Starting phenix.real_space_refine on Thu Nov 16 13:49:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg7_27417/11_2023/8dg7_27417_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg7_27417/11_2023/8dg7_27417.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg7_27417/11_2023/8dg7_27417.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg7_27417/11_2023/8dg7_27417.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg7_27417/11_2023/8dg7_27417_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dg7_27417/11_2023/8dg7_27417_updated.pdb" } resolution = 3.32 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= 0.035 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: 6 Type Number sf(0) Gaussians P 47 5.49 5 Mg 8 5.21 5 S 81 5.16 5 C 9722 2.51 5 N 2738 2.21 5 O 3013 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 292": "OE1" <-> "OE2" Residue "A TYR 529": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 630": "OD1" <-> "OD2" Residue "A ASP 907": "OD1" <-> "OD2" Residue "A GLU 916": "OE1" <-> "OE2" Residue "A GLU 1036": "OE1" <-> "OE2" Residue "A GLU 1047": "OE1" <-> "OE2" Residue "A PHE 1055": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1074": "OD1" <-> "OD2" Residue "A ASP 1098": "OD1" <-> "OD2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "A TYR 1148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1588": "OD1" <-> "OD2" Residue "A TYR 1815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1819": "OE1" <-> "OE2" Residue "A ASP 1841": "OD1" <-> "OD2" Residue "A GLU 1917": "OE1" <-> "OE2" Residue "A PHE 1978": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2002": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 2197": "OE1" <-> "OE2" Residue "K GLU 164": "OE1" <-> "OE2" Residue "K PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 177": "OD1" <-> "OD2" Residue "K PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 457": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 15609 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 13175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1635, 13175 Classifications: {'peptide': 1635} Link IDs: {'PTRANS': 98, 'TRANS': 1536} Chain breaks: 14 Chain: "E" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 456 Classifications: {'RNA': 21} Modifications used: {'rna3p_pur': 14, 'rna3p_pyr': 7} Link IDs: {'rna3p': 20} Chain: "F" Number of atoms: 532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 532 Classifications: {'RNA': 26} Modifications used: {'5*END': 1, 'rna3p_pur': 8, 'rna3p_pyr': 17} Link IDs: {'rna3p': 25} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "K" Number of atoms: 1417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1417 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 175} Chain breaks: 2 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 24 Unusual residues: {' MG': 3} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna2p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.83, per 1000 atoms: 0.57 Number of scatterers: 15609 At special positions: 0 Unit cell: (155.21, 126.99, 146.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 81 16.00 P 47 15.00 Mg 8 11.99 O 3013 8.00 N 2738 7.00 C 9722 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.56 Conformation dependent library (CDL) restraints added in 2.5 seconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3468 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 63 helices and 12 sheets defined 41.7% alpha, 7.5% beta 19 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 8.47 Creating SS restraints... Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 40 through 58 Processing helix chain 'A' and resid 80 through 87 Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 118 through 126 Processing helix chain 'A' and resid 146 through 157 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 188 through 199 Processing helix chain 'A' and resid 233 through 251 removed outlier: 3.848A pdb=" N SER A 247 " --> pdb=" O ASN A 243 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE A 248 " --> pdb=" O THR A 244 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP A 251 " --> pdb=" O SER A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 292 removed outlier: 4.390A pdb=" N LEU A 286 " --> pdb=" O VAL A 282 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU A 287 