Starting phenix.real_space_refine on Fri Feb 16 22:23:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfv_27415/02_2024/8dfv_27415.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfv_27415/02_2024/8dfv_27415.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfv_27415/02_2024/8dfv_27415.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfv_27415/02_2024/8dfv_27415.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfv_27415/02_2024/8dfv_27415.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dfv_27415/02_2024/8dfv_27415.pdb" } resolution = 3.06 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= -0.001 sd= 0.070 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 Ca 10 9.91 5 P 60 5.49 5 S 91 5.16 5 C 10365 2.51 5 N 2935 2.21 5 O 3249 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 1131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16710 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 13422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1664, 13422 Classifications: {'peptide': 1664} Link IDs: {'PTRANS': 97, 'TRANS': 1566} Chain breaks: 12 Chain: "E" Number of atoms: 1266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 1266 Classifications: {'RNA': 60} Modifications used: {'p5*END': 1, 'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 27, 'rna3p_pyr': 31} Link IDs: {'rna2p': 2, 'rna3p': 57} Chain: "K" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 2012 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 240} Chain breaks: 2 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' CA': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 9.09, per 1000 atoms: 0.54 Number of scatterers: 16710 At special positions: 0 Unit cell: (156.88, 130.38, 146.28, 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) Ca 10 19.99 S 91 16.00 P 60 15.00 O 3249 8.00 N 2935 7.00 C 10365 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.97 Conformation dependent library (CDL) restraints added in 2.8 seconds 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 19 sheets defined 46.8% alpha, 9.0% beta 19 base pairs and 39 stacking pairs defined. Time for finding SS restraints: 6.03 Creating SS restraints... Processing helix chain 'A' and resid 19 through 31 removed outlier: 3.784A pdb=" N GLU A 23 " --> pdb=" O ASP A 19 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLU A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 59 Processing helix chain 'A' and resid 79 through 88 removed outlier: 4.256A pdb=" N THR A 83 " --> pdb=" O CYS A 79 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET A 84 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 145 through 157 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 187 through 199 removed outlier: 3.578A pdb=" N LEU A 192 " --> pdb=" O LEU A 188 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 215 removed outlier: 3.535A pdb=" N VAL A 212 " --> pdb=" O ASP A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 252 removed outlier: 3.840A pdb=" N ASP A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 293 removed outlier: 4.535A pdb=" N VAL A 288 " --> pdb=" O ASN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 313 removed outlier: 4.198A pdb=" N HIS A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 344 removed outlier: 3.738A pdb=" N ALA A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N PHE A 343 " --> pdb=" O CYS A 339 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N HIS A 344 " --> pdb=" O GLU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 361 Processing helix chain 'A' and resid 362 through 375 Processing helix chain 'A' and resid 501 through 517 Processing helix chain 'A' and resid 520 through 524 removed outlier: 3.837A pdb=" N LYS A 523 " --> pdb=" O PRO A 520 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N PHE A 524 " --> pdb=" O ASP A 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 520 through 524' Processing helix chain 'A' and resid 540 through 560 removed outlier: 3.907A pdb=" N ARG A 557 " --> pdb=" O GLU A 553 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG A 559 " --> pdb=" O LEU A 555 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N MET A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.659A pdb=" N GLU A 573 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 601 removed outlier: 3.633A pdb=" N CYS A 599 " --> pdb=" O SER A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 760 through 785 Processing helix chain 'A' and resid 791 through 801 removed outlier: 3.570A pdb=" N GLN A 795 " --> pdb=" O PRO A 791 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 834 removed outlier: 4.091A pdb=" N ILE A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 904 Processing helix chain 'A' and resid 922 through 927 removed outlier: 3.516A pdb=" N GLU A 926 " --> pdb=" O PRO A 923 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N CYS A 927 " --> pdb=" O ASP A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 931 through 941 removed outlier: 3.792A pdb=" N GLU A 935 " --> pdb=" O GLU A 931 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1062 removed outlier: 3.705A pdb=" N ILE A1049 " --> pdb=" O THR A1045 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL A1050 " --> pdb=" O SER A1046 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1108 Processing helix chain 'A' and resid 1117 through 1124 removed outlier: 3.735A pdb=" N ARG A1121 " --> pdb=" O PRO A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1230 through 1234 removed outlier: 3.967A pdb=" N LYS A1234 " --> pdb=" O LEU A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1238 through 1242 removed outlier: 3.776A pdb=" N CYS A1242 " --> pdb=" O PRO A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1282 Proline residue: A1259 - end of helix Processing helix chain 'A' and resid 1524 through 1546 removed outlier: 4.648A pdb=" N GLN A1541 " --> pdb=" O ALA A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1568 through 1581 Processing helix chain 'A' and resid 1607 through 1616 Processing helix chain 'A' and resid 1620 through 1629 removed outlier: 4.053A pdb=" N LEU A1624 " --> pdb=" O ASN A1620 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N LYS A1626 " --> pdb=" O ASP A1622 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A1629 " --> pdb=" O ALA A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1636 through 1650 removed outlier: 3.510A pdb=" N HIS A1650 " --> pdb=" O TRP A1646 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 1768 through 1780 removed outlier: 3.775A pdb=" N HIS A1774 " --> pdb=" O GLY A1770 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1792 Processing helix chain 'A' and resid 1793 through 1797 Processing helix chain 'A' and resid 1838 through 1842 removed outlier: 4.025A pdb=" N ASP A1841 " --> pdb=" O ASP A1838 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ILE A1842 " --> pdb=" O LEU A1839 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1838 through 1842' Processing helix chain 'A' and resid 1847 through 1852 Processing helix chain 'A' and resid 1900 through 1931 Proline residue: A1920 - end of helix Processing helix chain 'A' and resid 1981 through 1990 removed outlier: 3.526A pdb=" N LEU A1990 " --> pdb=" O LEU A1986 " (cutoff:3.500A) 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: 3.792A pdb=" N ALA A2037 " --> pdb=" O PHE A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2055 through 2067 Processing helix chain 'A' and resid 2068 through 2079 Processing helix chain 'A' and resid 2089 through 2106 Processing helix chain 'A' and resid 2131 through 2149 removed outlier: 3.652A pdb=" N GLY A2135 " --> pdb=" O PRO A2131 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A2142 " --> pdb=" O PHE A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2155 through 2173 removed outlier: 3.696A pdb=" N VAL A2159 " --> pdb=" O VAL A2155 " (cutoff:3.500A) Proline residue: A2166 - end of helix removed outlier: 3.523A pdb=" N ASN A2173 " --> pdb=" O GLU A2169 " (cutoff:3.500A) Processing helix chain 'A' and resid 2178 through 2187 Processing helix chain 'A' and resid 2223 through 2239 Processing helix chain 'K' and resid 135 through 146 Processing helix chain 'K' and resid 188 through 204 Processing helix chain 'K' and resid 253 through 262 Processing helix chain 'K' and resid 300 through 319 Processing helix chain 'K' and resid 359 through 374 Processing helix chain 'K' and resid 376 through 384 removed outlier: 4.466A pdb=" N LEU K 380 " --> pdb=" O GLY K 376 " (cutoff:3.500A) Processing helix chain 'K' and resid 393 through 405 Processing helix chain 'K' and resid 443 through 464 Processing sheet with id=AA1, first strand: chain 'A' and resid 115 through 116 removed outlier: 7.831A pdb=" N LEU A 116 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N TYR A 67 " --> pdb=" O LEU A 116 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N VAL A 64 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ILE A 138 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N VAL A 66 " --> pdb=" O ILE A 138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 220 through 221 removed outlier: 6.220A pdb=" N HIS A 220 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE A 612 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL A 224 " --> pdb=" O VAL A 614 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 221 removed outlier: 6.220A pdb=" N HIS A 220 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE A 612 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL A 584 " --> pdb=" O VAL A 611 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU A 613 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ARG A 586 " --> pdb=" O LEU A 613 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AA5, first strand: chain 'A' and resid 805 through 806 Processing sheet with id=AA6, first strand: chain 'A' and resid 847 through 850 Processing sheet with id=AA7, first strand: chain 'A' and resid 853 through 854 Processing sheet with id=AA8, first strand: chain 'A' and resid 952 through 956 removed outlier: 3.572A pdb=" N TYR A 955 " --> pdb=" O HIS A1896 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS A1896 " --> pdb=" O TYR A 955 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1036 through 1042 removed outlier: 4.574A pdb=" N LEU A 976 " --> pdb=" O ALA A1038 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N GLU A1040 " --> pdb=" O CYS A 974 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N CYS A 974 " --> pdb=" O GLU A1040 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 981 through 986 removed outlier: 6.626A pdb=" N GLU A1030 " --> pdb=" O GLN A 984 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1072 through 1073 Processing sheet with id=AB3, first strand: chain 'A' and resid 1153 through 1155 removed outlier: 4.355A pdb=" N GLN A1235 " --> pdb=" O VAL A1194 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1673 through 1674 removed outlier: 3.780A pdb=" N ASN A1674 " --> pdb=" O GLN A1679 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN A1679 " --> pdb=" O ASN A1674 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1937 through 1940 removed outlier: 4.038A pdb=" N VAL A1964 " --> pdb=" O THR A1938 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 2191 through 2193 removed outlier: 3.893A pdb=" N LYS A2192 " --> pdb=" O ASP A2210 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A2210 " --> pdb=" O LYS A2192 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 2191 through 2193 removed outlier: 3.893A pdb=" N LYS A2192 " --> pdb=" O ASP A2210 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ASP A2210 " --> pdb=" O LYS A2192 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 152 through 160 removed outlier: 3.808A pdb=" N GLY K 152 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N ARG K 168 " --> pdb=" O VAL K 156 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE K 158 " --> pdb=" O THR K 166 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N THR K 166 " --> pdb=" O ILE K 158 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 268 through 273 removed outlier: 4.363A pdb=" N SER K 268 " --> pdb=" O SER K 288 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER K 288 " --> pdb=" O SER K 268 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N THR K 284 " --> pdb=" O GLU K 272 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 408 through 412 removed outlier: 4.205A pdb=" N GLU K 408 " --> pdb=" O SER K 430 " (cutoff:3.500A) 675 hydrogen bonds defined for protein. 