Starting phenix.real_space_refine on Sat Jun 14 13:37:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dg7_27417/06_2025/8dg7_27417.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dg7_27417/06_2025/8dg7_27417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dg7_27417/06_2025/8dg7_27417.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dg7_27417/06_2025/8dg7_27417.map" model { file = "/net/cci-nas-00/data/ceres_data/8dg7_27417/06_2025/8dg7_27417.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dg7_27417/06_2025/8dg7_27417.cif" } resolution = 3.32 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= 0.000 sd= 0.035 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 47 5.49 5 Mg 8 5.21 5 S 81 5.16 5 C 9722 2.51 5 N 2738 2.21 5 O 3013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 15609 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 13175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1635, 13175 Classifications: {'peptide': 1635} Link IDs: {'PTRANS': 98, 'TRANS': 1536} Chain breaks: 14 Chain: "E" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 456 Classifications: {'RNA': 21} Modifications used: {'rna3p_pur': 14, 'rna3p_pyr': 7} Link IDs: {'rna3p': 20} Chain: "F" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 532 Classifications: {'RNA': 26} Modifications used: {'5*END': 1, 'rna3p_pur': 8, 'rna3p_pyr': 17} Link IDs: {'rna3p': 25} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1417 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 175} Chain breaks: 2 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 24 Unusual residues: {' MG': 3, 'U5P%rna2p': 1} Classifications: {'RNA_mixed': 1, 'undetermined': 3} Modifications used: {'rna2p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.29, per 1000 atoms: 0.60 Number of scatterers: 15609 At special positions: 0 Unit cell: (155.21, 126.99, 146.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 81 16.00 P 47 15.00 Mg 8 11.99 O 3013 8.00 N 2738 7.00 C 9722 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.01 Conformation dependent library (CDL) restraints added in 2.6 seconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3468 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 16 sheets defined 47.7% alpha, 9.9% beta 19 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 7.77 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 Processing helix chain 'A' and resid 39 through 59 Processing helix chain 'A' and resid 79 through 88 removed outlier: 3.607A pdb=" N THR A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 88 " --> pdb=" O MET A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.817A pdb=" N ASP A 110 " --> pdb=" O CYS A 107 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR A 111 " --> pdb=" O TRP A 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 107 through 111' Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 145 through 158 Proline residue: A 154 - end of helix removed outlier: 3.867A pdb=" N ASN A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 200 Processing helix chain 'A' and resid 232 through 251 removed outlier: 3.848A pdb=" N SER A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 293 removed outlier: 4.390A pdb=" N LEU A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU A 287 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 288 " --> pdb=" O ASN A 284 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 313 removed outlier: 3.860A pdb=" N HIS A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 346 removed outlier: 3.501A pdb=" N ARG A 345 " --> pdb=" O HIS A 341 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS A 346 " --> pdb=" O ALA A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 362 through 375 removed outlier: 3.511A pdb=" N ARG A 366 " --> pdb=" O SER A 362 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N PHE A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 519 removed outlier: 3.564A pdb=" N ALA A 505 " --> pdb=" O GLN A 501 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ARG A 506 " --> pdb=" O ASN A 502 " (cutoff:3.500A) Processing helix chain 'A' and resid 540 through 560 removed outlier: 3.620A pdb=" N ALA A 544 " --> pdb=" O GLU A 540 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU A 553 " --> pdb=" O ARG A 549 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N MET A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.763A pdb=" N GLU A 573 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 598 Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 760 through 784 Processing helix chain 'A' and resid 791 through 802 removed outlier: 3.633A pdb=" N GLN A 795 " --> pdb=" O PRO A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 827 removed outlier: 3.876A pdb=" N ILE A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 904 Processing helix chain 'A' and resid 931 through 941 removed outlier: 4.262A pdb=" N ILE A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 1046 through 1062 removed outlier: 3.777A pdb=" N VAL A1050 " --> pdb=" O SER A1046 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN A1057 " --> pdb=" O ASN A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1108 removed outlier: 3.721A pdb=" N ASN A1108 " --> pdb=" O LEU A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1124 removed outlier: 3.854A pdb=" N ARG A1121 " --> pdb=" O PRO A1117 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN A1124 " --> pdb=" O GLU A1120 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1179 Processing helix chain 'A' and resid 1220 through 1230 Processing helix chain 'A' and resid 1238 through 1240 No H-bonds generated for 'chain 'A' and resid 1238 through 1240' Processing helix chain 'A' and resid 1248 through 1257 Processing helix chain 'A' and resid 1257 through 1282 removed outlier: 3.691A pdb=" N ILE A1261 " --> pdb=" O CYS A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1526 through 1548 removed outlier: 3.933A pdb=" N GLN A1533 " --> pdb=" O LEU A1529 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A1540 " --> pdb=" O ASN A1536 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A1541 " --> pdb=" O ALA A1537 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A1543 " --> pdb=" O GLU A1539 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLN A1544 " --> pdb=" O ARG A1540 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A1546 " --> pdb=" O TYR A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1567 through 1581 Processing helix chain 'A' and resid 1607 through 1616 Processing helix chain 'A' and resid 1624 through 1629 Processing helix chain 'A' and resid 1635 through 1650 Processing helix chain 'A' and resid 1722 through 1731 