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL A 288 " --> pdb=" O ASN A 284 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 312 removed outlier: 3.860A pdb=" N HIS A 304 " --> pdb=" O ARG A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 319 through 345 removed outlier: 3.501A pdb=" N ARG A 345 " --> pdb=" O HIS A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 504 through 518 Processing helix chain 'A' and resid 541 through 559 removed outlier: 3.520A pdb=" N GLU A 553 " --> pdb=" O ARG A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 572 No H-bonds generated for 'chain 'A' and resid 570 through 572' Processing helix chain 'A' and resid 593 through 597 Processing helix chain 'A' and resid 630 through 638 Processing helix chain 'A' and resid 760 through 783 Processing helix chain 'A' and resid 792 through 801 Processing helix chain 'A' and resid 822 through 826 removed outlier: 3.876A pdb=" N ILE A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 822 through 826' Processing helix chain 'A' and resid 886 through 903 Processing helix chain 'A' and resid 932 through 940 removed outlier: 4.262A pdb=" N ILE A 937 " --> pdb=" O GLU A 933 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1061 removed outlier: 3.592A pdb=" N ASN A1057 " --> pdb=" O ASN A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1107 Processing helix chain 'A' and resid 1118 through 1123 Processing helix chain 'A' and resid 1172 through 1179 Processing helix chain 'A' and resid 1221 through 1229 Processing helix chain 'A' and resid 1239 through 1241 No H-bonds generated for 'chain 'A' and resid 1239 through 1241' Processing helix chain 'A' and resid 1249 through 1256 Processing helix chain 'A' and resid 1258 through 1281 Processing helix chain 'A' and resid 1526 through 1548 removed outlier: 3.933A pdb=" N GLN A1533 " --> pdb=" O LEU A1529 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ARG A1540 " --> pdb=" O ASN A1536 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLN A1541 " --> pdb=" O ALA A1537 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN A1543 " --> pdb=" O GLU A1539 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLN A1544 " --> pdb=" O ARG A1540 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS A1546 " --> pdb=" O TYR A1542 " (cutoff:3.500A) Processing helix chain 'A' and resid 1567 through 1580 Processing helix chain 'A' and resid 1608 through 1615 Processing helix chain 'A' and resid 1624 through 1628 Processing helix chain 'A' and resid 1636 through 1649 Processing helix chain 'A' and resid 1723 through 1730 Processing helix chain 'A' and resid 1733 through 1735 No H-bonds generated for 'chain 'A' and resid 1733 through 1735' Processing helix chain 'A' and resid 1742 through 1763 removed outlier: 3.894A pdb=" N THR A1746 " --> pdb=" O GLU A1742 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ILE A1747 " --> pdb=" O ARG A1743 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N SER A1750 " --> pdb=" O THR A1746 " (cutoff:3.500A) Processing helix chain 'A' and resid 1769 through 1780 removed outlier: 4.181A pdb=" N HIS A1774 " --> pdb=" O GLY A1770 " (cutoff:3.500A) Processing helix chain 'A' and resid 1782 through 1791 Processing helix chain 'A' and resid 1820 through 1823 No H-bonds generated for 'chain 'A' and resid 1820 through 1823' Processing helix chain 'A' and resid 1836 through 1843 Processing helix chain 'A' and resid 1848 through 1853 Processing helix chain 'A' and resid 1900 through 1930 Proline residue: A1920 - end of helix Processing helix chain 'A' and resid 1982 through 1989 Processing helix chain 'A' and resid 1994 through 1998 Processing helix chain 'A' and resid 2008 through 2014 Processing helix chain 'A' and resid 2029 through 2048 removed outlier: 3.745A pdb=" N LEU A2034 " --> pdb=" O ARG A2030 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA A2037 " --> pdb=" O PHE A2033 " (cutoff:3.500A) Processing helix chain 'A' and resid 2056 through 2064 removed outlier: 3.691A pdb=" N LEU A2062 " --> pdb=" O ALA A2058 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG A2063 " --> pdb=" O LEU A2059 " (cutoff:3.500A) Processing helix chain 'A' and resid 2069 through 2078 Processing helix chain 'A' and resid 2082 through 2084 No H-bonds generated for 'chain 'A' and resid 2082 through 2084' Processing helix chain 'A' and