1950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 39 stacking parallelities Total time for adding SS restraints: 8.66 Time building geometry restraints manager: 7.43 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: 4007 1.33 - 1.45: 3761 1.45 - 1.57: 9176 1.57 - 1.69: 119 1.69 - 1.81: 126 Bond restraints: 17189 Sorted by residual: bond pdb=" CG ARG A 586 " pdb=" CD ARG A 586 " ideal model delta sigma weight residual 1.520 1.416 0.104 3.00e-02 1.11e+03 1.19e+01 bond pdb=" CD1 PHE A1996 " pdb=" CE1 PHE A1996 " ideal model delta sigma weight residual 1.382 1.286 0.096 3.00e-02 1.11e+03 1.02e+01 bond pdb=" CG1 ILE A2180 " pdb=" CD1 ILE A2180 " ideal model delta sigma weight residual 1.513 1.393 0.120 3.90e-02 6.57e+02 9.46e+00 bond pdb=" CG1 ILE A1898 " pdb=" CD1 ILE A1898 " ideal model delta sigma weight residual 1.513 1.399 0.114 3.90e-02 6.57e+02 8.49e+00 bond pdb=" CB PHE A1996 " pdb=" CG PHE A1996 " ideal model delta sigma weight residual 1.502 1.437 0.065 2.30e-02 1.89e+03 7.96e+00 ... (remaining 17184 not shown) Histogram of bond angle deviations from ideal: 97.09 - 104.52: 587 104.52 - 111.95: 7986 111.95 - 119.39: 6659 119.39 - 126.82: 7955 126.82 - 134.25: 382 Bond angle restraints: 23569 Sorted by residual: angle pdb=" OG1 THR A 851 " pdb=" CB THR A 851 " pdb=" CG2 THR A 851 " ideal model delta sigma weight residual 109.30 98.90 10.40 2.00e+00 2.50e-01 2.70e+01 angle pdb=" CB LEU A1930 " pdb=" CG LEU A1930 " pdb=" CD2 LEU A1930 " ideal model delta sigma weight residual 110.70 97.13 13.57 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C PHE A 3 " pdb=" N HIS A 4 " pdb=" CA HIS A 4 " ideal model delta sigma weight residual 121.54 129.92 -8.38 1.91e+00 2.74e-01 1.93e+01 angle pdb=" C PHE K 173 " pdb=" N LYS K 174 " pdb=" CA LYS K 174 " ideal model delta sigma weight residual 121.54 129.86 -8.32 1.91e+00 2.74e-01 1.90e+01 angle pdb=" N LYS A1227 " pdb=" CA LYS A1227 " pdb=" C LYS A1227 " ideal model delta sigma weight residual 110.80 119.96 -9.16 2.13e+00 2.20e-01 1.85e+01 ... (remaining 23564 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.93: 10132 31.93 - 63.87: 351 63.87 - 95.80: 35 95.80 - 127.74: 0 127.74 - 159.67: 1 Dihedral angle restraints: 10519 sinusoidal: 4886 harmonic: 5633 Sorted by residual: dihedral pdb=" O4' U E 1 " pdb=" C1' U E 1 " pdb=" N1 U E 1 " pdb=" C2 U E 1 " ideal model delta sinusoidal sigma weight residual 232.00 72.33 159.67 1 1.70e+01 3.46e-03 6.44e+01 dihedral pdb=" CA GLY A1661 " pdb=" C GLY A1661 " pdb=" N ASP A1662 " pdb=" CA ASP A1662 " ideal model delta harmonic sigma weight residual -180.00 -145.34 -34.66 0 5.00e+00 4.00e-02 4.81e+01 dihedral pdb=" CA PRO A 912 " pdb=" C PRO A 912 " pdb=" N ILE A 913 " pdb=" CA ILE A 913 " ideal model delta harmonic sigma weight residual -180.00 -148.80 -31.20 0 5.00e+00 4.00e-02 3.89e+01 ... (remaining 10516 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 2538 0.124 - 0.249: 128 0.249 - 0.373: 8 0.373 - 0.497: 0 0.497 - 0.622: 1 Chirality restraints: 2675 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 2.02 0.62 2.00e-01 2.50e+01 9.66e+00 chirality pdb=" CB VAL A2137 " pdb=" CA VAL A2137 " pdb=" CG1 VAL A2137 " pdb=" CG2 VAL A2137 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CB VAL A1934 " pdb=" CA VAL A1934 " pdb=" CG1 VAL A1934 " pdb=" CG2 VAL A1934 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.81e+00 ... (remaining 2672 not shown) Planarity restraints: 2827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A1814 " -0.025 2.00e-02 2.50e+03 3.39e-02 2.30e+01 pdb=" CG TYR A1814 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 TYR A1814 " -0.043 2.00e-02 2.50e+03 pdb=" CD2 TYR A1814 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A1814 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A1814 " -0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A1814 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A1814 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 863 " 0.032 2.00e-02 2.50e+03 2.87e-02 1.65e+01 pdb=" CG TYR A 863 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 TYR A 863 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR A 863 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 863 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A 863 " 0.015 2.00e-02 2.50e+03 pdb=" CZ TYR A 863 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 863 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A2020 " -0.060 5.00e-02 4.00e+02 8.95e-02 1.28e+01 pdb=" N PRO A2021 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO A2021 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A2021 " -0.050 5.00e-02 4.00e+02 ... (remaining 2824 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.74: 1997 2.74 - 3.28: 16136 3.28 - 3.82: 29426 3.82 - 4.36: 35292 4.36 - 4.90: 57676 Nonbonded interactions: 140527 Sorted by model distance: nonbonded pdb=" O LEU A1727 " pdb=" OG1 THR A1731 " model vdw 2.206 2.440 nonbonded pdb=" O ILE A1950 " pdb=" OG SER A1953 " model vdw 2.223 2.440 nonbonded pdb=" OH TYR A 832 " pdb=" OG SER A 871 " model vdw 2.233 2.440 nonbonded pdb=" O SER A1162 " pdb=" OG1 THR A1171 " model vdw 2.236 2.440 nonbonded pdb=" OG SER A1999 " pdb=" O HIS A2079 " model vdw 2.265 2.440 ... (remaining 140522 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.910 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: 9.100 Check model and map are aligned: 0.270 Set scattering table: 0.190 Process input model: 52.750 Find NCS groups from input model: 0.450 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6886 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 : 0.010 0.131 17189 Z= 0.654 Angle : 1.153 14.157 23569 Z= 0.589 Chirality : 0.064 0.622 2675 Planarity : 0.009 0.105 2827 Dihedral : 16.023 159.671 6859 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.32 % Allowed : 9.66 % Favored : 90.03 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -2.99 (0.18), residues: 1885 helix: -1.54 (0.15), residues: 843 sheet: -2.30 (0.36), residues: 198 loop : -2.27 (0.21), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP K 254 HIS 0.031 0.002 HIS A1896 PHE 0.054 0.005 PHE A2081 TYR 0.078 0.004 TYR A1814 ARG 0.016 0.001 ARG A1027 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ILE cc_start: 0.7547 (tt) cc_final: 0.6985 (mt) REVERT: A 524 PHE cc_start: 0.6621 (p90) cc_final: 0.6262 (p90) REVERT: A 580 LYS cc_start: 0.6821 (pttt) cc_final: 0.6470 (mmtp) REVERT: A 936 GLN cc_start: 0.7473 (tp40) cc_final: 0.7259 (tp-100) REVERT: A 1531 ILE cc_start: 0.5659 (mm) cc_final: 0.5430 (mt) REVERT: A 1818 LYS cc_start: 0.7669 (mttp) cc_final: 0.7398 (ptpt) REVERT: A 2067 VAL cc_start: 0.5822 (t) cc_final: 0.5544 (m) REVERT: K 176 LYS cc_start: 0.6323 (mmtt) cc_final: 0.6036 (ttpp) REVERT: K 311 ARG cc_start: 0.6867 (mtp85) cc_final: 0.6582 (mmm160) REVERT: K 369 LYS cc_start: 0.7885 (tmmt) cc_final: 0.7542 (tptp) REVERT: K 384 LYS cc_start: 0.8110 (mttp) cc_final: 0.7410 (tptt) outliers start: 0 outliers final: 0 residues processed: 294 average time/residue: 0.3385 time to fit residues: 143.4415 Evaluate side-chains 176 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 166 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 79 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 93 optimal weight: 0.8980 chunk 114 optimal weight: 3.9990 chunk 178 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 144 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 225 GLN A 245 HIS A 773 GLN A1142 ASN A1185 GLN ** A1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 194 HIS ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17189 Z= 0.267 Angle : 0.719 11.715 23569 Z= 0.365 Chirality : 0.043 0.184 2675 Planarity : 0.006 0.064 2827 Dihedral : 14.209 156.763 3004 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.75 % Favored : 91.88 % Rotamer: Outliers : 1.35 % Allowed : 8.64 % Favored : 90.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.19), residues: 1885 helix: -0.45 (0.17), residues: 868 sheet: -2.22 (0.36), residues: 198 loop : -2.03 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 94 HIS 0.011 0.001 HIS A1896 PHE 0.022 0.002 PHE A1707 TYR 0.023 0.002 TYR A 863 ARG 0.006 0.001 ARG A1027 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 207 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6131 (mm-30) cc_final: 0.5350 (mm-30) REVERT: A 81 ILE cc_start: 0.7656 (OUTLIER) cc_final: 0.7276 (tt) REVERT: A 191 MET cc_start: 0.6933 (ptp) cc_final: 0.6594 (ptp) REVERT: A 303 HIS cc_start: 0.6320 (OUTLIER) cc_final: 0.5391 (t70) REVERT: A 341 HIS cc_start: 0.7020 (m-70) cc_final: 0.6348 (m-70) REVERT: A 346 HIS cc_start: 0.6865 (m-70) cc_final: 0.6615 (m90) REVERT: A 524 PHE cc_start: 0.6436 (p90) cc_final: 0.6055 (p90) REVERT: A 580 LYS cc_start: 0.6924 (pttt) cc_final: 0.6464 (mmtm) REVERT: A 771 MET cc_start: 0.7716 (tpp) cc_final: 0.7489 (mmt) REVERT: A 930 LEU cc_start: 0.4556 (OUTLIER) cc_final: 0.4250 (pp) REVERT: A 1175 TYR cc_start: 0.6525 (p90) cc_final: 0.6199 (p90) REVERT: A 1531 ILE cc_start: 0.5390 (mm) cc_final: 0.5179 (mt) REVERT: A 1818 LYS cc_start: 0.7577 (mttp) cc_final: 0.7329 (ptpt) REVERT: A 2182 GLU cc_start: 0.6474 (tp30) cc_final: 0.6237 (tp30) REVERT: K 176 LYS cc_start: 0.6055 (mmtt) cc_final: 0.5763 (ttpp) REVERT: K 311 ARG cc_start: 0.6804 (mtp85) cc_final: 0.6557 (mmm160) outliers start: 23 outliers final: 10 residues processed: 218 average time/residue: 0.3709 time to fit residues: 118.6976 Evaluate side-chains 185 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 172 time to evaluate : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1079 GLU Chi-restraints excluded: chain A residue 1209 VAL Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 2097 ASP Chi-restraints excluded: chain A residue 2216 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 148 optimal weight: 0.0970 chunk 121 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 193 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 177 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 143 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 291 HIS A1142 ASN A1806 HIS ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17189 Z= 0.199 Angle : 0.645 10.131 23569 Z= 0.326 Chirality : 0.041 0.276 2675 Planarity : 0.005 0.063 2827 Dihedral : 13.931 160.380 3004 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.27 % Favored : 92.47 % Rotamer: Outliers : 1.65 % Allowed : 11.70 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.19), residues: 1885 helix: 0.11 (0.17), residues: 870 sheet: -2.27 (0.36), residues: 199 loop : -1.69 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 5 HIS 0.007 0.001 HIS A1896 PHE 0.019 0.002 PHE A1707 TYR 0.016 0.002 TYR A2224 ARG 0.005 0.000 ARG A 354 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 204 time to evaluate : 1.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ILE cc_start: 0.7556 (tt) cc_final: 0.7035 (mt) REVERT: A 191 MET cc_start: 0.6800 (ptp) cc_final: 0.6394 (ptp) REVERT: A 231 MET cc_start: 0.6229 (mmt) cc_final: 0.5940 (mmm) REVERT: A 303 HIS cc_start: 0.6156 (OUTLIER) cc_final: 0.5266 (t70) REVERT: A 341 HIS cc_start: 0.6896 (m-70) cc_final: 0.6163 (m-70) REVERT: A 524 PHE cc_start: 0.6407 (p90) cc_final: 0.5986 (p90) REVERT: A 580 LYS cc_start: 0.6855 (pttt) cc_final: 0.6438 (mmtm) REVERT: A 771 MET cc_start: 0.7749 (tpp) cc_final: 0.7540 (mmt) REVERT: A 930 LEU cc_start: 0.4512 (OUTLIER) cc_final: 0.4262 (pp) REVERT: A 977 TYR cc_start: 0.6583 (m-10) cc_final: 0.6275 (m-80) REVERT: A 1112 MET cc_start: 0.6507 (mpp) cc_final: 0.5767 (mpp) REVERT: A 1124 GLN cc_start: 0.6559 (pp30) cc_final: 0.6218 (mp10) REVERT: A 1175 TYR cc_start: 0.6532 (p90) cc_final: 0.6012 (p90) REVERT: A 2177 LYS cc_start: 0.7188 (mmtt) cc_final: 0.6936 (mttt) REVERT: A 2180 ILE cc_start: 0.6266 (OUTLIER) cc_final: 0.6006 (tp) REVERT: A 2182 GLU cc_start: 0.6467 (tp30) cc_final: 0.6190 (tp30) REVERT: A 2197 GLU cc_start: 0.6194 (mm-30) cc_final: 