Processing helix chain 'A' and resid 1732 through 1736 removed outlier: 3.735A pdb=" N ASN A1736 " --> pdb=" O SER A1733 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1764 removed outlier: 3.894A pdb=" N THR A1746 " --> pdb=" O GLU A1742 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE A1747 " --> pdb=" O ARG A1743 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER A1750 " --> pdb=" O THR A1746 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N TYR A1764 " --> pdb=" O LEU A1760 " (cutoff:3.500A) Processing helix chain 'A' and resid 1768 through 1781 removed outlier: 3.604A pdb=" N LEU A1772 " --> pdb=" O HIS A1768 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N HIS A1774 " --> pdb=" O GLY A1770 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA A1781 " --> pdb=" O SER A1777 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1792 Processing helix chain 'A' and resid 1819 through 1824 removed outlier: 3.601A pdb=" N LEU A1824 " --> pdb=" O LEU A1820 " (cutoff:3.500A) Processing helix chain 'A' and resid 1836 through 1844 Processing helix chain 'A' and resid 1847 through 1854 Processing helix chain 'A' and resid 1900 through 1931 Proline residue: A1920 - end of helix Processing helix chain 'A' and resid 1981 through 1990 Processing helix chain 'A' and resid 1993 through 1999 Processing helix chain 'A' and resid 2007 through 2015 Processing helix chain 'A' and resid 2028 through 2049 removed outlier: 3.745A pdb=" N LEU A2034 " --> pdb=" O ARG A2030 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA A2037 " --> pdb=" O PHE A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2056 through 2065 removed outlier: 3.691A pdb=" N LEU A2062 " --> pdb=" O ALA A2058 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG A2063 " --> pdb=" O LEU A2059 " (cutoff:3.500A) Processing helix chain 'A' and resid 2068 through 2079 Processing helix chain 'A' and resid 2081 through 2085 removed outlier: 3.646A pdb=" N PHE A2085 " --> pdb=" O HIS A2082 " (cutoff:3.500A) Processing helix chain 'A' and resid 2089 through 2106 Processing helix chain 'A' and resid 2131 through 2149 removed outlier: 3.673A pdb=" N ALA A2142 " --> pdb=" O PHE A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2152 through 2174 removed outlier: 4.108A pdb=" N VAL A2156 " --> pdb=" O SER A2152 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ASN A2162 " --> pdb=" O HIS A2158 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N MET A2163 " --> pdb=" O VAL A2159 " (cutoff:3.500A) Proline residue: A2166 - end of helix removed outlier: 3.650A pdb=" N SER A2174 " --> pdb=" O GLN A2170 " (cutoff:3.500A) Processing helix chain 'A' and resid 2178 through 2186 Processing helix chain 'A' and resid 2223 through 2239 Processing helix chain 'K' and resid 135 through 145 Processing helix chain 'K' and resid 146 through 148 No H-bonds generated for 'chain 'K' and resid 146 through 148' Processing helix chain 'K' and resid 188 through 205 Processing helix chain 'K' and resid 359 through 373 Processing helix chain 'K' and resid 376 through 385 removed outlier: 4.027A pdb=" N LEU K 380 " --> pdb=" O GLY K 376 " (cutoff:3.500A) Processing helix chain 'K' and resid 393 through 405 removed outlier: 3.790A pdb=" N LEU K 397 " --> pdb=" O ASP K 393 " (cutoff:3.500A) Processing helix chain 'K' and resid 443 through 462 Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 66 removed outlier: 5.975A pdb=" N VAL A 64 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU A 137 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 583 through 586 removed outlier: 6.351A pdb=" N VAL A 584 " --> pdb=" O VAL A 611 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU A 613 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ARG A 586 " --> pdb=" O LEU A 613 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS A 610 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N VAL A1585 " --> pdb=" O GLU A 221 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ILE A 223 " --> pdb=" O VAL A1585 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA4, first strand: chain 'A' and resid 849 through 855 Processing sheet with id=AA5, first strand: chain 'A' and resid 952 through 956 Processing sheet with id=AA6, first strand: chain 'A' and resid 1022 through 1026 removed outlier: 6.709A pdb=" N GLU A1030 " --> pdb=" O GLN A 984 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1022 through 1026 removed outlier: 6.709A pdb=" N GLU A1030 " --> pdb=" O GLN A 984 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N PHE A1008 " --> pdb=" O ILE A 979 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N LEU A 981 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 10.912A pdb=" N GLN A1006 " --> pdb=" O LEU A 981 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1072 through 1073 removed outlier: 3.626A pdb=" N LEU A1072 " --> pdb=" O TYR A1815 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1136 through 1138 removed outlier: 3.542A pdb=" N MET A1137 " --> pdb=" O THR A1243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1153 through 1155 removed outlier: 4.149A pdb=" N GLN A1235 " --> pdb=" O VAL A1194 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1937 through 1941 removed outlier: 3.690A pdb=" N VAL A1964 " --> pdb=" O THR A1938 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 2197 through 2198 removed outlier: 3.665A pdb=" N GLU A2197 " --> pdb=" O ARG A2206 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 2209 through 2211 Processing sheet with id=AB5, first strand: chain 'K' and resid 152 through 155 removed outlier: 4.184A pdb=" N GLY K 152 " --> pdb=" O SER K 172 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 152 through 155 removed outlier: 4.184A pdb=" N GLY K 152 " --> pdb=" O SER K 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'K' and resid 409 through 414 removed outlier: 4.759A pdb=" N GLN K 424 " --> pdb=" O ILE K 414 " (cutoff:3.500A) 654 hydrogen bonds defined for protein. 