Starting phenix.real_space_refine on Thu Sep 26 18:36:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgi_27423/09_2024/8dgi_27423.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgi_27423/09_2024/8dgi_27423.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgi_27423/09_2024/8dgi_27423.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgi_27423/09_2024/8dgi_27423.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgi_27423/09_2024/8dgi_27423.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgi_27423/09_2024/8dgi_27423.cif" } resolution = 3.94 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= 0.008 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: 4 Type Number sf(0) Gaussians S 74 5.16 5 C 8608 2.51 5 N 2384 2.21 5 O 2514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13580 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 12733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1582, 12733 Classifications: {'peptide': 1582} Link IDs: {'PTRANS': 96, 'TRANS': 1485} Chain breaks: 9 Chain: "N" Number of atoms: 847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 847 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 105} Time building chain proxies: 8.80, per 1000 atoms: 0.65 Number of scatterers: 13580 At special positions: 0 Unit cell: (153.12, 134.85, 135.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 74 16.00 O 2514 8.00 N 2384 7.00 C 8608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.01 Conformation dependent library (CDL) restraints added in 1.6 seconds 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3222 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 10 sheets defined 51.0% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 removed outlier: 3.774A pdb=" N ARG A 31 " --> pdb=" O THR A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 61 removed outlier: 3.823A pdb=" N LYS A 43 " --> pdb=" O HIS A 39 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ARG A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ARG A 60 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N HIS A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 88 Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.737A pdb=" N VAL A 135 " --> pdb=" O LEU A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 160 Proline residue: A 154 - end of helix removed outlier: 3.593A pdb=" N HIS A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.535A pdb=" N ARG A 168 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 184 through 200 Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 232 through 252 Processing helix chain 'A' and resid 255 through 260 Processing helix chain 'A' and resid 267 through 272 removed outlier: 4.004A pdb=" N ASP A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 293 Processing helix chain 'A' and resid 294 through 316 removed outlier: 4.114A pdb=" N LYS A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 316 " --> pdb=" O LEU A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 346 removed outlier: 3.515A pdb=" N TYR A 322 " --> pdb=" O HIS A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 361 removed outlier: 3.508A pdb=" N TYR A 360 " --> pdb=" O THR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 374 Processing helix chain 'A' and resid 501 through 517 Processing helix chain 'A' and resid 540 through 560 removed outlier: 3.855A pdb=" N MET A 560 " --> pdb=" O LYS A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 573 Processing helix chain 'A' and resid 592 through 603 removed outlier: 3.857A pdb=" N ALA A 603 " --> pdb=" O CYS A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 783 Processing helix chain 'A' and resid 791 through 802 Processing helix chain 'A' and resid 824 through 835 Processing helix chain 'A' and resid 884 through 904 Processing helix chain 'A' and resid 921 through 929 removed outlier: 5.266A pdb=" N GLU A 926 " --> pdb=" O PRO A 923 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N CYS A 927 " --> pdb=" O ASP A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1062 Processing helix chain 'A' and resid 1098 through 1108 Processing helix chain 'A' and resid 1117 through 1123 Processing helix chain 'A' and resid 1171 through 1180 Processing helix chain 'A' and resid 1204 through 1208 Processing helix chain 'A' and resid 1223 through 1231 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 1256 Processing helix chain 'A' and resid 1261 through 1268 removed outlier: 3.566A pdb=" N ILE A1265 " --> pdb=" O ILE A1261 " (cutoff:3.500A) Processing helix chain 'A' and resid 1269 through 1283 Processing helix chain 'A' and resid 1519 through 1535 removed outlier: 4.240A pdb=" N THR A1535 " --> pdb=" O ILE A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1537 through 1547 removed outlier: 3.612A pdb=" N GLN A1541 " --> pdb=" O ALA A1537 " (cutoff:3.500A) Processing helix chain 'A' and resid 1562 through 1579 removed outlier: 3.516A pdb=" N ARG A1566 " --> pdb=" O PRO A1562 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N SER A1570 " --> pdb=" O ARG A1566 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1616 Processing helix chain 'A' and resid 1620 through 1629 removed outlier: 3.722A pdb=" N LEU A1624 " --> pdb=" O ASN A1620 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1650 Processing helix chain 'A' and resid 1665 through 1669 removed outlier: 4.481A pdb=" N ASN A1668 " --> pdb=" O ASP A1665 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1731 removed outlier: 4.027A pdb=" N ILE A1726 " --> pdb=" O SER A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1764 removed outlier: 3.674A pdb=" N THR A1746 " --> pdb=" O GLU A1742 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ILE A1747 " --> pdb=" O ARG A1743 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N SER A1750 " --> pdb=" O THR A1746 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS A1753 " --> pdb=" O ASP A1749 