resid 2090 through 2105 Processing helix chain 'A' and resid 2132 through 2149 removed outlier: 3.673A pdb=" N ALA A2142 " --> pdb=" O PHE A2138 " (cutoff:3.500A) Processing helix chain 'A' and resid 2153 through 2173 removed outlier: 4.160A pdb=" N ASN A2162 " --> pdb=" O HIS A2158 " (cutoff:3.500A) removed outlier: 4.200A 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 2224 through 2238 Processing helix chain 'K' and resid 136 through 147 removed outlier: 4.257A pdb=" N ARG K 146 " --> pdb=" O GLU K 142 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ARG K 147 " --> pdb=" O LEU K 143 " (cutoff:3.500A) Processing helix chain 'K' and resid 189 through 204 Processing helix chain 'K' and resid 359 through 372 Processing helix chain 'K' and resid 377 through 384 Processing helix chain 'K' and resid 394 through 404 Processing helix chain 'K' and resid 444 through 463 Processing sheet with id= A, first strand: chain 'A' and resid 220 through 225 removed outlier: 3.770A pdb=" N HIS A 610 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 613 " --> pdb=" O ARG A 586 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 527 through 529 removed outlier: 6.439A pdb=" N VAL A 565 " --> pdb=" O GLN A 528 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 849 through 855 Processing sheet with id= D, first strand: chain 'A' and resid 952 through 956 Processing sheet with id= E, first strand: chain 'A' and resid 1095 through 1097 removed outlier: 10.912A pdb=" N GLN A1006 " --> pdb=" O LEU A 981 " (cutoff:3.500A) removed outlier: 9.052A pdb=" N LEU A 981 " --> pdb=" O GLN A1006 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N PHE A1008 " --> pdb=" O ILE A 979 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU A1030 " --> pdb=" O GLN A 984 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 1136 through 1138 removed outlier: 3.542A pdb=" N MET A1137 " --> pdb=" O THR A1243 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 1153 through 1155 removed outlier: 4.149A pdb=" N GLN A1235 " --> pdb=" O VAL A1194 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 1936 through 1941 removed outlier: 3.690A pdb=" N VAL A1964 " --> pdb=" O THR A1938 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 2209 through 2211 Processing sheet with id= J, first strand: chain 'A' and resid 64 through 66 removed outlier: 7.354A pdb=" N VAL A 66 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE A 138 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 152 through 155 removed outlier: 4.184A pdb=" N GLY K 152 " --> pdb=" O SER K 172 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N PHE K 180 " --> pdb=" O PHE K 173 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'K' and resid 409 through 414 removed outlier: 4.759A pdb=" N GLN K 424 " --> pdb=" O ILE K 414 " (cutoff:3.500A) 554 hydrogen bonds defined for protein. 1623 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 45 hydrogen bonds 90 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 6.97 Time building geometry restraints manager: 7.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4293 1.33 - 1.46: 4242 1.46 - 1.59: 7304 1.59 - 1.71: 85 1.71 - 1.84: 110 Bond restraints: 16034 Sorted by residual: bond pdb=" CG PRO A 78 " pdb=" CD PRO A 78 " ideal model delta sigma weight residual 1.503 1.414 0.089 3.40e-02 8.65e+02 6.92e+00 bond pdb=" C GLY A 879 " pdb=" N LEU A 880 " ideal model delta sigma weight residual 1.331 1.279 0.052 2.07e-02 2.33e+03 6.24e+00 bond pdb=" CB PRO A 78 " pdb=" CG PRO A 78 " ideal model delta sigma weight residual 1.492 1.615 -0.123 5.00e-02 4.00e+02 6.06e+00 bond pdb=" C SER A 871 " pdb=" N PRO A 872 " ideal model delta sigma weight residual 1.331 1.351 -0.019 7.90e-03 1.60e+04 5.96e+00 bond pdb=" CA GLU A 926 " pdb=" CB GLU A 926 " ideal model delta sigma weight residual 1.522 1.560 -0.038 1.86e-02 2.89e+03 4.13e+00 ... (remaining 16029 not shown) Histogram of bond angle deviations from ideal: 95.24 - 104.02: 427 104.02 - 112.81: 8552 112.81 - 121.60: 9291 121.60 - 130.39: 3574 130.39 - 139.17: 101 Bond angle restraints: 21945 Sorted by residual: angle pdb=" CA PRO A 78 " pdb=" N PRO A 78 " pdb=" CD PRO A 78 " ideal model delta sigma weight residual 112.00 98.76 13.24 1.40e+00 5.10e-01 8.95e+01 angle pdb=" CA LEU A1177 " pdb=" CB LEU A1177 " pdb=" CG LEU A1177 " ideal model delta sigma