Starting phenix.real_space_refine on Thu May 1 04:50:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2k_44111/05_2025/9b2k_44111.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2k_44111/05_2025/9b2k_44111.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b2k_44111/05_2025/9b2k_44111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2k_44111/05_2025/9b2k_44111.map" model { file = "/net/cci-nas-00/data/ceres_data/9b2k_44111/05_2025/9b2k_44111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2k_44111/05_2025/9b2k_44111.cif" } resolution = 3.67 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= 0.014 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: 5 Type Number sf(0) Gaussians P 74 5.49 5 S 16 5.16 5 C 6213 2.51 5 N 1802 2.21 5 O 2137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib" Total number of atoms: 10242 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 381 Classifications: {'RNA': 18} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 7, 'rna3p_pyr': 10} Link IDs: {'rna2p': 1, 'rna3p': 16} Chain: "B" Number of atoms: 1206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1206 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 5, 'rna2p_pyr': 2, 'rna3p_pur': 31, 'rna3p_pyr': 18} Link IDs: {'rna2p': 7, 'rna3p': 48} Chain breaks: 1 Chain: "P" Number of atoms: 8655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1062, 8655 Classifications: {'peptide': 1062} Link IDs: {'PTRANS': 27, 'TRANS': 1034} Chain breaks: 2 Time building chain proxies: 7.13, per 1000 atoms: 0.70 Number of scatterers: 10242 At special positions: 0 Unit cell: (85.4, 118.3, 139.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 74 15.00 O 2137 8.00 N 1802 7.00 C 6213 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 - 3.00 Amino acid : True - 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: 2.40 Conformation dependent library (CDL) restraints added in 1.2 seconds 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2022 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 7 sheets defined 52.6% alpha, 7.3% beta 18 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 3.29 Creating SS restraints... Processing helix chain 'P' and resid 58 through 64 Processing helix chain 'P' and resid 68 through 91 removed outlier: 4.180A pdb=" N ASN P 88 " --> pdb=" O GLU P 84 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU P 89 " --> pdb=" O ILE P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 103 removed outlier: 3.851A pdb=" N ARG P 100 " --> pdb=" O SER P 96 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU P 101 " --> pdb=" O PHE P 97 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU P 103 " --> pdb=" O HIS P 99 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 132 removed outlier: 4.291A pdb=" N GLU P 125 " --> pdb=" O ASN P 121 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL P 126 " --> pdb=" O ILE P 122 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ALA P 127 " --> pdb=" O VAL P 123 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N HIS P 129 " --> pdb=" O GLU P 125 " (cutoff:3.500A) Processing helix chain 'P' and resid 134 through 144 removed outlier: 4.001A pdb=" N LEU P 138 " --> pdb=" O THR P 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 150 through 164 Processing helix chain 'P' and resid 175 through 179 Processing helix chain 'P' and resid 181 through 196 Processing helix chain 'P' and resid 207 through 213 removed outlier: 3.554A pdb=" N ILE P 211 " --> pdb=" O ASP P 207 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 227 removed outlier: 4.044A pdb=" N LEU P 225 " --> pdb=" O ARG P 221 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE P 226 " --> pdb=" O LEU P 222 " (cutoff:3.500A) Processing helix chain 'P' and resid 236 through 245 Processing helix chain 'P' and resid 271 through 283 Processing helix chain 'P' and resid 284 through 287 Processing helix chain 'P' and resid 293 through 306 removed outlier: 3.813A pdb=" N ASP P 298 " --> pdb=" O LYS P 294 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA P 299 " --> pdb=" O ASN P 295 " (cutoff:3.500A) Processing helix chain 'P' and resid 315 through 342 Processing helix chain 'P' and resid 346 through 352 Processing helix chain 'P' and resid 358 through 365 Processing helix chain 'P' and resid 368 through 383 Proline residue: P 378 - end of helix Processing helix chain 'P' and resid 389 through 395 removed outlier: 3.511A pdb=" N ASN P 394 " --> pdb=" O LEU P 390 " (cutoff:3.500A) Processing helix chain 'P' and resid 411 through 426 removed outlier: 4.492A pdb=" N HIS P 415 " --> pdb=" O PRO P 411 " (cutoff:3.500A) Processing helix chain 'P' and resid 430 through 446 removed outlier: 4.227A pdb=" N LYS P 434 " --> pdb=" O TYR P 430 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASP P 435 " --> pdb=" O PRO P 431 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N GLU P 438 " --> pdb=" O LYS P 434 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LYS P 439 " --> pdb=" O ASP P 435 " (cutoff:3.500A) Processing helix chain 'P' and resid 719 through 727 removed outlier: 3.853A pdb=" N LEU P 727 " --> pdb=" O HIS P 723 " (cutoff:3.500A) Processing helix chain 'P' and resid 730 through 751 removed outlier: 3.652A pdb=" N LYS P 734 " --> pdb=" O SER P 730 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET P 751 " --> pdb=" O LEU P 747 " (cutoff:3.500A) Processing helix chain 'P' and resid 771 through 792 removed outlier: 4.216A pdb=" N SER P 777 " --> pdb=" O GLY P 773 " (cutoff:3.500A) Processing helix chain 'P' and resid 794 through 799 Processing helix chain 'P' and resid 802 through 807 removed outlier: 3.808A pdb=" N GLN P 807 " --> pdb=" O ASN P 803 " (cutoff:3.500A) Processing helix chain 'P' and resid 808 through 817 Processing helix chain 'P' and resid 851 through 853 No H-bonds generated for 'chain 'P' and resid 851 through 