Starting phenix.real_space_refine on Mon Nov 18 15:46:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ki7_37253/11_2024/8ki7_37253.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ki7_37253/11_2024/8ki7_37253.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ki7_37253/11_2024/8ki7_37253.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ki7_37253/11_2024/8ki7_37253.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ki7_37253/11_2024/8ki7_37253.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ki7_37253/11_2024/8ki7_37253.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.064 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 32 5.49 5 S 105 5.16 5 C 10557 2.51 5 N 2801 2.21 5 O 3289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 16784 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 16102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2003, 16102 Classifications: {'peptide': 2003} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 53, 'TRANS': 1949} Chain breaks: 6 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 24 Chain: "E" Number of atoms: 217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 217 Classifications: {'RNA': 10} Modifications used: {'p5*END': 1, 'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 5, 'rna3p_pyr': 2} Link IDs: {'rna2p': 2, 'rna3p': 7} Chain: "B" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 195 Classifications: {'RNA': 9} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 3} Link IDs: {'rna3p': 8} Chain: "F" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 270 Classifications: {'RNA': 13} Modifications used: {'rna2p_pyr': 2, 'rna3p_pur': 4, 'rna3p_pyr': 7} Link IDs: {'rna2p': 1, 'rna3p': 11} Time building chain proxies: 9.53, per 1000 atoms: 0.57 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: 4.48 Conformation dependent library (CDL) restraints added in 2.1 seconds 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3848 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 9 sheets defined 58.7% alpha, 5.4% beta 11 base pairs and 21 stacking pairs defined. Time for finding SS restraints: 5.65 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 4.136A pdb=" N ILE A 10 " --> pdb=" O ILE A 6 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU A 11 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A 12 " --> pdb=" O LYS A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 38 removed outlier: 3.861A pdb=" N ARG A 37 " --> pdb=" O ASP A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 69 removed outlier: 4.414A pdb=" N VAL A 46 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ILE A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 111 Processing helix chain 'A' and resid 125 through 140 Processing helix chain 'A' and resid 147 through 158 removed outlier: 4.173A pdb=" N GLU A 152 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG A 153 " --> pdb=" O ASP A 149 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 210 Processing helix chain 'A' and resid 220 through 224 Processing helix chain 'A' and resid 251 through 258 Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 259 through 268 Processing helix chain 'A' and resid 277 through 281 Processing helix chain 'A' and resid 285 through 307 removed outlier: 3.671A pdb=" N ILE A 299 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N GLU A 302 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 352 through 363 Processing helix chain 'A' and resid 367 through 371 removed outlier: 3.629A pdb=" N THR A 370 " --> pdb=" O HIS A 367 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N MET A 371 " --> pdb=" O ILE A 368 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 371' Processing helix chain 'A' and resid 374 through 390 Processing helix chain 'A' and resid 397 through 413 Processing helix chain 'A' and resid 415 through 432 removed outlier: 3.673A pdb=" N LYS A 432 " --> pdb=" O ARG A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 455 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.606A pdb=" N THR A 466 " --> pdb=" O LEU A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 502 Processing helix chain 'A' and resid 521 through 536 Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.943A pdb=" N GLU A 570 " --> pdb=" O LYS A 567 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TRP A 571 " --> pdb=" O SER A 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 567 through 571' Processing helix chain 'A' and resid 591 through 606 Processing helix chain 'A' and resid 610 through 626 removed outlier: 3.762A pdb=" N LYS A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 682 removed outlier: 3.661A pdb=" N ASN A 682 " --> pdb=" O PHE A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 700 removed outlier: 3.558A pdb=" N VAL A 694 " --> pdb=" O LYS A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 706 removed outlier: 3.837A pdb=" N CYS A 704 " --> pdb=" O ASN A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 729 Processing helix chain 'A' and resid 730 through 748 Processing helix chain 'A' and resid 796 through 804 Processing helix chain 'A' and resid 828 through 837 Processing helix chain 'A' and resid 837 through 853 Proline residue: A 843 - end of helix Processing helix chain 'A' and resid 853 through 863 Processing helix chain 'A' and resid 874 through 893 Processing helix chain 'A' and resid 896 through 908 removed outlier: 3.887A pdb=" N MET A 900 " --> pdb=" O LYS A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 927 Processing helix chain 'A' and resid 937 through 953 Processing helix chain 'A' and resid 991 through 1005 removed outlier: 3.668A pdb=" N LEU A 995 " --> pdb=" O THR A 991 " (cutoff:3.500A) Processing helix chain 'A' and resid 1012 through 1036 Proline residue: A1024 - end of helix removed outlier: 4.114A pdb=" N PHE A1031 " --> pdb=" O TRP A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1060 through 1075 Processing helix chain 'A' and resid 1077 through 1089 Processing helix chain 'A' and resid 1094 through 1097 Processing helix chain 'A' and resid 1098 through 1103 Processing helix chain 'A' and resid 1114 through 1124 Processing helix chain 'A' and resid 1126 through 1130 removed outlier: 3.714A pdb=" N ILE A1130 " --> pdb=" O ILE A1127 " (cutoff:3.500A) Processing helix chain 'A' and resid 1135 through 1151 Processing helix chain 'A' and resid 1151 through 1163 removed outlier: 3.956A pdb=" N LEU A1155 " --> pdb=" O GLU A1151 " (cutoff:3.500A) Processing helix chain 'A' and resid 1165 through 1178 removed outlier: 3.838A pdb=" N LEU A1169 " --> pdb=" O ASN A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1188 through 1195 removed