weight residual 116.30 137.81 -21.51 3.50e+00 8.16e-02 3.78e+01 angle pdb=" CA LEU A1642 " pdb=" CB LEU A1642 " pdb=" CG LEU A1642 " ideal model delta sigma weight residual 116.30 136.89 -20.59 3.50e+00 8.16e-02 3.46e+01 angle pdb=" C LEU A 116 " pdb=" N ARG A 117 " pdb=" CA ARG A 117 " ideal model delta sigma weight residual 122.38 139.17 -16.79 2.90e+00 1.19e-01 3.35e+01 angle pdb=" N PHE A2171 " pdb=" CA PHE A2171 " pdb=" CB PHE A2171 " ideal model delta sigma weight residual 110.28 119.13 -8.85 1.55e+00 4.16e-01 3.26e+01 ... (remaining 21940 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 8149 17.80 - 35.59: 1105 35.59 - 53.39: 319 53.39 - 71.18: 54 71.18 - 88.98: 17 Dihedral angle restraints: 9644 sinusoidal: 4309 harmonic: 5335 Sorted by residual: dihedral pdb=" CA ALA A 606 " pdb=" C ALA A 606 " pdb=" N PRO A 607 " pdb=" CA PRO A 607 " ideal model delta harmonic sigma weight residual 180.00 125.96 54.04 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" CA THR A1654 " pdb=" C THR A1654 " pdb=" N TYR A1655 " pdb=" CA TYR A1655 " ideal model delta harmonic sigma weight residual -180.00 -144.64 -35.36 0 5.00e+00 4.00e-02 5.00e+01 dihedral pdb=" CA MET K 462 " pdb=" C MET K 462 " pdb=" N THR K 463 " pdb=" CA THR K 463 " ideal model delta harmonic sigma weight residual 180.00 150.23 29.77 0 5.00e+00 4.00e-02 3.55e+01 ... (remaining 9641 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 2334 0.104 - 0.208: 150 0.208 - 0.313: 10 0.313 - 0.417: 2 0.417 - 0.521: 1 Chirality restraints: 2497 Sorted by residual: chirality pdb=" CB ILE A2180 " pdb=" CA ILE A2180 " pdb=" CG1 ILE A2180 " pdb=" CG2 ILE A2180 " both_signs ideal model delta sigma weight residual False 2.64 2.12 0.52 2.00e-01 2.50e+01 6.79e+00 chirality pdb=" CG LEU A 50 " pdb=" CB LEU A 50 " pdb=" CD1 LEU A 50 " pdb=" CD2 LEU A 50 " both_signs ideal model delta sigma weight residual False -2.59 -2.21 -0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" CG LEU A2075 " pdb=" CB LEU A2075 " pdb=" CD1 LEU A2075 " pdb=" CD2 LEU A2075 " both_signs ideal model delta sigma weight residual False -2.59 -2.24 -0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 2494 not shown) Planarity restraints: 2661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 77 " 0.105 5.00e-02 4.00e+02 1.48e-01 3.50e+01 pdb=" N PRO A 78 " -0.255 5.00e-02 4.00e+02 pdb=" CA PRO A 78 " 0.074 5.00e-02 4.00e+02 pdb=" CD PRO A 78 " 0.076 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 164 " 0.070 5.00e-02 4.00e+02 1.04e-01 1.75e+01 pdb=" N PRO A 165 " -0.181 5.00e-02 4.00e+02 pdb=" CA PRO A 165 " 0.055 5.00e-02 4.00e+02 pdb=" CD PRO A 165 " 0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 362 " -0.061 5.00e-02 4.00e+02 9.18e-02 1.35e+01 pdb=" N PRO A 363 " 0.159 5.00e-02 4.00e+02 pdb=" CA PRO A 363 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO A 363 " -0.050 5.00e-02 4.00e+02 ... (remaining 2658 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 172 2.56 - 3.15: 11676 3.15 - 3.73: 26216 3.73 - 4.32: 34084 4.32 - 4.90: 55066 Nonbonded interactions: 127214 Sorted by model distance: nonbonded pdb=" OE2 GLU A1745 " pdb="MG MG A2301 " model vdw 1.980 2.170 nonbonded pdb=" OE2 GLU A1908 " pdb="MG MG A2302 " model vdw 1.995 2.170 nonbonded pdb=" OP1 C F 39 " pdb="MG MG A2301 " model vdw 2.001 2.170 nonbonded pdb="MG MG A2304 " pdb=" O1P U5P E 101 " model vdw 2.024 2.170 nonbonded pdb=" OD1 ASP A1749 " pdb="MG MG A2302 " model vdw 2.034 2.170 ... (remaining 127209 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.020 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: 17.520 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 49.100 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 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 0.123 16034 Z= 0.427 Angle : 1.111 21.512 21945 Z= 0.554 Chirality : 0.056 0.521 2497 Planarity : 0.009 0.148 2661 Dihedral : 17.480 88.981 6176 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.65 % Favored : 91.24 % Rotamer: Outliers : 1.24 % Allowed : 31.43 % Favored : 67.33 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.18), residues: 1780 helix: -1.45 (0.16), residues: 811 sheet: -2.09 (0.36), residues: 190 loop : -2.04 (0.21), residues: 779 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 150 time to evaluate : 1.773 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 