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A1754 " --> pdb=" O SER A1750 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N THR A1758 " --> pdb=" O TYR A1754 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A1759 " --> pdb=" O ALA A1755 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR A1764 " --> pdb=" O LEU A1760 " (cutoff:3.500A) Processing helix chain 'A' and resid 1768 through 1780 removed outlier: 3.939A pdb=" N LEU A1772 " --> pdb=" O HIS A1768 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N HIS A1774 " --> pdb=" O GLY A1770 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1792 removed outlier: 3.806A pdb=" N LYS A1792 " --> pdb=" O LEU A1788 " (cutoff:3.500A) Processing helix chain 'A' and resid 1899 through 1914 removed outlier: 3.504A pdb=" N ILE A1903 " --> pdb=" O PRO A1899 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA A1904 " --> pdb=" O ASP A1900 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA A1909 " --> pdb=" O ASP A1905 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ILE A1911 " --> pdb=" O VAL A1907 " (cutoff:3.500A) Processing helix chain 'A' and resid 1920 through 1931 removed outlier: 3.581A pdb=" N MET A1927 " --> pdb=" O ALA A1923 " (cutoff:3.500A) Processing helix chain 'A' and resid 1981 through 1990 removed outlier: 4.340A pdb=" N LEU A1990 " --> pdb=" O LEU A1986 " (cutoff:3.500A) Processing helix chain 'A' and resid 1992 through 2001 removed outlier: 3.600A pdb=" N PHE A1996 " --> pdb=" O GLY A1992 " (cutoff:3.500A) Processing helix chain 'A' and resid 2007 through 2014 Processing helix chain 'A' and resid 2030 through 2050 removed outlier: 3.750A pdb=" N LEU A2034 " --> pdb=" O ARG A2030 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ALA A2037 " --> pdb=" O PHE A2033 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP A2050 " --> pdb=" O HIS A2046 " (cutoff:3.500A) Processing helix chain 'A' and resid 2055 through 2067 Processing helix chain 'A' and resid 2068 through 2079 removed outlier: 3.934A pdb=" N PHE A2072 " --> pdb=" O ASN A2068 " (cutoff:3.500A) Processing helix chain 'A' and resid 2091 through 2107 Processing helix chain 'A' and resid 2110 through 2121 removed outlier: 5.117A pdb=" N SER A2118 " --> pdb=" O TYR A2114 " (cutoff:3.500A) Processing helix chain 'A' and resid 2132 through 2149 removed outlier: 3.941A pdb=" N PHE A2138 " --> pdb=" O LEU A2134 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA A2142 " --> pdb=" O PHE A2138 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A2143 " --> pdb=" O GLU A2139 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER A2149 " --> pdb=" O ILE A2145 " (cutoff:3.500A) Processing helix chain 'A' and resid 2152 through 2172 removed outlier: 3.567A pdb=" N VAL A2156 " --> pdb=" O SER A2152 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ASN A2162 " --> pdb=" O HIS A2158 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N MET A2163 " --> pdb=" O VAL A2159 " (cutoff:3.500A) Proline residue: A2166 - end of helix Processing helix chain 'A' and resid 2178 through 2187 Processing helix chain 'A' and resid 2223 through 2240 Processing helix chain 'N' and resid 359 through 372 Processing helix chain 'N' and resid 376 through 385 Processing helix chain 'N' and resid 394 through 405 Processing helix chain 'N' and resid 443 through 463 Processing sheet with id=AA1, first strand: chain 'A' and resid 137 through 140 removed outlier: 5.435A pdb=" N ILE A 34 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 68 removed outlier: 6.438A pdb=" N SER A 65 " --> pdb=" O SER A 114 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU A 116 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N TYR A 67 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 527 through 529 removed outlier: 6.771A pdb=" N GLN A 528 " --> pdb=" O ILE A 567 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N VAL A1585 " --> pdb=" O GLU A 221 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE A 223 " --> pdb=" O VAL A1585 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 847 through 855 Processing sheet with id=AA5, first strand: chain 'A' and resid 1022 through 1026 removed outlier: 3.942A pdb=" N PHE A1022 " --> pdb=" O VAL A1033 " (cutoff:3.500A) removed outlier: 5.874A pdb=" N LYS A1032 " --> pdb=" O LEU A 983 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N LEU A 983 " --> pdb=" O LYS A1032 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N SER A1034 " --> pdb=" O LEU A 981 " (cutoff:3.500A) removed outlier: 5.258A pdb=" N LEU A 981 " --> pdb=" O SER A1034 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLU A1036 " --> pdb=" O ILE A 979 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ILE A 979 " --> pdb=" O GLU A1036 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N PHE A1008 " --> pdb=" O ILE A 979 " (cutoff:3.500A) removed outlier: 8.495A pdb=" N LEU A 981 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 10.060A pdb=" N GLN A1006 " --> pdb=" O LEU A 981 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1236 through 1237 removed outlier: 7.273A pdb=" N LEU A1191 " --> pdb=" O ILE A1154 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ILE A1154 " --> pdb=" O LEU A1191 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASP A1193 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1937 through 1940 Processing sheet with id=AA8, first strand: chain 'A' and resid 2191 through 2193 Processing sheet with id=AA9, first strand: chain 'A' and resid 2191 through 2193 Processing sheet with id=AB1, first strand: chain 'N' and resid 409 through 414 removed outlier: 4.551A pdb=" N GLN N 424 " --> pdb=" O ILE N 414 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1839 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.41 Time building geometry restraints manager: 3.