1905 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 7.66 Time building geometry restraints manager: 4.68 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: 4293 1.33 - 1.46: 4242 1.46 - 1.59: 7304 1.59 - 1.71: 85 1.71 - 1.84: 110 Bond restraints: 16034 Sorted by residual: bond pdb=" O5' U5P E 101 " pdb=" P U5P E 101 " ideal model delta sigma weight residual 1.711 1.589 0.122 2.00e-02 2.50e+03 3.70e+01 bond pdb=" CG PRO A 78 " pdb=" CD PRO A 78 " ideal model delta sigma weight residual 1.503 1.414 0.089 3.40e-02 8.65e+02 6.92e+00 bond pdb=" C GLY A 879 " pdb=" N LEU A 880 " ideal model delta sigma weight residual 1.331 1.279 0.052 2.07e-02 2.33e+03 6.24e+00 bond pdb=" CB PRO A 78 " pdb=" CG PRO A 78 " ideal model delta sigma weight residual 1.492 1.615 -0.123 5.00e-02 4.00e+02 6.06e+00 bond pdb=" C SER A 871 " pdb=" N PRO A 872 " ideal model delta sigma weight residual 1.331 1.351 -0.019 7.90e-03 1.60e+04 5.96e+00 ... (remaining 16029 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.30: 21699 4.30 - 8.60: 209 8.60 - 12.91: 31 12.91 - 17.21: 4 17.21 - 21.51: 2 Bond angle restraints: 21945 Sorted by residual: angle pdb=" CA PRO A 78 " pdb=" N PRO A 78 " pdb=" CD PRO A 78 " ideal model delta sigma weight residual 112.00 98.76 13.24 1.40e+00 5.10e-01 8.95e+01 angle pdb=" CA LEU A1177 " pdb=" CB LEU A1177 " pdb=" CG LEU A1177 " ideal model delta sigma weight residual 116.30 137.81 -21.51 3.50e+00 8.16e-02 3.78e+01 angle pdb=" CA LEU A1642 " pdb=" CB LEU A1642 " pdb=" CG LEU A1642 " ideal model delta sigma weight residual 116.30 136.89 -20.59 3.50e+00 8.16e-02 3.46e+01 angle pdb=" C LEU A 116 " pdb=" N ARG A 117 " pdb=" CA ARG A 117 " ideal model delta sigma weight residual 122.38 139.17 -16.79 2.90e+00 1.19e-01 3.35e+01 angle pdb=" N PHE A2171 " pdb=" CA PHE A2171 " pdb=" CB PHE A2171 " ideal model delta sigma weight residual 110.28 119.13 -8.85 1.55e+00 4.16e-01 3.26e+01 ... (remaining 21940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 8203 17.80 - 35.59: 1140 35.59 - 53.39: 350 53.39 - 71.18: 92 71.18 - 88.98: 27 Dihedral angle restraints: 9812 sinusoidal: 4477 harmonic: 5335 Sorted by residual: dihedral pdb=" CA ALA A 606 " pdb=" C ALA A 606 " pdb=" N PRO A 607 " pdb=" CA PRO A 607 " ideal model delta harmonic sigma weight residual 180.00 125.96 54.04 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" CA THR A1654 " pdb=" C THR A1654 " pdb=" N TYR A1655 " pdb=" CA TYR A1655 " ideal model delta harmonic sigma weight residual -180.00 -144.64 -35.36 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" CA MET K 462 " pdb=" C MET K 462 " pdb=" N THR K 463 " pdb=" CA THR K 463 " ideal model delta harmonic sigma weight residual 180.00 150.23 29.77 0 5.00e+00 4.00e-02 3.55e+01 ... (remaining 9809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2332 0.104 - 0.208: 151 0.208 - 0.313: 11 0.313 - 0.417: 2 0.417 - 0.521: 1 Chirality restraints: 2497 Sorted by residual: chirality pdb=" CB ILE A2180 " pdb=" CA ILE A2180 " pdb=" CG1 ILE A2180 " pdb=" CG2 ILE A2180 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.79e+00 chirality pdb=" CG LEU A 50 " pdb=" CB LEU A 50 " pdb=" CD1 LEU A 50 " pdb=" CD2 LEU A 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CG LEU A2075 " pdb=" CB LEU A2075 " pdb=" CD1 LEU A2075 " pdb=" CD2 LEU A2075 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 2494 not shown) Planarity restraints: 2661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 77 " 0.105 5.00e-02 4.00e+02 1.48e-01 3.50e+01 pdb=" N PRO A 78 " -0.255 5.00e-02 4.00e+02 pdb=" CA PRO A 78 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO A 78 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 164 " 0.070 5.00e-02 4.00e+02 1.04e-01 1.75e+01 pdb=" N PRO A 165 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 362 " -0.061 5.00e-02 4.00e+02 9.18e-02 1.35e+01 pdb=" N PRO A 363 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 363 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 363 " -0.050 5.00e-02 4.00e+02 ... (remaining 2658 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 169 2.56 - 3.15: 11613 3.15 - 3.73: 26136 3.73 - 4.32: 33915 4.32 - 4.90: 55045 Nonbonded interactions: 126878 Sorted by model distance: nonbonded pdb=" OE2 GLU A1745 " pdb="MG MG A2301 " model vdw 1.980 2.170 nonbonded pdb=" OE2 GLU A1908 " pdb="MG MG A2302 " model vdw 1.995 2.170 nonbonded pdb=" OP1 C F 39 " pdb="MG MG A2301 " model vdw 2.001 2.170 nonbonded pdb="MG MG A2304 " pdb=" O1P U5P E 101 " model vdw 2.024 2.170 nonbonded pdb=" OD1 ASP A1749 " pdb="MG MG A2302 " model vdw 2.034 2.170 ... (remaining 126873 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 30.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.770 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 44.790 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 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 : 0.007 0.123 16035 Z= 0.288 Angle : 1.111 21.512 21945 Z= 0.554 Chirality : 0.056 0.521 2497 Planarity : 0.009 0.148 2661 Dihedral : 18.481 88.981 6344 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.65 % Favored : 91.24 % Rotamer: Outliers : 1.24 % Allowed : 31.43 % Favored : 67.33 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.06 % 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: -2.75 (0.18), residues: 1780 helix: -1.45 (0.16), residues: 811 sheet: -2.09 (0.36), residues: 190 loop : -2.04 (0.21), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP A1929 HIS 0.011 0.002 HIS A1896 PHE 0.039 0.003 PHE A2171 TYR 0.037 0.003 TYR A 529 ARG 0.006 0.001 ARG A 866 Details of bonding type rmsd hydrogen bonds : bond 0.12576 ( 683) hydrogen bonds : angle 6.55780 ( 1995) covalent geometry : bond 0.00668 (16034) covalent geometry : angle 1.11086 (21945) Misc. bond : bond 0.04161 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 1.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7983 (tmm) REVERT: A 1769 GLU cc_start: 0.6320 (pp20) cc_final: 0.5959 (pm20) REVERT: A 1778 LYS cc_start: 0.8485 (mmtm) cc_final: 0.8269 (mmmm) REVERT: K 194 HIS cc_start: 0.6352 (t70) cc_final: 0.5383 (m170) REVERT: K 448 GLN cc_start: 0.7664 (tm130) cc_final: 0.7248 (tm-30) outliers start: 20 outliers final: 10 residues processed: 165 average time/residue: 0.3025 time to fit residues: 75.1896 Evaluate side-chains 152 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 1.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1658 MET Chi-restraints excluded: chain A residue 1671 HIS Chi-restraints excluded: chain A residue 1815 TYR Chi-restraints excluded: chain A residue 1903 ILE Chi-restraints excluded: chain A residue 2094 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 94 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 145 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 303 HIS ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.159814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.125737 restraints weight = 30711.146| |-----------------------------------------------------------------------------| r_work (start): 0.3926 rms_B_bonded: 3.20 r_work: 0.3756 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7083 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16035 Z= 0.217 Angle : 0.719 12.894 21945 Z= 0.360 Chirality : 0.043 0.186 2497 Planarity : 0.006 0.075 2661 Dihedral : 12.825 83.212 2739 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.09 % Favored : 91.80 % Rotamer: Outliers : 5.53 % Allowed : 27.08 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -2.01 (0.19), residues: 1780 helix: -0.49 (0.17), residues: 829 sheet: -1.96 (0.36), residues: 186 loop : -2.06 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1929 HIS 0.008 0.001 HIS K 450 PHE 0.019 0.002 PHE A2033 TYR 0.015 0.002 TYR A1655 ARG 0.008 0.001 ARG A 866 Details of bonding type rmsd hydrogen bonds : bond 0.04832 ( 683) hydrogen bonds : angle 5.00294 ( 1995) covalent geometry : bond 0.00503 (16034) covalent geometry : angle 0.71930 (21945) Misc. bond : bond 0.00217 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 148 time to evaluate : 1.