Starting phenix.real_space_refine on Mon Aug 5 15:48:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgj_27427/08_2024/8dgj_27427.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgj_27427/08_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_27427/08_2024/8dgj_27427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgj_27427/08_2024/8dgj_27427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgj_27427/08_2024/8dgj_27427.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgj_27427/08_2024/8dgj_27427.cif" } 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-5409/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: 8.16, per 1000 atoms: 0.60 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: 4.81 Conformation dependent library (CDL) restraints added in 2.6 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: 1.59 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: 5.09 Time building geometry restraints manager: 5.34 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 3.040 nonbonded pdb=" OH TYR A 863 " pdb=" OE1 GLN A 885 " model vdw 2.246 3.040 nonbonded pdb=" O PRO A 923 " pdb=" NH2 ARG A1933 " model vdw 2.266 3.120 nonbonded pdb=" O TYR A 82 " pdb=" OG1 THR A 86 " model vdw 2.268 3.040 ... (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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 37.640 Find NCS groups from input model: 0.250 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: 0.010 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.530 ------------------------------------------------------------------------------- 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 : 1.541 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: 0.2819 time to fit residues: 63.7306 Evaluate side-chains 109 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 108 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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: 0.6980 chunk 127 optimal weight: 0.9990 chunk 70 optimal weight: 7.9990 chunk 43 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 0.3980 chunk 50 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 152 optimal weight: 0.3980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 598 GLN A 813 HIS A 870 ASN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 GLN A1096 HIS A1526 GLN A1668 ASN A1768 HIS ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 454 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5477 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13873 Z= 0.182 Angle : 0.654 11.270 18808 Z= 0.335 Chirality : 0.042 0.145 2097 Planarity : 0.006 0.071 2447 Dihedral : 6.061 30.745 1855 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.58 % Favored : 94.18 % Rotamer: Outliers : 0.13 % Allowed : 4.53 % Favored : 95.33 % 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: -1.75 (0.19), residues: 1667 helix: -0.84 (0.17), residues: 792 sheet: -0.79 (0.39), residues: 166 loop : -1.50 (0.23), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 848 HIS 0.004 0.001 HIS A 341 PHE 0.020 0.001 PHE A1552 TYR 0.016 0.001 TYR A 863 ARG 0.006 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 171 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 169 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 THR cc_start: 0.8884 (t) cc_final: 0.8599 (m) REVERT: A 546 LEU cc_start: 0.7857 (mt) cc_final: 0.7428 (mt) REVERT: A 1025 PHE cc_start: 0.7112 (m-80) cc_final: 0.6907 (m-80) REVERT: A 1137 MET cc_start: 0.0148 (mmm) cc_final: -0.0442 (mmm) REVERT: A 1261 ILE cc_start: 0.4666 (mm) cc_final: 0.4352 (mt) outliers start: 2 outliers final: 0 residues processed: 170 average time/residue: 0.2756 time to fit residues: 68.1259 Evaluate side-chains 110 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 110 time to evaluate : 1.497 ------------------------------------------------------------------------------- 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: 0.7980 chunk 47 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 152 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 