= 0.159 Angle : 0.745 11.233 23244 Z= 0.383 Chirality : 0.046 0.222 2662 Planarity : 0.004 0.049 2811 Dihedral : 12.435 142.561 2659 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.34 % Favored : 92.46 % Rotamer: Outliers : 5.28 % Allowed : 25.37 % 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: 1076 sheet: 0.74 (0.54), residues: 96 loop : -2.22 (0.20), residues: 817 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 268 TYR 0.017 0.001 TYR A1465 PHE 0.032 0.002 PHE A1950 TRP 0.026 0.002 TRP A1958 HIS 0.005 0.001 HIS A1578 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (17147) covalent geometry : angle 0.74476 / 0.38 (23244) hydrogen bonds : bond 0.04220 / 2.76 ( 856) hydrogen bonds : angle 4.76774 / 3.30 ( 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 430 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 333 time to evaluate : 0.596 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: A 30 LEU cc_start: 0.9263 (tp) cc_final: 0.8933 (mp) REVERT: A 87 MET cc_start: 0.8067 (mtp) cc_final: 0.7840 (mtp) REVERT: A 140 LYS cc_start: 0.8757 (mttt) cc_final: 0.8188 (tmtt) REVERT: A 150 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.8126 (mt-10) REVERT: A 199 MET cc_start: 0.9318 (tpp) cc_final: 0.8573 (ttt) REVERT: A 200 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8412 (tt0) REVERT: A 298 LYS cc_start: 0.9324 (mttt) cc_final: 0.8757 (pttp) REVERT: A 378 ASP cc_start: 0.7789 (t0) cc_final: 0.7279 (t70) REVERT: A 480 LYS cc_start: 0.7134 (tmtt) cc_final: 0.6657 (tmtt) REVERT: A 677 LEU cc_start: 0.9282 (tp) cc_final: 0.8997 (tt) REVERT: A 684 ASP cc_start: 0.6559 (OUTLIER) cc_final: 0.5936 (m-30) REVERT: A 822 MET cc_start: 0.9108 (mmt) cc_final: 0.8366 (mmm) REVERT: A 882 ILE cc_start: 0.9397 (mt) cc_final: 0.9182 (mt) REVERT: A 900 MET cc_start: 0.7574 (mpp) cc_final: 0.6883 (mpp) REVERT: A 904 ASP cc_start: 0.8031 (m-30) cc_final: 0.7608 (m-30) REVERT: A 1376 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7819 (mt) REVERT: A 1398 MET cc_start: 0.7795 (tpp) cc_final: 0.7191 (mtt) REVERT: A 1470 MET cc_start: 0.8819 (tpp) cc_final: 0.8491 (tpp) REVERT: A 1534 CYS cc_start: 0.7937 (t) cc_final: 0.7598 (t) REVERT: A 1603 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.6942 (mp0) REVERT: A 1622 MET cc_start: 0.7895 (mmm) cc_final: 0.6221 (mmp) REVERT: A 1687 LEU cc_start: 0.8392 (tp) cc_final: 0.8188 (tp) REVERT: A 1691 LYS cc_start: 0.9274 (ptmt) cc_final: 0.9048 (ptpp) REVERT: A 1747 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8304 (pttm) REVERT: A 1748 PHE cc_start: 0.7523 (m-80) cc_final: 0.7059 (m-10) REVERT: A 1749 GLN cc_start: 0.8281 (mm-40) cc_final: 0.7379 (mm-40) REVERT: A 1929 MET cc_start: 0.8486 (mtm) cc_final: 0.7585 (ptt) outliers start: 97 outliers final: 60 residues processed: 398 average time/residue: 0.0956 time to fit residues: 61.6602 Evaluate side-chains 365 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 299 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 200 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 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 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 1199 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 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 1390 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 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: 1.9990 chunk 19 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 146 optimal weight: 0.6980 chunk 66 optimal weight: 0.2980 chunk 84 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 187 optimal weight: 0.2980 chunk 77 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 27 ASN A 38 ASN A 103 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS A 404 HIS A 606 ASN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 ASN A1074 ASN ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.122878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.095397 restraints weight = 44952.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.098681 restraints weight = 23203.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.100817 restraints weight = 14950.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.102209 restraints weight = 11178.