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4471 1.34 - 1.46: 2789 1.46 - 1.58: 6516 1.58 - 1.70: 3 1.70 - 1.82: 100 Bond restraints: 13879 Sorted by residual: bond pdb=" C GLU A 922 " pdb=" N PRO A 923 " ideal model delta sigma weight residual 1.336 1.376 -0.040 1.08e-02 8.57e+03 1.36e+01 bond pdb=" C LYS A2083 " pdb=" N PHE A2084 " ideal model delta sigma weight residual 1.332 1.374 -0.041 1.40e-02 5.10e+03 8.64e+00 bond pdb=" C VAL A2175 " pdb=" N PRO A2176 " ideal model delta sigma weight residual 1.334 1.401 -0.067 2.34e-02 1.83e+03 8.22e+00 bond pdb=" N ASP A 90 " pdb=" CA ASP A 90 " ideal model delta sigma weight residual 1.463 1.434 0.029 1.23e-02 6.61e+03 5.65e+00 bond pdb=" C VAL A2130 " pdb=" N PRO A2131 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 4.89e+00 ... (remaining 13874 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.42: 18426 3.42 - 6.83: 305 6.83 - 10.25: 67 10.25 - 13.66: 13 13.66 - 17.08: 5 Bond angle restraints: 18816 Sorted by residual: angle pdb=" N ARG A2030 " pdb=" CA ARG A2030 " pdb=" C ARG A2030 " ideal model delta sigma weight residual 114.75 106.58 8.17 1.26e+00 6.30e-01 4.20e+01 angle pdb=" CA ARG A1566 " pdb=" CB ARG A1566 " pdb=" CG ARG A1566 " ideal model delta sigma weight residual 114.10 125.30 -11.20 2.00e+00 2.50e-01 3.14e+01 angle pdb=" N PRO A 256 " pdb=" CD PRO A 256 " pdb=" CG PRO A 256 " ideal model delta sigma weight residual 103.20 95.23 7.97 1.50e+00 4.44e-01 2.82e+01 angle pdb=" CA PRO A 256 " pdb=" N PRO A 256 " pdb=" CD PRO A 256 " ideal model delta sigma weight residual 112.00 104.70 7.30 1.40e+00 5.10e-01 2.72e+01 angle pdb=" CA GLN N 406 " pdb=" CB GLN N 406 " pdb=" CG GLN N 406 " ideal model delta sigma weight residual 114.10 124.32 -10.22 2.00e+00 2.50e-01 2.61e+01 ... (remaining 18811 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.22: 7380 18.22 - 36.45: 888 36.45 - 54.67: 160 54.67 - 72.90: 30 72.90 - 91.12: 11 Dihedral angle restraints: 8469 sinusoidal: 3504 harmonic: 4965 Sorted by residual: dihedral pdb=" CA THR A1205 " pdb=" C THR A1205 " pdb=" N PRO A1206 " pdb=" CA PRO A1206 " ideal model delta harmonic sigma weight residual -180.00 -133.56 -46.44 0 5.00e+00 4.00e-02 8.63e+01 dihedral pdb=" CA LEU A2116 " pdb=" C LEU A2116 " pdb=" N LEU A2117 " pdb=" CA LEU A2117 " ideal model delta harmonic sigma weight residual 180.00 148.49 31.51 0 5.00e+00 4.00e-02 3.97e+01 dihedral pdb=" CA ILE A2110 " pdb=" C ILE A2110 " pdb=" N SER A2111 " pdb=" CA SER A2111 " ideal model delta harmonic sigma weight residual -180.00 -151.47 -28.53 0 5.00e+00 4.00e-02 3.26e+01 ... (remaining 8466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1750 0.069 - 0.139: 292 0.139 - 0.208: 45 0.208 - 0.278: 7 0.278 - 0.347: 4 Chirality restraints: 2098 Sorted by residual: chirality pdb=" CB VAL A 554 " pdb=" CA VAL A 554 " pdb=" CG1 VAL A 554 " pdb=" CG2 VAL A 554 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA MET A 161 " pdb=" N MET A 161 " pdb=" C MET A 161 " pdb=" CB MET A 161 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CA TYR A2041 " pdb=" N TYR A2041 " pdb=" C TYR A2041 " pdb=" CB TYR A2041 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 2095 not shown) Planarity restraints: 2448 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A2041 " 0.039 2.00e-02 2.50e+03 2.30e-02 1.06e+01 pdb=" CG TYR A2041 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A2041 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR A2041 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A2041 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR A2041 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A2041 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR A2041 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 532 " -0.016 2.00e-02 2.50e+03 3.11e-02 9.69e+00 pdb=" C ASP A 532 " 0.054 2.00e-02 2.50e+03 pdb=" O ASP A 532 " -0.021 2.00e-02 2.50e+03 pdb=" N ARG A 533 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU N 432 " 0.051 5.00e-02 4.00e+02 7.76e-02 9.65e+00 pdb=" N PRO N 433 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO N 433 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO N 433 " 0.038 5.00e-02 4.00e+02 ... (remaining 2445 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3153 2.79 - 3.32: 12530 3.32 - 3.85: 23811 3.85 - 4.37: 26896 4.37 - 4.90: 43684 Nonbonded interactions: 110074 Sorted by model distance: nonbonded pdb=" OG SER A1750 " pdb=" OD2 ASP A2040 " model vdw 2.263 3.040 nonbonded pdb=" O ASP A2040 " pdb=" OG1 THR A2044 " model vdw 2.268 3.040 nonbonded pdb=" OE1 GLU A 221 " pdb=" OH TYR A 596 " model vdw 2.275 3.040 nonbonded pdb=" O PRO A 868 " pdb=" OG SER A 871 " model vdw 2.291 3.040 nonbonded pdb=" OH TYR A2002 " pdb=" OD1 ASP A2148 " model vdw 2.306 3.040 ... (remaining 110069 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.700 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: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 33.490 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.060 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5162 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 13879 Z= 0.356 Angle : 1.162 17.078 18816 Z= 0.605 Chirality : 0.055 0.347 2098 Planarity : 0.009 0.087 2448 Dihedral : 15.934 91.123 5247 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.88 % Favored : 93.82 % Rotamer: Outliers : 0.67 % Allowed : 21.65 % Favored : 77.68 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -2.32 (0.18), residues: 1668 helix: -1.62 (0.15), residues: 791 sheet: -0.16 (0.38), residues: 189 loop : -1.68 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1968 HIS 0.015 0.001 HIS A 87 PHE 0.037 0.003 PHE A2072 TYR 0.039 0.002 TYR A2041 ARG 0.016 0.001 ARG A1566 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 132 time to evaluate : 1.578 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 315 LYS cc_start: 0.8179 (tmtt) cc_final: 0.7832 (tptp) outliers start: 10 outliers final: 3 residues processed: 137 average time/residue: 0.2740 time to fit residues: 54.6190 Evaluate side-chains 121 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 ARG Chi-restraints excluded: chain A residue 841 PHE Chi-restraints excluded: chain A residue 2054 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.0870 chunk 127 optimal weight: 0.6980 chunk 70 optimal weight: 20.0000 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 40.0000 chunk 68 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 152 optimal weight: 7.