Starting phenix.real_space_refine on Wed Sep 17 17:58:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b2k_44111/09_2025/9b2k_44111.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b2k_44111/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9b2k_44111/09_2025/9b2k_44111.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b2k_44111/09_2025/9b2k_44111.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b2k_44111/09_2025/9b2k_44111.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b2k_44111/09_2025/9b2k_44111.map" } resolution = 3.67 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.62, per 1000 atoms: 0.26 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: 1.03 Conformation dependent library (CDL) restraints added in 325.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.21 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: 2.13 Time building geometry restraints manager: 1.30 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: 5.870 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: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.460 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.120 ------------------------------------------------------------------------------- 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 : 16.72 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG P 884 TYR 0.023 0.002 TYR P1237 PHE 0.019 0.002 PHE P 916 TRP 0.009 0.001 TRP P 883 HIS 0.006 0.001 HIS P 137 Details of bonding type rmsd covalent geometry : bond 0.00399 (10577) covalent geometry : angle 0.87168 (14590) hydrogen bonds : bond 0.14699 ( 401) hydrogen bonds : angle 5.92156 ( 1130) *********************** 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 : 0.405 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: 0.6752 (m-30) outliers start: 10 outliers final: 1 residues processed: 159 average time/residue: 0.1320 time to fit residues: 28.1760 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 : 0.382 ------------------------------------------------------------------------------- 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 108 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** P 285 GLN ** P 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 413 GLN P 721 HIS ** P 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 771 GLN P 818 ASN P 985 HIS 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 = 0.4214 r_free = 0.4214 target = 0.080979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.062311 restraints weight = 71220.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.063864 restraints weight = 41317.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.064839 restraints weight = 29644.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.065470 restraints weight = 24281.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.065821 restraints weight = 21315.496| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6813 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 10577 Z= 0.282 Angle : 0.911 12.379 14590 Z= 0.463 Chirality : 0.046 0.245 1682 Planarity : 0.007 0.088 1593 Dihedral : 17.595 116.389 2277 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 20.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer: Outliers : 7.16 % Allowed : 24.32 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.81 (0.24), residues: 1056 helix: -0.82 (0.21), residues: 511 sheet: -1.54 (0.53), residues: 88 loop : -1.43 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG P1060 TYR 0.026 0.003 TYR P 988 PHE 0.022 0.003 PHE P1324 TRP 0.021 0.005 TRP P 18 HIS 0.016 0.002 HIS P 328 Details of bonding type rmsd covalent geometry : bond 0.00612 (10577) covalent geometry : angle 0.91101 (14590) hydrogen bonds : bond 0.07018 ( 401) hydrogen bonds : angle 6.01618 ( 1130) *********************** 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 139 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 71 time to evaluate : 0.457 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: P 173 ASP cc_start: 0.9166 (m-30) cc_final: 0.8327 (t70) REVERT: P 322 ILE cc_start: 0.4936 (OUTLIER) cc_final: 0.4688 (tt) REVERT: P 396 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8637 (tm-30) REVERT: P 879 MET cc_start: 0.8535 (mpp) cc_final: 0.8222 (mpp) REVERT: P 1043 MET cc_start: 0.7425 (mtm) cc_final: 0.6651 (mmp) REVERT: P 1357 GLU cc_start: 0.7671 (mt-10) cc_final: 0.6971 (mm-30) outliers start: 68 outliers final: 35 residues processed: 131 average time/residue: 0.1108 time to fit residues: 20.6629 Evaluate side-chains 95 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 58 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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 82 LEU Chi-restraints excluded: chain P residue 100 ARG Chi-restraints excluded: chain P residue 128 TYR Chi-restraints excluded: chain P residue 143 VAL 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 300 ILE Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 379 ILE Chi-restraints excluded: chain P residue 396 GLU Chi-restraints excluded: chain P residue 733 ILE Chi-restraints excluded: chain P residue 753 ARG Chi-restraints excluded: chain P residue 803 ASN Chi-restraints excluded: chain P residue 818 ASN Chi-restraints excluded: chain P residue 841 ILE Chi-restraints excluded: chain P residue 876 VAL Chi-restraints excluded: chain P residue 928 THR 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 1173 SER 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 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 42 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 103 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 121 ASN P 281 GLN P 818 ASN P 983 HIS P1241 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.081356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.062949 restraints weight = 72028.