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.103006 restraints weight = 9247.203| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.3274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17147 Z= 0.136 Angle : 0.707 10.803 23244 Z= 0.362 Chirality : 0.044 0.283 2662 Planarity : 0.004 0.042 2811 Dihedral : 12.332 142.970 2659 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.34 % Favored : 92.46 % Rotamer: Outliers : 5.44 % Allowed : 25.48 % Favored : 69.08 % 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: -0.93 (0.18), residues: 1989 helix: 0.35 (0.15), residues: 1075 sheet: 0.62 (0.52), residues: 100 loop : -2.12 (0.21), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 580 TYR 0.016 0.001 TYR A1447 PHE 0.029 0.002 PHE A1950 TRP 0.038 0.002 TRP A1958 HIS 0.004 0.001 HIS A1529 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 (17147) covalent geometry : angle 0.70723 / 0.36 (23244) hydrogen bonds : bond 0.03894 / 2.57 ( 856) hydrogen bonds : angle 4.67937 / 3.24 ( 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 441 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 341 time to evaluate : 0.521 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: 0.8220 (mtp) cc_final: 0.7978 (mtp) REVERT: A 114 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8132 (mm) REVERT: A 140 LYS cc_start: 0.8763 (mttt) cc_final: 0.8239 (tmtt) REVERT: A 150 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: A 179 LEU cc_start: 0.7106 (OUTLIER) cc_final: 0.6431 (tt) REVERT: A 199 MET cc_start: 0.9241 (tpp) cc_final: 0.8569 (ttt) REVERT: A 378 ASP cc_start: 0.7748 (t0) cc_final: 0.7349 (t70) REVERT: A 472 MET cc_start: 0.6390 (mpp) cc_final: 0.5695 (tpp) REVERT: A 480 LYS cc_start: 0.7026 (tmtt) cc_final: 0.6568 (tmtt) REVERT: A 684 ASP cc_start: 0.6291 (OUTLIER) cc_final: 0.5717 (m-30) REVERT: A 750 ARG cc_start: 0.8650 (tpp80) cc_final: 0.8426 (tpp80) REVERT: A 767 MET cc_start: 0.5942 (mmt) cc_final: 0.5544 (mmt) REVERT: A 882 ILE cc_start: 0.9388 (mt) cc_final: 0.9169 (mt) REVERT: A 890 MET cc_start: 0.8540 (tpp) cc_final: 0.7709 (tpp) REVERT: A 900 MET cc_start: 0.7325 (mpp) cc_final: 0.7051 (mpp) REVERT: A 1086 GLU cc_start: 0.6051 (mt-10) cc_final: 0.5629 (mt-10) REVERT: A 1305 MET cc_start: 0.9472 (OUTLIER) cc_final: 0.9258 (mtm) REVERT: A 1361 LEU cc_start: 0.8912 (tp) cc_final: 0.8688 (tp) REVERT: A 1376 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7781 (tt) REVERT: A 1398 MET cc_start: 0.7805 (tpp) cc_final: 0.7337 (mtp) REVERT: A 1403 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7982 (tp) REVERT: A 1470 MET cc_start: 0.8696 (tpp) cc_final: 0.8284 (tpp) REVERT: A 1534 CYS cc_start: 0.7914 (t) cc_final: 0.7584 (t) REVERT: A 1598 LYS cc_start: 0.7988 (OUTLIER) cc_final: 0.7734 (mmmt) REVERT: A 1622 MET cc_start: 0.7878 (mmm) cc_final: 0.6509 (mmp) REVERT: A 1675 TYR cc_start: 0.8861 (t80) cc_final: 0.8542 (t80) REVERT: A 1691 LYS cc_start: 0.9291 (ptmt) cc_final: 0.9064 (ptpp) REVERT: A 1747 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.8260 (pttp) REVERT: A 1749 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7408 (mm-40) REVERT: A 1779 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8486 (pt) REVERT: A 1841 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7624 (tmm-80) REVERT: A 1903 MET cc_start: 0.8549 (tpp) cc_final: 0.8283 (tpp) REVERT: A 1929 MET cc_start: 0.8418 (mtm) cc_final: 0.7543 (ptt) REVERT: A 1958 TRP cc_start: 0.5639 (m-90) cc_final: 0.5417 (m-90) outliers start: 100 outliers final: 50 residues processed: 407 average time/residue: 0.1033 time to fit residues: 66.5208 Evaluate side-chains 370 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 309 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 179 LEU 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 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 1305 MET Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1348 TYR Chi-restraints excluded: chain A residue 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 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 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: 7.9990 chunk 93 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 123 optimal weight: 4.9990 chunk 132 optimal weight: 0.0060 chunk 142 optimal weight: 0.8980 chunk 140 optimal weight: 1.9990 chunk 113 optimal weight: 7.9990 chunk 178 optimal weight: 7.9990 chunk 61 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- 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 358 HIS ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 998 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 GLN ** 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 = 0.3916 r_free = 0.3916 target = 0.121542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.095464 restraints weight = 43387.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.098705 restraints weight = 22030.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.100835 restraints weight = 13935.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.102153 restraints weight = 10187.