0.5746 (mt-10) REVERT: K 176 LYS cc_start: 0.5917 (mmtt) cc_final: 0.5638 (ttpp) REVERT: K 263 ARG cc_start: 0.4931 (mtp180) cc_final: 0.4313 (ptp-170) REVERT: K 311 ARG cc_start: 0.6799 (mtp85) cc_final: 0.6539 (mmm160) outliers start: 28 outliers final: 13 residues processed: 220 average time/residue: 0.3337 time to fit residues: 107.4973 Evaluate side-chains 196 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2097 ASP Chi-restraints excluded: chain A residue 2180 ILE Chi-restraints excluded: chain A residue 2216 THR Chi-restraints excluded: chain K residue 150 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 177 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 120 optimal weight: 0.9990 chunk 179 optimal weight: 0.6980 chunk 190 optimal weight: 6.9990 chunk 170 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 158 optimal weight: 0.4980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 984 GLN A1210 ASN A1977 HIS ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 17189 Z= 0.294 Angle : 0.680 9.658 23569 Z= 0.344 Chirality : 0.043 0.267 2675 Planarity : 0.005 0.060 2827 Dihedral : 13.800 159.367 3004 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.48 % Favored : 92.20 % Rotamer: Outliers : 2.35 % Allowed : 13.82 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.20), residues: 1885 helix: 0.25 (0.17), residues: 870 sheet: -2.30 (0.36), residues: 199 loop : -1.66 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 5 HIS 0.008 0.001 HIS A1896 PHE 0.021 0.002 PHE A1707 TYR 0.017 0.002 TYR A1175 ARG 0.009 0.000 ARG A1225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 185 time to evaluate : 1.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ILE cc_start: 0.7529 (tt) cc_final: 0.6792 (mp) REVERT: A 104 PHE cc_start: 0.7205 (m-80) cc_final: 0.6906 (m-80) REVERT: A 140 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8315 (mt) REVERT: A 231 MET cc_start: 0.6244 (mmt) cc_final: 0.5963 (mmm) REVERT: A 303 HIS cc_start: 0.6288 (OUTLIER) cc_final: 0.5511 (t70) REVERT: A 311 LYS cc_start: 0.8270 (mtmm) cc_final: 0.7601 (mptt) REVERT: A 346 HIS cc_start: 0.7076 (m90) cc_final: 0.6769 (m90) REVERT: A 524 PHE cc_start: 0.6488 (p90) cc_final: 0.5981 (p90) REVERT: A 580 LYS cc_start: 0.6809 (pttt) cc_final: 0.6389 (mmtm) REVERT: A 771 MET cc_start: 0.7775 (tpp) cc_final: 0.7569 (mmt) REVERT: A 930 LEU cc_start: 0.4682 (OUTLIER) cc_final: 0.4411 (pp) REVERT: A 969 VAL cc_start: 0.6498 (t) cc_final: 0.6209 (m) REVERT: A 977 TYR cc_start: 0.6633 (m-10) cc_final: 0.6352 (m-80) REVERT: A 1112 MET cc_start: 0.6606 (mpp) cc_final: 0.5822 (mpp) REVERT: A 1175 TYR cc_start: 0.6748 (p90) cc_final: 0.6000 (p90) REVERT: A 1666 ASN cc_start: 0.7085 (t0) cc_final: 0.5835 (t0) REVERT: A 2177 LYS cc_start: 0.7265 (mmtt) cc_final: 0.6967 (mttt) REVERT: A 2184 LEU cc_start: 0.6525 (OUTLIER) cc_final: 0.6082 (tt) REVERT: A 2197 GLU cc_start: 0.6198 (mm-30) cc_final: 0.5769 (mt-10) REVERT: K 263 ARG cc_start: 0.5092 (mtp180) cc_final: 0.4443 (ptp-170) REVERT: K 311 ARG cc_start: 0.6791 (mtp85) cc_final: 0.6527 (mmm160) outliers start: 40 outliers final: 27 residues processed: 210 average time/residue: 0.3236 time to fit residues: 99.9159 Evaluate side-chains 204 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 173 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 884 THR Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 949 THR Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1051 CYS Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1222 GLU Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1583 MET Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2097 ASP Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2216 THR Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 271 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 108 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 141 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 131 optimal weight: 0.1980 chunk 0 optimal weight: 9.9990 chunk 97 optimal weight: 0.8980 chunk 170 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A1589 GLN ** A1844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17189 Z= 0.200 Angle : 0.623 8.849 23569 Z= 0.312 Chirality : 0.040 0.148 2675 Planarity : 0.005 0.059 2827 Dihedral : 13.719 160.913 3004 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.31 % Favored : 93.37 % Rotamer: Outliers : 2.18 % Allowed : 15.40 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.20), residues: 1885 helix: 0.55 (0.18), residues: 865 sheet: -2.27 (0.36), residues: 199 loop : -1.50 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 5 HIS 0.006 0.001 HIS A1896 PHE 0.019 0.002 PHE A1996 TYR 0.017 0.001 TYR K 458 ARG 0.007 0.000 ARG A1225 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 199 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.6119 (mm-30) cc_final: 0.5802 (tp30) REVERT: A 104 PHE cc_start: 0.7213 (m-80) cc_final: 0.6894 (m-80) REVERT: A 126 GLU cc_start: 0.6519 (mm-30) cc_final: 0.6162 (mm-30) REVERT: A 231 MET cc_start: 0.6209 (mmt) cc_final: 0.5986 (mmm) REVERT: A 303 HIS cc_start: 0.6127 (OUTLIER) cc_final: 0.5287 (t70) REVERT: A 311 LYS cc_start: 0.8250 (mtmm) cc_final: 0.7634 (mptt) REVERT: A 341 HIS cc_start: 0.6925 (m-70) cc_final: 0.6713 (m170) REVERT: A 346 HIS cc_start: 0.7312 (m90) cc_final: 0.6986 (m90) REVERT: A 367 ARG cc_start: 0.7261 (mmm-85) cc_final: 0.7050 (mmm-85) REVERT: A 524 PHE cc_start: 0.6426 (p90) cc_final: 0.5930 (p90) REVERT: A 561 HIS cc_start: 0.5799 (m-70) cc_final: 0.5427 (m-70) REVERT: A 580 LYS cc_start: 0.6779 (pttt) cc_final: 0.6373 (mmtm) REVERT: A 930 LEU cc_start: 0.4772 (OUTLIER) cc_final: 0.4513 (pp) REVERT: A 969 VAL cc_start: 0.6555 (t) cc_final: 0.6273 (m) REVERT: A 977 TYR cc_start: 0.6532 (m-10) cc_final: 0.6209 (m-80) REVERT: A 1175 TYR cc_start: 0.6782 (p90) cc_final: 0.5935 (p90) REVERT: A 1529 LEU cc_start: 0.6535 (mt) cc_final: 0.6085 (mp) REVERT: A 2094 ASP cc_start: 0.6916 (OUTLIER) cc_final: 0.6391 (t70) REVERT: A 2177 LYS cc_start: 0.7201 (mmtt) cc_final: 0.6936 (mttt) REVERT: A 2182 GLU cc_start: 0.6359 (tp30) cc_final: 0.6152 (tp30) REVERT: A 2184 LEU cc_start: 0.6427 (OUTLIER) cc_final: 0.6039 (tt) REVERT: A 2197 GLU cc_start: 0.6153 (mm-30) cc_final: 0.5776 (mt-10) REVERT: K 176 LYS cc_start: 0.5928 (mmtt) cc_final: 0.5430 (ttpp) REVERT: K 263 ARG cc_start: 0.5135 (mtp180) cc_final: 0.4512 (ptp-170) REVERT: K 311 ARG cc_start: 0.6841 (mtp85) cc_final: 0.6561 (mmm160) outliers start: 37 outliers final: 22 residues processed: 220 average time/residue: 0.3335 time to fit residues: 107.3990 Evaluate side-chains 203 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 177 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 813 HIS Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1051 CYS Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1583 MET Chi-restraints excluded: chain A residue 1587 HIS Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2097 ASP Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2216 THR Chi-restraints excluded: chain K residue 144 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 171 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 111 optimal weight: 0.0270 chunk 47 optimal weight: 0.9980 chunk 190 optimal weight: 20.0000 chunk 158 optimal weight: 0.5980 chunk 88 optimal weight: 0.0670 chunk 15 optimal weight: 0.7980 chunk 63 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 245 HIS A1589 GLN ** A1656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 157 GLN ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.2796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17189 Z= 0.174 Angle : 0.613 8.341 23569 Z= 0.305 Chirality : 0.040 0.232 2675 Planarity : 0.004 0.057 2827 Dihedral : 13.619 162.839 3004 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.05 % Favored : 93.63 % Rotamer: Outliers : 2.47 % Allowed : 15.70 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.20), residues: 1885 helix: 0.84 (0.18), residues: 864 sheet: -2.09 (0.36), residues: 202 loop : -1.47 (0.23), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 5 HIS 0.010 0.001 HIS K 194 PHE 0.020 0.002 PHE A 45 TYR 0.024 0.001 TYR A 306 ARG 0.007 0.000 ARG A1225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 195 time to evaluate : 1.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 PHE cc_start: 0.7153 (m-80) cc_final: 0.6901 (m-80) REVERT: A 231 MET cc_start: 0.6178 (mmt) cc_final: 0.5964 (mmm) REVERT: A 303 HIS cc_start: 0.6072 (OUTLIER) cc_final: 0.5249 (t70) REVERT: A 306 TYR cc_start: 0.6028 (t80) cc_final: 0.5752 (t80) REVERT: A 311 LYS cc_start: 0.8196 (mtmm) cc_final: 0.7559 (mptt) REVERT: A 524 PHE cc_start: 0.6345 (p90) cc_final: 0.5886 (p90) REVERT: A 580 LYS cc_start: 0.6721 (pttt) cc_final: 0.6367 (mmtm) REVERT: A 930 LEU cc_start: 0.4739 (OUTLIER) cc_final: 0.4512 (pp) REVERT: A 969 VAL cc_start: 0.6107 (t) cc_final: 0.5907 (m) REVERT: A 977 TYR cc_start: 0.6409 (m-10) cc_final: 0.6104 (m-80) REVERT: A 1083 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.6943 (m-10) REVERT: A 1529 LEU cc_start: 0.6563 (mt) cc_final: 0.6145 (mp) REVERT: A 1673 LEU cc_start: 0.6019 (mp) cc_final: 0.5803 (mp) REVERT: A 1749 ASP cc_start: 0.7272 (t70) cc_final: 0.6664 (t0) REVERT: A 2036 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7321 (t0) REVERT: A 2177 LYS cc_start: 0.7142 (mmtt) cc_final: 0.6903 (mttt) REVERT: A 2184 LEU cc_start: 0.6382 (OUTLIER) cc_final: 0.6013 (tt) REVERT: A 2197 GLU cc_start: 0.6242 (mm-30) cc_final: 0.5839 (mt-10) REVERT: K 176 LYS cc_start: 0.6129 (mmtt) cc_final: 0.5574 (mmtp) REVERT: K 263 ARG cc_start: 0.5164 (mtp180) cc_final: 0.4488 (ptp-170) REVERT: K 311 ARG cc_start: 0.6875 (mtp85) cc_final: 0.6584 (mmm160) outliers start: 42 outliers final: 22 residues processed: 224 average time/residue: 0.3306 time to fit residues: 108.2402 Evaluate side-chains 203 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 176 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 225 GLN Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 930 LEU Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1051 CYS Chi-restraints excluded: chain A residue 1083 PHE Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1583 MET Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2097 ASP Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2209 VAL Chi-restraints excluded: chain A residue 2216 THR Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 150 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 21 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 160 optimal weight: 0.0970 chunk 106 optimal weight: 0.5980 chunk 189 optimal weight: 0.4980 chunk 118 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 87 optimal weight: 0.4980 chunk 117 optimal weight: 0.9980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A1589 GLN ** A1656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.2948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17189 Z= 0.183 Angle : 0.622 11.189 23569 Z= 0.307 Chirality : 0.040 0.295 2675 Planarity : 0.005 0.056 2827 Dihedral : 13.522 163.785 3004 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.10 % Favored : 93.58 % Rotamer: Outliers : 1.94 % Allowed : 16.81 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.20), residues: 1885 helix: 0.99 (0.18), residues: 862 sheet: -2.05 (0.36), residues: 202 loop : -1.41 (0.23), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A2157 HIS 0.007 0.001 HIS A 245 PHE 0.025 0.002 PHE A2171 TYR 0.023 0.001 TYR A 593 ARG 0.007 0.000 ARG A2098 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 188 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 GLU cc_start: 0.5909 (tp30) cc_final: 0.5676 (mm-30) REVERT: A 104 PHE cc_start: 0.7159 (m-80) cc_final: 0.6881 (m-80) REVERT: A 231 MET cc_start: 0.6164 (mmt) cc_final: 0.5963 (mmm) REVERT: A 303 HIS cc_start: 0.6045 (OUTLIER) cc_final: 0.5208 (t70) REVERT: A 311 LYS cc_start: 0.8220 (mtmm) cc_final: 0.7571 (mptt) REVERT: A 341 HIS cc_start: 0.6819 (m170) cc_final: 0.6479 (m90) REVERT: A 524 PHE cc_start: 0.6293 (p90) cc_final: 0.5921 (p90) REVERT: A 580 LYS cc_start: 0.6703 (pttt) cc_final: 0.6389 (mmtm) REVERT: A 816 THR cc_start: 0.6132 (OUTLIER) cc_final: 0.5698 (p) REVERT: A 977 