Starting phenix.real_space_refine on Sat Mar 16 03:11:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgj_27427/03_2024/8dgj_27427.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgj_27427/03_2024/8dgj_27427.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgj_27427/03_2024/8dgj_27427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgj_27427/03_2024/8dgj_27427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgj_27427/03_2024/8dgj_27427.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgj_27427/03_2024/8dgj_27427.pdb" } resolution = 4.02 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 73 5.16 5 C 8605 2.51 5 N 2383 2.21 5 O 2513 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 208": "OD1" <-> "OD2" Residue "A PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 278": "OD1" <-> "OD2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 319": "OE1" <-> "OE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 574": "OE1" <-> "OE2" Residue "A GLU 794": "OE1" <-> "OE2" Residue "A GLU 797": "OE1" <-> "OE2" Residue "A ASP 876": "OD1" <-> "OD2" Residue "A GLU 933": "OE1" <-> "OE2" Residue "A PHE 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1076": "OD1" <-> "OD2" Residue "A PHE 1131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1222": "OE1" <-> "OE2" Residue "A TYR 1263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1655": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1764": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1765": "OE1" <-> "OE2" Residue "A TYR 1797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1984": "OE1" <-> "OE2" Residue "A PHE 1996": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2004": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2041": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 2210": "OD1" <-> "OD2" Residue "N TYR 411": "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-5265/modules/chem_data/mon_lib" Total number of atoms: 13574 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 12727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1581, 12727 Classifications: {'peptide': 1581} Link IDs: {'PCIS': 1, 'PTRANS': 95, 'TRANS': 1484} 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: 7.20, per 1000 atoms: 0.53 Number of scatterers: 13574 At special positions: 0 Unit cell: (153.99, 137.46, 139.2, 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 73 16.00 O 2513 8.00 N 2383 7.00 C 8605 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: 5.15 Conformation dependent library (CDL) restraints added in 2.4 seconds 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 9 sheets defined 49.8% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 22 through 31 Processing helix chain 'A' and resid 39 through 61 removed outlier: 4.000A pdb=" N LYS A 43 " --> pdb=" O HIS A 39 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG A 56 " --> pdb=" O GLN A 52 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ARG A 57 " --> pdb=" O GLU A 53 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N HIS A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 Processing helix chain 'A' and resid 117 through 127 removed outlier: 3.615A pdb=" N THR A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 145 through 159 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.753A pdb=" N ALA A 181 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 199 Processing helix chain 'A' and resid 207 through 215 Processing helix chain 'A' and resid 232 through 251 Processing helix chain 'A' and resid 265 through 272 removed outlier: 4.062A pdb=" N LYS A 270 " --> pdb=" O MET A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 293 Processing helix chain 'A' and resid 294 through 316 removed outlier: 3.902A pdb=" N LYS A 311 " --> pdb=" O GLN A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 345 Processing helix chain 'A' and resid 353 through 361 Processing helix chain 'A' and resid 362 through 374 Processing helix chain 'A' and resid 501 through 517 Processing helix chain 'A' and resid 541 through 559 Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.511A pdb=" N GLU A 573 " --> pdb=" O SER A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 592 through 603 removed outlier: 4.000A pdb=" N TYR A 596 " --> pdb=" O THR A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 763 through 782 Processing helix chain 'A' and resid 783 through 785 No H-bonds generated for 'chain 'A' and resid 783 through 785' Processing helix chain 'A' and resid 791 through 801 Processing helix chain 'A' and resid 802 through 804 No H-bonds generated for 'chain 'A' and resid 802 through 804' Processing helix chain 'A' and resid 824 through 836 removed outlier: 3.668A pdb=" N LEU A 836 " --> pdb=" O TYR A 832 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 904 removed outlier: 3.656A pdb=" N ALA A 888 " --> pdb=" O THR A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 929 removed outlier: 3.642A pdb=" N GLU A 926 " --> pdb=" O PRO A 923 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N CYS A 927 " --> pdb=" O ASP A 924 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU A 929 " --> pdb=" O GLU A 926 " (cutoff:3.500A) Processing helix chain 'A' and resid 1045 through 1062 Processing helix chain 'A' and resid 1098 through 1108 removed outlier: 3.698A pdb=" N LEU A1102 " --> pdb=" O ASP A1098 " (cutoff:3.500A) Processing helix chain 'A' and resid 1117 through 1123 removed outlier: 3.556A pdb=" N ARG A1121 " --> pdb=" O PRO A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1171 through 1181 Processing helix chain 'A' and resid 1218 through 1222 removed outlier: 4.095A pdb=" N GLU A1221 " --> pdb=" O THR A1218 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU A1222 " --> pdb=" O SER A1219 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1218 through 1222' Processing helix chain 'A' and resid 1223 through 1232 Processing helix chain 'A' and resid 1248 through 1256 Processing helix chain 'A' and resid 1261 through 1281 removed outlier: 3.722A pdb=" N ASN A1266 " --> pdb=" O LEU A1262 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU A1270 " --> pdb=" O ASN A1266 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ALA A1271 " --> pdb=" O GLY A1267 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASP A1272 " --> pdb=" O LEU A1268 " (cutoff:3.500A) Processing helix chain 'A' and resid 1519 through 1535 removed outlier: 3.800A pdb=" N THR A1535 " --> pdb=" O ILE A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1538 through 1549 removed outlier: 4.526A pdb=" N LEU A1549 " --> pdb=" O THR A1545 " (cutoff:3.500A) Processing helix chain 'A' and resid 1561 through 1579 removed outlier: 3.779A pdb=" N ILE A1565 " --> pdb=" O GLU A1561 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ALA A1572 " --> pdb=" O GLU A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1608 through 1616 Processing helix chain 'A' and resid 1620 through 1629 removed outlier: 3.909A pdb=" N GLY A1629 " --> pdb=" O ALA A1625 " (cutoff:3.500A) Processing helix chain 'A' and resid 1635 through 1648 removed outlier: 3.714A pdb=" N LEU A1639 " --> pdb=" O LEU A1635 " (cutoff:3.500A) Processing helix chain 'A' and resid 1665 through 1669 removed outlier: 4.152A pdb=" N ASN A1668 " --> pdb=" O ASP A1665 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1730 removed outlier: 3.917A pdb=" N ILE A1726 " --> pdb=" O SER A1722 " (cutoff:3.500A) Processing helix chain 'A' and resid 1741 through 1763 removed outlier: 4.227A pdb=" N THR A1746 " --> pdb=" O GLU A1742 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ILE A1747 " --> pdb=" O ARG A1743 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N SER A1750 " --> pdb=" O THR A1746 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR A1754 " --> pdb=" O SER A1750 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N THR A1758 " --> pdb=" O TYR A1754 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N TYR A1759 " --> pdb=" O ALA A1755 " (cutoff:3.500A) Processing helix chain 'A' and resid 1768 through 1780 removed outlier: 4.331A pdb=" N LEU A1772 " --> pdb=" O HIS A1768 " (cutoff:3.500A) Processing helix chain 'A' and resid 1781 through 1793 Processing helix chain 'A' and resid 1899 through 1914 removed outlier: 3.741A pdb=" N ALA A1909 " --> pdb=" O ASP A1905 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ILE A1911 " --> pdb=" O VAL A1907 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY A1912 " --> pdb=" O GLU A1908 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A1913 " --> pdb=" O ALA A1909 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR A1914 " --> pdb=" O LEU A1910 " (cutoff:3.500A) Processing helix chain 'A' and resid 1920 through 1931 removed outlier: 4.214A pdb=" N LEU A1924 " --> pdb=" O PRO A1920 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU A1925 " --> pdb=" O ARG A1921 " (cutoff:3.500A) Processing helix chain 'A' and resid 1981 through 1989 Processing helix chain 'A' and resid 1992 through 2001 removed outlier: 3.935A pdb=" N PHE A1996 " --> pdb=" O GLY A1992 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A2000 " --> pdb=" O PHE A1996 " (cutoff:3.500A) Processing helix chain 'A' and resid 2007 through 2014 Processing helix chain 'A' and resid 2030 through 2049 removed outlier: 4.590A pdb=" N ALA A2037 " --> pdb=" O PHE A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2055 through 2067 removed outlier: 3.544A pdb=" N VAL A2067 " --> pdb=" O ARG A2063 " (cutoff:3.500A) Processing helix chain 'A' and resid 2068 through 2079 Processing helix chain 'A' and resid 2081 through 2085 removed outlier: 3.633A pdb=" N PHE A2084 " --> pdb=" O PHE A2081 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A2085 " --> pdb=" O HIS A2082 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2081 through 2085' Processing helix chain 'A' and resid 2091 through 2107 removed outlier: 3.806A pdb=" N ASN A2106 " --> pdb=" O ILE A2102 " (cutoff:3.500A) Processing helix chain 'A' and resid 2110 through 2119 Processing helix chain 'A' and resid 2132 through 2148 removed outlier: 4.660A pdb=" N PHE A2138 " --> pdb=" O LEU A2134 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLU A2139 " --> pdb=" O GLY A2135 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA A2142 " --> pdb=" O PHE A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2152 through 2174 removed outlier: 3.716A pdb=" N VAL A2156 " --> pdb=" O SER A2152 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N ASN A2162 " --> pdb=" O HIS A2158 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N MET A2163 " --> pdb=" O VAL A2159 " (cutoff:3.500A) Proline residue: A2166 - end of helix Processing helix chain 'A' and resid 2179 through 2185 Processing helix chain 'A' and resid 2223 through 2238 removed outlier: 3.716A pdb=" N ALA A2227 " --> pdb=" O ASN A2223 " (cutoff:3.500A) Processing helix chain 'N' and resid 359 through 371 Processing helix chain 'N' and resid 376 through 385 removed outlier: 3.661A pdb=" N LEU N 380 " --> pdb=" O GLY N 376 " (cutoff:3.500A) Processing helix chain 'N' and resid 393 through 405 Processing helix chain 'N' and resid 443 through 464 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 95 removed outlier: 6.065A pdb=" N VAL A 64 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N LEU A 137 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL A 139 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N CYS A 36 " --> pdb=" O GLU A 204 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 527 through 529 removed outlier: 6.727A pdb=" N GLN A 528 " --> pdb=" O ILE A 567 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA A 495 " --> pdb=" O LEU A 566 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 496 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A 584 " --> pdb=" O VAL A 611 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N LEU A 613 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG A 586 " --> pdb=" O LEU A 613 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N VAL A1585 " --> pdb=" O GLU A 221 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ILE A 223 " --> pdb=" O VAL A1585 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 847 through 855 Processing sheet with id=AA4, first strand: chain 'A' and resid 1022 through 1026 removed outlier: 3.721A pdb=" N PHE A1022 " --> pdb=" O VAL A1033 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N LYS A1032 " --> pdb=" O LEU A 983 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N LEU A 983 " --> pdb=" O LYS A1032 " (cutoff:3.500A) removed outlier: 7.580A pdb=" N SER A1034 " --> pdb=" O LEU A 981 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LEU A 981 " --> pdb=" O SER A1034 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N GLU A1036 " --> pdb=" O ILE A 979 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE A 979 " --> pdb=" O GLU A1036 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N PHE A1008 " --> pdb=" O ILE A 979 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N LEU A 981 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 9.601A pdb=" N GLN A1006 " --> pdb=" O LEU A 981 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1236 through 1237 removed outlier: 7.165A pdb=" N ASP A1193 " --> pdb=" O ALA A1152 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N VAL A1135 " --> pdb=" O HIS A1245 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1937 through 1941 Processing sheet with id=AA7, first strand: chain 'A' and resid 2192 through 2193 removed outlier: 3.510A pdb=" N GLU A2197 " --> pdb=" O ARG A2206 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 2192 through 2193 Processing sheet with id=AA9, first strand: chain 'N' and resid 409 through 413 618 hydrogen bonds defined for protein. 1788 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: 5.10 Time building geometry restraints manager: 5.