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.103197 restraints weight = 8352.325| |-----------------------------------------------------------------------------| r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3498 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= 0.142 Angle : 0.713 12.693 23244 Z= 0.361 Chirality : 0.044 0.321 2662 Planarity : 0.004 0.041 2811 Dihedral : 12.251 143.680 2655 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.39 % Favored : 92.41 % Rotamer: Outliers : 5.12 % Allowed : 25.64 % 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: -0.77 (0.19), residues: 1989 helix: 0.50 (0.15), residues: 1083 sheet: 0.67 (0.52), residues: 100 loop : -2.12 (0.21), residues: 806 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A1335 TYR 0.018 0.001 TYR A1465 PHE 0.028 0.001 PHE A1950 TRP 0.020 0.001 TRP A1958 HIS 0.003 0.001 HIS A1529 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (17147) covalent geometry : angle 0.71318 / 0.36 (23244) hydrogen bonds : bond 0.03794 / 2.49 ( 856) hydrogen bonds : angle 4.57293 / 3.16 ( 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 418 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 324 time to evaluate : 0.683 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 30 LEU cc_start: 0.9171 (tp) cc_final: 0.8939 (mt) REVERT: A 87 MET cc_start: 0.8251 (mtp) cc_final: 0.8007 (mtp) REVERT: A 114 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8160 (mm) REVERT: A 140 LYS cc_start: 0.8752 (mttt) cc_final: 0.8303 (ttpp) REVERT: A 199 MET cc_start: 0.9188 (tpp) cc_final: 0.8612 (ttt) REVERT: A 298 LYS cc_start: 0.9357 (mttt) cc_final: 0.8854 (pttp) REVERT: A 472 MET cc_start: 0.6715 (mpp) cc_final: 0.5975 (tpp) REVERT: A 480 LYS cc_start: 0.7029 (tmtt) cc_final: 0.6553 (tmtt) REVERT: A 495 ASN cc_start: 0.9075 (OUTLIER) cc_final: 0.8853 (p0) REVERT: A 684 ASP cc_start: 0.6319 (OUTLIER) cc_final: 0.5817 (m-30) REVERT: A 822 MET cc_start: 0.8993 (mmt) cc_final: 0.8394 (mmm) REVERT: A 882 ILE cc_start: 0.9393 (mt) cc_final: 0.9175 (mt) REVERT: A 890 MET cc_start: 0.8535 (tpp) cc_final: 0.8279 (tpp) REVERT: A 900 MET cc_start: 0.7390 (mpp) cc_final: 0.6788 (mpp) REVERT: A 1264 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8116 (mt-10) REVERT: A 1361 LEU cc_start: 0.8881 (tp) cc_final: 0.8670 (tp) REVERT: A 1376 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7755 (tt) REVERT: A 1398 MET cc_start: 0.7813 (tpp) cc_final: 0.7128 (mtp) REVERT: A 1403 LEU cc_start: 0.8401 (OUTLIER) cc_final: 0.7968 (tp) REVERT: A 1431 ASN cc_start: 0.6315 (t0) cc_final: 0.5926 (m-40) REVERT: A 1470 MET cc_start: 0.8679 (tpp) cc_final: 0.8250 (tpp) REVERT: A 1534 CYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7723 (t) REVERT: A 1598 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7684 (mmmt) REVERT: A 1691 LYS cc_start: 0.9296 (ptmt) cc_final: 0.9037 (ptpp) REVERT: A 1723 MET cc_start: 0.8751 (tpp) cc_final: 0.8377 (tpp) REVERT: A 1747 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8271 (pttp) REVERT: A 1749 GLN cc_start: 0.8243 (mm-40) cc_final: 0.7442 (mm-40) REVERT: A 1779 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8446 (pt) REVERT: A 1841 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7530 (tmm-80) REVERT: A 1903 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8181 (tpp) REVERT: A 1929 MET cc_start: 0.8396 (mtm) cc_final: 0.7580 (ptt) REVERT: A 1953 PHE cc_start: 0.7043 (m-80) cc_final: 0.6628 (m-80) REVERT: A 1983 LEU cc_start: 0.5817 (OUTLIER) cc_final: 0.4392 (tt) REVERT: A 1998 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8136 (tp) outliers start: 94 outliers final: 57 residues processed: 386 average time/residue: 0.1160 time to fit residues: 71.6289 Evaluate side-chains 363 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 293 time to evaluate : 0.663 ------------------------------------------------------------------------------- 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 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 442 THR 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 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 768 MET 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 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 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 1596 LEU Chi-restraints excluded: chain A residue 1598 LYS Chi-restraints excluded: chain A residue 1684 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 1903 MET 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 1961 VAL Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1983 LEU Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2061 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 112 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 152 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 168 optimal weight: 0.0970 chunk 158 optimal weight: 0.6980 chunk 100 optimal weight: 3.9990 chunk 147 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.122058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.096050 restraints weight = 43386.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.099288 restraints weight = 21951.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.101279 restraints weight = 13841.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.102799 restraints weight = 10234.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.103752 restraints weight = 8264.162| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17147 Z= 0.136 Angle : 0.712 11.644 23244 Z= 0.359 Chirality : 0.045 0.352 2662 Planarity : 0.004 0.039 2811 Dihedral : 12.193 143.731 2655 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.19 % Favored : 92.61 % Rotamer: Outliers : 4.46 % Allowed : 26.35 % Favored : 69.