Starting phenix.real_space_refine (version: 1.21rc1) on Fri Oct 6 20:11:05 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgj_27427/10_2023/8dgj_27427.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgj_27427/10_2023/8dgj_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_27427/10_2023/8dgj_27427.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgj_27427/10_2023/8dgj_27427.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgj_27427/10_2023/8dgj_27427.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dgj_27427/10_2023/8dgj_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 6.98, per 1000 atoms: 0.51 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: 5.23 Conformation dependent library (CDL) restraints added in 1.9 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: 1.42 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: 5.17 Time building geometry restraints manager: 5.71 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: 4.060 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: 15.050 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 37.190 Find NCS groups from input model: 0.370 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.810 ------------------------------------------------------------------------------- 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 *********************** 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 : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 155 average time/residue: 0.2900 time to fit residues: 65.5501 Evaluate side-chains 108 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.588 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3079 ------------------------------------------------------------------------------- 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 ** 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5559 moved from start: 0.1194 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= 0.198 Angle : 0.655 11.193 18808 Z= 0.335 Chirality : 0.042 0.153 2097 Planarity : 0.006 0.071 2447 Dihedral : 6.126 30.674 1855 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.00 % Favored : 93.70 % Rotamer: Outliers : 0.20 % Allowed : 5.33 % Favored : 94.47 % 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: -1.74 (0.19), residues: 1667 helix: -0.86 (0.17), residues: 787 sheet: -0.74 (0.40), residues: 160 loop : -1.45 (0.23), residues: 720 *********************** 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 165 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 162 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 164 average time/residue: 0.2995 time to fit residues: 70.9459 Evaluate side-chains 111 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.529 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1881 ------------------------------------------------------------------------------- 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: 0.9990 chunk 47 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 152 optimal weight: 8.9990 chunk 165 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 151 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 GLN ** 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 A1768 HIS A1960 ASN ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 454 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5537 moved from start: 0.1670 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= 0.196 Angle : 0.650 9.005 18808 Z= 0.328 Chirality : 0.043 0.154 2097 Planarity : 0.005 0.065 2447 Dihedral : 5.742 30.288 1855 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.36 % Favored : 93.40 % Rotamer: Outliers : 0.13 % Allowed : 4.40 % Favored : 95.47 % 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: -1.28 (0.20), residues: 1667 helix: -0.37 (0.17), residues: 789 sheet: -0.63 (0.39), residues: 167 loop : -1.33 (0.23), residues: 711 *********************** 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 158 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 156 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 158 average time/residue: 0.2897 time to fit residues: 67.2720 Evaluate side-chains 111 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.595 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.3390 ------------------------------------------------------------------------------- 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: 0.0370 chunk 114 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 72 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 153 optimal weight: 0.0020 chunk 162 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 145 optimal weight: 0.9990 chunk 43 optimal weight: 0.0060 overall best weight: 0.4086 ------------------------------------------------------------------------------- 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 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS ** A 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1185 GLN A1233 GLN A1526 GLN A1668 ASN ** A2087 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5429 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13873 Z= 0.162 Angle : 0.611 11.336 18808 Z= 0.307 Chirality : 0.042 0.196 2097 Planarity : 0.005 0.063 2447 Dihedral : 5.359 28.157 1855 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.00 % Favored : 93.76 % Rotamer: Outliers : 0.07 % Allowed : 3.40 % Favored : 96.53 % 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: -0.86 (0.20), residues: 1667 helix: 0.01 (0.18), residues: 792 sheet: -0.51 (0.39), residues: 166 loop : -1.16 (0.24), residues: 709 *********************** 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 162 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 161 time to evaluate : 1.