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4039 1.34 - 1.46: 3235 1.46 - 1.59: 6500 1.59 - 1.71: 0 1.71 - 1.84: 99 Bond restraints: 13873 Sorted by residual: bond pdb=" CA SER A1750 " pdb=" C SER A1750 " ideal model delta sigma weight residual 1.523 1.451 0.072 1.41e-02 5.03e+03 2.61e+01 bond pdb=" CA HIS A 610 " pdb=" CB HIS A 610 " ideal model delta sigma weight residual 1.525 1.487 0.039 1.29e-02 6.01e+03 8.95e+00 bond pdb=" C LEU A1258 " pdb=" N PRO A1259 " ideal model delta sigma weight residual 1.334 1.387 -0.053 2.34e-02 1.83e+03 5.09e+00 bond pdb=" CB PHE A2033 " pdb=" CG PHE A2033 " ideal model delta sigma weight residual 1.502 1.453 0.049 2.30e-02 1.89e+03 4.52e+00 bond pdb=" N LEU A1675 " pdb=" CA LEU A1675 " ideal model delta sigma weight residual 1.459 1.482 -0.023 1.15e-02 7.56e+03 4.11e+00 ... (remaining 13868 not shown) Histogram of bond angle deviations from ideal: 93.41 - 102.12: 32 102.12 - 110.83: 4593 110.83 - 119.54: 7449 119.54 - 128.25: 6614 128.25 - 136.96: 120 Bond angle restraints: 18808 Sorted by residual: angle pdb=" C GLN A2029 " pdb=" N ARG A2030 " pdb=" CA ARG A2030 " ideal model delta sigma weight residual 121.52 133.02 -11.50 1.74e+00 3.30e-01 4.37e+01 angle pdb=" CA LEU A 85 " pdb=" CB LEU A 85 " pdb=" CG LEU A 85 " ideal model delta sigma weight residual 116.30 136.96 -20.66 3.50e+00 8.16e-02 3.49e+01 angle pdb=" N ILE A2110 " pdb=" CA ILE A2110 " pdb=" C ILE A2110 " ideal model delta sigma weight residual 113.42 106.73 6.69 1.17e+00 7.31e-01 3.27e+01 angle pdb=" N GLU N 457 " pdb=" CA GLU N 457 " pdb=" CB GLU N 457 " ideal model delta sigma weight residual 110.40 118.56 -8.16 1.63e+00 3.76e-01 2.50e+01 angle pdb=" CA GLU N 457 " pdb=" CB GLU N 457 " pdb=" CG GLU N 457 " ideal model delta sigma weight residual 114.10 124.02 -9.92 2.00e+00 2.50e-01 2.46e+01 ... (remaining 18803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 7460 16.90 - 33.80: 838 33.80 - 50.69: 132 50.69 - 67.59: 21 67.59 - 84.49: 14 Dihedral angle restraints: 8465 sinusoidal: 3503 harmonic: 4962 Sorted by residual: dihedral pdb=" CA TYR A 215 " pdb=" C TYR A 215 " pdb=" N CYS A 216 " pdb=" CA CYS A 216 " ideal model delta harmonic sigma weight residual 180.00 145.20 34.80 0 5.00e+00 4.00e-02 4.84e+01 dihedral pdb=" CA LEU A1258 " pdb=" C LEU A1258 " pdb=" N PRO A1259 " pdb=" CA PRO A1259 " ideal model delta harmonic sigma weight residual 180.00 -148.00 -32.00 0 5.00e+00 4.00e-02 4.10e+01 dihedral pdb=" CA ASP A1665 " pdb=" C ASP A1665 " pdb=" N ASN A1666 " pdb=" CA ASN A1666 " ideal model delta harmonic sigma weight residual 180.00 148.14 31.86 0 5.00e+00 4.00e-02 4.06e+01 ... (remaining 8462 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1551 0.059 - 0.118: 424 0.118 - 0.178: 92 0.178 - 0.237: 22 0.237 - 0.296: 8 Chirality restraints: 2097 Sorted by residual: chirality pdb=" CB VAL A2100 " pdb=" CA VAL A2100 " pdb=" CG1 VAL A2100 " pdb=" CG2 VAL A2100 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.19e+00 chirality pdb=" CG LEU A2034 " pdb=" CB LEU A2034 " pdb=" CD1 LEU A2034 " pdb=" CD2 LEU A2034 " both_signs ideal model delta sigma weight residual False -2.59 -2.88 0.30 2.00e-01 2.50e+01 2.18e+00 chirality pdb=" CB ILE A1097 " pdb=" CA ILE A1097 " pdb=" CG1 ILE A1097 " pdb=" CG2 ILE A1097 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 2094 not shown) Planarity restraints: 2447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A1718 " -0.073 5.00e-02 4.00e+02 1.11e-01 1.98e+01 pdb=" N PRO A1719 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO A1719 " -0.060 5.00e-02 4.00e+02 pdb=" CD PRO A1719 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A2045 " 0.315 9.50e-02 1.11e+02 1.42e-01 1.30e+01 pdb=" NE ARG A2045 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A2045 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG A2045 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A2045 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A2020 " -0.050 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO A2021 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A2021 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A2021 " -0.042 5.00e-02 4.00e+02 ... (remaining 2444 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1625 2.75 - 3.29: 13294 3.29 - 3.83: 23480 3.83 - 4.36: 27075 4.36 - 4.90: 43566 Nonbonded interactions: 109040 Sorted by model distance: nonbonded pdb=" O GLU A2182 " pdb=" O GLU A2185 " model vdw 2.213 3.040 nonbonded pdb=" OG1 THR A1218 " pdb=" OE2 GLU A1221 " model vdw 2.231 2.440 nonbonded pdb=" OH TYR A 863 " pdb=" OE1 GLN A 885 " model vdw 2.246 2.440 nonbonded pdb=" O PRO A 923 " pdb=" NH2 ARG A1933 " model vdw 2.266 2.520 nonbonded pdb=" O TYR A 82 " pdb=" OG1 THR A 86 " model vdw 2.268 2.440 ... (remaining 109035 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.430 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 37.810 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 13873 Z= 0.446 Angle : 1.242 20.664 18808 Z= 0.663 Chirality : 0.061 0.296 2097 Planarity : 0.010 0.142 2447 Dihedral : 14.250 84.488 5245 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.38 % Favored : 92.32 % Rotamer: Outliers : 0.13 % Allowed : 0.80 % Favored : 99.07 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 1.03 % Twisted General : 0.32 % 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: -2.71 (0.18), residues: 1667 helix: -1.97 (0.15), residues: 764 sheet: -0.77 (0.38), residues: 165 loop : -1.70 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 