Starting phenix.real_space_refine on Thu Jul 2 10:00:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vg3_31964/07_2026/7vg3_31964.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vg3_31964/07_2026/7vg3_31964.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vg3_31964/07_2026/7vg3_31964.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vg3_31964/07_2026/7vg3_31964.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7vg3_31964/07_2026/7vg3_31964.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vg3_31964/07_2026/7vg3_31964.cif" model { file = "/net/cci-nas-00/data/ceres_data/7vg3_31964/07_2026/7vg3_31964.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vg3_31964/07_2026/7vg3_31964.cif" } resolution = 3.73 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= 0.005 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Zn 1 6.06 5 P 61 5.49 5 S 36 5.16 5 C 4913 2.51 5 N 1392 2.21 5 O 1713 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8118 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 860, 6800 Classifications: {'peptide': 860} Link IDs: {'PTRANS': 37, 'TRANS': 822} Chain breaks: 6 Chain: "C" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 636 Classifications: {'RNA': 30} Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 15, 'rna3p_pyr': 13} Link IDs: {'rna2p': 2, 'rna3p': 27} Chain: "D" Number of atoms: 679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 679 Classifications: {'RNA': 32} Modifications used: {'5*END': 1, 'rna3p_pur': 17, 'rna3p_pyr': 15} Link IDs: {'rna3p': 31} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3363 SG CYS A1091 37.744 55.435 37.136 1.00 56.47 S ATOM 3378 SG CYS A1093 41.924 55.592 37.534 1.00 61.85 S ATOM 3582 SG CYS A1119 39.383 53.825 40.277 1.00 46.05 S Time building chain proxies: 1.88, per 1000 atoms: 0.23 Number of scatterers: 8118 At special positions: 0 Unit cell: (115.92, 91.56, 99.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 Ca 2 19.99 S 36 16.00 P 61 15.00 O 1713 8.00 N 1392 7.00 C 4913 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: 0.69 Conformation dependent library (CDL) restraints added in 327.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A2003 " pdb="ZN ZN A2003 " - pdb=" ND1 HIS A1123 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1093 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1119 " pdb="ZN ZN A2003 " - pdb=" SG CYS A1091 " Number of angles added : 3 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1628 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 7 sheets defined 39.3% alpha, 12.7% beta 14 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 710 through 725 removed outlier: 3.730A pdb=" N TYR A 719 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE A 720 " --> pdb=" O LYS A 716 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLN A 721 " --> pdb=" O ALA A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 795 removed outlier: 3.609A pdb=" N ILE A 782 " --> pdb=" O ASP A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 879 through 888 removed outlier: 3.730A pdb=" N TYR A 888 " --> pdb=" O PHE A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 942 through 944 No H-bonds generated for 'chain 'A' and resid 942 through 944' Processing helix chain 'A' and resid 953 through 958 Processing helix chain 'A' and resid 961 through 972 removed outlier: 4.449A pdb=" N HIS A 967 " --> pdb=" O PRO A 963 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG A 968 " --> pdb=" O SER A 964 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 983 removed outlier: 3.547A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ASP A 983 " --> pdb=" O ARG A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 992 through 998 removed outlier: 3.680A pdb=" N ILE A 996 " --> pdb=" O SER A 992 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU A 998 " --> pdb=" O THR A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1011 through 1034 removed outlier: 3.520A pdb=" N GLU A1015 " --> pdb=" O MET A1011 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU A1017 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER A1020 " --> pdb=" O LEU A1016 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1050 removed outlier: 3.689A pdb=" N GLN A1045 " --> pdb=" O GLN A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1060 removed outlier: 3.669A pdb=" N THR A1060 " --> pdb=" O HIS A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1061 through 1063 No H-bonds generated for 'chain 'A' and resid 1061 through 1063' Processing helix chain 'A' and resid 1064 through 1068 removed outlier: 3.822A pdb=" N ILE A1068 " --> pdb=" O