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.19), residues: 1989 helix: 0.60 (0.16), residues: 1080 sheet: 0.63 (0.52), residues: 100 loop : -2.04 (0.21), residues: 809 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1335 TYR 0.025 0.001 TYR A1465 PHE 0.033 0.002 PHE A2067 TRP 0.048 0.002 TRP A1958 HIS 0.004 0.001 HIS A1529 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (17147) covalent geometry : angle 0.71173 / 0.36 (23244) hydrogen bonds : bond 0.03739 / 2.45 ( 856) hydrogen bonds : angle 4.55238 / 3.15 ( 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 399 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 317 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: A 114 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8020 (mm) REVERT: A 140 LYS cc_start: 0.8709 (mttt) cc_final: 0.8321 (ttpp) REVERT: A 199 MET cc_start: 0.9177 (tpp) cc_final: 0.8702 (ttt) REVERT: A 298 LYS cc_start: 0.9348 (mttt) cc_final: 0.8851 (pttp) REVERT: A 325 TYR cc_start: 0.6855 (m-10) cc_final: 0.6507 (m-10) REVERT: A 472 MET cc_start: 0.6792 (mpp) cc_final: 0.6560 (mpp) REVERT: A 480 LYS cc_start: 0.6996 (tmtt) cc_final: 0.6508 (tmtt) REVERT: A 495 ASN cc_start: 0.9052 (OUTLIER) cc_final: 0.8836 (p0) REVERT: A 587 MET cc_start: 0.8099 (pmm) cc_final: 0.7866 (pmm) REVERT: A 684 ASP cc_start: 0.6375 (OUTLIER) cc_final: 0.5824 (m-30) REVERT: A 767 MET cc_start: 0.6424 (OUTLIER) cc_final: 0.5931 (mmm) REVERT: A 878 LYS cc_start: 0.9304 (tttt) cc_final: 0.9095 (ttpp) REVERT: A 882 ILE cc_start: 0.9404 (mt) cc_final: 0.9192 (mt) REVERT: A 890 MET cc_start: 0.8525 (tpp) cc_final: 0.8268 (tpp) REVERT: A 900 MET cc_start: 0.7371 (mpp) cc_final: 0.6729 (mpp) REVERT: A 1022 ASN cc_start: 0.8071 (m-40) cc_final: 0.7843 (m-40) REVERT: A 1089 GLU cc_start: 0.9048 (mm-30) cc_final: 0.8758 (mm-30) REVERT: A 1335 ARG cc_start: 0.7481 (tpp-160) cc_final: 0.7206 (mmt90) REVERT: A 1376 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7766 (tt) REVERT: A 1403 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.7980 (tp) REVERT: A 1431 ASN cc_start: 0.6312 (t0) cc_final: 0.5910 (m-40) REVERT: A 1470 MET cc_start: 0.8644 (tpp) cc_final: 0.8170 (tpp) REVERT: A 1691 LYS cc_start: 0.9279 (ptmt) cc_final: 0.9070 (ptpp) REVERT: A 1723 MET cc_start: 0.8707 (tpp) cc_final: 0.8377 (tpp) REVERT: A 1747 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8291 (pttp) REVERT: A 1749 GLN cc_start: 0.8189 (mm-40) cc_final: 0.7388 (mm-40) REVERT: A 1819 MET cc_start: 0.9293 (tpp) cc_final: 0.9051 (tpp) REVERT: A 1841 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7515 (tmm-80) REVERT: A 1903 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8182 (tpp) REVERT: A 1929 MET cc_start: 0.8415 (mtm) cc_final: 0.7681 (ptt) REVERT: A 1983 LEU cc_start: 0.5814 (OUTLIER) cc_final: 0.4173 (tt) REVERT: A 2063 PHE cc_start: 0.7862 (t80) cc_final: 0.7149 (t80) outliers start: 82 outliers final: 53 residues processed: 368 average time/residue: 0.1038 time to fit residues: 62.1235 Evaluate side-chains 358 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 295 time to evaluate : 0.509 ------------------------------------------------------------------------------- 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 371 MET Chi-restraints excluded: chain A residue 374 GLN 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 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 767 MET Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 830 VAL Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1058 ILE 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 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 1468 CYS Chi-restraints excluded: chain A residue 1475 LYS Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1747 LYS Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 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 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: 3.9990 chunk 151 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 52 optimal weight: 0.0370 chunk 82 optimal weight: 1.9990 chunk 178 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 overall best weight: 2.0066 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.120356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.093214 restraints weight = 44268.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.096429 restraints weight = 22741.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.098528 restraints weight = 14558.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.099779 restraints weight = 10782.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.100734 restraints weight = 8952.608| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.3912 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= 0.166 Angle : 0.712 12.123 23244 Z= 0.362 Chirality : 0.045 0.325 2662 Planarity : 0.004 0.043 2811 Dihedral : 12.127 145.259 2653 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.34 % Favored : 92.46 % Rotamer: Outliers : 4.79 % Allowed : 26.73 % Favored : 68.