outlier: 3.736A pdb=" N ILE A1193 " --> pdb=" O THR A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1209 removed outlier: 3.968A pdb=" N VAL A1201 " --> pdb=" O HIS A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1222 through 1235 Processing helix chain 'A' and resid 1241 through 1247 removed outlier: 3.662A pdb=" N VAL A1245 " --> pdb=" O ASP A1241 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N MET A1246 " --> pdb=" O LEU A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1258 through 1271 Processing helix chain 'A' and resid 1300 through 1313 Processing helix chain 'A' and resid 1314 through 1320 Processing helix chain 'A' and resid 1331 through 1353 removed outlier: 4.148A pdb=" N ARG A1335 " --> pdb=" O ASP A1331 " (cutoff:3.500A) Processing helix chain 'A' and resid 1377 through 1385 removed outlier: 3.771A pdb=" N VAL A1381 " --> pdb=" O THR A1377 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE A1385 " --> pdb=" O VAL A1381 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1408 Processing helix chain 'A' and resid 1414 through 1428 Processing helix chain 'A' and resid 1434 through 1439 Processing helix chain 'A' and resid 1460 through 1478 Processing helix chain 'A' and resid 1505 through 1513 Processing helix chain 'A' and resid 1517 through 1532 Processing helix chain 'A' and resid 1565 through 1572 Processing helix chain 'A' and resid 1580 through 1598 removed outlier: 3.617A pdb=" N HIS A1591 " --> pdb=" O SER A1587 " (cutoff:3.500A) Processing helix chain 'A' and resid 1604 through 1620 Processing helix chain 'A' and resid 1630 through 1638 Processing helix chain 'A' and resid 1647 through 1651 Processing helix chain 'A' and resid 1657 through 1664 Processing helix chain 'A' and resid 1667 through 1682 Processing helix chain 'A' and resid 1686 through 1696 removed outlier: 4.033A pdb=" N SER A1696 " --> pdb=" O ASP A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1699 through 1714 Processing helix chain 'A' and resid 1717 through 1732 Processing helix chain 'A' and resid 1763 through 1770 removed outlier: 3.671A pdb=" N LEU A1767 " --> pdb=" O ASN A1763 " (cutoff:3.500A) Processing helix chain 'A' and resid 1770 through 1780 Processing helix chain 'A' and resid 1814 through 1829 removed outlier: 3.679A pdb=" N ASN A1829 " --> pdb=" O ILE A1825 " (cutoff:3.500A) Processing helix chain 'A' and resid 1830 through 1835 removed outlier: 3.839A pdb=" N ILE A1835 " --> pdb=" O GLU A1831 " (cutoff:3.500A) Processing helix chain 'A' and resid 1843 through 1850 Processing helix chain 'A' and resid 1867 through 1877 removed outlier: 3.950A pdb=" N ASP A1871 " --> pdb=" O LYS A1867 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS A1877 " --> pdb=" O VAL A1873 " (cutoff:3.500A) Processing helix chain 'A' and resid 1891 through 1904 Processing helix chain 'A' and resid 1910 through 1923 Processing helix chain 'A' and resid 1924 through 1936 Proline residue: A1932 - end of helix Processing helix chain 'A' and resid 1951 through 1965 removed outlier: 4.670A pdb=" N LYS A1957 " --> pdb=" O PHE A1953 " (cutoff:3.500A) Proline residue: A1960 - end of helix Processing helix chain 'A' and resid 1986 through 2008 Processing helix chain 'A' and resid 2018 through 2030 removed outlier: 3.980A pdb=" N ASN A2030 " --> pdb=" O PHE A2026 " (cutoff:3.500A) Processing helix chain 'A' and resid 2031 through 2043 Processing helix chain 'A' and resid 2052 through 2058 removed outlier: 3.775A pdb=" N ARG A2058 " --> pdb=" O THR A2054 " (cutoff:3.500A) Processing helix chain 'A' and resid 2059 through 2066 Processing helix chain 'A' and resid 2067 through 2069 No H-bonds generated for 'chain 'A' and resid 2067 through 2069' Processing sheet with id=AA1, first strand: chain 'A' and resid 167 through 172 removed outlier: 3.587A pdb=" N CYS A 180 " --> pdb=" O TYR A 171 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N PHE A 227 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 181 " --> pdb=" O PHE A 227 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N SER A 229 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 5.694A pdb=" N ILE A 183 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N VAL A 231 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ASP A 185 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N LEU A 233 " --> pdb=" O ASP A 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 214 through 215 Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 509 removed outlier: 6.914A pdb=" N ILE A 821 " --> pdb=" O TYR A 809 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N TYR A 811 " --> pdb=" O ILE A 819 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 819 " --> pdb=" O TYR A 811 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARG A 813 " --> pdb=" O ASN A 817 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASN A 817 " --> pdb=" O ARG A 813 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ALA A 788 " --> pdb=" O MET A 822 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET A 768 " --> pdb=" O LEU A 789 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1109 through 1110 removed outlier: 3.629A pdb=" N GLN A1109 " --> pdb=" O LYS A1219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1295 through 1299 removed outlier: 6.765A pdb=" N VAL A1281 " --> pdb=" O CYS A1412 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1484 through 1486 Processing sheet with id=AA7, first strand: chain 'A' and resid 1484 through 1486 Processing sheet with id=AA8, first strand: chain 'A' and resid 1548 through 1549 Processing sheet with id=AA9, first strand: chain 'A' and resid 1974 through 1975 removed outlier: 6.882A pdb=" N VAL A1974 " --> pdb=" O THR A2083 " (cutoff:3.500A) 832 hydrogen bonds defined for protein. 2433 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 52 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 21 stacking parallelities Total time for adding SS restraints: 7.80 Time building geometry restraints manager: 5.