853' Processing helix chain 'P' and resid 860 through 864 removed outlier: 3.931A pdb=" N ASN P 863 " --> pdb=" O SER P 860 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ARG P 864 " --> pdb=" O ASP P 861 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 860 through 864' Processing helix chain 'P' and resid 872 through 888 removed outlier: 4.261A pdb=" N VAL P 876 " --> pdb=" O SER P 872 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS P 877 " --> pdb=" O GLU P 873 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LYS P 878 " --> pdb=" O GLU P 874 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET P 879 " --> pdb=" O VAL P 875 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ASN P 881 " --> pdb=" O LYS P 877 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N TYR P 882 " --> pdb=" O LYS P 878 " (cutoff:3.500A) Processing helix chain 'P' and resid 893 through 901 Processing helix chain 'P' and resid 902 through 906 removed outlier: 3.733A pdb=" N ARG P 905 " --> pdb=" O LYS P 902 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLY P 906 " --> pdb=" O ALA P 903 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 902 through 906' Processing helix chain 'P' and resid 909 through 922 Processing helix chain 'P' and resid 925 through 940 removed outlier: 3.686A pdb=" N LYS P 929 " --> pdb=" O ARG P 925 " (cutoff:3.500A) Processing helix chain 'P' and resid 959 through 971 removed outlier: 4.408A pdb=" N VAL P 963 " --> pdb=" O LYS P 959 " (cutoff:3.500A) Processing helix chain 'P' and resid 981 through 1001 removed outlier: 3.594A pdb=" N ALA P 991 " --> pdb=" O ALA P 987 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA P 996 " --> pdb=" O VAL P 992 " (cutoff:3.500A) Processing helix chain 'P' and resid 1004 through 1009 removed outlier: 4.134A pdb=" N PHE P1008 " --> pdb=" O LEU P1004 " (cutoff:3.500A) Processing helix chain 'P' and resid 1025 through 1030 removed outlier: 3.512A pdb=" N ILE P1029 " --> pdb=" O SER P1025 " (cutoff:3.500A) Processing helix chain 'P' and resid 1041 through 1047 removed outlier: 3.739A pdb=" N ASN P1044 " --> pdb=" O ASN P1041 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N PHE P1045 " --> pdb=" O ILE P1042 " (cutoff:3.500A) Processing helix chain 'P' and resid 1076 through 1089 removed outlier: 3.933A pdb=" N PHE P1080 " --> pdb=" O LYS P1076 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA P1081 " --> pdb=" O GLY P1077 " (cutoff:3.500A) Processing helix chain 'P' and resid 1170 through 1177 removed outlier: 3.570A pdb=" N ASN P1177 " --> pdb=" O SER P1173 " (cutoff:3.500A) Processing helix chain 'P' and resid 1177 through 1186 Processing helix chain 'P' and resid 1207 through 1209 No H-bonds generated for 'chain 'P' and resid 1207 through 1209' Processing helix chain 'P' and resid 1229 through 1241 Processing helix chain 'P' and resid 1248 through 1262 removed outlier: 3.902A pdb=" N HIS P1262 " --> pdb=" O PHE P1258 " (cutoff:3.500A) Processing helix chain 'P' and resid 1264 through 1280 Processing helix chain 'P' and resid 1283 through 1297 Processing helix chain 'P' and resid 1301 through 1313 removed outlier: 3.570A pdb=" N GLU P1307 " --> pdb=" O ARG P1303 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASN P1308 " --> pdb=" O GLU P1304 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'P' and resid 954 through 957 removed outlier: 3.782A pdb=" N ILE P 759 " --> pdb=" O LYS P 954 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE P 956 " --> pdb=" O ILE P 759 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE P 7 " --> pdb=" O ASN P 758 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE P 11 " --> pdb=" O GLU P 762 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER P 6 " --> pdb=" O ILE P 21 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY P 8 " --> pdb=" O ALA P 19 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ALA P 19 " --> pdb=" O GLY P 8 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N ASP P 10 " --> pdb=" O GLY P 17 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY P 17 " --> pdb=" O ASP P 10 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'P' and resid 29 through 30 Processing sheet with id=AA3, first strand: chain 'P' and resid 35 through 36 removed outlier: 3.561A pdb=" N LEU P 35 " --> pdb=" O GLU P1357 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N THR P1358 " --> pdb=" O HIS P1349 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU P1203 " --> pdb=" O ILE P1348 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 837 through 840 removed outlier: 3.764A pdb=" N ASP P 837 " --> pdb=" O THR P 858 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR P 858 " --> pdb=" O ASP P 837 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP P 839 " --> pdb=" O VAL P 856 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL P 856 " --> pdb=" O ASP P 839 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'P' and resid 1063 through 1065 removed outlier: 6.627A pdb=" N GLU P1064 " --> pdb=" O VAL P1073 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'P' and resid 1157 through 1167 removed outlier: 3.740A pdb=" N VAL P1145 " --> pdb=" O GLU P1162 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU P1164 " --> pdb=" O VAL P1143 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ILE P1166 " --> pdb=" O TYR P1141 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR P1141 " --> pdb=" O ILE P1166 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU P1144 " --> pdb=" O ILE P1196 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE P1196 " --> pdb=" O LEU P1144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'P' and resid 1324 through 1325 removed outlier: 3.738A pdb=" N PHE P1324 " --> pdb=" O ILE P1331 " (cutoff:3.500A) 355 hydrogen bonds defined for protein. 