165 average time/residue: 0.2873 time to fit residues: 71.5147 Evaluate side-chains 149 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 139 time to evaluate : 1.558 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1638 time to fit residues: 5.1972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.6980 chunk 140 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 145 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 88 optimal weight: 0.0010 chunk 107 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 HIS ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.0913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16034 Z= 0.178 Angle : 0.616 12.189 21945 Z= 0.302 Chirality : 0.039 0.170 2497 Planarity : 0.005 0.069 2661 Dihedral : 7.681 81.812 2548 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.63 % Favored : 93.20 % Rotamer: Outliers : 3.85 % Allowed : 28.57 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -1.83 (0.19), residues: 1780 helix: -0.33 (0.17), residues: 813 sheet: -2.02 (0.37), residues: 180 loop : -1.90 (0.21), residues: 787 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 146 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 29 residues processed: 198 average time/residue: 0.2936 time to fit residues: 89.9332 Evaluate side-chains 159 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 130 time to evaluate : 1.697 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1793 time to fit residues: 11.5590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 0.5980 chunk 52 optimal weight: 8.9990 chunk 139 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 46 optimal weight: 0.0010 chunk 168 optimal weight: 7.9990 chunk 181 optimal weight: 6.9990 chunk 149 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 overall best weight: 1.1190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 163 HIS ** K 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16034 Z= 0.223 Angle : 0.622 12.789 21945 Z= 0.303 Chirality : 0.040 0.176 2497 Planarity : 0.005 0.064 2661 Dihedral : 7.519 82.968 2548 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 14.20 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.58 % Favored : 92.25 % Rotamer: Outliers : 3.79 % Allowed : 28.57 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -1.54 (0.19), residues: 1780 helix: 0.03 (0.18), residues: 814 sheet: -2.22 (0.36), residues: 190 loop : -1.81 (0.21), residues: 776 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 143 time to evaluate : 1.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 28 residues processed: 196 average time/residue: 0.2897 time to fit residues: 86.2847 Evaluate side-chains 159 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 131 time to evaluate : 1.761 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.1545 time to fit residues: 10.8876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 87 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 168 optimal weight: 6.9990 chunk 178 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 160 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 830 ASN ** A1006 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1671 HIS A1849 GLN A1891 ASN ** K 194 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16034 Z= 0.420 Angle : 0.756 13.965 21945 Z= 0.377 Chirality : 0.046 0.229 2497 Planarity : 0.006 0.066 2661 Dihedral : 7.910 83.414 2548 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.17 % Allowed : 9.38 % Favored : 90.45 % Rotamer: Outliers : 4.84 % Allowed : 29.19 % Favored : 65.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -1.86 (0.19), residues: 1780 helix: -0.31 (0.17), residues: 807 sheet: -2.24 (0.36), residues: 180 loop : -1.91 (0.21), residues: 793 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 136 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 49 residues processed: 201 average time/residue: 0.2641 time to fit residues: 81.7545 Evaluate side-chains 172 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 123 time to evaluate : 1.742 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 0.1706 time to fit residues: 17.3090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 133 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 91 optimal weight: 0.0170 chunk 160 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1849 GLN K 194 HIS ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6835 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16034 Z= 0.182 Angle : 0.624 14.288 21945 Z= 0.303 Chirality : 0.040 0.162 2497 Planarity : 0.004 0.063 2661 Dihedral : 7.458 84.124 2548 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.91 % Favored : 92.92 % Rotamer: Outliers : 2.86 % Allowed : 30.06 % Favored : 67.