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4123 1.33 - 1.46: 3648 1.46 - 1.58: 9142 1.58 - 1.70: 61 1.70 - 1.82: 173 Bond restraints: 17147 Sorted by residual: bond pdb=" C LEU A 912 " pdb=" N PRO A 913 " ideal model delta sigma weight residual 1.337 1.380 -0.044 9.80e-03 1.04e+04 1.98e+01 bond pdb=" C SER A1965 " pdb=" N PRO A1966 " ideal model delta sigma weight residual 1.334 1.397 -0.063 2.34e-02 1.83e+03 7.20e+00 bond pdb=" CB ILE A1724 " pdb=" CG2 ILE A1724 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.57e+00 bond pdb=" CB GLU A 715 " pdb=" CG GLU A 715 " ideal model delta sigma weight residual 1.520 1.574 -0.054 3.00e-02 1.11e+03 3.28e+00 bond pdb=" CB PHE A2026 " pdb=" CG PHE A2026 " ideal model delta sigma weight residual 1.502 1.542 -0.040 2.30e-02 1.89e+03 2.99e+00 ... (remaining 17142 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 22882 3.59 - 7.19: 294 7.19 - 10.78: 56 10.78 - 14.38: 9 14.38 - 17.97: 3 Bond angle restraints: 23244 Sorted by residual: angle pdb=" N ILE A 299 " pdb=" CA ILE A 299 " pdb=" C ILE A 299 " ideal model delta sigma weight residual 113.71 106.69 7.02 9.50e-01 1.11e+00 5.46e+01 angle pdb=" CB MET A2042 " pdb=" CG MET A2042 " pdb=" SD MET A2042 " ideal model delta sigma weight residual 112.70 130.67 -17.97 3.00e+00 1.11e-01 3.59e+01 angle pdb=" CG1 ILE A 791 " pdb=" CB ILE A 791 " pdb=" CG2 ILE A 791 " ideal model delta sigma weight residual 110.70 93.94 16.76 3.00e+00 1.11e-01 3.12e+01 angle pdb=" N ILE A 555 " pdb=" CA ILE A 555 " pdb=" C ILE A 555 " ideal model delta sigma weight residual 111.48 106.39 5.09 9.40e-01 1.13e+00 2.94e+01 angle pdb=" C PRO A 456 " pdb=" N ASN A 457 " pdb=" CA ASN A 457 " ideal model delta sigma weight residual 122.46 129.73 -7.27 1.41e+00 5.03e-01 2.66e+01 ... (remaining 23239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.40: 9601 26.40 - 52.80: 854 52.80 - 79.20: 88 79.20 - 105.59: 7 105.59 - 131.99: 1 Dihedral angle restraints: 10551 sinusoidal: 4626 harmonic: 5925 Sorted by residual: dihedral pdb=" O4' C F 12 " pdb=" C1' C F 12 " pdb=" N1 C F 12 " pdb=" C2 C F 12 " ideal model delta sinusoidal sigma weight residual 200.00 68.01 131.99 1 1.50e+01 4.44e-03 7.12e+01 dihedral pdb=" CA TYR A1044 " pdb=" C TYR A1044 " pdb=" N PRO A1045 " pdb=" CA PRO A1045 " ideal model delta harmonic sigma weight residual -180.00 -153.31 -26.69 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA GLY A1393 " pdb=" C GLY A1393 " pdb=" N GLU A1394 " pdb=" CA GLU A1394 " ideal model delta harmonic sigma weight residual 180.00 154.75 25.25 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 10548 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 2390 0.088 - 0.177: 249 0.177 - 0.265: 18 0.265 - 0.353: 3 0.353 - 0.441: 2 Chirality restraints: 2662 Sorted by residual: chirality pdb=" CG LEU A1510 " pdb=" CB LEU A1510 " pdb=" CD1 LEU A1510 " pdb=" CD2 LEU A1510 " both_signs ideal model delta sigma weight residual False -2.59 -2.15 -0.44 2.00e-01 2.50e+01 4.87e+00 chirality pdb=" CB ILE A 791 " pdb=" CA ILE A 791 " pdb=" CG1 ILE A 791 " pdb=" CG2 ILE A 791 " both_signs ideal model delta sigma weight residual False 2.64 3.00 -0.36 2.00e-01 2.50e+01 3.21e+00 chirality pdb=" CB ILE A 188 " pdb=" CA ILE A 188 " pdb=" CG1 ILE A 188 " pdb=" CG2 ILE A 188 " both_signs ideal model delta sigma weight residual False 2.64 2.30 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 2659 not shown) Planarity restraints: 2811 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 737 " 0.021 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" CG ASP A 737 " -0.073 2.00e-02 2.50e+03 pdb=" OD1 ASP A 737 " 0.026 2.00e-02 2.50e+03 pdb=" OD2 ASP A 737 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 363 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ASN A 363 " -0.055 2.00e-02 2.50e+03 pdb=" O ASN A 363 " 0.021 2.00e-02 2.50e+03 pdb=" N PHE A 364 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A1738 " -0.015 2.00e-02 2.50e+03 3.03e-02 9.17e+00 pdb=" C ASP A1738 " 0.052 2.00e-02 2.50e+03 pdb=" O ASP A1738 " -0.020 2.00e-02 2.50e+03 pdb=" N SER A1739 " -0.017 2.00e-02 2.50e+03 ... (remaining 2808 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 2098 2.76 - 3.29: 16478 3.29 - 3.83: 29477 3.83 - 4.36: 33137 4.36 - 4.90: 56789 Nonbonded interactions: 137979 Sorted by model distance: nonbonded pdb=" O PHE A2061 " pdb=" OG SER A2065 " model vdw 2.221 3.040 nonbonded pdb=" O MET A 472 " pdb=" OH TYR A 786 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR A1773 " pdb=" O LYS A1785 " model vdw 2.278 3.040 nonbonded pdb=" O GLY A1251 " pdb=" ND2 ASN A1839 " model vdw 2.288 3.120 nonbonded pdb=" OG SER A 477 " pdb=" O LEU A 680 " model vdw 2.291 3.040 ... (remaining 137974 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.470 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: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 44.640 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17147 Z= 0.301 Angle : 1.069 17.974 23244 Z= 0.557 Chirality : 0.056 0.441 2662 Planarity : 0.006 0.075 2811 Dihedral : 18.157 131.992 6703 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.34 % Favored : 92.46 % Rotamer: Outliers : 3.86 % Allowed : 23.19 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.08 (0.17), residues: 1989 helix: -0.89 (0.14), residues: 1050 sheet: 0.55 (0.54), residues: 100 loop : -2.22 (0.20), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 474 HIS 0.014 0.002 HIS A1529 PHE 0.051 0.003 PHE A1234 TYR 0.025 0.002 TYR A1938 ARG 0.015 0.001 ARG A1679 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 541 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ASP cc_start: 0.6885 (m-30) cc_final: 0.6534 (m-30) REVERT: A 822 MET cc_start: 0.8598 (mmt) cc_final: 0.8391 (mmm) REVERT: A 833 LEU cc_start: 0.8900 (tp) cc_final: 0.8627 (tt) REVERT: A 1028 GLU cc_start: 0.6857 (tm-30) cc_final: 0.6653 (tm-30) REVERT: A 1084 GLU cc_start: 0.7024 (pt0) cc_final: 0.6307 (pt0) REVERT: A 1376 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7873 (mt) REVERT: A 1534 CYS cc_start: 0.7585 (t) cc_final: 0.7242 (t) REVERT: A 1728 ASN cc_start: 0.7363 (t0) cc_final: 0.5486 (t0) REVERT: A 1747 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.6856 (pttt) REVERT: A 1992 ASP cc_start: 0.7181 (m-30) cc_final: 0.6886 (m-30) REVERT: A 2063 PHE cc_start: 0.5673 (t80) cc_final: 0.5101 (t80) outliers start: 71 outliers final: 28 residues processed: 581 average time/residue: 0.3093 time to fit residues: 269.6995 Evaluate side-chains 362 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 332 time to evaluate : 1.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 701 ASN Chi-restraints excluded: chain A residue 805 THR Chi-restraints excluded: chain A residue 1058 ILE Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 1661 LEU Chi-restraints excluded: chain A residue 1747 LYS Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1822 VAL Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2061 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 52 optimal weight: 7.9990 chunk 103 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 158 optimal weight: 2.9990 chunk 61 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 103 HIS A 358 HIS A 404 HIS A 697 ASN ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 ASN A1312 HIS A1457 ASN A1683 ASN A1749 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 17147 Z= 0.301 Angle : 0.770 12.390 23244 Z= 0.397 Chirality : 0.047 0.257 2662 Planarity : 0.005 0.062 2811 Dihedral : 12.521 138.829 2678 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.29 % Favored : 92.51 % Rotamer: Outliers : 6.04 % Allowed : 23.95 % Favored : 70.