Starting phenix.real_space_refine (version: dev) on Tue Feb 21 01:08:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgi_27423/02_2023/8dgi_27423.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgi_27423/02_2023/8dgi_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_27423/02_2023/8dgi_27423.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgi_27423/02_2023/8dgi_27423.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgi_27423/02_2023/8dgi_27423.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgi_27423/02_2023/8dgi_27423.pdb" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Process input model Symmetric amino acids flipped Residue "A ASP 105": "OD1" <-> "OD2" Residue "A GLU 196": "OE1" <-> "OE2" Residue "A ASP 208": "OD1" <-> "OD2" Residue "A TYR 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A ASP 251": "OD1" <-> "OD2" Residue "A ASP 278": "OD1" <-> "OD2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 545": "OE1" <-> "OE2" Residue "A GLU 547": "OE1" <-> "OE2" Residue "A ASP 562": "OD1" <-> "OD2" Residue "A ASP 577": "OD1" <-> "OD2" Residue "A GLU 799": "OE1" <-> "OE2" Residue "A ASP 821": "OD1" <-> "OD2" Residue "A ASP 839": "OD1" <-> "OD2" Residue "A PHE 841": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 854": "OE1" <-> "OE2" Residue "A GLU 916": "OE1" <-> "OE2" Residue "A PHE 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1040": "OE1" <-> "OE2" Residue "A PHE 1069": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1119": "OE1" <-> "OE2" Residue "A PHE 1131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1222": "OE1" <-> "OE2" Residue "A GLU 1229": "OE1" <-> "OE2" Residue "A GLU 1232": "OE1" <-> "OE2" Residue "A GLU 1240": "OE1" <-> "OE2" Residue "A PHE 1247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1558": "OD1" <-> "OD2" Residue "A GLU 1621": "OE1" <-> "OE2" Residue "A GLU 1641": "OE1" <-> "OE2" Residue "A TYR 1655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1665": "OD1" <-> "OD2" Residue "A PHE 1709": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1765": "OE1" <-> "OE2" Residue "A TYR 1786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1796": "OE1" <-> "OE2" Residue "A GLU 1804": "OE1" <-> "OE2" Residue "A GLU 1908": "OE1" <-> "OE2" Residue "A PHE 1926": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1942": "OD1" <-> "OD2" Residue "A GLU 1959": "OE1" <-> "OE2" Residue "A GLU 1998": "OE1" <-> "OE2" Residue "A TYR 2009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2048": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2050": "OD1" <-> "OD2" Residue "A PHE 2085": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2094": "OD1" <-> "OD2" Residue "A ASP 2097": "OD1" <-> "OD2" Residue "A GLU 2105": "OE1" <-> "OE2" Residue "A GLU 2113": "OE1" <-> "OE2" Residue "A GLU 2121": "OE1" <-> "OE2" Residue "A PHE 2138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2139": "OE1" <-> "OE2" Residue "A GLU 2167": "OE1" <-> "OE2" Residue "N PHE 407": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 419": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 8.46, per 1000 atoms: 0.62 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 - 3.50 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: 6.11 Conformation dependent library (CDL) restraints added in 2.3 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: 1.29 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: 8.14 Time building geometry restraints manager: 6.65 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: 94.49 - 102.46: 53 102.46 - 110.43: 3401 110.43 - 118.39: 7336 118.39 - 126.36: 7782 126.36 - 134.33: 244 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 2.440 nonbonded pdb=" O ASP A2040 " pdb=" OG1 THR A2044 " model vdw 2.268 2.440 nonbonded pdb=" OE1 GLU A 221 " pdb=" OH TYR A 596 " model vdw 2.275 2.440 nonbonded pdb=" O PRO A 868 " pdb=" OG SER A 871 " model vdw 2.291 2.440 nonbonded pdb=" OH TYR A2002 " pdb=" OD1 ASP A2148 " model vdw 2.306 2.440 ... (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 ========== 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 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. 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: 3.530 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: 15.650 Check model and map are aligned: 0.180 Process input model: 44.880 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Set scattering table: 0.160 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:4.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5221 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 % 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 *********************** 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 : 1.473 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 outliers start: 10 outliers final: 3 residues processed: 137 average time/residue: 0.2791 time to fit residues: 56.3529 Evaluate side-chains 121 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 118 time to evaluate : 1.581 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3055 time to fit residues: 3.5183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.1980 chunk 127 optimal weight: 0.6980 chunk 70 optimal weight: 20.0000 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 50.0000 chunk 68 optimal weight: 0.0980 chunk 131 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 20.0000 chunk 98 optimal weight: 0.0370 chunk 152 optimal weight: 0.8980 overall best weight: 0.3858 ------------------------------------------------------------------------------- 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 548 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1536 ASN A1668 ASN A1774 HIS A2012 GLN A2029 GLN A2054 HIS ** N 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5224 moved from start: 0.1080 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= 0.168 Angle : 0.635 10.116 18816 Z= 0.319 Chirality : 0.041 0.158 2098 Planarity : 0.005 0.068 2448 Dihedral : 5.229 43.096 1856 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.16 % Favored : 94.54 % Rotamer Outliers : 3.00 % 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: -0.97 (0.20), residues: 1668 helix: -0.19 (0.17), residues: 799 sheet: -0.06 (0.38), residues: 193 loop : -1.25 (0.24), residues: 676 *********************** 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 165 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 120 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 20 residues processed: 155 average time/residue: 0.2740 time to fit residues: 63.1626 Evaluate side-chains 130 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 1.614 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1306 time to fit residues: 7.2197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 0.1980 chunk 103 