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 161 average time/residue: 0.2905 time to fit residues: 68.1079 Evaluate side-chains 107 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.348 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.9294 ------------------------------------------------------------------------------- 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: 0.9990 chunk 92 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 112 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 82 optimal weight: 0.4980 chunk 145 optimal weight: 0.0060 chunk 40 optimal weight: 5.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- 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 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 304 HIS A 598 GLN ** A 773 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 853 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1196 HIS A1235 GLN ** A1526 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1668 ASN ** A2093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A2104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2106 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5489 moved from start: 0.2338 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= 0.187 Angle : 0.620 8.438 18808 Z= 0.311 Chirality : 0.042 0.154 2097 Planarity : 0.005 0.065 2447 Dihedral : 5.237 28.971 1855 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.66 % Favored : 93.10 % Rotamer: Outliers : 0.07 % Allowed : 2.60 % 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: -0.67 (0.20), residues: 1667 helix: 0.17 (0.18), residues: 793 sheet: -0.50 (0.39), residues: 166 loop : -1.04 (0.24), residues: 708 *********************** 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 164 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.3057 time to fit residues: 71.8535 Evaluate side-chains 106 residues out of total 1500 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 106 time to evaluate : 1.584 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.1916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/iotbx/cli_parser.py", line 881, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/programs/real_space_refine.py", line 192, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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-1.21rc1-5097/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: 57.9584 > 50: distance: 14 - 18: 11.656 distance: 18 - 19: 7.341 distance: 19 - 20: 9.061 distance: 20 - 21: 23.277 distance: 20 - 22: 16.867 distance: 22 - 23: 7.362 distance: 23 - 24: 3.847 distance: 23 - 26: 7.137 distance: 24 - 25: 7.654 distance: 24 - 33: 4.152 distance: 25 - 62: 10.024 distance: 27 - 28: 7.818 distance: 27 - 29: 7.647 distance: 28 - 30: 19.063 distance: 29 - 31: 16.896 distance: 30 - 32: 4.327 distance: 31 - 32: 7.473 distance: 33 - 34: 6.572 distance: 34 - 35: 12.401 distance: 34 - 37: 7.547 distance: 35 - 36: 10.034 distance: 35 - 42: 4.781 distance: 36 - 71: 38.320 distance: 37 - 38: 8.218 distance: 38 - 39: 6.738 distance: 39 - 40: 10.239 distance: 39 - 41: 3.838 distance: 42 - 43: 8.960 distance: 43 - 44: 5.988 distance: 44 - 45: 19.706 distance: 44 - 51: 15.679 distance: 45 - 80: 23.350 distance: 46 - 47: 17.779 distance: 47 - 48: 21.213 distance: 48 - 49: 11.330 distance: 51 - 52: 8.374 distance: 52 - 53: 15.378 distance: 52 - 55: 13.730 distance: 53 - 54: 16.527 distance: 53 - 62: 16.161 distance: 55 - 56: 4.634 distance: 56 - 57: 5.225 distance: 56 - 58: 16.067 distance: 57 - 59: 8.165 distance: 58 - 60: 5.392 distance: 59 - 61: 6.739 distance: 60 - 61: 14.052 distance: 62 - 63: 6.536 distance: 63 - 64: 13.126 distance: 63 - 66: 9.560 distance: 64 - 65: 12.931 distance: 64 - 71: 15.100 distance: 65 - 94: 4.802 distance: 66 - 67: 11.273 distance: 67 - 68: 19.157 distance: 68 - 69: 11.369 distance: 71 - 72: 13.362 distance: 72 - 73: 7.531 distance: 73 - 74: 7.078 distance: 73 - 80: 5.497 distance: 75 - 76: 4.314 distance: 76 - 77: 19.071 distance: 77 - 79: 5.723 distance: 81 - 82: 26.698 distance: 81 - 84: 14.242 distance: 82 - 83: 9.238 distance: 82 - 86: 8.804 distance: 84 - 85: 16.658 distance: 86 - 87: 16.519 distance: 87 - 88: 3.017 distance: 88 - 89: 39.739 distance: 88 - 94: 5.658 distance: 90 - 91: 12.921 distance: 91 - 92: 38.010 distance: 91 - 93: 23.642 distance: 94 - 95: 23.501 distance: 95 - 96: 22.745 distance: 96 - 97: 12.885 distance: 96 - 98: 29.728