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.18), residues: 1989 helix: 0.06 (0.15), residues: 1069 sheet: 1.03 (0.58), residues: 76 loop : -2.19 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1958 HIS 0.005 0.001 HIS A 404 PHE 0.035 0.002 PHE A 741 TYR 0.027 0.002 TYR A1465 ARG 0.006 0.001 ARG A1294 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 460 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 349 time to evaluate : 2.146 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 205 ASN cc_start: 0.8722 (p0) cc_final: 0.8463 (p0) REVERT: A 378 ASP cc_start: 0.6524 (t0) cc_final: 0.6265 (t70) REVERT: A 684 ASP cc_start: 0.4993 (OUTLIER) cc_final: 0.4746 (m-30) REVERT: A 809 TYR cc_start: 0.6444 (OUTLIER) cc_final: 0.6195 (m-80) REVERT: A 1267 MET cc_start: 0.7606 (mmm) cc_final: 0.7065 (mmt) REVERT: A 1376 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7865 (mt) REVERT: A 1398 MET cc_start: 0.6469 (tpp) cc_final: 0.5779 (mtt) REVERT: A 1534 CYS cc_start: 0.7718 (t) cc_final: 0.7474 (t) REVERT: A 1554 GLU cc_start: 0.6810 (mt-10) cc_final: 0.6086 (mt-10) REVERT: A 1585 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8559 (tt) REVERT: A 1622 MET cc_start: 0.7176 (mmm) cc_final: 0.5719 (mmp) outliers start: 111 outliers final: 56 residues processed: 430 average time/residue: 0.2653 time to fit residues: 181.3484 Evaluate side-chains 357 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 297 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 15 THR Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 473 THR Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 670 CYS Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 684 ASP Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 792 VAL Chi-restraints excluded: chain A residue 809 TYR Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1305 MET Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1348 TYR Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1580 SER Chi-restraints excluded: chain A residue 1585 LEU Chi-restraints excluded: chain A residue 1596 LEU 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 1832 THR Chi-restraints excluded: chain A residue 1880 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1931 ILE Chi-restraints excluded: chain A residue 1955 THR Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2061 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 124 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 198 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 chunk 182 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN A 103 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 358 HIS ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1728 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17147 Z= 0.206 Angle : 0.711 13.067 23244 Z= 0.361 Chirality : 0.044 0.188 2662 Planarity : 0.004 0.051 2811 Dihedral : 12.166 136.270 2653 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 15.82 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.19 % Favored : 92.61 % Rotamer: Outliers : 4.46 % Allowed : 25.48 % Favored : 70.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.18), residues: 1989 helix: 0.26 (0.15), residues: 1089 sheet: 0.48 (0.52), residues: 103 loop : -2.21 (0.21), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A1958 HIS 0.004 0.001 HIS A1529 PHE 0.032 0.002 PHE A1950 TYR 0.014 0.001 TYR A1620 ARG 0.005 0.001 ARG A 899 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 343 time to evaluate : 1.882 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 378 ASP cc_start: 0.6552 (t0) cc_final: 0.6340 (t70) REVERT: A 552 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7409 (pm20) REVERT: A 890 MET cc_start: 0.7634 (tpp) cc_final: 0.7414 (tpp) REVERT: A 1086 GLU cc_start: 0.6163 (mt-10) cc_final: 0.5832 (mt-10) REVERT: A 1267 MET cc_start: 0.7533 (mmm) cc_final: 0.7040 (mmp) REVERT: A 1376 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7662 (mt) REVERT: A 1398 MET cc_start: 0.6435 (tpp) cc_final: 0.5779 (mtp) REVERT: A 1403 LEU cc_start: 0.7965 (mm) cc_final: 0.7512 (tp) REVERT: A 1534 CYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7448 (t) REVERT: A 1585 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8435 (tt) REVERT: A 1748 PHE cc_start: 0.6715 (m-80) cc_final: 0.6470 (m-10) REVERT: A 1841 ARG cc_start: 0.7835 (OUTLIER) cc_final: 0.7564 (tmm-80) REVERT: A 1998 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7334 (tp) outliers start: 82 outliers final: 46 residues processed: 398 average time/residue: 0.2691 time to fit residues: 169.2930 Evaluate side-chains 362 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 310 time to evaluate : 1.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 119 LYS Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 670 CYS Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 753 THR 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 1023 VAL Chi-restraints excluded: chain A residue 1167 LEU Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1348 TYR Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1376 LEU Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1385 ILE Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1411 VAL Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1446 THR Chi-restraints excluded: chain A residue 1451 MET Chi-restraints excluded: chain A residue 1534 CYS Chi-restraints excluded: chain A residue 1585 LEU Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1822 VAL Chi-restraints excluded: chain A residue 1832 THR Chi-restraints excluded: chain A residue 1841 ARG Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1920 LEU Chi-restraints excluded: chain A residue 1948 TYR Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2061 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 5.9990 chunk 138 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 184 optimal weight: 0.0670 chunk 195 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 174 optimal weight: 8.9990 chunk 52 optimal weight: 4.9990 overall best weight: 4.