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 165 optimal weight: 0.1980 chunk 136 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 97 GLN A 548 HIS ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 773 GLN A1067 GLN ** A1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1768 HIS A2054 HIS ** N 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5415 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 13879 Z= 0.215 Angle : 0.656 11.264 18816 Z= 0.325 Chirality : 0.043 0.182 2098 Planarity : 0.005 0.066 2448 Dihedral : 5.080 44.723 1856 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.94 % Favored : 93.82 % Rotamer Outliers : 2.73 % 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: -0.51 (0.21), residues: 1668 helix: 0.26 (0.18), residues: 807 sheet: -0.27 (0.40), residues: 181 loop : -0.99 (0.25), residues: 680 *********************** 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 168 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 127 time to evaluate : 1.655 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 outliers start: 41 outliers final: 20 residues processed: 160 average time/residue: 0.2604 time to fit residues: 62.8455 Evaluate side-chains 135 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 1.484 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1306 time to fit residues: 6.9236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 8.9990 chunk 114 optimal weight: 5.9990 chunk 79 optimal weight: 0.0870 chunk 16 optimal weight: 4.9990 chunk 72 optimal weight: 40.0000 chunk 102 optimal weight: 4.9990 chunk 153 optimal weight: 40.0000 chunk 162 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 145 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 overall best weight: 2.5964 ------------------------------------------------------------------------------- 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 A 548 HIS ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 HIS A 992 ASN A1656 ASN A1766 ASN ** A1977 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1988 GLN ** A2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2093 ASN ** N 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 448 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5791 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.072 13879 Z= 0.404 Angle : 0.854 11.529 18816 Z= 0.429 Chirality : 0.048 0.214 2098 Planarity : 0.006 0.069 2448 Dihedral : 5.923 45.174 1856 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 27.01 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.21 % Favored : 91.61 % Rotamer Outliers : 4.13 % Cbeta Deviations : 0.00 % 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: -1.00 (0.20), residues: 1668 helix: -0.13 (0.18), residues: 800 sheet: -0.89 (0.40), residues: 171 loop : -1.11 (0.24), residues: 697 *********************** 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 181 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 119 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 34 residues processed: 172 average time/residue: 0.2537 time to fit residues: 66.3258 Evaluate side-chains 143 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 109 time to evaluate : 1.607 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.1555 time to fit residues: 11.6361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.7980 chunk 2 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 82 optimal weight: 1.9990 chunk 145 optimal weight: 0.4980 chunk 40 optimal weight: 6.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 548 HIS ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1988 GLN ** N 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5581 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.067 13879 Z= 0.211 Angle : 0.679 12.054 18816 Z= 0.332 Chirality : 0.043 0.198 2098 Planarity : 0.005 0.066 2448 Dihedral : 5.293 44.889 1856 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.83 % Favored : 92.99 % Rotamer Outliers : 2.27 % Cbeta Deviations : 0.00 % 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: -0.66 (0.21), residues: 1668 helix: 0.27 (0.18), residues: 806 sheet: -0.86 (0.39), residues: 173 loop : -1.07 (0.25), residues: 689 *********************** 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 157 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 123 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 15 residues processed: 152 average time/residue: 0.2560 time to fit residues: 59.7732 Evaluate side-chains 123 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 1.649 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1363 time to fit residues: 6.1613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 75 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 85 optimal weight: 0.0070 overall best weight: 2.8006 ------------------------------------------------------------------------------- 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 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1643 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1988 GLN ** A2022 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2103 GLN ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 454 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5884 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.083 13879 Z= 0.430 Angle : 0.870 12.333 18816 Z= 0.437 Chirality : 0.049 0.343 2098 Planarity : 0.006 0.068 2448 Dihedral : 5.953 45.385 1856 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 29.04 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.87 % Favored : 90.89 % Rotamer Outliers : 3.40 % Cbeta Deviations : 0.00 % 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: -1.20 (0.20), residues: 1668 helix: -0.26 (0.17), residues: 798 sheet: -1.18 (0.39), residues: 169 loop : -1.21 (0.24), residues: 701 *********************** 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 162 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 111 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 51 outliers final: 33 residues processed: 155 average time/residue: 0.2594 time to fit residues: 61.0959 Evaluate side-chains 138 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 105 time to evaluate : 1.636 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.1417 time to fit residues: 10.6981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 92 optimal weight: 7.9990 chunk 118 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 136 optimal weight: 0.5980 chunk 90 optimal weight: 10.0000 chunk 161 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 98 optimal weight: 7.9990 chunk 74 optimal weight: 6.