1038 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 46 hydrogen bonds 92 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 4.32 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2961 1.34 - 1.46: 2224 1.46 - 1.58: 5215 1.58 - 1.70: 146 1.70 - 1.82: 31 Bond restraints: 10577 Sorted by residual: bond pdb=" N LYS P 65 " pdb=" CA LYS P 65 " ideal model delta sigma weight residual 1.456 1.527 -0.071 1.40e-02 5.10e+03 2.55e+01 bond pdb=" CA SER P 409 " pdb=" CB SER P 409 " ideal model delta sigma weight residual 1.530 1.476 0.054 1.69e-02 3.50e+03 1.01e+01 bond pdb=" N LEU P 334 " pdb=" CA LEU P 334 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.17e-02 7.31e+03 8.93e+00 bond pdb=" N LEU P 306 " pdb=" CA LEU P 306 " ideal model delta sigma weight residual 1.463 1.500 -0.037 1.27e-02 6.20e+03 8.40e+00 bond pdb=" C LEU P 64 " pdb=" N LYS P 65 " ideal model delta sigma weight residual 1.328 1.370 -0.042 1.51e-02 4.39e+03 7.79e+00 ... (remaining 10572 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 14306 2.54 - 5.08: 219 5.08 - 7.61: 39 7.61 - 10.15: 21 10.15 - 12.69: 5 Bond angle restraints: 14590 Sorted by residual: angle pdb=" O3' A B 14 " pdb=" C3' A B 14 " pdb=" C2' A B 14 " ideal model delta sigma weight residual 109.50 98.46 11.04 1.50e+00 4.44e-01 5.42e+01 angle pdb=" C4' A B 14 " pdb=" C3' A B 14 " pdb=" O3' A B 14 " ideal model delta sigma weight residual 109.40 118.16 -8.76 1.50e+00 4.44e-01 3.41e+01 angle pdb=" CA ARG P 63 " pdb=" C ARG P 63 " pdb=" N LEU P 64 " ideal model delta sigma weight residual 118.27 109.14 9.13 1.59e+00 3.96e-01 3.30e+01 angle pdb=" N ASN P 407 " pdb=" CA ASN P 407 " pdb=" C ASN P 407 " ideal model delta sigma weight residual 111.56 103.78 7.78 1.38e+00 5.25e-01 3.18e+01 angle pdb=" C ARG P 63 " pdb=" N LEU P 64 " pdb=" CA LEU P 64 " ideal model delta sigma weight residual 123.24 114.87 8.37 1.54e+00 4.22e-01 2.95e+01 ... (remaining 14585 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.19: 5666 22.19 - 44.38: 655 44.38 - 66.56: 187 66.56 - 88.75: 31 88.75 - 110.94: 6 Dihedral angle restraints: 6545 sinusoidal: 3420 harmonic: 3125 Sorted by residual: dihedral pdb=" O4' A B 14 " pdb=" C1' A B 14 " pdb=" N9 A B 14 " pdb=" C4 A B 14 " ideal model delta sinusoidal sigma weight residual -106.00 -175.61 69.61 1 1.70e+01 3.46e-03 2.16e+01 dihedral pdb=" C ARG P 307 " pdb=" N ARG P 307 " pdb=" CA ARG P 307 " pdb=" CB ARG P 307 " ideal model delta harmonic sigma weight residual -122.60 -112.46 -10.14 0 2.50e+00 1.60e-01 1.64e+01 dihedral pdb=" CA VAL P1280 " pdb=" C VAL P1280 " pdb=" N ILE P1281 " pdb=" CA ILE P1281 " ideal model delta harmonic sigma weight residual 180.00 -159.99 -20.01 0 5.00e+00 4.00e-02 1.60e+01 ... (remaining 6542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1466 0.065 - 0.131: 199 0.131 - 0.196: 12 0.196 - 0.261: 2 0.261 - 0.327: 3 Chirality restraints: 1682 Sorted by residual: chirality pdb=" CA ARG P 307 " pdb=" N ARG P 307 " pdb=" C ARG P 307 " pdb=" CB ARG P 307 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA GLU P1268 " pdb=" N GLU P1268 " pdb=" C GLU P1268 " pdb=" CB GLU P1268 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB VAL P 339 " pdb=" CA VAL P 339 " pdb=" CG1 VAL P 339 " pdb=" CG2 VAL P 339 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 1679 not shown) Planarity restraints: 1593 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG P 63 " 0.065 2.00e-02 2.50e+03 1.30e-01 1.69e+02 pdb=" C ARG P 63 " -0.225 2.00e-02 2.50e+03 pdb=" O ARG P 63 " 0.088 2.00e-02 2.50e+03 pdb=" N LEU P 64 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE P 305 " 0.030 2.00e-02 2.50e+03 5.75e-02 3.31e+01 pdb=" C ILE P 305 " -0.100 2.00e-02 2.50e+03 pdb=" O ILE P 305 " 0.036 2.00e-02 2.50e+03 pdb=" N LEU P 306 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR P 249 " -0.046 5.00e-02 4.00e+02 6.96e-02 7.76e+00 pdb=" N PRO P 250 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO P 250 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO P 250 " -0.038 5.00e-02 4.00e+02 ... (remaining 1590 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 362 2.69 - 3.24: 10090 3.24 - 3.79: 16218 3.79 - 4.35: 20344 4.35 - 4.90: 30642 Nonbonded interactions: 77656 Sorted by model distance: nonbonded pdb=" O GLU P1271 " pdb=" OG SER P1274 " model vdw 2.137 3.040 nonbonded pdb=" OH TYR P 5 " pdb=" O HIS P 754 " model vdw 2.228 3.040 nonbonded pdb=" OG SER P 909 " pdb=" OD2 ASP P 912 " model vdw 2.233 3.040 nonbonded pdb=" O GLN P 774 " pdb=" OG SER P 777 " model vdw 2.238 3.040 nonbonded pdb=" OE2 GLU P 762 " pdb=" OG SER P 960 " model vdw 2.273 3.040 ... (remaining 77651 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.340 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4157 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 : 0.004 0.098 10577 Z= 0.208 Angle : 0.872 12.687 14590 Z= 0.471 Chirality : 0.045 0.327 1682 Planarity : 0.006 0.130 1593 Dihedral : 19.384 110.940 4523 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.19 % Allowed : 6.82 % Favored : 92.99 % Rotamer: Outliers : 1.05 % Allowed : 28.11 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.25), residues: 1056 helix: -0.31 (0.22), residues: 508 sheet: -0.83 (0.49), residues: 118 loop : -1.75 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP P 883 HIS 0.006 0.001 HIS P 137 PHE 0.019 0.002 PHE P 916 TYR 0.023 0.002 TYR P1237 ARG 0.006 0.001 ARG P 884 Details of bonding type rmsd hydrogen bonds : bond 0.14699 ( 401) hydrogen bonds : angle 5.92156 ( 1130) covalent geometry : bond 0.00399 (10577) covalent geometry : angle 0.87168 (14590) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 404 THR cc_start: 0.4229 (p) cc_final: 0.3370 (m) REVERT: P 965 ASP cc_start: 0.7705 (m-30) cc_final: 0.6755 (m-30) outliers start: 10 outliers final: 1 residues processed: 159 average time/residue: 0.2695 time to fit residues: 57.6708 Evaluate side-chains 75 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 306 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 28 optimal weight: 0.0970 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 87 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 53 optimal weight: 5.9990 chunk 65 optimal weight: 0.0010 chunk 101 optimal weight: 2.9990 overall best weight: 2.