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS A 167 ASN A 266 HIS A 491 ASN A 790 HIS ** A 919 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 ASN ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1628 ASN A1982 ASN ** A2030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 17147 Z= 0.396 Angle : 0.818 11.858 23244 Z= 0.425 Chirality : 0.048 0.216 2662 Planarity : 0.005 0.049 2811 Dihedral : 12.477 143.283 2651 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 18.87 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.60 % Favored : 91.20 % Rotamer: Outliers : 6.70 % Allowed : 24.39 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.19), residues: 1989 helix: 0.42 (0.15), residues: 1094 sheet: 0.35 (0.48), residues: 111 loop : -2.12 (0.21), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 474 HIS 0.006 0.001 HIS A 790 PHE 0.040 0.003 PHE A 741 TYR 0.018 0.002 TYR A 706 ARG 0.008 0.001 ARG A1597 *********************** 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 440 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 317 time to evaluate : 2.173 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 472 MET cc_start: 0.5317 (mpp) cc_final: 0.4978 (mpp) REVERT: A 937 ASP cc_start: 0.7479 (OUTLIER) cc_final: 0.7265 (p0) REVERT: A 1086 GLU cc_start: 0.5500 (mt-10) cc_final: 0.5254 (mt-10) REVERT: A 1335 ARG cc_start: 0.6515 (mpt180) cc_final: 0.6299 (mmt-90) REVERT: A 1398 MET cc_start: 0.6732 (tpp) cc_final: 0.6327 (mtp) REVERT: A 1451 MET cc_start: 0.7680 (mtm) cc_final: 0.7443 (mtm) REVERT: A 1688 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7407 (tm-30) REVERT: A 1850 MET cc_start: 0.8123 (ttp) cc_final: 0.7901 (ttp) REVERT: A 1913 SER cc_start: 0.8444 (OUTLIER) cc_final: 0.8234 (m) REVERT: A 1954 GLN cc_start: 0.7044 (tp40) cc_final: 0.6644 (tp40) REVERT: A 1958 TRP cc_start: 0.4819 (m-90) cc_final: 0.4319 (m-90) outliers start: 123 outliers final: 78 residues processed: 403 average time/residue: 0.2624 time to fit residues: 169.2775 Evaluate side-chains 356 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 275 time to evaluate : 1.839 ------------------------------------------------------------------------------- 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 150 GLU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 320 HIS Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 477 SER Chi-restraints excluded: chain A residue 491 ASN Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 579 THR 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 745 LEU Chi-restraints excluded: chain A residue 784 VAL 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 912 LEU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1062 LEU Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1218 LEU Chi-restraints excluded: chain A residue 1223 VAL Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1281 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 1390 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 1464 VAL Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1487 THR Chi-restraints excluded: chain A residue 1498 THR Chi-restraints excluded: chain A residue 1521 MET Chi-restraints excluded: chain A residue 1580 SER Chi-restraints excluded: chain A residue 1589 SER Chi-restraints excluded: chain A residue 1592 VAL Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1650 MET Chi-restraints excluded: chain A residue 1663 ILE Chi-restraints excluded: chain A residue 1688 GLU Chi-restraints excluded: chain A residue 1720 ASP Chi-restraints excluded: chain A residue 1724 ILE Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1909 ASP Chi-restraints excluded: chain A residue 1913 SER 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 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2073 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 2 optimal weight: 30.0000 chunk 145 optimal weight: 7.9990 chunk 80 optimal weight: 0.6980 chunk 166 optimal weight: 0.4980 chunk 134 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 99 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 103 HIS A 260 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 ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.4370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17147 Z= 0.218 Angle : 0.739 13.006 23244 Z= 0.372 Chirality : 0.045 0.241 2662 Planarity : 0.004 0.045 2811 Dihedral : 12.177 137.336 2645 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 16.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.14 % Favored : 92.66 % Rotamer: Outliers : 5.28 % Allowed : 26.57 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.19), residues: 1989 helix: 0.57 (0.15), residues: 1084 sheet: 0.61 (0.49), residues: 108 loop : -1.98 (0.22), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1958 HIS 0.006 0.001 HIS A1529 PHE 0.032 0.002 PHE A1950 TYR 0.023 0.002 TYR A 325 ARG 0.003 0.000 ARG A 899 *********************** 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 409 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 312 time to evaluate : 2.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 200 GLU cc_start: 0.7836 (pp20) cc_final: 0.6821 (pp20) REVERT: A 273 LEU cc_start: 0.7903 (OUTLIER) cc_final: 0.7613 (mm) REVERT: A 408 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.7121 (mmpt) REVERT: A 472 MET cc_start: 0.4952 (mpp) cc_final: 0.4560 (tpp) REVERT: A 587 MET cc_start: 0.7599 (pmm) cc_final: 0.6923 (pmm) REVERT: A 937 ASP cc_start: 0.7115 (OUTLIER) cc_final: 0.6911 (p0) REVERT: A 1267 MET cc_start: 0.7618 (mmm) cc_final: 0.7211 (mmt) REVERT: A 1398 MET cc_start: 0.6670 (tpp) cc_final: 0.6014 (mtp) REVERT: A 1749 GLN cc_start: 0.7942 (tp-100) cc_final: 0.7284 (tp40) REVERT: A 1913 SER cc_start: 0.8402 (OUTLIER) cc_final: 0.8157 (m) REVERT: A 1998 LEU cc_start: 0.7949 (tp) cc_final: 0.7652 (tp) outliers start: 97 outliers final: 64 residues processed: 376 average time/residue: 0.2666 time to fit residues: 159.4974 Evaluate side-chains 355 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 287 time to evaluate : 1.874 ------------------------------------------------------------------------------- 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 223 ASP Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 273 LEU 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 408 LYS Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 493 ILE Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 670 CYS Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 792 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 937 ASP Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 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 1382 LEU Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1397 LEU Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1583 ASP Chi-restraints excluded: chain A residue 1596 LEU Chi-restraints excluded: chain A residue 1650 MET Chi-restraints excluded: chain A residue 1672 ILE Chi-restraints