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.064540 restraints weight = 40877.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.065558 restraints weight = 29117.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.066217 restraints weight = 23644.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.066635 restraints weight = 20731.262| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6758 moved from start: 0.6209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10577 Z= 0.132 Angle : 0.655 10.679 14590 Z= 0.327 Chirality : 0.039 0.192 1682 Planarity : 0.004 0.054 1593 Dihedral : 17.206 110.907 2275 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.95 % Allowed : 24.21 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.15 (0.25), residues: 1056 helix: -0.07 (0.23), residues: 510 sheet: -1.13 (0.53), residues: 95 loop : -1.40 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 938 TYR 0.015 0.002 TYR P 359 PHE 0.029 0.001 PHE P1008 TRP 0.011 0.003 TRP P 883 HIS 0.008 0.001 HIS P 328 Details of bonding type rmsd covalent geometry : bond 0.00285 (10577) covalent geometry : angle 0.65462 (14590) hydrogen bonds : bond 0.04442 ( 401) hydrogen bonds : angle 5.36515 ( 1130) *********************** 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 107 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 60 time to evaluate : 0.387 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: 0.8851 (m-30) cc_final: 0.8477 (t70) REVERT: P 419 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9199 (mt) REVERT: P 879 MET cc_start: 0.8448 (mpp) cc_final: 0.8073 (mpp) REVERT: P 1043 MET cc_start: 0.7445 (mtm) cc_final: 0.6626 (mmp) outliers start: 47 outliers final: 25 residues processed: 102 average time/residue: 0.1049 time to fit residues: 15.5492 Evaluate side-chains 79 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 53 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 317 LEU Chi-restraints excluded: chain P residue 335 LEU Chi-restraints excluded: chain P residue 336 LYS Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 379 ILE Chi-restraints excluded: chain P residue 419 LEU Chi-restraints excluded: chain P residue 721 HIS Chi-restraints excluded: chain P residue 753 ARG Chi-restraints excluded: chain P residue 803 ASN Chi-restraints excluded: chain P residue 818 ASN Chi-restraints excluded: chain P residue 841 ILE Chi-restraints excluded: chain P residue 997 LEU Chi-restraints excluded: chain P residue 1138 THR 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 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 77 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 1 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 chunk 57 optimal weight: 7.9990 chunk 30 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 86 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 415 HIS P1066 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.078619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.060614 restraints weight = 71792.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.061996 restraints weight = 46052.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.062540 restraints weight = 31175.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.062577 restraints weight = 30532.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.062687 restraints weight = 27418.910| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.7397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10577 Z= 0.161 Angle : 0.651 12.399 14590 Z= 0.330 Chirality : 0.040 0.205 1682 Planarity : 0.005 0.049 1593 Dihedral : 17.126 110.132 2275 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 5.16 % Allowed : 25.05 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.20 (0.25), residues: 1056 helix: -0.18 (0.22), residues: 518 sheet: -0.97 (0.49), residues: 107 loop : -1.40 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 139 TYR 0.026 0.002 TYR P 72 PHE 0.020 0.002 PHE P1008 TRP 0.011 0.003 TRP P1074 HIS 0.007 0.001 HIS P 328 Details of bonding type rmsd covalent geometry : bond 0.00346 (10577) covalent geometry : angle 0.65120 (14590) hydrogen bonds : bond 0.04915 ( 401) hydrogen bonds : angle 5.24273 ( 1130) *********************** 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 113 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 64 time to evaluate : 0.367 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: 0.8878 (m-30) cc_final: 0.8465 (t70) REVERT: P 322 ILE cc_start: 0.5297 (OUTLIER) cc_final: 0.5051 (tt) REVERT: P 359 TYR cc_start: 0.8759 (t80) cc_final: 0.8348 (t80) REVERT: P 879 MET cc_start: 0.8543 (mpp) cc_final: 0.8037 (mpp) REVERT: P 1043 MET cc_start: 0.7539 (mtm) cc_final: 0.6752 (mmp) REVERT: P 1045 PHE cc_start: 0.8681 (OUTLIER) cc_final: 0.8436 (p90) outliers start: 49 outliers final: 30 residues processed: 105 average time/residue: 0.1073 time to fit residues: 16.2652 Evaluate side-chains 87 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 55 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 100 ARG 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 151 LEU Chi-restraints excluded: chain P residue 234 LYS Chi-restraints excluded: chain P residue 241 LEU Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 336 LYS Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 379 ILE 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 818 ASN Chi-restraints excluded: chain P residue 841 ILE Chi-restraints excluded: chain P residue 891 LEU Chi-restraints excluded: chain P residue 928 THR 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 1026 GLU 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 1275 GLU Chi-restraints excluded: chain P residue 1353 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 62 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 26 optimal weight: 0.0370 chunk 111 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 overall best weight: 3.0066 ------------------------------------------------------------------------------- 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 920 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.076040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.058715 restraints weight = 71524.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.059375 restraints weight = 39429.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.059542 restraints weight = 31894.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.060023 restraints weight = 28848.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.060053 restraints weight = 27906.611| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.8582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10577 Z= 0.175 Angle : 0.656 11.283 14590 Z= 0.335 Chirality : 0.041 0.214 1682 Planarity : 0.005 0.048 1593 Dihedral : 17.180 107.853 2275 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 5.37 % Allowed : 24.74 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.36 (0.25), residues: 1056 helix: -0.29 (0.22), residues: 522 sheet: -1.51 (0.50), residues: 99 loop : -1.39 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 820 TYR 0.016 0.002 TYR P 359 PHE 0.023 0.002 PHE P1181 TRP 0.013 0.003 TRP P1074 HIS 0.008 0.001 HIS P1349 Details of bonding type rmsd covalent geometry : bond 0.00380 (10577) covalent geometry : angle 0.65612 (14590) hydrogen bonds : bond 0.05028 ( 401) hydrogen bonds : angle 5.30181 ( 1130) *********************** 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 108 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 57 time to evaluate : 0.450 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: 0.8932 (m-30) cc_final: 0.8490 (t70) REVERT: P 359 TYR cc_start: 0.8771 (t80) cc_final: 0.8239 (t80) REVERT: P 879 MET cc_start: 0.8497 (mpp) cc_final: 0.8135 (mpp) REVERT: P 1043 MET cc_start: 0.7459 (mtm) cc_final: 0.6788 (mmp) outliers start: 51 outliers final: 32 residues processed: 103 average time/residue: 0.1079 time to fit residues: 16.0621 Evaluate side-chains 81 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 49 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 38 THR 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 151 LEU Chi-restraints excluded: chain P residue 155 TYR Chi-restraints excluded: chain P residue 234 LYS Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 335 LEU Chi-restraints excluded: chain P residue 336 LYS Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 379 ILE Chi-restraints excluded: chain P residue 404 THR Chi-restraints excluded: chain P residue 445 THR 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 928 THR 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 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 1187 TYR Chi-restraints excluded: chain P residue 1213 MET Chi-restraints excluded: chain P residue 1275 GLU Chi-restraints excluded: chain P residue 1312 LEU Chi-restraints excluded: chain P residue 1338 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 20.0000 chunk 24 optimal weight: 0.6980 chunk 93 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 55 optimal weight: 20.0000 chunk 15 optimal weight: 7.9990 chunk 90 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.8384 ------------------------------------------------------------------------------- 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 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 415 HIS ** P 721 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 723 HIS ** P 990 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 = 0.4147 r_free = 0.4147 target = 0.076357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.059244 restraints weight = 72827.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.060128 restraints weight = 38553.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.060417 restraints weight = 30073.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.060582 restraints weight = 27382.