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 HIS A 773 GLN A 895 GLN ** A1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1774 HIS ** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2029 GLN A2054 HIS N 389 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5317 moved from start: 0.1212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 13879 Z= 0.229 Angle : 0.705 11.013 18816 Z= 0.356 Chirality : 0.043 0.168 2098 Planarity : 0.006 0.069 2448 Dihedral : 5.663 43.418 1864 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.28 % Favored : 94.48 % Rotamer: Outliers : 3.00 % Allowed : 18.65 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -1.18 (0.20), residues: 1668 helix: -0.40 (0.17), residues: 805 sheet: -0.21 (0.38), residues: 193 loop : -1.29 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 848 HIS 0.009 0.001 HIS A2087 PHE 0.023 0.002 PHE A2085 TYR 0.032 0.002 TYR A2041 ARG 0.005 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 127 time to evaluate : 1.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.5526 (OUTLIER) cc_final: 0.4990 (pp) REVERT: A 286 LEU cc_start: 0.5082 (mt) cc_final: 0.4723 (mt) REVERT: A 315 LYS cc_start: 0.7912 (tmtt) cc_final: 0.7709 (tptp) REVERT: A 1137 MET cc_start: 0.1725 (OUTLIER) cc_final: 0.1257 (mmp) REVERT: A 1776 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6710 (ttm170) REVERT: A 1975 LEU cc_start: 0.4908 (tp) cc_final: 0.4434 (mt) REVERT: A 2138 PHE cc_start: 0.4447 (t80) cc_final: 0.3511 (t80) outliers start: 45 outliers final: 22 residues processed: 162 average time/residue: 0.2735 time to fit residues: 64.3672 Evaluate side-chains 139 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 114 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 201 CYS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1768 HIS Chi-restraints excluded: chain A residue 1776 ARG Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1973 SER Chi-restraints excluded: chain A residue 2028 TYR Chi-restraints excluded: chain A residue 2034 LEU Chi-restraints excluded: chain A residue 2046 HIS Chi-restraints excluded: chain A residue 2069 ASN Chi-restraints excluded: chain A residue 2070 THR Chi-restraints excluded: chain A residue 2089 SER Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain N residue 392 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 152 optimal weight: 4.9990 chunk 165 optimal weight: 0.0870 chunk 136 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 122 optimal weight: 2.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 HIS ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1067 GLN ** A1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2054 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5397 moved from start: 0.1870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13879 Z= 0.232 Angle : 0.688 11.124 18816 Z= 0.340 Chirality : 0.044 0.212 2098 Planarity : 0.005 0.068 2448 Dihedral : 5.264 44.600 1856 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.41 % Favored : 93.35 % Rotamer: Outliers : 4.00 % Allowed : 18.25 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.69 (0.21), residues: 1668 helix: 0.11 (0.18), residues: 806 sheet: -0.47 (0.39), residues: 181 loop : -1.03 (0.25), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 848 HIS 0.008 0.001 HIS A2087 PHE 0.022 0.002 PHE A 45 TYR 0.026 0.002 TYR A2028 ARG 0.006 0.000 ARG A 550 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 121 time to evaluate : 1.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.5498 (OUTLIER) cc_final: 0.5033 (pp) REVERT: A 286 LEU cc_start: 0.5333 (mt) cc_final: 0.4923 (mt) REVERT: A 572 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6576 (tt) REVERT: A 1137 MET cc_start: 0.1727 (OUTLIER) cc_final: 0.1212 (mmp) REVERT: A 1749 ASP cc_start: 0.7577 (t0) cc_final: 0.7213 (t0) REVERT: A 1776 ARG cc_start: 0.6980 (OUTLIER) cc_final: 0.6735 (ttm170) REVERT: A 2020 THR cc_start: 0.6510 (OUTLIER) cc_final: 0.5288 (t) REVERT: A 2041 TYR cc_start: 0.5584 (t80) cc_final: 0.5327 (t80) REVERT: N 462 MET cc_start: 0.8203 (OUTLIER) cc_final: 0.7925 (mtt) outliers start: 60 outliers final: 31 residues processed: 168 average time/residue: 0.2478 time to fit residues: 62.4662 Evaluate side-chains 143 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 106 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 572 LEU Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1768 HIS Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1776 ARG Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 1973 SER Chi-restraints excluded: chain A residue 2020 THR Chi-restraints excluded: chain A residue 2028 TYR Chi-restraints excluded: chain A residue 2034 LEU Chi-restraints excluded: chain A residue 2046 HIS Chi-restraints excluded: chain A residue 2069 ASN Chi-restraints excluded: chain A residue 2070 THR Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2158 HIS Chi-restraints excluded: chain N residue 392 ILE Chi-restraints excluded: chain N residue 462 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 153 optimal weight: 40.0000 chunk 162 optimal weight: 5.9990 chunk 80 optimal weight: 20.0000 chunk 145 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 HIS ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1533 GLN A1559 GLN A1656 ASN ** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2012 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2093 ASN A2103 GLN ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 448 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5834 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.097 13879 Z= 0.503 Angle : 0.961 13.326 18816 Z= 0.486 Chirality : 0.051 0.238 2098 Planarity : 0.007 0.072 2448 Dihedral : 6.292 45.637 1856 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 26.