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.54 (0.19), residues: 1989 helix: 0.68 (0.16), residues: 1088 sheet: 0.77 (0.49), residues: 112 loop : -2.06 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1597 TYR 0.030 0.002 TYR A1465 PHE 0.029 0.002 PHE A1950 TRP 0.017 0.002 TRP A 474 HIS 0.004 0.001 HIS A1578 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (17147) covalent geometry : angle 0.71240 / 0.36 (23244) hydrogen bonds : bond 0.03805 / 2.49 ( 856) hydrogen bonds : angle 4.50298 / 3.12 ( 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 389 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 301 time to evaluate : 0.401 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: 0.9288 (tp) cc_final: 0.9019 (pp) REVERT: A 114 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7960 (mm) REVERT: A 140 LYS cc_start: 0.8713 (mttt) cc_final: 0.8313 (ttpp) REVERT: A 199 MET cc_start: 0.9219 (tpp) cc_final: 0.8785 (ttt) REVERT: A 325 TYR cc_start: 0.6597 (m-10) cc_final: 0.6221 (m-10) REVERT: A 378 ASP cc_start: 0.7964 (t0) cc_final: 0.7452 (t0) REVERT: A 408 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7499 (mmpt) REVERT: A 450 GLU cc_start: 0.8798 (tt0) cc_final: 0.8422 (tp30) REVERT: A 472 MET cc_start: 0.6892 (mpp) cc_final: 0.6444 (mpp) REVERT: A 480 LYS cc_start: 0.7038 (tmtt) cc_final: 0.6507 (tmtt) REVERT: A 495 ASN cc_start: 0.9089 (OUTLIER) cc_final: 0.8870 (p0) REVERT: A 684 ASP cc_start: 0.6728 (OUTLIER) cc_final: 0.6147 (m-30) REVERT: A 767 MET cc_start: 0.6762 (OUTLIER) cc_final: 0.5854 (mmm) REVERT: A 878 LYS cc_start: 0.9316 (tttt) cc_final: 0.9097 (ttpp) REVERT: A 890 MET cc_start: 0.8586 (tpp) cc_final: 0.8301 (tpp) REVERT: A 900 MET cc_start: 0.7448 (mpp) cc_final: 0.6722 (mpp) REVERT: A 1005 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7662 (ttt) REVERT: A 1319 GLN cc_start: 0.8616 (mt0) cc_final: 0.8076 (tm-30) REVERT: A 1376 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7697 (mt) REVERT: A 1403 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8071 (tp) REVERT: A 1431 ASN cc_start: 0.6519 (t0) cc_final: 0.6020 (m-40) REVERT: A 1451 MET cc_start: 0.7965 (mtm) cc_final: 0.7686 (mtm) REVERT: A 1470 MET cc_start: 0.8620 (tpp) cc_final: 0.8169 (tpp) REVERT: A 1691 LYS cc_start: 0.9287 (ptmt) cc_final: 0.9085 (ptpp) REVERT: A 1723 MET cc_start: 0.8702 (tpp) cc_final: 0.8489 (tpp) REVERT: A 1748 PHE cc_start: 0.7611 (m-10) cc_final: 0.7339 (m-10) REVERT: A 1749 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7565 (mm-40) REVERT: A 1903 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8207 (tpp) REVERT: A 1929 MET cc_start: 0.8492 (mtm) cc_final: 0.7795 (ptt) REVERT: A 1983 LEU cc_start: 0.6093 (OUTLIER) cc_final: 0.4124 (tt) REVERT: A 2063 PHE cc_start: 0.8028 (t80) cc_final: 0.7164 (t80) outliers start: 88 outliers final: 60 residues processed: 357 average time/residue: 0.0955 time to fit residues: 55.4388 Evaluate side-chains 351 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 281 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 442 THR Chi-restraints excluded: chain A residue 495 ASN 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 610 SER Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 670 CYS Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 767 MET Chi-restraints excluded: chain A residue 768 MET 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 881 LEU 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 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 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 1364 LEU 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 1589 SER Chi-restraints excluded: chain A residue 1592 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 1832 THR 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 1983 LEU Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2043 ILE Chi-restraints excluded: chain A residue 2061 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 84 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 183 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 176 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 160 optimal weight: 0.0570 chunk 29 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 overall best weight: 0.7702 ------------------------------------------------------------------------------- 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 ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.121428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.095241 restraints weight = 43584.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.098485 restraints weight = 22107.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.100608 restraints weight = 13929.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.101920 restraints weight = 10195.