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.060690 restraints weight = 25744.451| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.8996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10577 Z= 0.127 Angle : 0.619 11.517 14590 Z= 0.311 Chirality : 0.039 0.205 1682 Planarity : 0.004 0.066 1593 Dihedral : 17.094 103.861 2275 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 4.53 % Allowed : 25.68 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.14 (0.25), residues: 1056 helix: 0.06 (0.23), residues: 518 sheet: -1.61 (0.48), residues: 103 loop : -1.45 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 63 TYR 0.018 0.001 TYR P 72 PHE 0.011 0.001 PHE P 119 TRP 0.010 0.002 TRP P1074 HIS 0.011 0.001 HIS P 721 Details of bonding type rmsd covalent geometry : bond 0.00274 (10577) covalent geometry : angle 0.61934 (14590) hydrogen bonds : bond 0.04190 ( 401) hydrogen bonds : angle 4.99411 ( 1130) *********************** 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 101 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 58 time to evaluate : 0.390 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: 0.8927 (m-30) cc_final: 0.8513 (t0) REVERT: P 762 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.5672 (tp30) REVERT: P 879 MET cc_start: 0.8452 (mpp) cc_final: 0.8102 (mpp) REVERT: P 1043 MET cc_start: 0.7389 (mtm) cc_final: 0.6723 (mmp) outliers start: 43 outliers final: 30 residues processed: 97 average time/residue: 0.1153 time to fit residues: 15.7727 Evaluate side-chains 81 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 50 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 37 ASN Chi-restraints excluded: chain P residue 38 THR 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 151 LEU Chi-restraints excluded: chain P residue 155 TYR Chi-restraints excluded: chain P residue 221 ARG Chi-restraints excluded: chain P residue 288 ASP Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 323 LYS Chi-restraints excluded: chain P residue 336 LYS Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 379 ILE 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 928 THR 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 1213 MET Chi-restraints excluded: chain P residue 1275 GLU Chi-restraints excluded: chain P residue 1361 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 23 optimal weight: 0.0970 chunk 102 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 108 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 106 optimal weight: 0.9990 chunk 51 optimal weight: 6.9990 chunk 95 optimal weight: 8.9990 chunk 21 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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 721 HIS P 818 ASN ** P 990 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 = 0.4134 r_free = 0.4134 target = 0.075555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.057761 restraints weight = 72207.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.059125 restraints weight = 38472.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.059272 restraints weight = 28270.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.059512 restraints weight = 25824.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.059549 restraints weight = 24048.127| |-----------------------------------------------------------------------------| r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.9376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10577 Z= 0.133 Angle : 0.603 10.263 14590 Z= 0.307 Chirality : 0.039 0.163 1682 Planarity : 0.004 0.058 1593 Dihedral : 17.079 102.340 2275 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 3.89 % Allowed : 27.37 % Favored : 68.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.06 (0.25), residues: 1056 helix: 0.16 (0.23), residues: 518 sheet: -1.61 (0.49), residues: 103 loop : -1.45 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 63 TYR 0.018 0.001 TYR P 359 PHE 0.008 0.001 PHE P1008 TRP 0.012 0.002 TRP P1074 HIS 0.004 0.001 HIS P 328 Details of bonding type rmsd covalent geometry : bond 0.00289 (10577) covalent geometry : angle 0.60289 (14590) hydrogen bonds : bond 0.04349 ( 401) hydrogen bonds : angle 4.92863 ( 1130) *********************** 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 92 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 55 time to evaluate : 0.398 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 173 ASP cc_start: 0.8954 (m-30) cc_final: 0.8561 (t0) REVERT: P 762 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.5681 (tp30) REVERT: P 879 MET cc_start: 0.8452 (mpp) cc_final: 0.7925 (mpp) REVERT: P 1043 MET cc_start: 0.7400 (mtm) cc_final: 0.6773 (mmp) outliers start: 37 outliers final: 29 residues processed: 88 average time/residue: 0.1182 time to fit residues: 14.6909 Evaluate side-chains 80 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 50 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 141 LYS 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 234 LYS Chi-restraints excluded: chain P residue 237 LEU Chi-restraints excluded: chain P residue 288 ASP Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 323 LYS Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain P residue 336 LYS Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 379 ILE Chi-restraints excluded: chain P residue 396 GLU 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 1045 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 97 optimal weight: 10.0000 chunk 95 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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 726 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 990 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 = 0.4128 r_free = 0.4128 target = 0.075527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.056370 restraints weight = 72300.