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.51 % Favored : 91.31 % Rotamer: Outliers : 6.93 % Allowed : 18.12 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.19 % 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: -1.56 (0.20), residues: 1668 helix: -0.60 (0.17), residues: 798 sheet: -1.23 (0.38), residues: 184 loop : -1.36 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 848 HIS 0.014 0.002 HIS A 179 PHE 0.034 0.003 PHE A1552 TYR 0.046 0.003 TYR A2028 ARG 0.010 0.001 ARG A1264 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 112 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.6520 (OUTLIER) cc_final: 0.6145 (pp) REVERT: A 873 LEU cc_start: 0.6075 (OUTLIER) cc_final: 0.5758 (mp) REVERT: A 1137 MET cc_start: 0.2436 (mmp) cc_final: 0.1726 (mmp) REVERT: A 1749 ASP cc_start: 0.7870 (t0) cc_final: 0.7638 (t0) REVERT: A 1776 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6446 (ttm170) REVERT: A 2094 ASP cc_start: 0.5423 (OUTLIER) cc_final: 0.4447 (p0) outliers start: 104 outliers final: 68 residues processed: 200 average time/residue: 0.2373 time to fit residues: 71.9033 Evaluate side-chains 174 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 102 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ASP Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 252 HIS Chi-restraints excluded: chain A residue 297 CYS Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 560 MET Chi-restraints excluded: chain A residue 563 CYS Chi-restraints excluded: chain A residue 564 ASN Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 782 LEU Chi-restraints excluded: chain A residue 783 SER Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 843 LYS Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 871 SER Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 1041 ARG Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1238 VAL Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1276 LYS Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1550 ILE Chi-restraints excluded: chain A residue 1623 VAL Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1774 HIS Chi-restraints excluded: chain A residue 1776 ARG Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1896 HIS Chi-restraints excluded: chain A residue 1917 GLU Chi-restraints excluded: chain A residue 2015 THR Chi-restraints excluded: chain A residue 2020 THR Chi-restraints excluded: chain A residue 2025 THR Chi-restraints excluded: chain A residue 2028 TYR Chi-restraints excluded: chain A residue 2034 LEU Chi-restraints excluded: chain A residue 2036 ASP Chi-restraints excluded: chain A residue 2043 ILE Chi-restraints excluded: chain A residue 2046 HIS Chi-restraints excluded: chain A residue 2069 ASN Chi-restraints excluded: chain A residue 2070 THR Chi-restraints excluded: chain A residue 2071 ILE Chi-restraints excluded: chain A residue 2089 SER Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2113 GLU Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2153 LEU Chi-restraints excluded: chain A residue 2158 HIS Chi-restraints excluded: chain A residue 2175 VAL Chi-restraints excluded: chain N residue 392 ILE Chi-restraints excluded: chain N residue 427 VAL Chi-restraints excluded: chain N residue 462 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 2 optimal weight: 0.3980 chunk 120 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 138 optimal weight: 0.5980 chunk 112 optimal weight: 0.0970 chunk 0 optimal weight: 3.9990 chunk 82 optimal weight: 6.9990 chunk 145 optimal weight: 0.2980 chunk 40 optimal weight: 0.2980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1536 ASN A1671 HIS A1766 ASN A1782 ASN ** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2012 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5485 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 13879 Z= 0.203 Angle : 0.697 11.882 18816 Z= 0.341 Chirality : 0.044 0.189 2098 Planarity : 0.005 0.068 2448 Dihedral : 5.397 44.736 1856 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.24 % Favored : 93.71 % Rotamer: Outliers : 3.20 % Allowed : 20.79 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.87 (0.21), residues: 1668 helix: 0.06 (0.18), residues: 809 sheet: -0.93 (0.39), residues: 175 loop : -1.14 (0.25), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1139 HIS 0.009 0.001 HIS A2087 PHE 0.020 0.002 PHE A2138 TYR 0.023 0.002 TYR A2009 ARG 0.004 0.000 ARG A 170 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 117 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.6205 (OUTLIER) cc_final: 0.5814 (pp) REVERT: A 204 GLU cc_start: 0.7555 (tp30) cc_final: 0.7183 (pt0) REVERT: A 286 LEU cc_start: 0.5642 (mt) cc_final: 0.5268 (mt) REVERT: A 873 LEU cc_start: 0.5631 (OUTLIER) cc_final: 0.5170 (mp) REVERT: A 1011 LEU cc_start: 0.7338 (tp) cc_final: 0.7104 (mm) REVERT: A 1041 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.7109 (mmp-170) REVERT: A 1137 MET cc_start: 0.2372 (OUTLIER) cc_final: 0.1740 (mmp) REVERT: A 1633 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6620 (pp20) REVERT: A 2094 ASP cc_start: 0.4945 (OUTLIER) cc_final: 0.4472 (p0) outliers start: 48 outliers final: 27 residues processed: 158 average time/residue: 0.2527 time to fit residues: 59.6563 Evaluate side-chains 135 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 102 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 GLU Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 1041 ARG Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1633 GLU Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1760 LEU Chi-restraints excluded: chain A residue 1768 HIS Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 1973 SER Chi-restraints excluded: chain A residue 2046 HIS Chi-restraints excluded: chain A residue 2070 THR Chi-restraints excluded: chain A residue 2089 SER Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2158 HIS Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain N residue 392 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 10.0000 chunk 146 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 40 optimal weight: 0.9980 chunk 162 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 75 optimal weight: 20.0000 chunk 13 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 HIS ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 454 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5574 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 13879 Z= 0.239 Angle : 0.713 13.139 18816 Z= 0.350 Chirality : 0.045 0.419 2098 Planarity : 0.005 0.068 2448 Dihedral : 5.327 44.864 1856 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.43 % Favored : 92.51 % Rotamer: Outliers : 3.93 % Allowed : 20.79 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.82 (0.21), residues: 1668 helix: 0.14 (0.18), residues: 810 sheet: -0.94 (0.39), residues: 175 loop : -1.15 (0.25), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1968 HIS 0.008 0.001 HIS A2087 PHE 0.021 0.002 PHE A2138 TYR 0.030 0.002 TYR A1567 ARG 0.007 0.000 ARG A1566 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 114 time to evaluate : 1.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.6338 (OUTLIER) cc_final: 0.5934 (pp) REVERT: A 204 GLU cc_start: 0.7647 (tp30) cc_final: 0.7219 (pt0) REVERT: A 510 GLU cc_start: 0.7373 (tt0) cc_final: 0.7087 (tt0) REVERT: A 873 LEU cc_start: 0.5882 (OUTLIER) cc_final: 0.5459 (mp) REVERT: A 1137 MET cc_start: 0.2446 (OUTLIER) cc_final: 0.1776 (mmp) REVERT: A 1542 TYR cc_start: 0.6994 (m-80) cc_final: 0.6742 (m-80) REVERT: A 1633 GLU cc_start: 0.7392 (OUTLIER) cc_final: 0.6619 (pp20) REVERT: A 2094 ASP cc_start: 0.5060 (OUTLIER) cc_final: 0.4653 (p0) outliers start: 59 outliers final: 46 residues processed: 165 average time/residue: 0.2429 time to fit residues: 61.1855 Evaluate side-chains 156 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 105 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 25 LEU 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 83 THR Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 1041 ARG Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1567 TYR Chi-restraints excluded: chain A residue 1633 GLU Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1768 HIS Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 1896 HIS Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 1968 TRP Chi-restraints excluded: chain A residue 2020 THR Chi-restraints excluded: chain A residue 2034 LEU Chi-restraints excluded: chain A residue 2046 HIS Chi-restraints excluded: chain A residue 2070 THR Chi-restraints excluded: chain A residue 2094 ASP Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2110 ILE Chi-restraints excluded: chain A residue 2158 HIS Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain N residue 364 VAL Chi-restraints excluded: chain N residue 392 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 92 optimal weight: 0.0970 chunk 118 optimal weight: 0.6980 chunk 91 optimal weight: 0.1980 chunk 136 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 161 optimal weight: 0.8980 chunk 101 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 74 optimal weight: 5.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 548 HIS ** A 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2093 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5438 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13879 Z= 0.182 Angle : 0.671 12.953 18816 Z= 0.327 Chirality : 0.043 0.266 2098 Planarity : 0.005 0.067 2448 Dihedral : 5.071 44.876 1856 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.94 % Favored : 94.00 % Rotamer: Outliers : 3.80 % Allowed : 21.19 % Favored : 75.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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 (0.21), residues: 1668 helix: 0.37 (0.18), residues: 810 sheet: -0.79 (0.39), residues: 168 loop : -1.08 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1139 HIS 0.011 0.001 HIS A2087 PHE 0.023 0.001 PHE A 45 TYR 0.026 0.001 TYR A1567 ARG 0.004 0.000 ARG A1566 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 116 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.6222 (OUTLIER) cc_final: 0.5813 (pp) REVERT: A 204 GLU cc_start: 0.7558 (tp30) cc_final: 0.7082 (pt0) REVERT: A 286 LEU cc_start: 0.5415 (mt) cc_final: 0.4939 (mt) REVERT: A 510 GLU cc_start: 0.7353 (tt0) cc_final: 0.7081 (tt0) REVERT: A 873 LEU cc_start: 0.5701 (OUTLIER) cc_final: 0.5387 (mp) REVERT: A 1041 ARG cc_start: 0.7399 (OUTLIER) cc_final: 0.7131 (mmp-170) REVERT: A 1137 MET cc_start: 0.2349 (OUTLIER) cc_final: 0.1659 (mmp) REVERT: A 1633 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6602 (pp20) REVERT: A 1749 ASP cc_start: 0.7387 (t0) cc_final: 0.6783 (t0) REVERT: A 2041 TYR cc_start: 0.5868 (t80) cc_final: 0.5655 (t80) REVERT: A 2153 LEU cc_start: 0.2517 (OUTLIER) cc_final: 0.1819 (mp) REVERT: A 2167 GLU cc_start: 0.6880 (pp20) cc_final: 0.5724 (tt0) outliers start: 57 outliers final: 41 residues processed: 163 average time/residue: 0.2303 time to fit residues: 57.8557 Evaluate side-chains 154 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 107 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 83 THR Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 1041 ARG Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1567 TYR Chi-restraints excluded: chain A residue 1633 GLU Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1768 HIS Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 1896 HIS Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 1968 TRP Chi-restraints excluded: chain A residue 1973 SER Chi-restraints excluded: chain A residue 2046 HIS Chi-restraints excluded: chain A residue 2070 THR Chi-restraints excluded: chain A residue 2089 SER Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2153 LEU Chi-restraints excluded: chain A residue 2158 HIS Chi-restraints excluded: chain A residue 2205 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.7980 chunk 64 optimal weight: 0.0010 chunk 96 optimal weight: 10.0000 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 110 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 127 optimal weight: 0.0020 chunk 147 optimal weight: 7.