GLN A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1133 through 1146 removed outlier: 3.516A pdb=" N ILE A1139 " --> pdb=" O ALA A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1150 through 1159 removed outlier: 3.824A pdb=" N MET A1154 " --> pdb=" O ALA A1150 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET A1155 " --> pdb=" O SER A1151 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A1159 " --> pdb=" O MET A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1176 Processing helix chain 'A' and resid 1190 through 1196 removed outlier: 4.243A pdb=" N LYS A1194 " --> pdb=" O GLU A1190 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN A1196 " --> pdb=" O GLU A1192 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1208 removed outlier: 3.725A pdb=" N LEU A1205 " --> pdb=" O ALA A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1243 removed outlier: 3.786A pdb=" N SER A1229 " --> pdb=" O PHE A1225 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A1240 " --> pdb=" O THR A1236 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN A1241 " --> pdb=" O ARG A1237 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR A1242 " --> pdb=" O HIS A1238 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR A1243 " --> pdb=" O LEU A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1259 removed outlier: 3.847A pdb=" N ASP A1253 " --> pdb=" O GLY A1249 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N CYS A1258 " --> pdb=" O LEU A1254 " (cutoff:3.500A) Processing helix chain 'A' and resid 1260 through 1271 removed outlier: 3.576A pdb=" N VAL A1269 " --> pdb=" O ALA A1265 " (cutoff:3.500A) Processing helix chain 'A' and resid 1273 through 1277 removed outlier: 3.597A pdb=" N HIS A1276 " --> pdb=" O LEU A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1281 through 1293 removed outlier: 3.711A pdb=" N GLN A1287 " --> pdb=" O VAL A1283 " (cutoff:3.500A) Processing helix chain 'A' and resid 1316 through 1329 removed outlier: 3.729A pdb=" N ALA A1322 " --> pdb=" O VAL A1318 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A1323 " --> pdb=" O GLU A1319 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU A1326 " --> pdb=" O ALA A1322 " (cutoff:3.500A) Processing helix chain 'A' and resid 1335 through 1344 Proline residue: A1342 - end of helix Processing helix chain 'A' and resid 1356 through 1369 removed outlier: 3.871A pdb=" N SER A1367 " --> pdb=" O GLU A1363 " (cutoff:3.500A) Processing helix chain 'A' and resid 1407 through 1422 removed outlier: 3.659A pdb=" N GLN A1419 " --> pdb=" O HIS A1415 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS A1422 " --> pdb=" O THR A1418 " (cutoff:3.500A) Processing helix chain 'A' and resid 1475 through 1488 Processing helix chain 'A' and resid 1544 through 1562 removed outlier: 3.540A pdb=" N GLU A1561 " --> pdb=" O LEU A1557 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG A1562 " --> pdb=" O TYR A1558 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 629 through 631 removed outlier: 3.639A pdb=" N ARG A1124 " --> pdb=" O HIS A 631 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 687 through 691 removed outlier: 3.564A pdb=" N SER A 700 " --> pdb=" O ASP A 658 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP A 658 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA A 650 " --> pdb=" O LEU A 709 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 687 through 691 removed outlier: 3.564A pdb=" N SER A 700 " --> pdb=" O ASP A 658 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP A 658 " --> pdb=" O SER A 700 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER A 670 " --> pdb=" O VAL A 766 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 938 through 941 removed outlier: 3.515A pdb=" N MET A 900 " --> pdb=" O LEU A 941 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 901 " --> pdb=" O GLU A 858 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE A 856 " --> pdb=" O LYS A 903 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N VAL A 845 " --> pdb=" O TYR A 854 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE A 856 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N LEU A 843 " --> pdb=" O ILE A 856 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N VAL A 844 " --> pdb=" O ILE A 949 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1372 through 1377 removed outlier: 3.628A pdb=" N GLN A1384 " --> pdb=" O SER A1377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1372 through 1377 removed outlier: 3.628A pdb=" N GLN A1384 " --> pdb=" O SER A1377 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1494 through 1498 removed outlier: 3.950A pdb=" N THR A1522 " --> pdb=" O SER A1498 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N TYR A1537 " --> pdb=" O ILE A1525 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A1535 " --> pdb=" O LEU A1527 " (cutoff:3.500A) 240 hydrogen bonds defined for protein. 