TYR cc_start: 0.6350 (m-10) cc_final: 0.6050 (m-80) REVERT: A 1083 PHE cc_start: 0.7241 (OUTLIER) cc_final: 0.6894 (m-10) REVERT: A 1529 LEU cc_start: 0.6578 (mt) cc_final: 0.6243 (mp) REVERT: A 1633 GLU cc_start: 0.6117 (OUTLIER) cc_final: 0.5711 (pm20) REVERT: A 1673 LEU cc_start: 0.5954 (mp) cc_final: 0.5665 (mp) REVERT: A 2036 ASP cc_start: 0.7559 (OUTLIER) cc_final: 0.7319 (t0) REVERT: A 2184 LEU cc_start: 0.6422 (OUTLIER) cc_final: 0.6140 (tt) REVERT: A 2197 GLU cc_start: 0.6224 (mm-30) cc_final: 0.5852 (mt-10) REVERT: K 176 LYS cc_start: 0.6256 (mmtt) cc_final: 0.5704 (mmtp) REVERT: K 263 ARG cc_start: 0.4908 (mtp180) cc_final: 0.4393 (ptp-170) REVERT: K 311 ARG cc_start: 0.6857 (mtp85) cc_final: 0.6583 (mmm160) outliers start: 33 outliers final: 20 residues processed: 207 average time/residue: 0.3472 time to fit residues: 104.9267 Evaluate side-chains 198 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 172 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1051 CYS Chi-restraints excluded: chain A residue 1071 MET Chi-restraints excluded: chain A residue 1083 PHE Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1583 MET Chi-restraints excluded: chain A residue 1633 GLU Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2209 VAL Chi-restraints excluded: chain A residue 2216 THR Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 150 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 75 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 120 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A1589 GLN ** A1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6768 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 17189 Z= 0.212 Angle : 0.641 10.927 23569 Z= 0.317 Chirality : 0.041 0.259 2675 Planarity : 0.005 0.054 2827 Dihedral : 13.481 162.815 3004 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.26 % Favored : 93.42 % Rotamer: Outliers : 2.18 % Allowed : 16.58 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.20), residues: 1885 helix: 0.99 (0.18), residues: 858 sheet: -2.06 (0.35), residues: 202 loop : -1.37 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 5 HIS 0.008 0.001 HIS A 245 PHE 0.032 0.002 PHE A 45 TYR 0.020 0.001 TYR A 111 ARG 0.008 0.000 ARG A1225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 176 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 PHE cc_start: 0.7168 (m-80) cc_final: 0.6891 (m-80) REVERT: A 231 MET cc_start: 0.6144 (mmt) cc_final: 0.5944 (mmm) REVERT: A 303 HIS cc_start: 0.6062 (OUTLIER) cc_final: 0.5249 (t70) REVERT: A 311 LYS cc_start: 0.8245 (mtmm) cc_final: 0.7587 (mptt) REVERT: A 341 HIS cc_start: 0.6876 (m170) cc_final: 0.6506 (m90) REVERT: A 524 PHE cc_start: 0.6342 (p90) cc_final: 0.5883 (p90) REVERT: A 580 LYS cc_start: 0.6729 (pttt) cc_final: 0.6406 (mmtm) REVERT: A 816 THR cc_start: 0.6091 (OUTLIER) cc_final: 0.5650 (p) REVERT: A 1083 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6858 (m-10) REVERT: A 1529 LEU cc_start: 0.6563 (mt) cc_final: 0.6240 (mp) REVERT: A 2036 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.7365 (t0) REVERT: A 2177 LYS cc_start: 0.7176 (mmtt) cc_final: 0.6908 (mttt) REVERT: A 2184 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.6131 (tt) REVERT: A 2197 GLU cc_start: 0.6240 (mm-30) cc_final: 0.5864 (mt-10) REVERT: K 176 LYS cc_start: 0.6218 (mmtt) cc_final: 0.5636 (mmtp) REVERT: K 311 ARG cc_start: 0.6906 (mtp85) cc_final: 0.6661 (mmm160) outliers start: 37 outliers final: 24 residues processed: 201 average time/residue: 0.3185 time to fit residues: 95.1203 Evaluate side-chains 200 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 171 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TRP Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1051 CYS Chi-restraints excluded: chain A residue 1083 PHE Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1583 MET Chi-restraints excluded: chain A residue 1633 GLU Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2184 LEU Chi-restraints excluded: chain A residue 2209 VAL Chi-restraints excluded: chain A residue 2216 THR Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 271 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 181 optimal weight: 0.0270 chunk 165 optimal weight: 0.9990 chunk 176 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 77 optimal weight: 0.2980 chunk 138 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 159 optimal weight: 0.0070 chunk 167 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1235 GLN A1589 GLN ** A1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6705 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17189 Z= 0.169 Angle : 0.627 13.509 23569 Z= 0.307 Chirality : 0.040 0.325 2675 Planarity : 0.005 0.058 2827 Dihedral : 13.414 165.107 3004 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.32 % Allowed : 6.10 % Favored : 93.58 % Rotamer: Outliers : 1.70 % Allowed : 17.11 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.20), residues: 1885 helix: 1.08 (0.18), residues: 868 sheet: -1.83 (0.36), residues: 195 loop : -1.33 (0.23), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2157 HIS 0.007 0.001 HIS A 245 PHE 0.033 0.002 PHE A 45 TYR 0.026 0.001 TYR A 593 ARG 0.008 0.000 ARG A2098 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 184 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 PHE cc_start: 0.7160 (m-80) cc_final: 0.6862 (m-80) REVERT: A 124 LEU cc_start: 0.6827 (mm) cc_final: 0.6594 (mm) REVERT: A 303 HIS cc_start: 0.5946 (OUTLIER) cc_final: 0.5091 (t70) REVERT: A 306 TYR cc_start: 0.5890 (t80) cc_final: 0.5525 (t80) REVERT: A 311 LYS cc_start: 0.8270 (mtmm) cc_final: 0.7625 (mmtt) REVERT: A 341 HIS cc_start: 0.6799 (m170) cc_final: 0.6424 (m90) REVERT: A 580 LYS cc_start: 0.6716 (pttt) cc_final: 0.6428 (mmtm) REVERT: A 816 THR cc_start: 0.6257 (OUTLIER) cc_final: 0.5833 (p) REVERT: A 867 LEU cc_start: 0.7870 (mt) cc_final: 0.7647 (mt) REVERT: A 977 TYR cc_start: 0.6249 (m-10) cc_final: 0.6035 (m-80) REVERT: A 1083 PHE cc_start: 0.7226 (OUTLIER) cc_final: 0.6882 (m-10) REVERT: A 1223 THR cc_start: 0.6761 (OUTLIER) cc_final: 0.6494 (m) REVERT: A 1529 LEU cc_start: 