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1656 ASN ** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5438 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13879 Z= 0.181 Angle : 0.666 13.992 18816 Z= 0.323 Chirality : 0.043 0.190 2098 Planarity : 0.005 0.067 2448 Dihedral : 4.942 44.686 1856 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.47 % Favored : 93.47 % Rotamer: Outliers : 3.93 % Allowed : 21.12 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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 (0.21), residues: 1668 helix: 0.52 (0.18), residues: 805 sheet: -0.64 (0.39), residues: 171 loop : -1.01 (0.25), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1968 HIS 0.009 0.001 HIS A 87 PHE 0.026 0.002 PHE A 45 TYR 0.025 0.001 TYR A1567 ARG 0.004 0.000 ARG A1566 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 122 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.6218 (OUTLIER) cc_final: 0.5827 (pp) REVERT: A 204 GLU cc_start: 0.7532 (tp30) cc_final: 0.7035 (pt0) REVERT: A 510 GLU cc_start: 0.7410 (tt0) cc_final: 0.7170 (tt0) REVERT: A 873 LEU cc_start: 0.5677 (OUTLIER) cc_final: 0.5377 (mp) REVERT: A 1041 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.7221 (mmp-170) REVERT: A 1137 MET cc_start: 0.2438 (OUTLIER) cc_final: 0.1836 (mmm) REVERT: A 1149 PHE cc_start: 0.8632 (m-80) cc_final: 0.8117 (m-80) REVERT: A 1633 GLU cc_start: 0.7368 (OUTLIER) cc_final: 0.6667 (pp20) REVERT: A 1749 ASP cc_start: 0.7321 (t0) cc_final: 0.6774 (t0) REVERT: A 2153 LEU cc_start: 0.2528 (OUTLIER) cc_final: 0.2309 (mp) REVERT: A 2167 GLU cc_start: 0.7017 (pp20) cc_final: 0.5831 (tt0) outliers start: 59 outliers final: 44 residues processed: 169 average time/residue: 0.2487 time to fit residues: 64.2634 Evaluate side-chains 165 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 115 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 83 THR Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 1041 ARG Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1137 MET Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1567 TYR Chi-restraints excluded: chain A residue 1633 GLU Chi-restraints excluded: chain A residue 1658 MET Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1768 HIS Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 1896 HIS Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 1968 TRP Chi-restraints excluded: chain A residue 2020 THR Chi-restraints excluded: chain A residue 2046 HIS Chi-restraints excluded: chain A residue 2070 THR Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2136 ASP Chi-restraints excluded: chain A residue 2153 LEU Chi-restraints excluded: chain A residue 2158 HIS Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain N residue 364 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 5.9990 chunk 141 optimal weight: 0.8980 chunk 150 optimal weight: 2.9990 chunk 90 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 118 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 136 optimal weight: 0.9990 chunk 142 optimal weight: 0.9980 chunk 99 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 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 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN ** A 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1977 HIS A2029 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5446 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13879 Z= 0.193 Angle : 0.686 14.138 18816 Z= 0.331 Chirality : 0.043 0.235 2098 Planarity : 0.005 0.067 2448 Dihedral : 4.914 44.980 1856 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 15.20 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.29 % Favored : 93.65 % Rotamer: Outliers : 3.53 % Allowed : 22.05 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.37 (0.21), residues: 1668 helix: 0.53 (0.18), residues: 807 sheet: -0.67 (0.39), residues: 171 loop : -0.98 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1929 HIS 0.010 0.001 HIS A 87 PHE 0.033 0.002 PHE A 841 TYR 0.027 0.002 TYR A1542 ARG 0.005 0.000 ARG A1566 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 118 time to evaluate : 1.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.6989 (pmm) cc_final: 0.6704 (pmm) REVERT: A 178 LEU cc_start: 0.6257 (OUTLIER) cc_final: 0.5898 (pp) REVERT: A 510 GLU cc_start: 0.7517 (tt0) cc_final: 0.7185 (tt0) REVERT: A 873 LEU cc_start: 0.5701 (OUTLIER) cc_final: 0.5404 (mp) REVERT: A 1149 PHE cc_start: 0.8609 (m-80) cc_final: 0.8180 (m-80) REVERT: A 1633 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6590 (pp20) REVERT: A 1749 ASP cc_start: 0.7336 (t0) cc_final: 0.6763 (t0) REVERT: A 2020 THR cc_start: 0.6530 (OUTLIER) cc_final: 0.5211 (t) REVERT: A 2167 GLU cc_start: 0.7022 (pp20) cc_final: 0.6043 (tt0) outliers start: 53 outliers final: 41 residues processed: 161 average time/residue: 0.2496 time to fit residues: 61.9470 Evaluate side-chains 156 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 111 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 83 THR Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 1081 CYS Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1567 TYR Chi-restraints excluded: chain A residue 1633 GLU Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1768 HIS Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 1896 HIS Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 1968 TRP Chi-restraints excluded: chain A residue 2020 