excluded: chain A residue 1684 LYS Chi-restraints excluded: chain A residue 1724 ILE Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1822 VAL Chi-restraints excluded: chain A residue 1824 ASP Chi-restraints excluded: chain A residue 1865 THR Chi-restraints excluded: chain A residue 1913 SER Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1920 LEU Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 2061 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 114 optimal weight: 0.8980 chunk 48 optimal weight: 0.3980 chunk 195 optimal weight: 4.9990 chunk 162 optimal weight: 0.7980 chunk 90 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 64 optimal weight: 0.4980 chunk 102 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17147 Z= 0.191 Angle : 0.729 13.723 23244 Z= 0.364 Chirality : 0.044 0.211 2662 Planarity : 0.004 0.048 2811 Dihedral : 11.995 136.727 2640 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.89 % Favored : 91.91 % Rotamer: Outliers : 5.06 % Allowed : 27.33 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.19), residues: 1989 helix: 0.55 (0.16), residues: 1088 sheet: 0.60 (0.47), residues: 117 loop : -2.06 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1952 HIS 0.006 0.001 HIS A1529 PHE 0.030 0.002 PHE A2067 TYR 0.021 0.001 TYR A1620 ARG 0.003 0.000 ARG A1597 *********************** 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 407 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 314 time to evaluate : 1.924 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 200 GLU cc_start: 0.7878 (pp20) cc_final: 0.7644 (pp20) REVERT: A 273 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7690 (mm) REVERT: A 378 ASP cc_start: 0.6510 (t0) cc_final: 0.6308 (t70) REVERT: A 408 LYS cc_start: 0.7238 (OUTLIER) cc_final: 0.6965 (mmpt) REVERT: A 472 MET cc_start: 0.4993 (mpp) cc_final: 0.4642 (tpp) REVERT: A 587 MET cc_start: 0.7527 (pmm) cc_final: 0.6968 (pmm) REVERT: A 890 MET cc_start: 0.7680 (tpp) cc_final: 0.7476 (tpp) REVERT: A 937 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6861 (p0) REVERT: A 1262 MET cc_start: 0.6784 (tpp) cc_final: 0.6559 (tpp) REVERT: A 1267 MET cc_start: 0.7747 (mmm) cc_final: 0.6868 (mmt) REVERT: A 1348 TYR cc_start: 0.6017 (OUTLIER) cc_final: 0.5750 (t80) REVERT: A 1585 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8531 (tt) REVERT: A 1687 LEU cc_start: 0.7958 (tp) cc_final: 0.7366 (tp) REVERT: A 1841 ARG cc_start: 0.7823 (OUTLIER) cc_final: 0.7459 (tmm-80) REVERT: A 1998 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7724 (tp) REVERT: A 2063 PHE cc_start: 0.6671 (t80) cc_final: 0.5812 (t80) outliers start: 93 outliers final: 62 residues processed: 373 average time/residue: 0.2637 time to fit residues: 157.9801 Evaluate side-chains 360 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 291 time to evaluate : 2.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 670 CYS Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 766 SER Chi-restraints excluded: chain A residue 784 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 937 ASP Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1310 ILE 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 1397 LEU Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1583 ASP Chi-restraints excluded: chain A residue 1585 LEU Chi-restraints excluded: chain A residue 1672 ILE Chi-restraints excluded: chain A residue 1684 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 1841 ARG Chi-restraints excluded: chain A residue 1865 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 1974 VAL Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2043 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 2.9990 chunk 22 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 142 optimal weight: 0.0470 chunk 110 optimal weight: 10.0000 chunk 164 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 194 optimal weight: 7.9990 chunk 121 optimal weight: 5.9990 chunk 118 optimal weight: 0.7980 chunk 89 optimal weight: 9.9990 overall best weight: 1.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 HIS ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1063 ASN ** A1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1863 GLN ** A2030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 17147 Z= 0.246 Angle : 0.755 12.837 23244 Z= 0.378 Chirality : 0.045 0.223 2662 Planarity : 0.004 0.048 2811 Dihedral : 12.040 139.092 2640 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.09 % Favored : 91.70 % Rotamer: Outliers : 5.01 % Allowed : 27.38 % Favored : 67.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.19), residues: 1989 helix: 0.60 (0.16), residues: 1089 sheet: 0.64 (0.47), residues: 117 loop : -1.89 (0.22), residues: 783 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A1958 HIS 0.005 0.001 HIS A1529 PHE 0.035 0.002 PHE A1748 TYR 0.017 0.001 TYR A1620 ARG 0.006 0.000 ARG A1597 *********************** 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 397 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 305 time to evaluate : 1.837 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 200 GLU cc_start: 0.7950 (pp20) cc_final: 0.7010 (pp20) REVERT: A 273 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7579 (mm) REVERT: A 378 ASP cc_start: 0.6650 (t0) cc_final: 0.6437 (t70) REVERT: A 408 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.7064 (mmpt) REVERT: A 472 MET cc_start: 0.5281 (mpp) cc_final: 0.4893 (mpp) REVERT: A 587 MET cc_start: 0.7552 (pmm) cc_final: 0.7049 (pmm) REVERT: A 937 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6945 (p0) REVERT: A 1267 MET cc_start: 0.7727 (mmm) cc_final: 0.6910 (mmt) REVERT: A 1451 MET cc_start: 0.7227 (mtm) cc_final: 0.6979 (mtm) REVERT: A 1585 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8538 (tt) REVERT: A 1841 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7434 (tmm-80) REVERT: A 1998 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7732 (tp) REVERT: A 2063 PHE cc_start: 0.6774 (t80) cc_final: 0.5858 (t80) outliers start: 92 outliers final: 68 residues processed: 366 average time/residue: 0.2693 time to fit residues: 156.3604 Evaluate side-chains 361 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 287 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 124 VAL 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 273 LEU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 408 LYS Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 616 LEU 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 784 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 906 MET Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1305 MET 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 