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 37 ASN ** P 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN P 265 GLN P 281 GLN P 285 GLN P 413 GLN P 721 HIS ** P 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 771 GLN P 818 ASN ** P 985 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 990 ASN P1254 GLN P1262 HIS P1297 HIS P1305 GLN P1350 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.084917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.065959 restraints weight = 69790.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.067624 restraints weight = 40022.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.068679 restraints weight = 28367.118| |-----------------------------------------------------------------------------| r_work (final): 0.3858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10577 Z= 0.195 Angle : 0.777 13.238 14590 Z= 0.391 Chirality : 0.042 0.179 1682 Planarity : 0.006 0.093 1593 Dihedral : 17.189 114.016 2277 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 5.58 % Allowed : 24.74 % Favored : 69.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.24), residues: 1056 helix: -0.37 (0.22), residues: 510 sheet: -1.30 (0.52), residues: 95 loop : -1.39 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP P 883 HIS 0.012 0.002 HIS P 328 PHE 0.020 0.002 PHE P 375 TYR 0.021 0.002 TYR P1141 ARG 0.019 0.001 ARG P1060 Details of bonding type rmsd hydrogen bonds : bond 0.05290 ( 401) hydrogen bonds : angle 5.46072 ( 1130) covalent geometry : bond 0.00426 (10577) covalent geometry : angle 0.77658 (14590) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 69 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 161 MET cc_start: 0.8811 (mmm) cc_final: 0.8570 (mmt) REVERT: P 173 ASP cc_start: 0.9060 (m-30) cc_final: 0.8501 (t70) REVERT: P 359 TYR cc_start: 0.8599 (t80) cc_final: 0.8392 (t80) REVERT: P 879 MET cc_start: 0.8587 (mpp) cc_final: 0.8258 (mpp) REVERT: P 1043 MET cc_start: 0.7500 (mtm) cc_final: 0.6768 (mmp) REVERT: P 1062 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7715 (tp) outliers start: 53 outliers final: 25 residues processed: 114 average time/residue: 0.2924 time to fit residues: 47.2043 Evaluate side-chains 88 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 37 ASN Chi-restraints excluded: chain P residue 43 ILE Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 72 TYR Chi-restraints excluded: chain P residue 100 ARG Chi-restraints excluded: chain P residue 128 TYR Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 211 ILE Chi-restraints excluded: chain P residue 225 LEU Chi-restraints excluded: chain P residue 266 LEU Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 379 ILE Chi-restraints excluded: chain P residue 803 ASN Chi-restraints excluded: chain P residue 818 ASN Chi-restraints excluded: chain P residue 992 VAL Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1062 LEU Chi-restraints excluded: chain P residue 1080 PHE Chi-restraints excluded: chain P residue 1094 ILE Chi-restraints excluded: chain P residue 1138 THR Chi-restraints excluded: chain P residue 1168 ILE Chi-restraints excluded: chain P residue 1169 MET Chi-restraints excluded: chain P residue 1173 SER Chi-restraints excluded: chain P residue 1346 THR Chi-restraints excluded: chain P residue 1348 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 48 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 88 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 84 optimal weight: 8.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 121 ASN P 844 GLN P 983 HIS P1241 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.083674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.064630 restraints weight = 71163.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.066265 restraints weight = 40543.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.067286 restraints weight = 28729.540| |-----------------------------------------------------------------------------| r_work (final): 0.3843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6660 moved from start: 0.5076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10577 Z= 0.130 Angle : 0.628 11.653 14590 Z= 0.313 Chirality : 0.038 0.186 1682 Planarity : 0.005 0.058 1593 Dihedral : 17.011 111.496 2275 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 4.11 % Allowed : 23.47 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.91 (0.25), residues: 1056 helix: 0.16 (0.23), residues: 506 sheet: -1.15 (0.53), residues: 99 loop : -1.28 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP P1074 HIS 0.009 0.001 HIS P 328 PHE 0.025 0.001 PHE P1008 TYR 0.019 0.001 TYR P1265 ARG 0.006 0.001 ARG P 753 Details of bonding type rmsd hydrogen bonds : bond 0.04253 ( 401) hydrogen bonds : angle 5.13459 ( 1130) covalent geometry : bond 0.00281 (10577) covalent geometry : angle 0.62848 (14590) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 67 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 173 ASP cc_start: 0.8820 (m-30) cc_final: 0.8506 (t0) REVERT: P 879 MET cc_start: 0.8546 (mpp) cc_final: 0.8138 (mpp) REVERT: P 929 LYS cc_start: 0.7803 (mttt) cc_final: 0.7515 (mttt) REVERT: P 1043 MET cc_start: 0.7636 (mtm) cc_final: 0.6769 (mmp) outliers start: 39 outliers final: 27 residues processed: 101 average time/residue: 0.2071 time to fit residues: 31.3173 Evaluate side-chains 87 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 37 ASN Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 72 TYR Chi-restraints excluded: chain P residue 128 TYR Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 