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.102908 restraints weight = 8371.823| |-----------------------------------------------------------------------------| r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17147 Z= 0.137 Angle : 0.718 13.794 23244 Z= 0.361 Chirality : 0.045 0.347 2662 Planarity : 0.004 0.044 2811 Dihedral : 12.099 143.987 2649 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.49 % Favored : 92.31 % Rotamer: Outliers : 4.41 % Allowed : 27.33 % Favored : 68.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.52 (0.19), residues: 1989 helix: 0.70 (0.16), residues: 1086 sheet: 0.86 (0.50), residues: 112 loop : -2.05 (0.22), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1597 TYR 0.035 0.001 TYR A1465 PHE 0.029 0.001 PHE A1950 TRP 0.012 0.001 TRP A 412 HIS 0.005 0.001 HIS A1529 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (17147) covalent geometry : angle 0.71827 / 0.36 (23244) hydrogen bonds : bond 0.03723 / 2.46 ( 856) hydrogen bonds : angle 4.48176 / 3.11 ( 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 384 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 303 time to evaluate : 0.436 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: 0.9266 (tp) cc_final: 0.9061 (pp) REVERT: A 114 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7862 (mm) REVERT: A 199 MET cc_start: 0.9222 (tpp) cc_final: 0.8741 (ttt) REVERT: A 378 ASP cc_start: 0.7917 (t0) cc_final: 0.7395 (t0) REVERT: A 408 LYS cc_start: 0.7731 (OUTLIER) cc_final: 0.7440 (mmpt) REVERT: A 450 GLU cc_start: 0.8749 (tt0) cc_final: 0.8397 (tp30) REVERT: A 472 MET cc_start: 0.6870 (mpp) cc_final: 0.6612 (mpp) REVERT: A 480 LYS cc_start: 0.6996 (tmtt) cc_final: 0.6464 (tmtt) REVERT: A 495 ASN cc_start: 0.9074 (OUTLIER) cc_final: 0.8847 (p0) REVERT: A 684 ASP cc_start: 0.6550 (OUTLIER) cc_final: 0.6061 (m-30) REVERT: A 890 MET cc_start: 0.8559 (tpp) cc_final: 0.8233 (tpp) REVERT: A 900 MET cc_start: 0.7358 (mpp) cc_final: 0.6669 (mpp) REVERT: A 1005 MET cc_start: 0.7753 (OUTLIER) cc_final: 0.7486 (ttt) REVERT: A 1319 GLN cc_start: 0.8591 (mt0) cc_final: 0.8024 (tm-30) REVERT: A 1431 ASN cc_start: 0.6426 (t0) cc_final: 0.5962 (m-40) REVERT: A 1451 MET cc_start: 0.8034 (mtm) cc_final: 0.7817 (mtm) REVERT: A 1470 MET cc_start: 0.8639 (tpp) cc_final: 0.8279 (tpp) REVERT: A 1819 MET cc_start: 0.9220 (tpp) cc_final: 0.9007 (tpp) REVERT: A 1903 MET cc_start: 0.8527 (OUTLIER) cc_final: 0.8167 (tpp) REVERT: A 1929 MET cc_start: 0.8435 (mtm) cc_final: 0.7804 (ptt) REVERT: A 1983 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.5924 (tt) REVERT: A 2063 PHE cc_start: 0.7995 (t80) cc_final: 0.7142 (t80) outliers start: 81 outliers final: 57 residues processed: 358 average time/residue: 0.0991 time to fit residues: 57.4850 Evaluate side-chains 350 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 286 time to evaluate : 0.488 ------------------------------------------------------------------------------- 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 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 442 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 767 MET Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 992 LEU 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 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 1311 GLU Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1348 TYR Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1364 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1475 LYS Chi-restraints excluded: chain A residue 1487 THR Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1627 VAL 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 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 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: 0.1980 chunk 48 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 195 optimal weight: 0.5980 chunk 105 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 137 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 55 optimal weight: 0.5980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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** A1863 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.121109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.094136 restraints weight = 44104.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.097368 restraints weight = 22513.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.099458 restraints weight = 14375.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.100807 restraints weight = 10669.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.101615 restraints weight = 8785.309| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 17147 Z= 0.151 Angle : 0.733 13.464 23244 Z= 0.370 Chirality : 0.045 0.346 2662 Planarity : 0.004 0.046 2811 Dihedral : 12.064 144.763 2647 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.59 % Favored : 92.21 % Rotamer: Outliers : 3.97 % Allowed : 27.93 % Favored : 68.