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.057907 restraints weight = 41300.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 65)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.058891 restraints weight = 29632.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.059486 restraints weight = 24163.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.059899 restraints weight = 21377.778| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.9743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10577 Z= 0.124 Angle : 0.615 11.074 14590 Z= 0.308 Chirality : 0.039 0.227 1682 Planarity : 0.004 0.050 1593 Dihedral : 17.034 99.563 2275 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.58 % Allowed : 27.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.93 (0.25), residues: 1056 helix: 0.31 (0.23), residues: 510 sheet: -1.47 (0.49), residues: 101 loop : -1.44 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 63 TYR 0.018 0.001 TYR P 72 PHE 0.008 0.001 PHE P 352 TRP 0.010 0.002 TRP P1074 HIS 0.007 0.001 HIS P 721 Details of bonding type rmsd covalent geometry : bond 0.00275 (10577) covalent geometry : angle 0.61464 (14590) hydrogen bonds : bond 0.04061 ( 401) hydrogen bonds : angle 4.80775 ( 1130) *********************** 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 87 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 53 time to evaluate : 0.414 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 173 ASP cc_start: 0.8886 (m-30) cc_final: 0.8543 (t0) REVERT: P 879 MET cc_start: 0.8397 (mpp) cc_final: 0.7904 (mpp) REVERT: P 1043 MET cc_start: 0.7326 (mtm) cc_final: 0.6733 (mmp) outliers start: 34 outliers final: 28 residues processed: 83 average time/residue: 0.1114 time to fit residues: 13.1852 Evaluate side-chains 79 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 51 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 35 LEU 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 221 ARG Chi-restraints excluded: chain P residue 234 LYS Chi-restraints excluded: chain P residue 237 LEU Chi-restraints excluded: chain P residue 288 ASP Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 323 LYS Chi-restraints excluded: chain P residue 332 LEU Chi-restraints excluded: chain P residue 336 LYS Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 445 THR 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 1006 SER Chi-restraints excluded: chain P residue 1045 PHE 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 97 optimal weight: 0.9980 chunk 67 optimal weight: 3.9990 chunk 31 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 56 optimal weight: 6.9990 chunk 39 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 415 HIS ** P 990 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 = 0.4063 r_free = 0.4063 target = 0.072318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.053610 restraints weight = 73639.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.054992 restraints weight = 42848.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.055884 restraints weight = 30903.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.056472 restraints weight = 25497.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.056834 restraints weight = 22581.898| |-----------------------------------------------------------------------------| r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 1.0591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10577 Z= 0.192 Angle : 0.702 10.736 14590 Z= 0.358 Chirality : 0.041 0.186 1682 Planarity : 0.005 0.049 1593 Dihedral : 17.354 100.509 2275 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 4.11 % Allowed : 26.63 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.25), residues: 1056 helix: -0.24 (0.22), residues: 524 sheet: -1.90 (0.45), residues: 113 loop : -1.42 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 63 TYR 0.017 0.002 TYR P 72 PHE 0.014 0.002 PHE P 966 TRP 0.014 0.003 TRP P1074 HIS 0.006 0.001 HIS P 116 Details of bonding type rmsd covalent geometry : bond 0.00419 (10577) covalent geometry : angle 0.70156 (14590) hydrogen bonds : bond 0.05705 ( 401) hydrogen bonds : angle 5.23063 ( 1130) *********************** 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 95 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 56 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 165 ARG cc_start: 0.8027 (ptt180) cc_final: 0.7762 (ptp-170) REVERT: P 173 ASP cc_start: 0.8859 (m-30) cc_final: 0.8530 (t0) REVERT: P 879 MET cc_start: 0.8317 (mpp) cc_final: 0.7831 (mpp) REVERT: P 1043 MET cc_start: 0.7394 (mtm) cc_final: 0.7108 (mmp) outliers start: 39 outliers final: 32 residues processed: 92 average time/residue: 0.1083 time to fit residues: 13.8539 Evaluate side-chains 79 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 47 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 37 ASN 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 