699 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 68 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 0.89 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2151 1.34 - 1.46: 2021 1.46 - 1.58: 4059 1.58 - 1.70: 122 1.70 - 1.82: 54 Bond restraints: 8407 Sorted by residual: bond pdb=" P U C 1 " pdb=" OP3 U C 1 " ideal model delta sigma weight residual 1.480 1.606 -0.126 2.00e-02 2.50e+03 3.95e+01 bond pdb=" N SER A1212 " pdb=" CA SER A1212 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.69e+00 bond pdb=" N ASN A1405 " pdb=" CA ASN A1405 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.48e+00 bond pdb=" N HIS A1197 " pdb=" CA HIS A1197 " ideal model delta sigma weight residual 1.455 1.490 -0.034 1.18e-02 7.18e+03 8.43e+00 bond pdb=" N LEU A 746 " pdb=" CA LEU A 746 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.29e-02 6.01e+03 8.43e+00 ... (remaining 8402 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 11006 2.25 - 4.50: 556 4.50 - 6.75: 58 6.75 - 9.01: 32 9.01 - 11.26: 6 Bond angle restraints: 11658 Sorted by residual: angle pdb=" N ALA A 758 " pdb=" CA ALA A 758 " pdb=" C ALA A 758 " ideal model delta sigma weight residual 114.75 107.13 7.62 1.26e+00 6.30e-01 3.65e+01 angle pdb=" N PRO A 757 " pdb=" CA PRO A 757 " pdb=" C PRO A 757 " ideal model delta sigma weight residual 112.47 123.73 -11.26 2.06e+00 2.36e-01 2.99e+01 angle pdb=" C HIS A1211 " pdb=" N SER A1212 " pdb=" CA SER A1212 " ideal model delta sigma weight residual 121.54 131.66 -10.12 1.91e+00 2.74e-01 2.81e+01 angle pdb=" N ALA A1072 " pdb=" CA ALA A1072 " pdb=" C ALA A1072 " ideal model delta sigma weight residual 114.75 108.32 6.43 1.26e+00 6.30e-01 2.60e+01 angle pdb=" C THR A1404 " pdb=" N ASN A1405 " pdb=" CA ASN A1405 " ideal model delta sigma weight residual 121.54 130.44 -8.90 1.91e+00 2.74e-01 2.17e+01 ... (remaining 11653 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.41: 4855 35.41 - 70.82: 89 70.82 - 106.23: 2 106.23 - 141.64: 0 141.64 - 177.06: 1 Dihedral angle restraints: 4947 sinusoidal: 2442 harmonic: 2505 Sorted by residual: dihedral pdb=" O4' U C 1 " pdb=" C1' U C 1 " pdb=" N1 U C 1 " pdb=" C2 U C 1 " ideal model delta sinusoidal sigma weight residual -128.00 49.06 -177.06 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" CA PRO A1356 " pdb=" C PRO A1356 " pdb=" N PRO A1357 " pdb=" CA PRO A1357 " ideal model delta harmonic sigma weight residual -180.00 -153.10 -26.90 0 5.00e+00 4.00e-02 2.89e+01 dihedral pdb=" CA PHE A 830 " pdb=" C PHE A 830 " pdb=" N ALA A 831 " pdb=" CA ALA A 831 " ideal model delta harmonic sigma weight residual 180.00 153.96 26.04 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 4944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1115 0.069 - 0.138: 195 0.138 - 0.207: 44 0.207 - 0.276: 7 0.276 - 0.345: 4 Chirality restraints: 1365 Sorted by residual: chirality pdb=" CA PRO A 757 " pdb=" N PRO A 757 " pdb=" C PRO A 757 " pdb=" CB PRO A 757 " both_signs ideal model delta sigma weight residual False 2.72 2.37 0.34 2.00e-01 2.50e+01 2.97e+00 chirality pdb=" CA PHE A 759 " pdb=" N PHE A 759 " pdb=" C PHE A 759 " pdb=" CB PHE A 759 " both_signs ideal model delta sigma weight residual False 2.51 2.85 -0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CB VAL A 951 " pdb=" CA VAL A 951 " pdb=" CG1 VAL A 951 " pdb=" CG2 VAL A 951 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.64e+00 ... (remaining 1362 not shown) Planarity restraints: 1263 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 756 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.25e+00 pdb=" C HIS A 756 " 0.053 2.00e-02 2.50e+03 pdb=" O HIS A 756 " -0.020 2.00e-02 2.50e+03 pdb=" N PRO A 757 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 851 " 0.013 2.00e-02 2.50e+03 2.66e-02 7.08e+00 pdb=" C GLY A 851 " -0.046 2.00e-02 2.50e+03 pdb=" O GLY A 851 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG A 852 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 951 " 0.042 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO A 952 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 952 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 952 " 0.036 5.00e-02 4.00e+02 ... (remaining 1260 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 31 2.53 - 3.12: 5552 3.12 - 3.71: 12743 3.71 - 4.31: 16753 4.31 - 4.90: 26612 Nonbonded interactions: 61691 Sorted by model distance: nonbonded pdb=" OP1 U C 25 " pdb="CA CA A2002 " model vdw 1.935 2.510 nonbonded pdb=" OE2 GLU A1224 " pdb="CA CA A2002 " model vdw 2.153 2.510 nonbonded pdb=" OP1 A D 9 " pdb="CA CA A2001 " model vdw 2.221 2.510 nonbonded pdb=" OE2 GLU A1015 " pdb="CA CA A2001 " model vdw 2.248 2.510 nonbonded pdb=" OG SER A 855 " pdb=" O LYS A 903 " model vdw 2.271 3.040 ... (remaining 61686 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: 0.