151 LEU Chi-restraints excluded: chain P residue 155 TYR Chi-restraints excluded: chain P residue 266 LEU Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 335 LEU Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 379 ILE Chi-restraints excluded: chain P residue 721 HIS Chi-restraints excluded: chain P residue 733 ILE Chi-restraints excluded: chain P residue 803 ASN Chi-restraints excluded: chain P residue 818 ASN Chi-restraints excluded: chain P residue 992 VAL Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1138 THR Chi-restraints excluded: chain P residue 1173 SER Chi-restraints excluded: chain P residue 1213 MET Chi-restraints excluded: chain P residue 1275 GLU Chi-restraints excluded: chain P residue 1338 SER Chi-restraints excluded: chain P residue 1348 ILE Chi-restraints excluded: chain P residue 1361 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 81 optimal weight: 0.0770 chunk 66 optimal weight: 0.9990 chunk 15 optimal weight: 7.9990 chunk 94 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 0.2980 chunk 52 optimal weight: 4.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 402 GLN P 415 HIS P 980 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.083649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.066225 restraints weight = 70176.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.067353 restraints weight = 40077.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.067921 restraints weight = 26172.237| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.5698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 10577 Z= 0.104 Angle : 0.570 9.785 14590 Z= 0.283 Chirality : 0.037 0.180 1682 Planarity : 0.004 0.049 1593 Dihedral : 16.811 108.700 2275 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.79 % Allowed : 24.00 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.57 (0.26), residues: 1056 helix: 0.50 (0.23), residues: 508 sheet: -0.39 (0.54), residues: 95 loop : -1.36 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 883 HIS 0.005 0.001 HIS P 328 PHE 0.019 0.001 PHE P 375 TYR 0.014 0.001 TYR P1265 ARG 0.004 0.000 ARG P1333 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 401) hydrogen bonds : angle 4.78536 ( 1130) covalent geometry : bond 0.00216 (10577) covalent geometry : angle 0.56975 (14590) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 66 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 173 ASP cc_start: 0.8939 (m-30) cc_final: 0.8581 (t70) REVERT: P 762 GLU cc_start: 0.6415 (OUTLIER) cc_final: 0.5492 (tp30) REVERT: P 879 MET cc_start: 0.8530 (mpp) cc_final: 0.8032 (mpp) REVERT: P 1043 MET cc_start: 0.7529 (mtm) cc_final: 0.6681 (mmp) REVERT: P 1357 GLU cc_start: 0.7432 (mt-10) cc_final: 0.6751 (mm-30) outliers start: 36 outliers final: 21 residues processed: 97 average time/residue: 0.2379 time to fit residues: 33.4525 Evaluate side-chains 79 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 72 TYR Chi-restraints excluded: chain P residue 123 VAL Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 155 TYR Chi-restraints excluded: chain P residue 234 LYS Chi-restraints excluded: chain P residue 306 LEU Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 336 LYS Chi-restraints excluded: chain P residue 445 THR Chi-restraints excluded: chain P residue 721 HIS Chi-restraints excluded: chain P residue 762 GLU Chi-restraints excluded: chain P residue 803 ASN Chi-restraints excluded: chain P residue 891 LEU Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1026 GLU Chi-restraints excluded: chain P residue 1168 ILE Chi-restraints excluded: chain P residue 1173 SER Chi-restraints excluded: chain P residue 1275 GLU Chi-restraints excluded: chain P residue 1338 SER Chi-restraints excluded: chain P residue 1348 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 20 optimal weight: 0.0870 chunk 39 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 85 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 74 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 43 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 415 HIS P 768 GLN P 818 ASN P 980 ASN P1066 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.077353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.060252 restraints weight = 71600.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.061275 restraints weight = 42793.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.061173 restraints weight = 33979.278| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.7803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10577 Z= 0.199 Angle : 0.707 11.478 14590 Z= 0.365 Chirality : 0.041 0.199 1682 Planarity : 0.005 0.045 1593 Dihedral : 17.231 111.414 2275 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 4.63 % Allowed : 24.21 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.25), residues: 1056 helix: 0.06 (0.23), residues: 504 sheet: -1.11 (0.50), residues: 108 loop : -1.35 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP P1074 HIS 0.010 0.002 HIS P 328 PHE 0.027 0.002 PHE P 429 TYR 0.017 0.002 TYR P 430 ARG 0.007 0.001 ARG P 75 Details of bonding type rmsd hydrogen bonds : bond 0.05847 ( 401) hydrogen bonds : angle 5.33549 ( 1130) covalent geometry : bond 0.00414 (10577) covalent geometry : angle 0.70735 (14590) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 65 time to evaluate : 1.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 173 ASP cc_start: 0.9049 (m-30) cc_final: 0.8641 (t70) REVERT: P 879 MET cc_start: 0.8533 (mpp) cc_final: 0.8168 (mpp) REVERT: P 1043 MET cc_start: 0.7509 (mtm) cc_final: 0.6765 (mmp) REVERT: P 1045 PHE cc_start: 0.8667 (OUTLIER) cc_final: 0.8339 (p90) outliers start: 44 outliers final: 29 residues processed: 101 average time/residue: 0.3094 time to fit residues: 47.4941 Evaluate side-chains 87 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 57 time to evaluate : 2.