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.7967 (m-80) REVERT: A 801 PHE cc_start: 0.4032 (OUTLIER) cc_final: 0.3552 (m-80) REVERT: A 899 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7272 (tp30) REVERT: A 1240 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.6200 (mp0) REVERT: A 1289 ILE cc_start: 0.5175 (OUTLIER) cc_final: 0.4212 (tp) REVERT: A 1778 LYS cc_start: 0.8595 (mmtm) cc_final: 0.8387 (mmmm) REVERT: A 2036 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7592 (t0) REVERT: A 2098 ARG cc_start: 0.6171 (ttm-80) cc_final: 0.5868 (ttp80) REVERT: K 170 ARG cc_start: 0.6919 (mtp180) cc_final: 0.6486 (mtp180) outliers start: 89 outliers final: 47 residues processed: 223 average time/residue: 0.2747 time to fit residues: 92.6113 Evaluate side-chains 185 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 132 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 185 LEU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1716 VAL Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1851 CYS Chi-restraints excluded: chain A residue 1894 SER Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 2020 THR Chi-restraints excluded: chain A residue 2032 GLU Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2050 ASP Chi-restraints excluded: chain A residue 2066 LEU Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2095 VAL Chi-restraints excluded: chain A residue 2105 GLU Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2159 VAL Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2180 ILE Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2236 LEU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 174 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 107 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 136 optimal weight: 8.9990 chunk 3 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 161 optimal weight: 0.5980 chunk 140 optimal weight: 0.0050 chunk 134 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN A1185 GLN ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.157797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.125465 restraints weight = 30677.817| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 3.06 r_work: 0.3756 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16035 Z= 0.205 Angle : 0.692 13.535 21945 Z= 0.344 Chirality : 0.043 0.218 2497 Planarity : 0.005 0.066 2661 Dihedral : 12.604 84.686 2726 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.26 % Favored : 91.63 % Rotamer: Outliers : 7.08 % Allowed : 25.84 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -1.73 (0.19), residues: 1780 helix: -0.18 (0.17), residues: 827 sheet: -1.94 (0.35), residues: 191 loop : -1.97 (0.22), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1929 HIS 0.007 0.001 HIS A 901 PHE 0.019 0.002 PHE A2033 TYR 0.014 0.002 TYR A1815 ARG 0.007 0.001 ARG A1211 Details of bonding type rmsd hydrogen bonds : bond 0.04675 ( 683) hydrogen bonds : angle 4.81361 ( 1995) covalent geometry : bond 0.00472 (16034) covalent geometry : angle 0.69164 (21945) Misc. bond : bond 0.00144 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 146 time to evaluate : 1.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.6832 (tt) REVERT: A 53 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7417 (mp0) REVERT: A 123 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.7853 (m-80) REVERT: A 140 LEU cc_start: 0.7541 (OUTLIER) cc_final: 0.7296 (pp) REVERT: A 801 PHE cc_start: 0.4032 (OUTLIER) cc_final: 0.3564 (m-80) REVERT: A 899 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7264 (tp30) REVERT: A 1289 ILE cc_start: 0.5269 (OUTLIER) cc_final: 0.4280 (tp) REVERT: A 1778 LYS cc_start: 0.8650 (mmtm) cc_final: 0.8445 (mmmm) REVERT: A 2031 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7375 (tt) REVERT: A 2036 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7587 (t0) REVERT: A 2098 ARG cc_start: 0.6090 (ttm-80) cc_final: 0.5814 (ttp80) REVERT: K 158 ILE cc_start: 0.6646 (OUTLIER) cc_final: 0.6384 (pt) REVERT: K 170 ARG cc_start: 0.6987 (mtp180) cc_final: 0.6570 (mtp180) outliers start: 114 outliers final: 62 residues processed: 240 average time/residue: 0.2656 time to fit residues: 98.0533 Evaluate side-chains 210 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 138 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 223 ILE Chi-restraints excluded: chain A residue 231 MET Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 865 LEU Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1211 ARG Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1298 MET Chi-restraints excluded: chain A residue 1532 ILE Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1655 TYR Chi-restraints excluded: chain A residue 1658 MET Chi-restraints excluded: chain A residue 1716 VAL Chi-restraints excluded: chain A residue 1731 THR Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1756 ILE Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1851 CYS Chi-restraints excluded: chain A residue 1894 SER Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1950 ILE Chi-restraints excluded: chain A residue 1970 THR Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2159 VAL Chi-restraints excluded: chain A residue 2180 ILE Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2236 LEU Chi-restraints excluded: chain K residue 158 ILE Chi-restraints excluded: chain K residue 173 PHE Chi-restraints excluded: chain K residue 174 LYS Chi-restraints excluded: chain K residue 379 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 10 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 157 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 116 optimal weight: 0.0170 overall best weight: 0.9222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 501 GLN A 627 GLN A1062 ASN A1736 ASN ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.160134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.128439 restraints weight = 30514.856| |-----------------------------------------------------------------------------| r_work (start): 0.3995 rms_B_bonded: 3.10 r_work: 0.3801 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16035 Z= 0.144 Angle : 0.643 13.713 21945 Z= 0.315 Chirality : 0.041 0.185 2497 Planarity : 0.005 0.064 2661 Dihedral : 12.424 85.954 2726 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.08 % Favored : 92.81 % Rotamer: Outliers : 6.21 % Allowed : 27.95 % Favored : 65.