52 optimal weight: 0.3980 chunk 122 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 HIS A1185 GLN A1233 GLN ** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1668 ASN ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5462 moved from start: 0.1838 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= 0.183 Angle : 0.636 8.790 18808 Z= 0.322 Chirality : 0.043 0.141 2097 Planarity : 0.005 0.063 2447 Dihedral : 5.600 29.722 1855 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.76 % Favored : 94.00 % Rotamer: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % 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: -1.20 (0.20), residues: 1667 helix: -0.29 (0.17), residues: 793 sheet: -0.53 (0.39), residues: 162 loop : -1.33 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 848 HIS 0.005 0.001 HIS A1670 PHE 0.020 0.001 PHE A1552 TYR 0.028 0.001 TYR A 498 ARG 0.010 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 159 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 ASP cc_start: 0.6590 (t0) cc_final: 0.6339 (t0) REVERT: A 529 TYR cc_start: 0.7472 (p90) cc_final: 0.7125 (p90) REVERT: A 530 THR cc_start: 0.8897 (t) cc_final: 0.8511 (m) REVERT: A 546 LEU cc_start: 0.7723 (mt) cc_final: 0.7291 (mt) REVERT: A 882 MET cc_start: 0.5038 (tpp) cc_final: 0.3919 (tpp) REVERT: A 1137 MET cc_start: 0.0126 (mmm) cc_final: -0.0446 (mmm) REVERT: A 1261 ILE cc_start: 0.4595 (mm) cc_final: 0.4211 (mt) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2836 time to fit residues: 66.2146 Evaluate side-chains 108 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.536 ------------------------------------------------------------------------------- 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: 6.9990 chunk 114 optimal weight: 3.9990 chunk 79 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 72 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 153 optimal weight: 1.9990 chunk 162 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS A 503 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 HIS A1526 GLN A1668 ASN ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 454 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5531 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13873 Z= 0.223 Angle : 0.651 10.907 18808 Z= 0.330 Chirality : 0.043 0.268 2097 Planarity : 0.005 0.064 2447 Dihedral : 5.482 28.423 1855 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.66 % Favored : 93.10 % Rotamer: Outliers : 0.07 % Allowed : 4.13 % Favored : 95.80 % 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: -0.99 (0.20), residues: 1667 helix: -0.11 (0.18), residues: 793 sheet: -0.59 (0.39), residues: 163 loop : -1.21 (0.24), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 848 HIS 0.006 0.001 HIS A2158 PHE 0.020 0.002 PHE A1552 TYR 0.019 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 165 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 1.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 TYR cc_start: 0.7473 (p90) cc_final: 0.7133 (p90) REVERT: A 546 LEU cc_start: 0.7708 (mt) cc_final: 0.7461 (mt) REVERT: A 882 MET cc_start: 0.5295 (tpp) cc_final: 0.4279 (tpp) REVERT: A 925 TRP cc_start: 0.5789 (m100) cc_final: 0.5586 (m100) REVERT: A 1025 PHE cc_start: 0.7182 (m-80) cc_final: 0.6890 (m-80) REVERT: A 1041 ARG cc_start: 0.6504 (mmt-90) cc_final: 0.6258 (mmt-90) REVERT: A 1137 MET cc_start: 0.0016 (mmm) cc_final: -0.0535 (mmm) REVERT: A 1261 ILE cc_start: 0.4643 (mm) cc_final: 0.4213 (mt) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.2701 time to fit residues: 64.8370 Evaluate side-chains 112 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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: 0.9980 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: 0.8980 chunk 0 optimal weight: 8.9990 chunk 82 optimal weight: 9.9990 chunk 145 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS ** A 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 HIS A1147 GLN A1196 HIS A1235 GLN ** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2106 ASN N 454 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5597 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13873 Z= 0.257 Angle : 0.686 8.331 18808 Z= 0.345 Chirality : 0.044 0.169 2097 Planarity : 0.005 0.063 2447 Dihedral : 5.542 26.910 1855 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.02 % Favored : 92.74 % Rotamer: Outliers : 0.07 % Allowed : 3.27 % Favored : 96.67 % 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: -1.04 (0.20), residues: 1667 helix: -0.18 (0.17), residues: 796 sheet: -0.58 (0.40), residues: 152 loop : -1.19 (0.23), residues: 719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A1252 HIS 0.010 0.001 HIS A2016 PHE 0.020 0.002 PHE A1552 TYR 0.018 0.002 TYR A2028 ARG 0.011 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: 1 poor density : 156 time to evaluate : 1.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 LEU cc_start: 0.7740 (mt) cc_final: 0.7511 (mt) REVERT: A 882 MET cc_start: 0.5201 (tpp) cc_final: 0.4414 (tpp) REVERT: A 1025 PHE cc_start: 0.7197 (m-80) cc_final: 0.6863 (m-80) REVERT: A 1041 ARG cc_start: 0.6535 (mmt-90) cc_final: 0.6143 (mpt180) REVERT: A 1137 MET cc_start: -0.0105 (mmm) cc_final: -0.0717 (mmm) REVERT: A 1526 GLN cc_start: 0.6808 (pp30) cc_final: 0.6516 (pp30) outliers start: 1 outliers final: 0 residues processed: 157 average time/residue: 0.2759 time to fit residues: 62.7257 Evaluate side-chains 103 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.456 ------------------------------------------------------------------------------- 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: 0.0050 chunk 146 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 95 optimal weight: 0.2980 chunk 40 optimal weight: 7.9990 chunk 162 optimal weight: 2.9990 chunk 134 optimal weight: 0.0870 chunk 75 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 0.9990 chunk 85 optimal weight: 30.0000 overall best weight: 0.3972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS A 309 ASN A1096 HIS ** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1668 ASN ** A2053 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5421 moved from start: 0.2762 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= 0.171 Angle : 0.631 8.814 18808 Z= 0.315 Chirality : 0.042 0.178 2097 Planarity : 0.005 0.064 2447 Dihedral : 5.147 26.948 1855 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.40 % Favored : 94.36 % Rotamer: Outliers : 0.07 % Allowed : 1.93 % Favored : 98.00 % 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: -0.64 (0.20), residues: 1667 helix: 0.21 (0.18), residues: 793 sheet: -0.60 (0.39), residues: 158 loop : -1.01 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1252 HIS 0.008 0.001 HIS A 341 PHE 0.018 0.001 PHE A1552 TYR 0.017 0.001 TYR A2028 ARG 0.009 0.000 ARG A 151 *********************** 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 : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 530 THR cc_start: 0.8900 (t) cc_final: 0.8496 (m) REVERT: A 546 LEU cc_start: 0.7749 (mt) cc_final: 0.7531 (mt) REVERT: A 882 MET cc_start: 0.4898 (tpp) cc_final: 0.4119 (tpp) REVERT: A 1025 PHE cc_start: 0.7101 (m-80) cc_final: 0.6775 (m-80) REVERT: A 1137 MET cc_start: -0.0282 (mmm) cc_final: -0.0634 (mmm) REVERT: A 1526 GLN cc_start: 0.6790 (pp30) cc_final: 0.6588 (pp30) outliers start: 1 outliers final: 0 residues processed: 163 average time/residue: 0.2814 time to fit residues: 67.0060 Evaluate side-chains 113 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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: 3.9990 chunk 18 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 118 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 161 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 ASN A 304 HIS ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1096 HIS A1174 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 ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 454 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5752 