848 HIS 0.010 0.002 HIS A2046 PHE 0.043 0.004 PHE A2084 TYR 0.033 0.003 TYR A 29 ARG 0.015 0.001 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 882 MET cc_start: 0.5388 (tpp) cc_final: 0.4314 (tpp) REVERT: A 1137 MET cc_start: -0.0292 (mmm) cc_final: -0.0734 (mmm) REVERT: A 1782 ASN cc_start: 0.6639 (OUTLIER) cc_final: 0.5851 (t0) outliers start: 2 outliers final: 0 residues processed: 155 average time/residue: 0.2739 time to fit residues: 61.6283 Evaluate side-chains 109 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 1.520 ------------------------------------------------------------------------------- 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: 0.9980 chunk 127 optimal weight: 0.7980 chunk 70 optimal weight: 9.9990 chunk 43 optimal weight: 0.0970 chunk 85 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 152 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN A 598 GLN ** A 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 813 HIS ** A 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 HIS A1526 GLN A1668 ASN ** A1768 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5559 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13873 Z= 0.200 Angle : 0.655 11.251 18808 Z= 0.335 Chirality : 0.042 0.152 2097 Planarity : 0.006 0.071 2447 Dihedral : 6.113 30.499 1855 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.18 % Favored : 93.52 % Rotamer: Outliers : 0.20 % Allowed : 5.13 % Favored : 94.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.74 (0.19), residues: 1667 helix: -0.85 (0.17), residues: 788 sheet: -0.76 (0.40), residues: 160 loop : -1.47 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 848 HIS 0.004 0.001 HIS A 291 PHE 0.020 0.001 PHE A1552 TYR 0.015 0.002 TYR A2028 ARG 0.007 0.001 ARG A2045 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 164 time to evaluate : 1.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.7077 (pp30) REVERT: A 530 THR cc_start: 0.8994 (t) cc_final: 0.8650 (m) REVERT: A 546 LEU cc_start: 0.7868 (mt) cc_final: 0.7424 (mt) REVERT: A 882 MET cc_start: 0.5195 (tpp) cc_final: 0.4380 (tpp) REVERT: A 1137 MET cc_start: 0.0192 (mmm) cc_final: -0.0380 (mmm) REVERT: A 1261 ILE cc_start: 0.4661 (mm) cc_final: 0.4311 (mt) outliers start: 3 outliers final: 0 residues processed: 166 average time/residue: 0.2819 time to fit residues: 67.4107 Evaluate side-chains 112 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 111 time to evaluate : 1.693 ------------------------------------------------------------------------------- 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: 0.0470 chunk 47 optimal weight: 0.5980 chunk 126 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 152 optimal weight: 0.0670 chunk 165 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1668 ASN A1670 HIS A1768 HIS A1960 ASN ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5464 moved from start: 0.1714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 13873 Z= 0.167 Angle : 0.623 8.594 18808 Z= 0.315 Chirality : 0.042 0.142 2097 Planarity : 0.005 0.063 2447 Dihedral : 5.584 30.977 1855 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.88 % Favored : 93.88 % Rotamer: Outliers : 0.13 % Allowed : 3.93 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.17 (0.20), residues: 1667 helix: -0.26 (0.17), residues: 789 sheet: -0.53 (0.39), residues: 161 loop : -1.33 (0.23), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1252 HIS 0.006 0.001 HIS A1670 PHE 0.019 0.001 PHE A1552 TYR 0.031 0.001 TYR A 498 ARG 0.013 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 164 time to evaluate : 1.679 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: A 529 TYR cc_start: 0.7453 (p90) cc_final: 0.6652 (p90) REVERT: A 546 LEU cc_start: 0.7719 (mt) cc_final: 0.7275 (mt) REVERT: A 882 MET cc_start: 0.5104 (tpp) cc_final: 0.4179 (tpp) REVERT: A 1137 MET cc_start: -0.0077 (mmm) cc_final: -0.0682 (mmm) REVERT: A 1261 ILE cc_start: 0.4609 (mm) cc_final: 0.4228 (mt) outliers start: 2 outliers final: 1 residues processed: 165 average time/residue: 0.2712 time to fit residues: 65.3076 Evaluate side-chains 114 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 1.516 ------------------------------------------------------------------------------- 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: 0.0000 chunk 114 optimal weight: 9.9990 chunk 79 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 102 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 162 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS A 503 HIS ** A 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 GLN A1147 GLN ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1233 GLN A1526 GLN ** A1656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 454 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5691 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13873 Z= 0.304 Angle : 0.726 9.977 18808 Z= 0.369 Chirality : 0.045 0.145 2097 Planarity : 0.006 0.064 2447 Dihedral : 5.807 29.711 1855 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.92 % Favored : 91.84 % Rotamer: Outliers : 0.07 % Allowed : 4.47 % Favored : 95.