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -1.29 (0.20), residues: 1780 helix: 0.20 (0.18), residues: 816 sheet: -1.82 (0.39), residues: 167 loop : -1.74 (0.22), residues: 797 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 148 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 17 residues processed: 186 average time/residue: 0.2766 time to fit residues: 79.4222 Evaluate side-chains 145 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.620 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1650 time to fit residues: 7.4016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 60 optimal weight: 0.8980 chunk 161 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 chunk 104 optimal weight: 0.6980 chunk 44 optimal weight: 0.0040 chunk 178 optimal weight: 9.9990 chunk 148 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1053 ASN A1062 ASN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1891 ASN ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 438 HIS K 448 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16034 Z= 0.185 Angle : 0.623 14.051 21945 Z= 0.299 Chirality : 0.039 0.164 2497 Planarity : 0.004 0.062 2661 Dihedral : 7.285 85.522 2548 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.36 % Favored : 92.47 % Rotamer: Outliers : 2.05 % Allowed : 30.50 % Favored : 67.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: 1780 helix: 0.45 (0.18), residues: 815 sheet: -1.89 (0.38), residues: 179 loop : -1.59 (0.22), residues: 786 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 149 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 12 residues processed: 172 average time/residue: 0.2861 time to fit residues: 75.4227 Evaluate side-chains 147 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 1.756 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1953 time to fit residues: 6.6764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 172 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 101 optimal weight: 6.9990 chunk 130 optimal weight: 0.5980 chunk 150 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 178 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1891 ASN ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6823 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16034 Z= 0.202 Angle : 0.640 14.634 21945 Z= 0.305 Chirality : 0.040 0.208 2497 Planarity : 0.004 0.061 2661 Dihedral : 7.274 86.528 2548 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.30 % Favored : 92.53 % Rotamer: Outliers : 1.93 % Allowed : 30.81 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -0.98 (0.20), residues: 1780 helix: 0.49 (0.18), residues: 814 sheet: -1.85 (0.38), residues: 179 loop : -1.56 (0.22), residues: 787 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 138 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 12 residues processed: 165 average time/residue: 0.2914 time to fit residues: 73.3302 Evaluate side-chains 146 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 134 time to evaluate : 1.623 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1599 time to fit residues: 5.9872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 71 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 34 optimal weight: 0.0050 chunk 113 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 162 optimal weight: 0.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1006 GLN A1062 ASN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1891 ASN ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6798 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16034 Z= 0.185 Angle : 0.627 14.777 21945 Z= 0.300 Chirality : 0.040 0.174 2497 Planarity : 0.004 0.061 2661 Dihedral : 7.206 87.362 2548 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.13 % Favored : 92.70 % Rotamer: Outliers : 0.87 % Allowed : 31.49 % Favored : 67.