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.19), residues: 1989 helix: 0.78 (0.16), residues: 1088 sheet: 0.86 (0.49), residues: 112 loop : -2.07 (0.22), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 193 TYR 0.037 0.001 TYR A1465 PHE 0.030 0.002 PHE A1950 TRP 0.042 0.002 TRP A1958 HIS 0.005 0.001 HIS A1529 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (17147) covalent geometry : angle 0.73251 / 0.37 (23244) hydrogen bonds : bond 0.03789 / 2.50 ( 856) hydrogen bonds : angle 4.44901 / 3.09 ( 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 362 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 289 time to evaluate : 0.809 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: 0.9331 (tp) cc_final: 0.9128 (pp) REVERT: A 114 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7912 (mm) REVERT: A 140 LYS cc_start: 0.8720 (mttt) cc_final: 0.8386 (ttpp) REVERT: A 199 MET cc_start: 0.9294 (tpp) cc_final: 0.8776 (ttt) REVERT: A 378 ASP cc_start: 0.7967 (t0) cc_final: 0.7461 (t0) REVERT: A 408 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7487 (mmpt) REVERT: A 450 GLU cc_start: 0.8798 (tt0) cc_final: 0.8464 (tp30) REVERT: A 472 MET cc_start: 0.7062 (mpp) cc_final: 0.6584 (mpp) REVERT: A 480 LYS cc_start: 0.7040 (tmtt) cc_final: 0.6666 (tmtt) REVERT: A 495 ASN cc_start: 0.9108 (OUTLIER) cc_final: 0.8862 (p0) REVERT: A 587 MET cc_start: 0.7969 (pmm) cc_final: 0.7686 (pmm) REVERT: A 684 ASP cc_start: 0.6606 (OUTLIER) cc_final: 0.6160 (m-30) REVERT: A 890 MET cc_start: 0.8588 (tpp) cc_final: 0.8259 (tpp) REVERT: A 900 MET cc_start: 0.7372 (mpp) cc_final: 0.6697 (mpp) REVERT: A 1005 MET cc_start: 0.7678 (OUTLIER) cc_final: 0.7413 (ttt) REVERT: A 1319 GLN cc_start: 0.8593 (mt0) cc_final: 0.8005 (tm-30) REVERT: A 1398 MET cc_start: 0.6870 (mtp) cc_final: 0.6629 (mtt) REVERT: A 1431 ASN cc_start: 0.6661 (t0) cc_final: 0.6126 (m-40) REVERT: A 1903 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8142 (tpp) REVERT: A 1929 MET cc_start: 0.8486 (mtm) cc_final: 0.7807 (ptt) REVERT: A 2063 PHE cc_start: 0.8094 (t80) cc_final: 0.7160 (t80) outliers start: 73 outliers final: 57 residues processed: 337 average time/residue: 0.0980 time to fit residues: 54.3744 Evaluate side-chains 345 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 282 time to evaluate : 0.646 ------------------------------------------------------------------------------- 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 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 442 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 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 767 MET Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 881 LEU Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 992 LEU 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 1216 THR Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1311 GLU Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1348 TYR Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1364 LEU 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 1475 LYS Chi-restraints excluded: chain A residue 1487 THR Chi-restraints excluded: chain A residue 1498 THR Chi-restraints excluded: chain A residue 1589 SER Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 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 1920 LEU Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL 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: 6.9990 chunk 5 optimal weight: 5.9990 chunk 145 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 174 optimal weight: 0.2980 chunk 14 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 7 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 overall best weight: 3.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 HIS ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 HIS A 491 ASN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1863 GLN A2030 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.116063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.089535 restraints weight = 44278.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.092563 restraints weight = 22574.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.094548 restraints weight = 14463.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.095834 restraints weight = 10750.