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.20), residues: 1667 helix: -0.40 (0.17), residues: 794 sheet: -0.22 (0.43), residues: 139 loop : -1.37 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 848 HIS 0.012 0.002 HIS A1670 PHE 0.022 0.002 PHE A1926 TYR 0.024 0.002 TYR A 498 ARG 0.011 0.001 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 TYR cc_start: 0.7601 (p90) cc_final: 0.7127 (p90) REVERT: A 546 LEU cc_start: 0.7750 (mt) cc_final: 0.7371 (mt) REVERT: A 1025 PHE cc_start: 0.7265 (m-80) cc_final: 0.6999 (m-80) REVERT: A 1137 MET cc_start: 0.0038 (mmm) cc_final: -0.0587 (mmm) outliers start: 1 outliers final: 0 residues processed: 155 average time/residue: 0.2990 time to fit residues: 65.9248 Evaluate side-chains 104 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.635 ------------------------------------------------------------------------------- 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: 2.9990 chunk 92 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 6.9990 chunk 138 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 82 optimal weight: 8.9990 chunk 145 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS ** A1185 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1196 HIS A1235 GLN ** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1656 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1774 HIS A2093 ASN ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 454 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5859 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 13873 Z= 0.419 Angle : 0.855 12.019 18808 Z= 0.434 Chirality : 0.048 0.212 2097 Planarity : 0.007 0.075 2447 Dihedral : 6.346 30.576 1855 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 27.76 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.36 % Favored : 90.34 % Rotamer: Outliers : 0.13 % Allowed : 4.73 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.81 (0.19), residues: 1667 helix: -0.81 (0.17), residues: 789 sheet: -0.72 (0.41), residues: 154 loop : -1.65 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A1252 HIS 0.017 0.002 HIS A 144 PHE 0.025 0.003 PHE A2146 TYR 0.038 0.003 TYR A 863 ARG 0.018 0.001 ARG A 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 155 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 GLU cc_start: 0.5978 (tp30) cc_final: 0.5400 (tp30) REVERT: A 546 LEU cc_start: 0.7827 (mt) cc_final: 0.7545 (mt) REVERT: A 882 MET cc_start: 0.5733 (tpp) cc_final: 0.4649 (tpp) REVERT: A 1025 PHE cc_start: 0.7135 (m-80) cc_final: 0.6860 (m-80) REVERT: A 2114 TYR cc_start: 0.6080 (OUTLIER) cc_final: 0.5467 (p90) outliers start: 2 outliers final: 0 residues processed: 157 average time/residue: 0.2983 time to fit residues: 66.8653 Evaluate side-chains 114 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 113 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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: 7.9990 chunk 32 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 162 optimal weight: 3.9990 chunk 134 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 0.0970 chunk 85 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1185 GLN ** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1656 ASN ** A1668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2087 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 454 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5704 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13873 Z= 0.245 Angle : 0.698 10.247 18808 Z= 0.353 Chirality : 0.044 0.154 2097 Planarity : 0.005 0.066 2447 Dihedral : 5.785 28.515 1855 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 21.41 Ramachandran Plot: Outliers : 0.30 % Allowed : 7.26 % Favored : 92.44 % Rotamer: Outliers : 0.07 % Allowed : 2.27 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.20), residues: 1667 helix: -0.31 (0.18), residues: 783 sheet: -0.36 (0.45), residues: 130 loop : -1.34 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1252 HIS 0.009 0.001 HIS A2016 PHE 0.020 0.002 PHE A2084 TYR 0.021 0.002 TYR A2028 ARG 0.011 0.001 ARG A 345 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 1.