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 13873 Z= 0.370 Angle : 0.809 11.685 18808 Z= 0.408 Chirality : 0.047 0.173 2097 Planarity : 0.006 0.065 2447 Dihedral : 5.762 28.597 1855 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.16 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % 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: -1.12 (0.20), residues: 1667 helix: -0.29 (0.17), residues: 799 sheet: -0.93 (0.40), residues: 152 loop : -1.10 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 848 HIS 0.015 0.002 HIS A2016 PHE 0.023 0.002 PHE A1926 TYR 0.023 0.002 TYR A 67 ARG 0.012 0.001 ARG A 18 *********************** 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 151 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 529 TYR cc_start: 0.7616 (p90) cc_final: 0.7118 (p90) REVERT: A 546 LEU cc_start: 0.7802 (mt) cc_final: 0.7584 (mt) REVERT: A 863 TYR cc_start: 0.3783 (m-10) cc_final: 0.3337 (m-80) REVERT: A 882 MET cc_start: 0.5119 (tpp) cc_final: 0.4371 (tpp) REVERT: A 1025 PHE cc_start: 0.7225 (m-80) cc_final: 0.6840 (m-80) REVERT: A 1071 MET cc_start: -0.1929 (tpt) cc_final: -0.3754 (mmt) REVERT: A 1137 MET cc_start: 0.0176 (mmm) cc_final: -0.0052 (mmm) REVERT: A 1150 TYR cc_start: 0.5427 (m-80) cc_final: 0.4875 (m-80) REVERT: A 1526 GLN cc_start: 0.7017 (pp30) cc_final: 0.6696 (pp30) REVERT: A 1732 MET cc_start: 0.2776 (mmm) cc_final: 0.2490 (mmt) REVERT: A 2054 HIS cc_start: 0.7012 (m-70) cc_final: 0.6665 (m-70) REVERT: N 398 LEU cc_start: 0.8426 (tp) cc_final: 0.8158 (tp) outliers start: 0 outliers final: 0 residues processed: 151 average time/residue: 0.2577 time to fit residues: 57.9051 Evaluate side-chains 107 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.4247 > 50: distance: 25 - 167: 17.074 distance: 51 - 153: 12.936 distance: 59 - 156: 3.536 distance: 92 - 96: 15.999 distance: 96 - 97: 17.679 distance: 96 - 102: 26.573 distance: 97 - 98: 20.872 distance: 97 - 100: 20.758 distance: 98 - 99: 34.109 distance: 98 - 103: 14.074 distance: 100 - 101: 26.726 distance: 101 - 102: 29.931 distance: 103 - 104: 15.383 distance: 104 - 105: 7.407 distance: 104 - 107: 20.947 distance: 105 - 106: 31.474 distance: 105 - 108: 7.757 distance: 108 - 109: 14.139 distance: 108 - 114: 18.269 distance: 109 - 110: 22.884 distance: 109 - 112: 26.668 distance: 110 - 111: 13.101 distance: 110 - 115: 26.343 distance: 112 - 113: 31.252 distance: 113 - 114: 10.105 distance: 115 - 116: 9.489 distance: 115 - 121: 6.919 distance: 116 - 117: 9.522 distance: 116 - 119: 9.238 distance: 117 - 118: 9.371 distance: 117 - 122: 10.735 distance: 119 - 120: 7.936 distance: 120 - 121: 15.697 distance: 122 - 123: 16.683 distance: 123 - 124: 4.590 distance: 123 - 126: 14.547 distance: 124 - 125: 5.841 distance: 124 - 127: 6.496 distance: 127 - 128: 7.192 distance: 128 - 129: 11.067 distance: 128 - 131: 3.924 distance: 129 - 130: 16.816 distance: 129 - 135: 4.128 distance: 131 - 132: 5.320 distance: 132 - 133: 8.689 distance: 132 - 134: 12.603 distance: 135 - 136: 4.536 distance: 136 - 137: 10.376 distance: 136 - 139: 19.367 distance: 137 - 138: 21.100 distance: 137 - 146: 4.543 distance: 139 - 140: 14.168 distance: 140 - 141: 5.188 distance: 141 - 142: 5.135 distance: 142 - 143: 5.406 distance: 143 - 144: 10.523 distance: 143 - 145: 13.811 distance: 146 - 147: 12.723 distance: 146 - 152: 19.982 distance: 147 - 148: 11.091 distance: 147 - 150: 9.537 distance: 148 - 149: 23.651 distance: 148 - 153: 27.708 distance: 150 - 151: 9.995 distance: 151 - 152: 15.828 distance: 153 - 154: 12.181 distance: 154 - 155: 6.527 distance: 154 - 157: 14.690 distance: 155 - 156: 8.708 distance: 155 - 164: 11.295 distance: 157 - 158: 23.972 distance: 158 - 159: 21.622 distance: 159 - 160: 21.452 distance: 160 - 161: 9.536 distance: 161 - 162: 8.833 distance: 161 - 163: 11.696 distance: 164 - 165: 10.073 distance: 165 - 166: 12.563 distance: 165 - 168: 13.727 distance: 166 - 167: 16.793 distance: 166 - 172: 10.148 distance: 168 - 169: 23.297 distance: 168 - 170: 21.119 distance: 169 - 171: 36.322