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.096526 restraints weight = 8860.529| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 17147 Z= 0.257 Angle : 0.816 13.024 23244 Z= 0.415 Chirality : 0.048 0.340 2662 Planarity : 0.004 0.050 2811 Dihedral : 12.244 146.927 2645 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.55 % Favored : 91.25 % Rotamer: Outliers : 3.86 % Allowed : 28.42 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.58 (0.19), residues: 1989 helix: 0.66 (0.16), residues: 1103 sheet: 0.78 (0.51), residues: 105 loop : -2.13 (0.22), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1597 TYR 0.016 0.002 TYR A 95 PHE 0.043 0.002 PHE A1849 TRP 0.025 0.002 TRP A1958 HIS 0.008 0.001 HIS A1578 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.26 (17147) covalent geometry : angle 0.81620 / 0.41 (23244) hydrogen bonds : bond 0.04152 / 2.76 ( 856) hydrogen bonds : angle 4.60341 / 3.19 ( 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 355 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 284 time to evaluate : 0.561 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: 0.9359 (tp) cc_final: 0.9121 (pp) REVERT: A 114 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7951 (mm) REVERT: A 140 LYS cc_start: 0.8817 (mttt) cc_final: 0.8483 (ttpp) REVERT: A 199 MET cc_start: 0.9283 (tpp) cc_final: 0.8786 (ttt) REVERT: A 378 ASP cc_start: 0.8032 (t0) cc_final: 0.7581 (t0) REVERT: A 408 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7558 (mmpt) REVERT: A 450 GLU cc_start: 0.8841 (tt0) cc_final: 0.8544 (tp30) REVERT: A 480 LYS cc_start: 0.7241 (tmtt) cc_final: 0.6895 (tmtt) REVERT: A 495 ASN cc_start: 0.9092 (OUTLIER) cc_final: 0.8857 (p0) REVERT: A 587 MET cc_start: 0.8031 (pmm) cc_final: 0.7777 (pmm) REVERT: A 684 ASP cc_start: 0.6845 (OUTLIER) cc_final: 0.6174 (m-30) REVERT: A 900 MET cc_start: 0.7730 (mpp) cc_final: 0.6962 (mpp) REVERT: A 951 MET cc_start: 0.8793 (ttm) cc_final: 0.8579 (ttp) REVERT: A 1319 GLN cc_start: 0.8601 (mt0) cc_final: 0.8050 (tm-30) REVERT: A 1416 ASP cc_start: 0.8571 (p0) cc_final: 0.8227 (p0) REVERT: A 1660 PRO cc_start: 0.9453 (Cg_exo) cc_final: 0.9179 (Cg_endo) REVERT: A 1728 ASN cc_start: 0.8914 (t0) cc_final: 0.8530 (m-40) REVERT: A 1779 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8630 (pt) REVERT: A 1819 MET cc_start: 0.9171 (tpp) cc_final: 0.8940 (tpp) REVERT: A 1826 MET cc_start: 0.8124 (mmp) cc_final: 0.7866 (mmm) REVERT: A 1903 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.7956 (tpp) REVERT: A 1929 MET cc_start: 0.8525 (mtm) cc_final: 0.7780 (ptt) REVERT: A 2063 PHE cc_start: 0.8202 (t80) cc_final: 0.7140 (t80) outliers start: 71 outliers final: 53 residues processed: 329 average time/residue: 0.1015 time to fit residues: 54.3760 Evaluate side-chains 323 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 264 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 208 LYS Chi-restraints excluded: chain A residue 239 MET 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 411 ILE 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 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 767 MET 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 992 LEU Chi-restraints excluded: chain A residue 1023 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 1311 GLU Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1348 TYR Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 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 1498 THR Chi-restraints excluded: chain A residue 1589 SER Chi-restraints excluded: chain A residue 1592 VAL 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 1903 MET Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 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: 0.9990 chunk 74 optimal weight: 0.8980 chunk 7 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 chunk 137 optimal weight: 4.9990 chunk 35 optimal weight: 0.1980 chunk 0 optimal weight: 20.0000 chunk 190 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- 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** ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1615 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.119128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.092949 restraints weight = 43542.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.096110 restraints weight = 22060.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.098236 restraints weight = 13998.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.099504 restraints weight = 10284.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.100518 restraints weight = 8456.308| |-----------------------------------------------------------------------------| r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17147 Z= 0.149 Angle : 0.786 14.664 23244 Z= 0.390 Chirality : 0.046 0.365 2662 Planarity : 0.004 0.048 2811 Dihedral : 12.212 144.003 2643 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.74 % Favored : 92.06 % Rotamer: Outliers : 3.05 % Allowed : 29.83 % Favored : 67.12 % 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: -0.53 (0.19), residues: 1989 helix: 0.69 (0.16), residues: 1088 sheet: 0.96 (0.50), residues: 113 loop : -2.09 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 153 TYR 0.021 0.001 TYR A1675 PHE 0.053 0.002 PHE A 478 TRP 0.017 0.001 TRP A1027 HIS 0.006 0.001 HIS A1529 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (17147) covalent geometry : angle 0.78622 / 0.39 (23244) hydrogen bonds : bond 0.03900 / 2.59 ( 856) hydrogen bonds : angle 4.53912 / 3.16 ( 2485) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2680.60 seconds wall clock time: 47 minutes 29.84 seconds (2849.84 seconds total)