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -0.88 (0.20), residues: 1780 helix: 0.59 (0.18), residues: 809 sheet: -1.66 (0.39), residues: 172 loop : -1.56 (0.22), residues: 799 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 148 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 156 average time/residue: 0.2724 time to fit residues: 65.1904 Evaluate side-chains 148 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 140 time to evaluate : 1.561 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1538 time to fit residues: 4.3951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 170 optimal weight: 7.9990 chunk 155 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 100 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 chunk 165 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2079 HIS ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6862 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16034 Z= 0.255 Angle : 0.673 15.279 21945 Z= 0.323 Chirality : 0.041 0.222 2497 Planarity : 0.004 0.062 2661 Dihedral : 7.315 88.110 2548 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.81 % Favored : 92.02 % Rotamer: Outliers : 0.75 % Allowed : 31.55 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -1.01 (0.20), residues: 1780 helix: 0.51 (0.18), residues: 805 sheet: -1.79 (0.38), residues: 179 loop : -1.63 (0.22), residues: 796 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 5 residues processed: 145 average time/residue: 0.3211 time to fit residues: 71.2545 Evaluate side-chains 142 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 137 time to evaluate : 1.694 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1699 time to fit residues: 3.9132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 175 optimal weight: 0.3980 chunk 107 optimal weight: 0.6980 chunk 83 optimal weight: 0.9980 chunk 122 optimal weight: 2.9990 chunk 184 optimal weight: 6.9990 chunk 169 optimal weight: 4.9990 chunk 146 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 113 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 chunk 116 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN ** K 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16034 Z= 0.177 Angle : 0.643 15.452 21945 Z= 0.307 Chirality : 0.040 0.179 2497 Planarity : 0.004 0.061 2661 Dihedral : 7.169 88.482 2548 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.30 % Favored : 92.53 % Rotamer: Outliers : 0.31 % Allowed : 31.99 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.20), residues: 1780 helix: 0.69 (0.18), residues: 804 sheet: -1.71 (0.38), residues: 179 loop : -1.54 (0.22), residues: 797 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 145 time to evaluate : 1.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 148 average time/residue: 0.2910 time to fit residues: 65.8998 Evaluate side-chains 143 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 1.807 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1549 time to fit residues: 3.1992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 0.6980 chunk 44 optimal weight: 3.9990 chunk 135 optimal weight: 5.9990 chunk 21 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 0.9990 chunk 61 optimal weight: 0.0270 chunk 150 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 610 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 895 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1062 ASN ** A1080 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 405 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.162551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.129265 restraints weight = 30702.760| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 3.15 r_work: 0.3822 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16034 Z= 0.209 Angle : 0.648 15.691 21945 Z= 0.310 Chirality : 0.040 0.191 2497 Planarity : 0.004 0.061 2661 Dihedral : 7.189 89.552 2548 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.75 % Favored : 92.08 % Rotamer: Outliers : 0.37 % Allowed : 32.48 % Favored : 67.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.97 % Cis-general : 0.00 % Twisted Proline : 0.97 % 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: -0.80 (0.20), residues: 1780 helix: 0.70 (0.18), residues: 804 sheet: -1.68 (0.38), residues: 179 loop : -1.54 (0.22), residues: 797 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3442.64 seconds wall clock time: 64 minutes 32.18 seconds (3872.18 seconds total)