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 PHE cc_start: 0.7351 (t80) cc_final: 0.7131 (t80) REVERT: A 529 TYR cc_start: 0.7495 (p90) cc_final: 0.7045 (p90) REVERT: A 882 MET cc_start: 0.5529 (tpp) cc_final: 0.4667 (tpp) REVERT: A 1025 PHE cc_start: 0.7198 (m-80) cc_final: 0.6911 (m-80) REVERT: A 1526 GLN cc_start: 0.7035 (pp30) cc_final: 0.6623 (pp30) REVERT: A 1798 MET cc_start: 0.8037 (ppp) cc_final: 0.7693 (ppp) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.2843 time to fit residues: 66.4449 Evaluate side-chains 113 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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: 5.9990 chunk 18 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 118 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 161 optimal weight: 0.0000 chunk 101 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- 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 304 HIS ** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2106 ASN ** 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: 0.5692 moved from start: 0.3163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13873 Z= 0.243 Angle : 0.694 8.930 18808 Z= 0.349 Chirality : 0.044 0.148 2097 Planarity : 0.005 0.067 2447 Dihedral : 5.604 30.370 1855 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.10 % Favored : 91.66 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.07 (0.20), residues: 1667 helix: -0.18 (0.18), residues: 786 sheet: -0.88 (0.42), residues: 149 loop : -1.14 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A1252 HIS 0.007 0.001 HIS A2016 PHE 0.018 0.002 PHE A2084 TYR 0.022 0.002 TYR A2028 ARG 0.007 0.001 ARG A2045 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 1.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 509 PHE cc_start: 0.7403 (t80) cc_final: 0.7135 (t80) REVERT: A 529 TYR cc_start: 0.7371 (p90) cc_final: 0.6912 (p90) REVERT: A 546 LEU cc_start: 0.7910 (mt) cc_final: 0.7379 (mt) REVERT: A 882 MET cc_start: 0.5784 (tpp) cc_final: 0.5021 (tpp) REVERT: A 1025 PHE cc_start: 0.7122 (m-80) cc_final: 0.6897 (m-80) REVERT: A 1071 MET cc_start: -0.2188 (tpt) cc_final: -0.3966 (mmt) REVERT: A 1526 GLN cc_start: 0.7030 (pp30) cc_final: 0.6688 (pp30) REVERT: A 1798 MET cc_start: 0.7982 (ppp) cc_final: 0.7442 (ppp) REVERT: N 398 LEU cc_start: 0.8422 (tp) cc_final: 0.8134 (tp) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.2782 time to fit residues: 64.1778 Evaluate side-chains 113 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.488 ------------------------------------------------------------------------------- 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: 0.0770 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 48 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 80 optimal weight: 0.0070 chunk 15 optimal weight: 0.0030 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 overall best weight: 0.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS ** A 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 HIS ** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2106 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: 0.5501 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13873 Z= 0.176 Angle : 0.651 9.350 18808 Z= 0.327 Chirality : 0.043 0.188 2097 Planarity : 0.005 0.067 2447 Dihedral : 5.186 28.224 1855 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.82 % Favored : 94.06 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.20), residues: 1667 helix: 0.17 (0.18), residues: 785 sheet: -0.78 (0.41), residues: 154 loop : -0.99 (0.24), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP A1252 HIS 0.008 0.001 HIS A2087 PHE 0.020 0.001 PHE A2084 TYR 0.018 0.001 TYR A2028 ARG 0.008 0.001 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 1.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 LEU cc_start: 0.7830 (mt) cc_final: 0.7331 (mt) REVERT: A 1071 MET cc_start: -0.2165 (tpt) cc_final: -0.4025 (mmt) REVERT: A 1526 GLN cc_start: 0.6812 (pp30) cc_final: 0.6494 (pp30) REVERT: A 1798 MET cc_start: 0.7714 (ppp) cc_final: 0.6999 (ppp) REVERT: N 398 LEU cc_start: 0.8394 (tp) cc_final: 0.8132 (tp) outliers start: 0 outliers final: 0 residues processed: 167 average time/residue: 0.2817 time to fit residues: 68.7806 Evaluate side-chains 119 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.606 ------------------------------------------------------------------------------- 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: 0.0870 chunk 141 optimal weight: 2.9990 chunk 150 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 118 optimal weight: 0.6980 chunk 46 optimal weight: 0.3980 chunk 136 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 159 optimal weight: 10.0000 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS A 598 GLN ** A 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2087 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A2106 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5531 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13873 Z= 0.176 Angle : 0.635 9.366 18808 Z= 0.317 Chirality : 0.043 0.276 2097 Planarity : 0.005 0.065 2447 Dihedral : 5.048 28.990 1855 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.42 % Favored : 93.46 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1667 