1468 CYS Chi-restraints excluded: chain A residue 1487 THR Chi-restraints excluded: chain A residue 1585 LEU Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 1663 ILE Chi-restraints excluded: chain A residue 1672 ILE Chi-restraints excluded: chain A residue 1724 ILE Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1822 VAL Chi-restraints excluded: chain A residue 1841 ARG Chi-restraints excluded: chain A residue 1865 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1920 LEU Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 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 120 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 116 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 9.9990 chunk 37 optimal weight: 0.9990 chunk 123 optimal weight: 8.9990 chunk 132 optimal weight: 0.9980 chunk 96 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 153 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.5050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 17147 Z= 0.296 Angle : 0.800 12.927 23244 Z= 0.400 Chirality : 0.046 0.228 2662 Planarity : 0.004 0.049 2811 Dihedral : 12.202 140.440 2640 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.45 % Favored : 91.35 % Rotamer: Outliers : 4.84 % Allowed : 28.09 % Favored : 67.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.19), residues: 1989 helix: 0.59 (0.16), residues: 1091 sheet: 0.41 (0.47), residues: 111 loop : -1.99 (0.22), residues: 787 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A1958 HIS 0.005 0.001 HIS A1578 PHE 0.035 0.002 PHE A 741 TYR 0.018 0.002 TYR A 95 ARG 0.005 0.001 ARG A1597 *********************** 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: 89 poor density : 295 time to evaluate : 1.839 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 200 GLU cc_start: 0.7922 (pp20) cc_final: 0.7042 (pp20) REVERT: A 273 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7559 (mm) REVERT: A 378 ASP cc_start: 0.6694 (t0) cc_final: 0.6477 (t70) REVERT: A 472 MET cc_start: 0.5678 (mpp) cc_final: 0.5421 (mpp) REVERT: A 587 MET cc_start: 0.7636 (pmm) cc_final: 0.7206 (pmm) REVERT: A 684 ASP cc_start: 0.5274 (OUTLIER) cc_final: 0.4657 (m-30) REVERT: A 937 ASP cc_start: 0.7255 (OUTLIER) cc_final: 0.7042 (p0) REVERT: A 1267 MET cc_start: 0.7743 (mmm) cc_final: 0.6966 (mmt) REVERT: A 1748 PHE cc_start: 0.6402 (m-80) cc_final: 0.6153 (m-10) REVERT: A 1826 MET cc_start: 0.7539 (mmt) cc_final: 0.7252 (mmm) REVERT: A 1998 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7879 (tp) outliers start: 89 outliers final: 72 residues processed: 353 average time/residue: 0.2766 time to fit residues: 158.0166 Evaluate side-chains 351 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 275 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 365 CYS Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 616 LEU 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 784 VAL Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 792 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 906 MET Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1110 SER Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1305 MET 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 1365 SER Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1391 THR Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1487 THR Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 1663 ILE Chi-restraints excluded: chain A residue 1672 ILE Chi-restraints excluded: chain A residue 1720 ASP Chi-restraints excluded: chain A residue 1724 ILE Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1822 VAL Chi-restraints excluded: chain A residue 1865 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 1998 LEU Chi-restraints excluded: chain A residue 2043 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 4.9990 chunk 186 optimal weight: 4.9990 chunk 170 optimal weight: 0.0060 chunk 181 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 chunk 55 optimal weight: 8.9990 chunk 163 optimal weight: 0.5980 chunk 171 optimal weight: 6.9990 chunk 180 optimal weight: 2.9990 overall best weight: 1.5202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17147 Z= 0.228 Angle : 0.787 15.679 23244 Z= 0.389 Chirality : 0.046 0.220 2662 Planarity : 0.004 0.050 2811 Dihedral : 12.196 138.310 2640 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.59 % Favored : 92.21 % Rotamer: Outliers : 4.08 % Allowed : 29.12 % Favored : 66.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.19), residues: 1989 helix: 0.53 (0.16), residues: 1096 sheet: 0.41 (0.47), residues: 118 loop : -1.98 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1958 HIS 0.006 0.001 HIS A1529 PHE 0.030 0.002 PHE A1950 TYR 0.019 0.001 TYR A 168 ARG 0.004 0.000 ARG A 899 *********************** 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 380 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 305 time to evaluate : 1.993 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 200 GLU cc_start: 0.7924 (pp20) cc_final: 0.7027 (pp20) REVERT: A 239 MET cc_start: 0.5678 (mmp) cc_final: 0.5473 (mmt) REVERT: A 273 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7538 (mm) REVERT: A 587 MET cc_start: 0.7584 (pmm) cc_final: 0.7170 (pmm) REVERT: A 937 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6785 (p0) REVERT: A 1005 MET cc_start: 0.7343 (ttm) cc_final: 0.7121 (ttt) REVERT: A 1267 MET cc_start: 0.7737 (mmm) cc_final: 0.7031 (mmt) REVERT: A 1451 MET cc_start: 0.7254 (mtm) cc_final: 0.7053 (mtm) REVERT: A 1583 ASP cc_start: 0.6537 (t0) cc_final: 0.6288 (t0) REVERT: A 1748 PHE cc_start: 0.6245 (m-80) cc_final: 0.6003 (m-10) REVERT: A 1826 MET cc_start: 0.7526 (mmt) cc_final: 0.7049 (mmm) REVERT: A 1841 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7511 (tmm-80) REVERT: A 1954 GLN cc_start: 0.6834 (tp40) cc_final: 0.6555 (tp40) REVERT: A 1958 TRP cc_start: 0.4727 (m-90) cc_final: 0.4407 (m-90) outliers start: 75 outliers final: 65 residues processed: 356 average time/residue: 0.2725 time to fit residues: 154.0423 Evaluate side-chains 355 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 287 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 616 LEU 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 784 VAL Chi-restraints excluded: chain A residue 789 LEU 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 906 MET Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 995 LEU Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1201 VAL Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1260 LEU Chi-restraints excluded: chain A residue 1305 MET 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 1444 