THR Chi-restraints excluded: chain A residue 2046 HIS Chi-restraints excluded: chain A residue 2070 THR Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2158 HIS Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain N residue 364 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.8980 chunk 75 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 167 optimal weight: 0.9980 chunk 154 optimal weight: 9.9990 chunk 133 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 102 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2082 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5574 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 13879 Z= 0.255 Angle : 0.732 14.159 18816 Z= 0.356 Chirality : 0.044 0.225 2098 Planarity : 0.005 0.066 2448 Dihedral : 5.115 45.154 1856 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.13 % Favored : 92.81 % Rotamer: Outliers : 3.53 % Allowed : 21.99 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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: -0.52 (0.21), residues: 1668 helix: 0.42 (0.18), residues: 812 sheet: -0.95 (0.38), residues: 176 loop : -1.02 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1968 HIS 0.009 0.001 HIS A 87 PHE 0.027 0.002 PHE A 45 TYR 0.029 0.002 TYR A1542 ARG 0.006 0.000 ARG A1566 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3336 Ramachandran restraints generated. 1668 Oldfield, 0 Emsley, 1668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 115 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 LEU cc_start: 0.6047 (OUTLIER) cc_final: 0.5771 (pp) REVERT: A 510 GLU cc_start: 0.7561 (tt0) cc_final: 0.7240 (tt0) REVERT: A 873 LEU cc_start: 0.5917 (OUTLIER) cc_final: 0.5538 (mp) REVERT: A 1137 MET cc_start: 0.2284 (mmm) cc_final: 0.1462 (mmp) REVERT: A 1633 GLU cc_start: 0.7264 (OUTLIER) cc_final: 0.6490 (pp20) REVERT: A 1749 ASP cc_start: 0.7529 (t0) cc_final: 0.7017 (t0) REVERT: A 2167 GLU cc_start: 0.7113 (pp20) cc_final: 0.6053 (tt0) REVERT: A 2182 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8656 (mm-30) outliers start: 53 outliers final: 47 residues processed: 160 average time/residue: 0.2285 time to fit residues: 56.9070 Evaluate side-chains 162 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 112 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 83 THR Chi-restraints excluded: chain A residue 87 HIS Chi-restraints excluded: chain A residue 90 ASP Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 303 HIS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 571 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 592 THR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 768 VAL Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 801 PHE Chi-restraints excluded: chain A residue 821 ASP Chi-restraints excluded: chain A residue 841 PHE Chi-restraints excluded: chain A residue 863 TYR Chi-restraints excluded: chain A residue 869 ILE Chi-restraints excluded: chain A residue 873 LEU Chi-restraints excluded: chain A residue 878 VAL Chi-restraints excluded: chain A residue 1081 CYS Chi-restraints excluded: chain A residue 1088 VAL Chi-restraints excluded: chain A residue 1192 LEU Chi-restraints excluded: chain A residue 1261 ILE Chi-restraints excluded: chain A residue 1282 LEU Chi-restraints excluded: chain A residue 1567 TYR Chi-restraints excluded: chain A residue 1633 GLU Chi-restraints excluded: chain A residue 1747 ILE Chi-restraints excluded: chain A residue 1757 THR Chi-restraints excluded: chain A residue 1768 HIS Chi-restraints excluded: chain A residue 1769 GLU Chi-restraints excluded: chain A residue 1780 VAL Chi-restraints excluded: chain A residue 1801 THR Chi-restraints excluded: chain A residue 1896 HIS Chi-restraints excluded: chain A residue 1927 MET Chi-restraints excluded: chain A residue 1968 TRP Chi-restraints excluded: chain A residue 2020 THR Chi-restraints excluded: chain A residue 2046 HIS Chi-restraints excluded: chain A residue 2070 THR Chi-restraints excluded: chain A residue 2089 SER Chi-restraints excluded: chain A residue 2100 VAL Chi-restraints excluded: chain A residue 2134 LEU Chi-restraints excluded: chain A residue 2158 HIS Chi-restraints excluded: chain A residue 2205 VAL Chi-restraints excluded: chain N residue 364 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 133 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 137 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 117 optimal weight: 0.6980 chunk 7 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 862 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5137 r_free = 0.5137 target = 0.192514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4906 r_free = 0.4906 target = 0.172768 restraints weight = 37687.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4880 r_free = 0.4880 target = 0.172680 restraints weight = 42523.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.173938 restraints weight = 33941.218| |-----------------------------------------------------------------------------| r_work (final): 0.4920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5017 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 13879 Z= 0.196 Angle : 0.702 14.188 18816 Z= 0.337 Chirality : 0.044 0.219 2098 Planarity : 0.005 0.067 2448 Dihedral : 4.963 44.996 1856 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.94 % Favored : 94.00 % Rotamer: Outliers : 3.33 % Allowed : 22.58 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.03 % Cis-general : 0.00 % Twisted Proline : 1.03 % 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 (0.21), residues: 1668 helix: 0.51 (0.18), residues: 811 sheet: -0.94 (0.38), residues: 175 loop : -0.95 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1968 HIS 0.010 0.001 HIS A 87 PHE 0.023 0.002 PHE A 841 TYR 0.029 0.002 TYR A1542 ARG 0.005 0.000 ARG A1566 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2605.90 seconds wall clock time: 48 minutes 11.72 seconds (2891.72 seconds total)