0.6524 (mt) cc_final: 0.6211 (mp) REVERT: A 1633 GLU cc_start: 0.6094 (OUTLIER) cc_final: 0.5740 (pm20) REVERT: A 2036 ASP cc_start: 0.7572 (OUTLIER) cc_final: 0.7340 (t0) REVERT: A 2197 GLU cc_start: 0.6207 (mm-30) cc_final: 0.5891 (mt-10) REVERT: K 176 LYS cc_start: 0.6175 (mmtt) cc_final: 0.5637 (mmtp) REVERT: K 311 ARG cc_start: 0.6921 (mtp85) cc_final: 0.6693 (mmm160) outliers start: 29 outliers final: 20 residues processed: 201 average time/residue: 0.3073 time to fit residues: 93.3913 Evaluate side-chains 197 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 171 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TRP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1083 PHE Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1583 MET Chi-restraints excluded: chain A residue 1633 GLU Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2209 VAL Chi-restraints excluded: chain A residue 2216 THR Chi-restraints excluded: chain A residue 2223 ASN Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 271 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 114 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 chunk 180 optimal weight: 0.8980 chunk 156 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 95 optimal weight: 0.0070 chunk 124 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 overall best weight: 0.7202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS ** A 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1589 GLN ** A1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 17189 Z= 0.204 Angle : 0.647 13.305 23569 Z= 0.318 Chirality : 0.040 0.316 2675 Planarity : 0.005 0.055 2827 Dihedral : 13.347 164.144 3004 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.21 % Favored : 93.42 % Rotamer: Outliers : 1.70 % Allowed : 17.23 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.20), residues: 1885 helix: 1.08 (0.18), residues: 866 sheet: -1.83 (0.36), residues: 195 loop : -1.33 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 5 HIS 0.008 0.001 HIS A 179 PHE 0.038 0.002 PHE A 45 TYR 0.022 0.001 TYR A 306 ARG 0.009 0.000 ARG A1114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3770 Ramachandran restraints generated. 1885 Oldfield, 0 Emsley, 1885 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 172 time to evaluate : 1.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 PHE cc_start: 0.7225 (m-80) cc_final: 0.6910 (m-80) REVERT: A 124 LEU cc_start: 0.6899 (mm) cc_final: 0.6690 (mm) REVERT: A 303 HIS cc_start: 0.6018 (OUTLIER) cc_final: 0.5164 (t70) REVERT: A 306 TYR cc_start: 0.5858 (t80) cc_final: 0.5480 (t80) REVERT: A 311 LYS cc_start: 0.8290 (mtmm) cc_final: 0.7638 (mmtt) REVERT: A 341 HIS cc_start: 0.6823 (m170) cc_final: 0.6423 (m90) REVERT: A 580 LYS cc_start: 0.6729 (pttt) cc_final: 0.6420 (mmtm) REVERT: A 816 THR cc_start: 0.6208 (OUTLIER) cc_final: 0.5777 (p) REVERT: A 1083 PHE cc_start: 0.7214 (OUTLIER) cc_final: 0.6854 (m-10) REVERT: A 1223 THR cc_start: 0.6797 (OUTLIER) cc_final: 0.6549 (m) REVERT: A 1666 ASN cc_start: 0.8138 (p0) cc_final: 0.7938 (p0) REVERT: A 2036 ASP cc_start: 0.7551 (OUTLIER) cc_final: 0.7326 (t0) REVERT: A 2197 GLU cc_start: 0.6220 (mm-30) cc_final: 0.5900 (mt-10) REVERT: K 311 ARG cc_start: 0.6911 (mtp85) cc_final: 0.6687 (mmm160) outliers start: 29 outliers final: 24 residues processed: 191 average time/residue: 0.3067 time to fit residues: 88.9976 Evaluate side-chains 198 residues out of total 1701 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 169 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TRP Chi-restraints excluded: chain A residue 84 MET Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 816 THR Chi-restraints excluded: chain A residue 839 ASP Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 913 ILE Chi-restraints excluded: chain A residue 993 THR Chi-restraints excluded: chain A residue 1051 CYS Chi-restraints excluded: chain A residue 1083 PHE Chi-restraints excluded: chain A residue 1154 ILE Chi-restraints excluded: chain A residue 1223 THR Chi-restraints excluded: chain A residue 1583 MET Chi-restraints excluded: chain A residue 1633 GLU Chi-restraints excluded: chain A residue 1754 TYR Chi-restraints excluded: chain A residue 1816 VAL Chi-restraints excluded: chain A residue 1896 HIS Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2209 VAL Chi-restraints excluded: chain A residue 2216 THR Chi-restraints excluded: chain A residue 2223 ASN Chi-restraints excluded: chain K residue 144 LEU Chi-restraints excluded: chain K residue 150 THR Chi-restraints excluded: chain K residue 271 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 197 random chunks: chunk 47 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 23 optimal weight: 8.9990 chunk 43 optimal weight: 0.2980 chunk 156 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 160 optimal weight: 0.0030 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 5.9990 chunk 137 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS A 341 HIS A1589 GLN ** A1590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1844 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 383 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.189679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.157200 restraints weight = 26555.183| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 2.54 r_work: 0.3968 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 17189 Z= 0.179 Angle : 0.634 13.280 23569 Z= 0.312 Chirality : 0.040 0.355 2675 Planarity : 0.005 0.057 2827 Dihedral : 13.293 164.882 3004 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.37 % Allowed : 6.21 % Favored : 93.42 % Rotamer: Outliers : 1.76 % Allowed : 17.40 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.20), residues: 1885 helix: 1.14 (0.18), residues: 865 sheet: -1.77 (0.36), residues: 195 loop : -1.33 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A2157 HIS 0.007 0.001 HIS A 245 PHE 0.055 0.002 PHE A2171 TYR 0.021 0.001 TYR A 306 ARG 0.009 0.000 ARG A2098 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3623.69 seconds wall clock time: 66 minutes 48.67 seconds (4008.67 seconds total)