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -1.34 (0.19), residues: 1780 helix: 0.22 (0.18), residues: 826 sheet: -1.95 (0.36), residues: 194 loop : -1.80 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1929 HIS 0.008 0.001 HIS A 901 PHE 0.013 0.001 PHE A2033 TYR 0.012 0.001 TYR A 325 ARG 0.005 0.000 ARG A1211 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 683) hydrogen bonds : angle 4.54656 ( 1995) covalent geometry : bond 0.00327 (16034) covalent geometry : angle 0.64283 (21945) Misc. bond : bond 0.00093 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 146 time to evaluate : 1.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: A 84 MET cc_start: 0.7523 (tpp) cc_final: 0.7289 (tpp) REVERT: A 123 TYR cc_start: 0.8306 (OUTLIER) cc_final: 0.8046 (m-80) REVERT: A 140 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7253 (pp) REVERT: A 801 PHE cc_start: 0.4059 (OUTLIER) cc_final: 0.3589 (m-80) REVERT: A 1240 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.6212 (mp0) REVERT: A 1289 ILE cc_start: 0.5225 (OUTLIER) cc_final: 0.4261 (tp) REVERT: A 1733 SER cc_start: 0.8573 (p) cc_final: 0.8298 (t) REVERT: A 2036 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7538 (t0) REVERT: K 158 ILE cc_start: 0.6669 (tt) cc_final: 0.6411 (pt) outliers start: 100 outliers final: 58 residues processed: 226 average time/residue: 0.2688 time to fit residues: 93.1163 Evaluate side-chains 197 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 132 time to evaluate : 1.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1211 ARG Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1218 THR Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1529 LEU Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1655 TYR Chi-restraints excluded: chain A residue 1658 MET Chi-restraints excluded: chain A residue 1668 ASN Chi-restraints excluded: chain A residue 1716 VAL Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1851 CYS Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1990 LEU Chi-restraints excluded: chain A residue 2020 THR Chi-restraints excluded: chain A residue 2032 GLU Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2105 GLU Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain A residue 2234 CYS Chi-restraints excluded: chain A residue 2236 LEU Chi-restraints excluded: chain K residue 174 LYS Chi-restraints excluded: chain K residue 379 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 0.4980 chunk 158 optimal weight: 4.9990 chunk 72 optimal weight: 0.0980 chunk 31 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 141 optimal weight: 0.8980 chunk 89 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2079 HIS ** K 405 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 = 0.4436 r_free = 0.4436 target = 0.161556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.129544 restraints weight = 30868.144| |-----------------------------------------------------------------------------| r_work (start): 0.4010 rms_B_bonded: 3.12 r_work: 0.3814 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.1849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16035 Z= 0.128 Angle : 0.636 14.269 21945 Z= 0.309 Chirality : 0.040 0.178 2497 Planarity : 0.004 0.062 2661 Dihedral : 12.258 87.634 2723 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.91 % Favored : 92.98 % Rotamer: Outliers : 6.96 % Allowed : 26.96 % Favored : 66.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -1.13 (0.20), residues: 1780 helix: 0.42 (0.18), residues: 828 sheet: -1.78 (0.37), residues: 194 loop : -1.76 (0.22), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1929 HIS 0.008 0.001 HIS A 901 PHE 0.014 0.001 PHE A 248 TYR 0.014 0.001 TYR A 325 ARG 0.007 0.000 ARG A2098 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 683) hydrogen bonds : angle 4.39042 ( 1995) covalent geometry : bond 0.00292 (16034) covalent geometry : angle 0.63567 (21945) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 149 time to evaluate : 1.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7300 (mp0) REVERT: A 84 MET cc_start: 0.7441 (tpp) cc_final: 0.7232 (tpp) REVERT: A 141 GLU cc_start: 0.7554 (pt0) cc_final: 0.7139 (tt0) REVERT: A 529 TYR cc_start: 0.6890 (OUTLIER) cc_final: 0.6503 (p90) REVERT: A 801 PHE cc_start: 0.4065 (OUTLIER) cc_final: 0.3623 (m-80) REVERT: A 1240 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.6224 (mp0) REVERT: A 1289 ILE cc_start: 0.5356 (OUTLIER) cc_final: 0.4374 (tp) REVERT: A 2036 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7557 (t0) REVERT: A 2151 MET cc_start: 0.6099 (OUTLIER) cc_final: 0.5708 (mtt) REVERT: K 158 ILE cc_start: 0.6724 (tt) cc_final: 0.6320 (pt) REVERT: K 170 ARG cc_start: 0.7132 (mtp180) cc_final: 0.6528 (mtp180) outliers start: 112 outliers final: 65 residues processed: 242 average time/residue: 0.2614 time to fit residues: 97.1722 Evaluate side-chains 210 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 138 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 102 ILE Chi-restraints excluded: chain A residue 123 TYR Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 959 ILE Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1655 TYR Chi-restraints excluded: chain A residue 1658 MET Chi-restraints excluded: chain A residue 1668 ASN Chi-restraints excluded: chain A residue 1671 HIS Chi-restraints excluded: chain A residue 1716 VAL Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1970 THR Chi-restraints excluded: chain A residue 1990 LEU Chi-restraints excluded: chain A residue 2020 THR Chi-restraints excluded: chain A residue 2032 GLU Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2050 ASP Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2083 LYS Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2105 GLU Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2151 MET Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2190 THR Chi-restraints excluded: chain A residue 2234 CYS Chi-restraints excluded: chain A residue 2236 LEU Chi-restraints excluded: chain K residue 379 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 68 optimal weight: 0.3980 chunk 93 optimal weight: 0.1980 chunk 48 optimal weight: 10.0000 chunk 73 optimal weight: 0.5980 chunk 117 optimal weight: 0.2980 chunk 161 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 45 optimal weight: 8.9990 chunk 