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 128 TYR Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 234 LYS Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 335 LEU Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 404 THR Chi-restraints excluded: chain P residue 721 HIS Chi-restraints excluded: chain P residue 803 ASN Chi-restraints excluded: chain P residue 841 ILE Chi-restraints excluded: chain P residue 891 LEU Chi-restraints excluded: chain P residue 992 VAL Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 998 ILE Chi-restraints excluded: chain P residue 1045 PHE Chi-restraints excluded: chain P residue 1138 THR Chi-restraints excluded: chain P residue 1160 VAL Chi-restraints excluded: chain P residue 1168 ILE Chi-restraints excluded: chain P residue 1187 TYR Chi-restraints excluded: chain P residue 1213 MET Chi-restraints excluded: chain P residue 1238 LEU Chi-restraints excluded: chain P residue 1275 GLU Chi-restraints excluded: chain P residue 1338 SER Chi-restraints excluded: chain P residue 1348 ILE Chi-restraints excluded: chain P residue 1353 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 30 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 23 optimal weight: 0.0010 chunk 47 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 0.0470 chunk 91 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.1086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 415 HIS ** P 768 GLN ** 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 = 0.4194 r_free = 0.4194 target = 0.079207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.060062 restraints weight = 70407.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.061673 restraints weight = 40016.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.062688 restraints weight = 28480.880| |-----------------------------------------------------------------------------| r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.7978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 10577 Z= 0.109 Angle : 0.596 10.317 14590 Z= 0.299 Chirality : 0.039 0.199 1682 Planarity : 0.004 0.047 1593 Dihedral : 16.961 105.735 2275 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.95 % Allowed : 26.63 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.62 (0.26), residues: 1056 helix: 0.42 (0.24), residues: 501 sheet: -0.59 (0.52), residues: 101 loop : -1.26 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP P 18 HIS 0.004 0.001 HIS P 328 PHE 0.014 0.001 PHE P 375 TYR 0.014 0.001 TYR P 72 ARG 0.003 0.000 ARG P1333 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 401) hydrogen bonds : angle 4.89287 ( 1130) covalent geometry : bond 0.00236 (10577) covalent geometry : angle 0.59632 (14590) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 63 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 173 ASP cc_start: 0.9041 (m-30) cc_final: 0.8703 (t70) REVERT: P 359 TYR cc_start: 0.8698 (t80) cc_final: 0.8130 (t80) REVERT: P 879 MET cc_start: 0.8494 (mpp) cc_final: 0.7936 (mpp) REVERT: P 1043 MET cc_start: 0.7363 (mtm) cc_final: 0.6614 (mmp) outliers start: 28 outliers final: 19 residues processed: 86 average time/residue: 0.2152 time to fit residues: 27.5235 Evaluate side-chains 76 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 155 TYR Chi-restraints excluded: chain P residue 234 LYS Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 404 THR Chi-restraints excluded: chain P residue 445 THR Chi-restraints excluded: chain P residue 721 HIS Chi-restraints excluded: chain P residue 803 ASN Chi-restraints excluded: chain P residue 891 LEU Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 998 ILE Chi-restraints excluded: chain P residue 1026 GLU Chi-restraints excluded: chain P residue 1138 THR Chi-restraints excluded: chain P residue 1275 GLU Chi-restraints excluded: chain P residue 1353 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 26 optimal weight: 8.9990 chunk 106 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 111 optimal weight: 6.9990 chunk 20 optimal weight: 4.9990 chunk 30 optimal weight: 0.4980 chunk 46 optimal weight: 0.0060 chunk 67 optimal weight: 9.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 228 GLN ** P 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 980 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.079149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.062258 restraints weight = 71103.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.063013 restraints weight = 41211.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.063365 restraints weight = 33416.310| |-----------------------------------------------------------------------------| r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.8256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10577 Z= 0.103 Angle : 0.568 10.676 14590 Z= 0.283 Chirality : 0.038 0.164 1682 Planarity : 0.003 0.048 1593 Dihedral : 16.839 103.582 2275 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 3.16 % Allowed : 26.11 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.26), residues: 1056 helix: 0.56 (0.24), residues: 502 sheet: -0.66 (0.57), residues: 89 loop : -1.29 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP P 18 HIS 0.005 0.001 HIS P1349 PHE 0.016 0.001 PHE P1181 TYR 0.011 0.001 TYR P 72 ARG 0.005 0.000 ARG P1359 Details of bonding type rmsd hydrogen bonds : bond 0.03659 ( 401) hydrogen bonds : angle 4.71513 ( 1130) covalent geometry : bond 0.00220 (10577) covalent geometry : angle 0.56822 (14590) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 161 MET cc_start: 0.8782 (mmm) cc_final: 0.8558 (mpp) REVERT: P 173 ASP cc_start: 0.9055 (m-30) cc_final: 0.8733 (t70) REVERT: P 762 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.5576 (tp30) REVERT: P 879 MET cc_start: 0.8475 (mpp) cc_final: 0.7949 (mpp) REVERT: P 1043 MET cc_start: 0.7353 (mtm) cc_final: 0.6660 (mmp) REVERT: P 1213 MET cc_start: 0.6885 (OUTLIER) cc_final: 0.6448 (mmm) outliers start: 30 outliers final: 20 residues processed: 87 average time/residue: 0.2025 time to fit residues: 26.6859 Evaluate side-chains 81 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 155 TYR Chi-restraints excluded: chain P residue 237 LEU Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 445 THR Chi-restraints excluded: chain P residue 762 GLU Chi-restraints excluded: chain P residue 803 ASN Chi-restraints excluded: chain P residue 841 ILE Chi-restraints excluded: chain P residue 891 LEU Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 998 ILE Chi-restraints excluded: chain P residue 1025 SER Chi-restraints excluded: chain P residue 1045 PHE Chi-restraints excluded: chain P residue 1138 THR Chi-restraints excluded: chain P residue 1160 VAL Chi-restraints excluded: chain P residue 1168 ILE Chi-restraints excluded: chain P residue 1213 MET Chi-restraints excluded: chain P residue 1275 GLU Chi-restraints excluded: chain P residue 1353 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 52 optimal weight: 1.9990 chunk 109 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 18 optimal weight: 0.2980 chunk 34 optimal weight: 10.0000 chunk 41 optimal weight: 7.9990 chunk 32 optimal weight: 0.0470 chunk 24 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 726 ASN P 768 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.080199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.061213 restraints weight = 70301.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.062889 restraints weight = 39115.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.063943 restraints weight = 27564.797| |-----------------------------------------------------------------------------| r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.8394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10577 Z= 0.096 Angle : 0.574 12.639 14590 Z= 0.280 Chirality : 0.038 0.298 1682 Planarity : 0.003 0.047 1593 Dihedral : 16.711 100.941 2275 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 2.63 % Allowed : 27.26 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.37 (0.26), residues: 1056 helix: 0.70 (0.24), residues: 506 sheet: -0.36 (0.59), residues: 87 loop : -1.27 (0.27), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP P 18 HIS 0.003 0.001 HIS P 328 PHE 0.013 0.001 PHE P 375 TYR 0.014 0.001 TYR P 359 ARG 0.003 0.000 ARG P1333 Details of bonding type rmsd hydrogen bonds : bond 0.03273 ( 401) hydrogen bonds : angle 4.54918 ( 1130) covalent geometry : bond 0.00202 (10577) covalent geometry : angle 0.57385 (14590) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 66 ARG cc_start: 0.2784 (mmt180) cc_final: 0.2439 (mmt180) REVERT: P 173 ASP cc_start: 0.8887 (m-30) cc_final: 0.8673 (t70) REVERT: P 359 TYR cc_start: 0.8579 (t80) cc_final: 0.8042 (t80) REVERT: P 762 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.5568 (tp30) REVERT: P 879 MET cc_start: 0.8418 (mpp) cc_final: 0.7908 (mpp) REVERT: P 1043 MET cc_start: 0.7300 (mtm) cc_final: 0.6585 (mmp) outliers start: 25 outliers final: 20 residues processed: 86 average time/residue: 0.2061 time to fit residues: 26.5844 Evaluate side-chains 80 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 59 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 155 TYR Chi-restraints excluded: chain P residue 288 ASP Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 445 THR Chi-restraints excluded: chain P residue 726 ASN Chi-restraints excluded: chain P residue 762 GLU Chi-restraints excluded: chain P residue 803 ASN Chi-restraints excluded: chain P residue 841 ILE Chi-restraints excluded: chain P residue 891 LEU Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 998 ILE Chi-restraints excluded: chain P residue 1025 SER Chi-restraints excluded: chain P residue 1026 GLU Chi-restraints excluded: chain P residue 1138 THR Chi-restraints excluded: chain P residue 1160 VAL Chi-restraints excluded: chain P residue 1213 MET Chi-restraints excluded: chain P residue 1275 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 15 optimal weight: 9.9990 chunk 46 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 4 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 84 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 14 ASN ** P 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 415 HIS P 723 HIS ** P 808 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.074142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.057445 restraints weight = 73137.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.058129 restraints weight = 41335.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.058551 restraints weight = 34118.768| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.9513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10577 Z= 0.226 Angle : 0.726 10.595 14590 Z= 0.374 Chirality : 0.042 0.314 1682 Planarity : 0.005 0.062 1593 Dihedral : 17.136 106.362 2275 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 19.