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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 252 HIS ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1643 ASN A1988 GLN ** N 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5738 moved from start: 0.3988 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= 0.266 Angle : 0.734 13.383 18816 Z= 0.360 Chirality : 0.045 0.250 2098 Planarity : 0.005 0.066 2448 Dihedral : 5.519 45.480 1856 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 23.06 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.31 % Favored : 92.51 % Rotamer Outliers : 0.93 % Cbeta Deviations : 0.00 % 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: -0.99 (0.21), residues: 1668 helix: 0.04 (0.18), residues: 795 sheet: -1.16 (0.38), residues: 175 loop : -1.24 (0.25), residues: 698 *********************** 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 136 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 122 time to evaluate : 1.585 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 130 average time/residue: 0.2495 time to fit residues: 50.2351 Evaluate side-chains 119 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 1.467 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1297 time to fit residues: 4.1065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.0370 chunk 64 optimal weight: 3.9990 chunk 96 optimal weight: 9.9990 chunk 48 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 102 optimal weight: 5.9990 chunk 110 optimal weight: 0.0030 chunk 80 optimal weight: 8.9990 chunk 15 optimal weight: 0.0870 chunk 127 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 overall best weight: 0.3446 ------------------------------------------------------------------------------- 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 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 992 ASN ** A1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 389 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5526 moved from start: 0.3868 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= 0.182 Angle : 0.691 13.593 18816 Z= 0.334 Chirality : 0.044 0.238 2098 Planarity : 0.004 0.066 2448 Dihedral : 5.079 44.706 1856 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 17.75 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.35 % Favored : 93.53 % Rotamer Outliers : 0.53 % 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: -0.56 (0.21), residues: 1668 helix: 0.42 (0.18), residues: 799 sheet: -1.03 (0.38), residues: 179 loop : -1.03 (0.25), residues: 690 *********************** 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 133 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 131 average time/residue: 0.2635 time to fit residues: 52.9908 Evaluate side-chains 115 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 1.658 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1657 time to fit residues: 3.2320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 8.9990 chunk 141 optimal weight: 0.6980 chunk 150 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 142 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 159 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 252 HIS A 334 GLN ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1671 HIS ** A1960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.4004 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= 0.200 Angle : 0.685 14.064 18816 Z= 0.332 Chirality : 0.043 0.247 2098 Planarity : 0.004 0.066 2448 Dihedral : 4.996 45.109 1856 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.59 % Favored : 93.29 % Rotamer Outliers : 0.60 % 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: -0.43 (0.21), residues: 1668 helix: 0.51 (0.18), residues: 805 sheet: -0.94 (0.39), residues: 177 loop : -0.96 (0.25), residues: 686 *********************** 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 129 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 120 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 125 average time/residue: 0.2639 time to fit residues: 50.2114 Evaluate side-chains 119 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 114 time to evaluate : 1.696 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1367 time to fit residues: 3.6548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 6.9990 chunk 75 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 105 optimal weight: 0.0970 chunk 141 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1988 GLN A2158 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5649 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 13879 Z= 0.227 Angle : 0.710 13.933 18816 Z= 0.344 Chirality : 0.044 0.267 2098 Planarity : 0.004 0.066 2448 Dihedral : 5.076 45.195 1856 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.89 % Favored : 92.99 % Rotamer Outliers : 0.47 % 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: -0.50 (0.21), residues: 1668 helix: 0.47 (0.18), residues: 803 sheet: -0.96 (0.39), residues: 177 loop : -1.02 (0.25), residues: 688 ********************** 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 126 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 119 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 123 average time/residue: 0.2549 time to fit residues: 48.5074 Evaluate side-chains 122 residues out of total 1501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 1.664 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1406 time to fit residues: 3.6302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 8.9990 chunk 122 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 137 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 117 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 252 HIS ** A 598 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2158 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5122 r_free = 0.5122 target = 0.191127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.172264 restraints weight = 37644.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4868 r_free = 0.4868 target = 0.171641 restraints weight = 44918.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4889 r_free = 0.4889 target = 0.173490 restraints weight = 36895.149| |-----------------------------------------------------------------------------| r_work (final): 0.4914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5057 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 13879 Z= 0.198 Angle : 0.703 14.082 18816 Z= 0.338 Chirality : 0.044 0.275 2098 Planarity : 0.004 0.066 2448 Dihedral : 4.981 45.144 1856 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.06 % Favored : 93.82 % Rotamer Outliers : 0.47 % 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: -0.44 (0.21), residues: 1668 helix: 0.55 (0.18), residues: 801 sheet: -0.95 (0.39), residues: 177 loop : -1.03 (0.25), residues: 690 =============================================================================== Job complete usr+sys time: 2432.17 seconds wall clock time: 45 minutes 25.77 seconds (2725.77 seconds total)