164 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 501 GLN A1643 ASN K 163 HIS ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4456 r_free = 0.4456 target = 0.163164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.131250 restraints weight = 30692.303| |-----------------------------------------------------------------------------| r_work (start): 0.4030 rms_B_bonded: 3.06 r_work: 0.3843 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16035 Z= 0.115 Angle : 0.627 13.954 21945 Z= 0.304 Chirality : 0.040 0.183 2497 Planarity : 0.004 0.061 2661 Dihedral : 12.176 89.303 2723 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 11.66 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.69 % Favored : 93.20 % Rotamer: Outliers : 5.96 % Allowed : 27.64 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -0.89 (0.20), residues: 1780 helix: 0.64 (0.18), residues: 832 sheet: -1.81 (0.37), residues: 195 loop : -1.62 (0.22), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1929 HIS 0.007 0.001 HIS A 901 PHE 0.017 0.001 PHE K 173 TYR 0.019 0.001 TYR A1890 ARG 0.007 0.000 ARG A1211 Details of bonding type rmsd hydrogen bonds : bond 0.03625 ( 683) hydrogen bonds : angle 4.24062 ( 1995) covalent geometry : bond 0.00261 (16034) covalent geometry : angle 0.62731 (21945) Misc. bond : bond 0.00036 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 152 time to evaluate : 1.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.7284 (mp0) REVERT: A 801 PHE cc_start: 0.4012 (OUTLIER) cc_final: 0.3583 (m-80) REVERT: A 899 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7194 (tp30) REVERT: A 1240 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.6421 (mp0) REVERT: A 1634 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7992 (tp) REVERT: A 2036 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7341 (t0) REVERT: A 2151 MET cc_start: 0.6064 (OUTLIER) cc_final: 0.5833 (mmt) REVERT: A 2169 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7357 (mp0) REVERT: K 170 ARG cc_start: 0.7061 (mtp180) cc_final: 0.6494 (mtp180) outliers start: 96 outliers final: 58 residues processed: 230 average time/residue: 0.2564 time to fit residues: 91.5518 Evaluate side-chains 207 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 141 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 16 THR Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 221 GLU Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1655 TYR Chi-restraints excluded: chain A residue 1658 MET Chi-restraints excluded: chain A residue 1716 VAL Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1894 SER Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1990 LEU Chi-restraints excluded: chain A residue 2020 THR Chi-restraints excluded: chain A residue 2032 GLU Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2050 ASP Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2083 LYS Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2105 GLU Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2151 MET Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2169 GLU Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2234 CYS Chi-restraints excluded: chain K residue 173 PHE Chi-restraints excluded: chain K residue 379 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 56 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 144 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 501 GLN ** A 870 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.161570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.129271 restraints weight = 30878.314| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 3.07 r_work: 0.3812 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16035 Z= 0.140 Angle : 0.664 15.021 21945 Z= 0.319 Chirality : 0.042 0.321 2497 Planarity : 0.004 0.061 2661 Dihedral : 12.123 89.203 2721 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.25 % Favored : 92.64 % Rotamer: Outliers : 5.53 % Allowed : 28.14 % Favored : 66.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -0.86 (0.20), residues: 1780 helix: 0.65 (0.18), residues: 830 sheet: -1.66 (0.37), residues: 194 loop : -1.63 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1929 HIS 0.007 0.001 HIS A 901 PHE 0.016 0.001 PHE A2171 TYR 0.017 0.001 TYR A 325 ARG 0.005 0.000 ARG A1211 Details of bonding type rmsd hydrogen bonds : bond 0.03825 ( 683) hydrogen bonds : angle 4.31782 ( 1995) covalent geometry : bond 0.00323 (16034) covalent geometry : angle 0.66439 (21945) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 150 time to evaluate : 1.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7647 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: A 141 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7171 (tt0) REVERT: A 231 MET cc_start: 0.7952 (tpp) cc_final: 0.7746 (mmm) REVERT: A 529 TYR cc_start: 0.6959 (OUTLIER) cc_final: 0.6629 (p90) REVERT: A 1240 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6464 (mp0) REVERT: A 1289 ILE cc_start: 0.5429 (OUTLIER) cc_final: 0.4451 (tp) REVERT: A 1634 LEU cc_start: 0.8219 (OUTLIER) cc_final: 0.8010 (tp) REVERT: A 2036 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7569 (t0) REVERT: A 2151 MET cc_start: 0.6246 (OUTLIER) cc_final: 0.6029 (mmt) REVERT: A 2169 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: K 170 ARG cc_start: 0.7042 (mtp180) cc_final: 0.6445 (mtp180) REVERT: K 394 TYR cc_start: 0.5647 (m-80) cc_final: 0.5403 (m-80) outliers start: 89 outliers final: 64 residues processed: 227 average time/residue: 0.2711 time to fit residues: 94.4794 Evaluate side-chains 211 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 138 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 771 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain A residue 1171 THR Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1211 ARG Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1240 GLU Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1634 LEU Chi-restraints excluded: chain A residue 1655 TYR Chi-restraints excluded: chain A residue 1671 HIS Chi-restraints excluded: chain A residue 1716 VAL Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1894 SER Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1970 THR Chi-restraints excluded: chain A residue 1990 LEU Chi-restraints excluded: chain A residue 2020 THR Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2032 GLU Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2050 ASP Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2083 LYS Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2095 VAL Chi-restraints excluded: chain A residue 2105 GLU Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2151 MET Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2169 