THR Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1487 THR Chi-restraints excluded: chain A residue 1627 VAL Chi-restraints excluded: chain A residue 1672 ILE Chi-restraints excluded: chain A residue 1724 ILE Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1770 MET Chi-restraints excluded: chain A residue 1779 LEU Chi-restraints excluded: chain A residue 1822 VAL Chi-restraints excluded: chain A residue 1841 ARG Chi-restraints excluded: chain A residue 1865 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1931 ILE Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 2043 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 133 optimal weight: 0.3980 chunk 201 optimal weight: 20.0000 chunk 185 optimal weight: 0.0870 chunk 160 optimal weight: 0.5980 chunk 16 optimal weight: 5.9990 chunk 123 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.5327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 17147 Z= 0.218 Angle : 0.801 14.065 23244 Z= 0.393 Chirality : 0.045 0.210 2662 Planarity : 0.004 0.050 2811 Dihedral : 12.183 138.074 2640 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.64 % Favored : 92.21 % Rotamer: Outliers : 3.59 % Allowed : 30.32 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.19), residues: 1989 helix: 0.51 (0.16), residues: 1094 sheet: 0.38 (0.47), residues: 119 loop : -1.94 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A1958 HIS 0.006 0.001 HIS A1529 PHE 0.029 0.002 PHE A1950 TYR 0.039 0.001 TYR A1675 ARG 0.005 0.000 ARG A 153 ********************** 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 370 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 304 time to evaluate : 2.119 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 200 GLU cc_start: 0.7845 (pp20) cc_final: 0.6966 (pp20) REVERT: A 273 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7414 (mm) REVERT: A 493 ILE cc_start: 0.8182 (mm) cc_final: 0.7971 (mm) REVERT: A 587 MET cc_start: 0.7499 (pmm) cc_final: 0.7097 (pmm) REVERT: A 937 ASP cc_start: 0.7048 (OUTLIER) cc_final: 0.6845 (p0) REVERT: A 994 ASP cc_start: 0.7351 (m-30) cc_final: 0.7136 (m-30) REVERT: A 1005 MET cc_start: 0.7336 (ttm) cc_final: 0.7133 (ttt) REVERT: A 1348 TYR cc_start: 0.5891 (OUTLIER) cc_final: 0.5545 (t80) REVERT: A 1398 MET cc_start: 0.5551 (mtp) cc_final: 0.5300 (mtt) REVERT: A 1451 MET cc_start: 0.7219 (mtm) cc_final: 0.6949 (mtm) REVERT: A 1826 MET cc_start: 0.7400 (mmt) cc_final: 0.7075 (mmm) REVERT: A 1841 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7703 (tmm-80) outliers start: 66 outliers final: 56 residues processed: 348 average time/residue: 0.2693 time to fit residues: 149.3227 Evaluate side-chains 344 residues out of total 1848 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 284 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 150 GLU Chi-restraints excluded: chain A residue 223 ASP Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 316 VAL Chi-restraints excluded: chain A residue 333 ILE Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 356 ILE Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 474 TRP Chi-restraints excluded: chain A residue 534 LEU Chi-restraints excluded: chain A residue 562 VAL Chi-restraints excluded: chain A residue 566 LYS Chi-restraints excluded: chain A residue 571 TRP Chi-restraints excluded: chain A residue 585 PHE Chi-restraints excluded: chain A residue 604 VAL Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 610 SER Chi-restraints excluded: chain A residue 654 HIS Chi-restraints excluded: chain A residue 670 CYS Chi-restraints excluded: chain A residue 681 HIS Chi-restraints excluded: chain A residue 784 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 906 MET Chi-restraints excluded: chain A residue 912 LEU Chi-restraints excluded: chain A residue 937 ASP Chi-restraints excluded: chain A residue 1023 VAL Chi-restraints excluded: chain A residue 1031 PHE Chi-restraints excluded: chain A residue 1107 CYS Chi-restraints excluded: chain A residue 1144 LEU Chi-restraints excluded: chain A residue 1216 THR Chi-restraints excluded: chain A residue 1220 SER Chi-restraints excluded: chain A residue 1237 MET Chi-restraints excluded: chain A residue 1245 VAL Chi-restraints excluded: chain A residue 1307 LEU Chi-restraints excluded: chain A residue 1311 GLU Chi-restraints excluded: chain A residue 1339 THR Chi-restraints excluded: chain A residue 1348 TYR Chi-restraints excluded: chain A residue 1359 SER Chi-restraints excluded: chain A residue 1382 LEU Chi-restraints excluded: chain A residue 1444 THR Chi-restraints excluded: chain A residue 1464 VAL Chi-restraints excluded: chain A residue 1468 CYS Chi-restraints excluded: chain A residue 1487 THR 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 1841 ARG Chi-restraints excluded: chain A residue 1865 THR Chi-restraints excluded: chain A residue 1917 CYS Chi-restraints excluded: chain A residue 1931 ILE Chi-restraints excluded: chain A residue 1950 PHE Chi-restraints excluded: chain A residue 1961 VAL Chi-restraints excluded: chain A residue 1974 VAL Chi-restraints excluded: chain A residue 2043 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 6.9990 chunk 170 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 147 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 160 optimal weight: 0.0870 chunk 67 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 ASN ** A1059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1316 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1615 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2030 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.117096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.089758 restraints weight = 44744.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.092835 restraints weight = 22933.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.094889 restraints weight = 14782.329| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.5495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17147 Z= 0.266 Angle : 0.808 14.227 23244 Z= 0.398 Chirality : 0.046 0.207 2662 Planarity : 0.004 0.049 2811 Dihedral : 12.222 140.077 2640 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.20 % Favored : 91.65 % Rotamer: Outliers : 3.59 % Allowed : 30.76 % Favored : 65.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.19), residues: 1989 helix: 0.52 (0.16), residues: 1095 sheet: 0.36 (0.48), residues: 120 loop : -2.03 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1952 HIS 0.008 0.001 HIS A1466 PHE 0.030 0.002 PHE A1950 TYR 0.040 0.002 TYR A1675 ARG 0.005 0.000 ARG A 153 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3767.50 seconds wall clock time: 70 minutes 14.36 seconds (4214.36 seconds total)