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 3.58 % Allowed : 26.84 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.25), residues: 1056 helix: -0.03 (0.23), residues: 501 sheet: -1.60 (0.51), residues: 101 loop : -1.30 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP P1074 HIS 0.007 0.002 HIS P 721 PHE 0.016 0.002 PHE P 966 TYR 0.020 0.002 TYR P 981 ARG 0.004 0.001 ARG P 403 Details of bonding type rmsd hydrogen bonds : bond 0.06369 ( 401) hydrogen bonds : angle 5.31203 ( 1130) covalent geometry : bond 0.00481 (10577) covalent geometry : angle 0.72601 (14590) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 60 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 173 ASP cc_start: 0.8961 (m-30) cc_final: 0.8651 (t70) REVERT: P 359 TYR cc_start: 0.8656 (t80) cc_final: 0.8204 (t80) REVERT: P 762 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6326 (tp30) REVERT: P 879 MET cc_start: 0.8342 (mpp) cc_final: 0.7812 (mpp) REVERT: P 1043 MET cc_start: 0.7437 (mtm) cc_final: 0.6924 (mmp) outliers start: 34 outliers final: 23 residues processed: 91 average time/residue: 0.2438 time to fit residues: 31.8969 Evaluate side-chains 76 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 128 TYR Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 155 TYR Chi-restraints excluded: chain P residue 199 ASN Chi-restraints excluded: chain P residue 221 ARG Chi-restraints excluded: chain P residue 291 LEU Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 379 ILE Chi-restraints excluded: chain P residue 762 GLU Chi-restraints excluded: chain P residue 803 ASN Chi-restraints excluded: chain P residue 841 ILE Chi-restraints excluded: chain P residue 891 LEU Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 998 ILE Chi-restraints excluded: chain P residue 1025 SER Chi-restraints excluded: chain P residue 1138 THR Chi-restraints excluded: chain P residue 1160 VAL Chi-restraints excluded: chain P residue 1168 ILE Chi-restraints excluded: chain P residue 1169 MET Chi-restraints excluded: chain P residue 1275 GLU Chi-restraints excluded: chain P residue 1338 SER Chi-restraints excluded: chain P residue 1353 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 0.5980 chunk 92 optimal weight: 9.9990 chunk 8 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 70 optimal weight: 0.0060 chunk 88 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 overall best weight: 1.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 415 HIS P 723 HIS ** P 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.075722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.058449 restraints weight = 72203.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.059310 restraints weight = 41048.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.059638 restraints weight = 33957.810| |-----------------------------------------------------------------------------| r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7137 moved from start: 0.9649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10577 Z= 0.129 Angle : 0.661 12.945 14590 Z= 0.326 Chirality : 0.040 0.332 1682 Planarity : 0.004 0.046 1593 Dihedral : 16.951 101.663 2275 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.32 % Allowed : 28.42 % Favored : 69.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.91 (0.25), residues: 1056 helix: 0.23 (0.23), residues: 507 sheet: -1.58 (0.50), residues: 103 loop : -1.24 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP P1074 HIS 0.004 0.001 HIS P 328 PHE 0.015 0.001 PHE P1045 TYR 0.017 0.001 TYR P 136 ARG 0.004 0.000 ARG P 63 Details of bonding type rmsd hydrogen bonds : bond 0.04325 ( 401) hydrogen bonds : angle 4.97964 ( 1130) covalent geometry : bond 0.00285 (10577) covalent geometry : angle 0.66063 (14590) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 173 ASP cc_start: 0.9047 (m-30) cc_final: 0.8767 (t70) REVERT: P 359 TYR cc_start: 0.8704 (t80) cc_final: 0.8173 (t80) REVERT: P 762 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.6124 (tp30) REVERT: P 879 MET cc_start: 0.8411 (mpp) cc_final: 0.7866 (mpp) REVERT: P 1043 MET cc_start: 0.7335 (mtm) cc_final: 0.6788 (mmp) outliers start: 22 outliers final: 19 residues processed: 79 average time/residue: 0.2280 time to fit residues: 26.3528 Evaluate side-chains 75 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 48 ILE Chi-restraints excluded: chain P residue 126 VAL Chi-restraints excluded: chain P residue 142 LEU Chi-restraints excluded: chain P residue 155 TYR Chi-restraints excluded: chain P residue 221 ARG Chi-restraints excluded: chain P residue 237 LEU Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 762 GLU Chi-restraints excluded: chain P residue 803 ASN Chi-restraints excluded: chain P residue 841 ILE Chi-restraints excluded: chain P residue 891 LEU Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 998 ILE Chi-restraints excluded: chain P residue 1138 THR Chi-restraints excluded: chain P residue 1160 VAL Chi-restraints excluded: chain P residue 1275 GLU Chi-restraints excluded: chain P residue 1329 THR Chi-restraints excluded: chain P residue 1338 SER Chi-restraints excluded: chain P residue 1353 THR Chi-restraints excluded: chain P residue 1361 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 0.2980 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 90 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 199 ASN ** P 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 415 HIS ** P 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.076869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.057941 restraints weight = 71095.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.059535 restraints weight = 39971.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.060570 restraints weight = 28302.796| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.9770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10577 Z= 0.106 Angle : 0.633 13.448 14590 Z= 0.308 Chirality : 0.039 0.309 1682 Planarity : 0.004 0.048 1593 Dihedral : 16.767 97.192 2275 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 1.89 % Allowed : 29.26 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.57 (0.26), residues: 1056 helix: 0.57 (0.24), residues: 505 sheet: -1.19 (0.52), residues: 100 loop : -1.23 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 18 HIS 0.004 0.001 HIS P 328 PHE 0.015 0.001 PHE P1045 TYR 0.017 0.001 TYR P1010 ARG 0.003 0.000 ARG P 152 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 401) hydrogen bonds : angle 4.71814 ( 1130) covalent geometry : bond 0.00233 (10577) covalent geometry : angle 0.63346 (14590) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5230.10 seconds wall clock time: 92 minutes 47.34 seconds (5567.34 seconds total)