helix: 0.31 (0.18), residues: 790 sheet: -0.75 (0.41), residues: 154 loop : -0.94 (0.24), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A1252 HIS 0.005 0.001 HIS A 503 PHE 0.019 0.001 PHE A1552 TYR 0.018 0.001 TYR A2028 ARG 0.010 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 1.641 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: A 290 LEU cc_start: 0.5285 (tp) cc_final: 0.5061 (tp) REVERT: A 882 MET cc_start: 0.5906 (tpp) cc_final: 0.5035 (tpp) REVERT: A 1025 PHE cc_start: 0.7144 (m-80) cc_final: 0.6826 (m-80) REVERT: A 1071 MET cc_start: -0.2035 (tpt) cc_final: -0.3941 (mmt) REVERT: A 1526 GLN cc_start: 0.6782 (pp30) cc_final: 0.6553 (pp30) REVERT: A 1798 MET cc_start: 0.7731 (ppp) cc_final: 0.7350 (ppp) REVERT: A 2054 HIS cc_start: 0.6990 (m-70) cc_final: 0.6754 (m-70) REVERT: N 398 LEU cc_start: 0.8456 (tp) cc_final: 0.8199 (tp) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2848 time to fit residues: 69.5714 Evaluate side-chains 115 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 1.479 ------------------------------------------------------------------------------- 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: 0.9990 chunk 75 optimal weight: 7.9990 chunk 110 optimal weight: 0.8980 chunk 167 optimal weight: 10.0000 chunk 154 optimal weight: 6.9990 chunk 133 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 102 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 chunk 141 optimal weight: 0.0980 overall best weight: 0.9986 ------------------------------------------------------------------------------- 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 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 HIS A1147 GLN ** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2106 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5581 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13873 Z= 0.206 Angle : 0.661 13.369 18808 Z= 0.331 Chirality : 0.043 0.339 2097 Planarity : 0.005 0.064 2447 Dihedral : 5.086 28.491 1855 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.96 % Favored : 92.92 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.20), residues: 1667 helix: 0.31 (0.18), residues: 788 sheet: -0.73 (0.40), residues: 154 loop : -0.92 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 848 HIS 0.014 0.001 HIS A1196 PHE 0.018 0.002 PHE A1552 TYR 0.019 0.001 TYR A2028 ARG 0.009 0.001 ARG A 151 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3334 Ramachandran restraints generated. 1667 Oldfield, 0 Emsley, 1667 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 1.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 882 MET cc_start: 0.5826 (tpp) cc_final: 0.5057 (tpp) REVERT: A 1025 PHE cc_start: 0.7191 (m-80) cc_final: 0.6847 (m-80) REVERT: A 1041 ARG cc_start: 0.6690 (mmt180) cc_final: 0.6092 (mmp-170) REVERT: A 1526 GLN cc_start: 0.6859 (pp30) cc_final: 0.6536 (pp30) REVERT: A 1798 MET cc_start: 0.7776 (ppp) cc_final: 0.7259 (ppp) REVERT: N 398 LEU cc_start: 0.8505 (tp) cc_final: 0.8235 (tp) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2943 time to fit residues: 69.4137 Evaluate side-chains 113 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.565 ------------------------------------------------------------------------------- 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: 2.9990 chunk 122 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 133 optimal weight: 6.9990 chunk 55 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 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 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 454 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.172353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.153964 restraints weight = 41719.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.153144 restraints weight = 53211.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.154028 restraints weight = 50110.791| |-----------------------------------------------------------------------------| r_work (final): 0.4627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5457 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 13873 Z= 0.233 Angle : 0.687 17.326 18808 Z= 0.342 Chirality : 0.044 0.288 2097 Planarity : 0.005 0.064 2447 Dihedral : 5.196 28.817 1855 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 20.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.68 % Favored : 92.20 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.20), residues: 1667 helix: 0.23 (0.18), residues: 787 sheet: -0.48 (0.42), residues: 142 loop : -0.98 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 848 HIS 0.009 0.001 HIS A2016 PHE 0.024 0.002 PHE A2085 TYR 0.032 0.001 TYR A 498 ARG 0.009 0.001 ARG A 151 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2721.25 seconds wall clock time: 50 minutes 14.70 seconds (3014.70 seconds total)