GLU Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2234 CYS Chi-restraints excluded: chain A residue 2236 LEU Chi-restraints excluded: chain K residue 379 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 163 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 108 optimal weight: 0.6980 chunk 38 optimal weight: 10.0000 chunk 74 optimal weight: 0.0570 chunk 146 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 GLN ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 870 ASN ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.161533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.129574 restraints weight = 30449.096| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 3.01 r_work: 0.3813 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6980 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16035 Z= 0.140 Angle : 0.662 15.331 21945 Z= 0.318 Chirality : 0.041 0.295 2497 Planarity : 0.004 0.061 2661 Dihedral : 12.097 88.399 2721 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.97 % Favored : 92.92 % Rotamer: Outliers : 5.34 % Allowed : 28.20 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -0.81 (0.20), residues: 1780 helix: 0.69 (0.18), residues: 832 sheet: -1.67 (0.38), residues: 193 loop : -1.61 (0.22), residues: 755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A1929 HIS 0.007 0.001 HIS A 901 PHE 0.027 0.001 PHE K 407 TYR 0.018 0.002 TYR A 325 ARG 0.005 0.000 ARG A 526 Details of bonding type rmsd hydrogen bonds : bond 0.03797 ( 683) hydrogen bonds : angle 4.36402 ( 1995) covalent geometry : bond 0.00326 (16034) covalent geometry : angle 0.66233 (21945) Misc. bond : bond 0.00073 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 140 time to evaluate : 1.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: A 141 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7037 (tt0) REVERT: A 529 TYR cc_start: 0.6878 (OUTLIER) cc_final: 0.6130 (p90) REVERT: A 1289 ILE cc_start: 0.5407 (OUTLIER) cc_final: 0.4438 (tp) REVERT: A 1747 ILE cc_start: 0.8022 (OUTLIER) cc_final: 0.7761 (tp) REVERT: A 2036 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7573 (t0) REVERT: K 170 ARG cc_start: 0.7046 (mtp180) cc_final: 0.6439 (mtp180) outliers start: 86 outliers final: 67 residues processed: 212 average time/residue: 0.2655 time to fit residues: 87.3428 Evaluate side-chains 209 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 136 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 53 GLU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 141 GLU Chi-restraints excluded: chain A residue 309 ASN Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain A residue 899 GLU Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1163 CYS Chi-restraints excluded: chain A residue 1171 THR Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1211 ARG Chi-restraints excluded: chain A residue 1216 LEU Chi-restraints excluded: chain A residue 1243 THR Chi-restraints excluded: chain A residue 1265 ILE Chi-restraints excluded: chain A residue 1289 ILE Chi-restraints excluded: chain A residue 1655 TYR Chi-restraints excluded: chain A residue 1658 MET Chi-restraints excluded: chain A residue 1671 HIS Chi-restraints excluded: chain A residue 1716 VAL Chi-restraints excluded: chain A residue 1739 ILE Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1894 SER Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1970 THR Chi-restraints excluded: chain A residue 1990 LEU Chi-restraints excluded: chain A residue 2020 THR Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2032 GLU Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2050 ASP Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2083 LYS Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2095 VAL Chi-restraints excluded: chain A residue 2105 GLU Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2234 CYS Chi-restraints excluded: chain A residue 2236 LEU Chi-restraints excluded: chain K residue 379 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 51 optimal weight: 0.6980 chunk 145 optimal weight: 0.6980 chunk 45 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 9 optimal weight: 0.0570 chunk 24 optimal weight: 0.6980 chunk 52 optimal weight: 0.0010 chunk 55 optimal weight: 0.0670 chunk 150 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.2042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 GLN A 582 ASN ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.165799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.134668 restraints weight = 30562.696| |-----------------------------------------------------------------------------| r_work (start): 0.4081 rms_B_bonded: 2.97 r_work: 0.3897 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6845 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 16035 Z= 0.107 Angle : 0.642 14.751 21945 Z= 0.305 Chirality : 0.040 0.282 2497 Planarity : 0.004 0.059 2661 Dihedral : 11.969 87.223 2719 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.52 % Favored : 93.37 % Rotamer: Outliers : 3.73 % Allowed : 29.94 % Favored : 66.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -0.58 (0.20), residues: 1780 helix: 0.90 (0.18), residues: 833 sheet: -1.45 (0.39), residues: 184 loop : -1.55 (0.22), residues: 763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1929 HIS 0.007 0.001 HIS A 901 PHE 0.022 0.001 PHE A2171 TYR 0.019 0.001 TYR A 325 ARG 0.006 0.000 ARG A2098 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 683) hydrogen bonds : angle 4.17049 ( 1995) covalent geometry : bond 0.00241 (16034) covalent geometry : angle 0.64243 (21945) Misc. bond : bond 0.00034 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 154 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 TYR cc_start: 0.6730 (OUTLIER) cc_final: 0.5888 (p90) REVERT: A 1655 TYR cc_start: 0.2126 (OUTLIER) cc_final: 0.1614 (p90) REVERT: A 2011 LEU cc_start: 0.8563 (tp) cc_final: 0.8293 (mm) REVERT: A 2036 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7391 (t0) REVERT: A 2066 LEU cc_start: 0.6969 (OUTLIER) cc_final: 0.6669 (tt) REVERT: A 2169 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: K 170 ARG cc_start: 0.6928 (mtp180) cc_final: 0.6444 (mtp180) REVERT: K 194 HIS cc_start: 0.6521 (OUTLIER) cc_final: 0.4694 (m170) outliers start: 60 outliers final: 40 residues processed: 204 average time/residue: 0.2577 time to fit residues: 81.2462 Evaluate side-chains 185 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 139 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1211 ARG Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1655 TYR Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1894 SER Chi-restraints excluded: chain A residue 1970 