155 TYR Chi-restraints excluded: chain P residue 221 ARG Chi-restraints excluded: chain P residue 234 LYS Chi-restraints excluded: chain P residue 237 LEU Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 322 ILE Chi-restraints excluded: chain P residue 323 LYS Chi-restraints excluded: chain P residue 336 LYS Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 396 GLU Chi-restraints excluded: chain P residue 445 THR 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 928 THR 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 1006 SER Chi-restraints excluded: chain P residue 1026 GLU Chi-restraints excluded: chain P residue 1144 LEU Chi-restraints excluded: chain P residue 1160 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 72 optimal weight: 0.0470 chunk 88 optimal weight: 0.9990 chunk 3 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 55 optimal weight: 0.0470 chunk 105 optimal weight: 0.9980 chunk 38 optimal weight: 3.9990 overall best weight: 0.5776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 402 GLN ** P 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 415 HIS P 980 ASN ** P 990 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 = 0.4134 r_free = 0.4134 target = 0.075375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.057298 restraints weight = 72258.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.058887 restraints weight = 37100.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.059709 restraints weight = 26643.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.059808 restraints weight = 24084.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.059859 restraints weight = 21524.454| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 1.0561 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 : 0.632 11.823 14590 Z= 0.313 Chirality : 0.040 0.193 1682 Planarity : 0.004 0.051 1593 Dihedral : 16.988 93.834 2275 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.00 % Allowed : 29.16 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.89 (0.26), residues: 1056 helix: 0.28 (0.23), residues: 510 sheet: -1.29 (0.50), residues: 102 loop : -1.39 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 63 TYR 0.020 0.001 TYR P 136 PHE 0.008 0.001 PHE P 119 TRP 0.013 0.002 TRP P 18 HIS 0.004 0.001 HIS P 721 Details of bonding type rmsd covalent geometry : bond 0.00233 (10577) covalent geometry : angle 0.63153 (14590) hydrogen bonds : bond 0.03684 ( 401) hydrogen bonds : angle 4.78672 ( 1130) ********************** 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 72 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 53 time to evaluate : 0.334 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 165 ARG cc_start: 0.7357 (ptt180) cc_final: 0.6954 (ptp-170) REVERT: P 173 ASP cc_start: 0.8913 (m-30) cc_final: 0.8645 (t0) REVERT: P 879 MET cc_start: 0.8343 (mpp) cc_final: 0.7874 (mpp) REVERT: P 1043 MET cc_start: 0.7259 (mtm) cc_final: 0.6870 (mmp) REVERT: P 1213 MET cc_start: 0.6862 (mmp) cc_final: 0.6568 (mmp) outliers start: 19 outliers final: 16 residues processed: 70 average time/residue: 0.1291 time to fit residues: 12.5320 Evaluate side-chains 70 residues out of total 950 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 155 TYR Chi-restraints excluded: chain P residue 221 ARG Chi-restraints excluded: chain P residue 317 LEU Chi-restraints excluded: chain P residue 336 LYS Chi-restraints excluded: chain P residue 375 PHE Chi-restraints excluded: chain P residue 445 THR 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 1026 GLU Chi-restraints excluded: chain P residue 1160 VAL Chi-restraints excluded: chain P residue 1275 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 0.4980 chunk 3 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 57 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 990 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 = 0.075384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.057829 restraints weight = 72596.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.058938 restraints weight = 40092.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.059722 restraints weight = 27745.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.059797 restraints weight = 24625.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.059864 restraints weight = 22472.811| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 1.0639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 10577 Z= 0.106 Angle : 0.640 17.107 14590 Z= 0.308 Chirality : 0.039 0.238 1682 Planarity : 0.004 0.052 1593 Dihedral : 16.846 91.277 2275 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.11 % Allowed : 29.47 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.71 (0.26), residues: 1056 helix: 0.43 (0.23), residues: 510 sheet: -1.11 (0.49), residues: 103 loop : -1.32 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 403 TYR 0.020 0.001 TYR P 72 PHE 0.012 0.001 PHE P1045 TRP 0.009 0.001 TRP P 18 HIS 0.004 0.001 HIS P 160 Details of bonding type rmsd covalent geometry : bond 0.00233 (10577) covalent geometry : angle 0.63970 (14590) hydrogen bonds : bond 0.03685 ( 401) hydrogen bonds : angle 4.69622 ( 1130) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3104.64 seconds wall clock time: 54 minutes 8.44 seconds (3248.44 seconds total)