THR Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2050 ASP Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2066 LEU Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2105 GLU Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2169 GLU Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2234 CYS Chi-restraints excluded: chain K residue 194 HIS Chi-restraints excluded: chain K residue 379 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 21 optimal weight: 2.9990 chunk 102 optimal weight: 0.0020 chunk 120 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 36 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 GLN ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1062 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 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 = 0.4461 r_free = 0.4461 target = 0.163566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.131777 restraints weight = 30663.193| |-----------------------------------------------------------------------------| r_work (start): 0.4040 rms_B_bonded: 3.04 r_work: 0.3849 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6919 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16035 Z= 0.126 Angle : 0.665 15.692 21945 Z= 0.317 Chirality : 0.041 0.281 2497 Planarity : 0.004 0.060 2661 Dihedral : 11.970 85.367 2719 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.57 % Favored : 93.31 % Rotamer: Outliers : 3.48 % Allowed : 30.12 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -0.54 (0.20), residues: 1780 helix: 0.91 (0.18), residues: 835 sheet: -1.30 (0.39), residues: 179 loop : -1.56 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1929 HIS 0.010 0.001 HIS K 360 PHE 0.019 0.001 PHE K 407 TYR 0.018 0.001 TYR A 306 ARG 0.004 0.000 ARG A 526 Details of bonding type rmsd hydrogen bonds : bond 0.03532 ( 683) hydrogen bonds : angle 4.25742 ( 1995) covalent geometry : bond 0.00290 (16034) covalent geometry : angle 0.66534 (21945) Misc. bond : bond 0.00046 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 141 time to evaluate : 1.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 TYR cc_start: 0.6789 (OUTLIER) cc_final: 0.5948 (p90) REVERT: A 760 LEU cc_start: 0.8411 (tp) cc_final: 0.8208 (pp) REVERT: A 1655 TYR cc_start: 0.2108 (OUTLIER) cc_final: 0.1510 (p90) REVERT: A 2011 LEU cc_start: 0.8594 (tp) cc_final: 0.8330 (mm) REVERT: A 2036 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7420 (t0) REVERT: A 2066 LEU cc_start: 0.7013 (OUTLIER) cc_final: 0.6766 (tt) REVERT: K 170 ARG cc_start: 0.6929 (mtp180) cc_final: 0.6457 (mtp180) REVERT: K 194 HIS cc_start: 0.6520 (OUTLIER) cc_final: 0.4680 (m170) outliers start: 56 outliers final: 46 residues processed: 189 average time/residue: 0.2606 time to fit residues: 76.1709 Evaluate side-chains 187 residues out of total 1610 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 136 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 HIS Chi-restraints excluded: chain A residue 33 THR Chi-restraints excluded: chain A residue 37 LEU Chi-restraints excluded: chain A residue 61 HIS Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 126 GLU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 529 TYR Chi-restraints excluded: chain A residue 534 VAL Chi-restraints excluded: chain A residue 548 HIS Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 628 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 880 LEU Chi-restraints excluded: chain A residue 894 LEU Chi-restraints excluded: chain A residue 897 CYS Chi-restraints excluded: chain A residue 1010 ILE Chi-restraints excluded: chain A residue 1069 PHE Chi-restraints excluded: chain A residue 1084 ILE Chi-restraints excluded: chain A residue 1180 TYR Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1198 SER Chi-restraints excluded: chain A residue 1211 ARG Chi-restraints excluded: chain A residue 1237 LEU Chi-restraints excluded: chain A residue 1655 TYR Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1773 SER Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1843 LYS Chi-restraints excluded: chain A residue 1848 VAL Chi-restraints excluded: chain A residue 1941 LEU Chi-restraints excluded: chain A residue 1970 THR Chi-restraints excluded: chain A residue 2031 LEU Chi-restraints excluded: chain A residue 2032 GLU Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2050 ASP Chi-restraints excluded: chain A residue 2055 SER Chi-restraints excluded: chain A residue 2066 LEU Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2105 GLU Chi-restraints excluded: chain A residue 2130 VAL Chi-restraints excluded: chain A residue 2168 ILE Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2234 CYS Chi-restraints excluded: chain A residue 2236 LEU Chi-restraints excluded: chain K residue 194 HIS Chi-restraints excluded: chain K residue 379 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 134 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 chunk 90 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 chunk 72 optimal weight: 5.9990 chunk 34 optimal weight: 0.0060 chunk 39 optimal weight: 3.9990 chunk 139 optimal weight: 0.0470 chunk 115 optimal weight: 0.7980 chunk 181 optimal weight: 2.9990 overall best weight: 0.4694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 501 GLN ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 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 = 0.4496 r_free = 0.4496 target = 0.167444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.135705 restraints weight = 30509.970| |-----------------------------------------------------------------------------| r_work (start): 0.4073 rms_B_bonded: 3.08 r_work: 0.3886 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6893 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16035 Z= 0.117 Angle : 0.664 15.821 21945 Z= 0.314 Chirality : 0.041 0.271 2497 Planarity : 0.004 0.059 2661 Dihedral : 11.945 84.239 2719 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.52 % Favored : 93.37 % Rotamer: Outliers : 3.73 % Allowed : 29.88 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -0.48 (0.20), residues: 1780 helix: 0.95 (0.18), residues: 835 sheet: -1.26 (0.39), residues: 184 loop : -1.50 (0.23), residues: 761 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A1929 HIS 0.008 0.001 HIS K 360 PHE 0.025 0.001 PHE A2171 TYR 0.018 0.001 TYR A 774 ARG 0.006 0.000 ARG A2098 Details of bonding type rmsd hydrogen bonds : bond 0.03425 ( 683) hydrogen bonds : angle 4.17611 ( 1995) covalent geometry : bond 0.00266 (16034) covalent geometry : angle 0.66428 (21945) Misc. bond : bond 0.00038 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9115.98 seconds wall clock time: 157 minutes 26.61 seconds (9446.61 seconds total)