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.140 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 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 : 0.010 0.661 8411 Z= 0.461 Angle : 1.175 24.018 11661 Z= 0.657 Chirality : 0.060 0.345 1365 Planarity : 0.007 0.064 1263 Dihedral : 12.986 177.055 3319 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.59 % Allowed : 10.76 % Favored : 88.65 % Rotamer: Outliers : 5.13 % Allowed : 7.37 % Favored : 87.50 % Cbeta Deviations : 0.25 % 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 are not related in a simple way. whole: -4.51 (0.22), residues: 846 helix: -3.42 (0.19), residues: 331 sheet: -0.92 (0.57), residues: 87 loop : -3.12 (0.24), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 968 TYR 0.019 0.002 TYR A1370 PHE 0.025 0.003 PHE A 989 TRP 0.017 0.003 TRP A1078 HIS 0.010 0.002 HIS A 631 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.35 ( 8407) covalent geometry : angle 1.14757 / 0.65 (11658) hydrogen bonds : bond 0.24549 / 16.49 ( 263) hydrogen bonds : angle 7.98510 / 5.24 ( 767) metal coordination : bond 0.37256 / 18.50 ( 4) metal coordination : angle 15.72470 / 7.00 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 126 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 624 SER cc_start: 0.8856 (p) cc_final: 0.8599 (t) REVERT: A 731 LYS cc_start: 0.8648 (ptmt) cc_final: 0.8280 (ptmm) REVERT: A 746 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8747 (tt) REVERT: A 914 ASP cc_start: 0.8155 (p0) cc_final: 0.7852 (p0) REVERT: A 966 MET cc_start: 0.8072 (mtm) cc_final: 0.7848 (mtp) REVERT: A 969 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8575 (tm) REVERT: A 1112 THR cc_start: 0.8111 (p) cc_final: 0.7861 (t) REVERT: A 1213 SER cc_start: 0.7024 (OUTLIER) cc_final: 0.6731 (p) REVERT: A 1403 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.6952 (pp30) REVERT: A 1492 MET cc_start: 0.8223 (tpp) cc_final: 0.7899 (tpt) REVERT: A 1526 THR cc_start: 0.9043 (t) cc_final: 0.8746 (p) outliers start: 39 outliers final: 16 residues processed: 151 average time/residue: 0.0984 time to fit residues: 19.6696 Evaluate side-chains 95 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1198 GLU Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1206 LYS Chi-restraints excluded: chain A residue 1213 SER Chi-restraints excluded: chain A residue 1214 LEU Chi-restraints excluded: chain A residue 1216 GLU Chi-restraints excluded: chain A residue 1219 SER Chi-restraints excluded: chain A residue 1220 TYR Chi-restraints excluded: chain A residue 1403 GLN Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1407 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 74 optimal weight: 0.2980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 722 GLN A 783 ASN A 967 HIS A 977 GLN A 988 ASN A1029 HIS A1054 ASN A1110 ASN A1260 ASN A1403 GLN A1405 ASN A1460 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.135949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.111062 restraints weight = 14032.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.114355 restraints weight = 7741.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.116576 restraints weight = 5366.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.117799 restraints weight = 4260.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.118741 restraints weight = 3720.685| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 8411 Z= 0.119 Angle : 0.650 9.032 11661 Z= 0.333 Chirality : 0.040 0.164 1365 Planarity : 0.005 0.085 1263 Dihedral : 10.637 177.635 1699 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.51 % Favored : 91.25 % Rotamer: Outliers : 4.74 % Allowed : 12.37 % Favored : 82.89 % 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 are not related in a simple way. whole: -3.41 (0.25), residues: 846 helix: -1.90 (0.24), residues: 341 sheet: -1.14 (0.49), residues: 112 loop : -2.93 (0.26), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1215 TYR 0.019 0.001 TYR A1181 PHE 0.011 0.001 PHE A 989 TRP 0.013 0.002 TRP A 643 HIS 0.010 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 ( 8407) covalent geometry : angle 0.64911 / 0.33 (11658) hydrogen bonds : bond 0.04419 / 2.95 ( 263) hydrogen bonds : angle 4.76299 / 3.17 ( 767) metal coordination : bond 0.00604 / 0.28 ( 4) metal coordination : angle 2.71303 / 1.14 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 100 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 624 SER cc_start: 0.8760 (p) cc_final: 0.8490 (t) REVERT: A 731 LYS cc_start: 0.8700 (ptmt) cc_final: 0.8308 (ptmm) REVERT: A 759 PHE cc_start: 0.7723 (OUTLIER) cc_final: 0.7019 (m-80) REVERT: A 914 ASP cc_start: 0.8220 (p0) cc_final: 0.7900 (p0) REVERT: A 966 MET cc_start: 0.7918 (mtm) cc_final: 0.7662 (mtp) REVERT: A 983 ASP cc_start: 0.7382 (t70) cc_final: 0.7180 (p0) REVERT: A 1112 THR cc_start: 0.8204 (p) cc_final: 0.7958 (t) REVERT: A 1331 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8377 (mt) outliers start: 36 outliers final: 20 residues processed: 132 average time/residue: 0.0681 time to fit residues: 13.1749 Evaluate side-chains 97 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 657 PHE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1220 TYR Chi-restraints excluded: chain A residue 1331 LEU Chi-restraints excluded: chain A residue 1403 GLN Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1407 LEU Chi-restraints excluded: chain A residue 1525 ILE Chi-restraints excluded: chain A residue 1529 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 18 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1196 GLN A1482 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.132813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.107855 restraints weight = 14182.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.110952 restraints weight = 8156.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.112986 restraints weight = 5795.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.114072 restraints weight = 4675.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.115092 restraints weight = 4121.316| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8411 Z= 0.171 Angle : 0.655 9.875 11661 Z= 0.336 Chirality : 0.041 0.164 1365 Planarity : 0.005 0.061 1263 Dihedral : 9.828 176.428 1683 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.57 % Favored : 90.31 % Rotamer: Outliers : 6.45 % Allowed : 13.29 % Favored : 80.26 % 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 are not related in a simple way. whole: -2.69 (0.27), residues: 846 helix: -0.90 (0.28), residues: 331 sheet: -1.50 (0.48), residues: 112 loop : -2.65 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1215 TYR 0.014 0.001 TYR A1181 PHE 0.017 0.002 PHE A 759 TRP 0.011 0.002 TRP A1078 HIS 0.014 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 ( 8407) covalent geometry : angle 0.65219 / 0.34 (11658) hydrogen bonds : bond 0.04428 / 2.93 ( 263) hydrogen bonds : angle 4.39367 / 2.94 ( 767) metal coordination : bond 0.01131 / 0.56 ( 4) metal coordination : angle 3.77334 / 1.53 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 81 time to evaluate : 0.283 Fit side-chains REVERT: A 624 SER cc_start: 0.8829 (p) cc_final: 0.8542 (t) REVERT: A 731 LYS cc_start: 0.8746 (ptmt) cc_final: 0.8361 (ptmm) REVERT: A 828 ILE cc_start: 0.1518 (OUTLIER) cc_final: 0.1121 (tp) REVERT: A 914 ASP cc_start: 0.8163 (p0) cc_final: 0.7814 (p0) REVERT: A 966 MET cc_start: 0.8059 (mtm) cc_final: 0.7655 (mtp) REVERT: A 983 ASP cc_start: 0.7458 (t70) cc_final: 0.7242 (p0) REVERT: A 1154 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8389 (tpp) REVERT: A 1174 ASN cc_start: 0.6256 (m110) cc_final: 0.6032 (m110) REVERT: A 1175 ARG cc_start: 0.6703 (OUTLIER) cc_final: 0.5957 (mmm160) REVERT: A 1379 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.6826 (p0) REVERT: A 1526 THR cc_start: 0.9087 (t) cc_final: 0.8749 (p) outliers start: 49 outliers final: 30 residues processed: 121 average time/residue: 0.0668 time to fit residues: 11.6684 Evaluate side-chains 106 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 72 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 657 PHE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 753 SER Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 902 LEU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1028 CYS Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1154 MET Chi-restraints excluded: chain A residue 1175 ARG Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1379 ASP Chi-restraints excluded: chain A residue 1404 THR Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1494 THR Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1525 ILE Chi-restraints excluded: chain A residue 1529 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 896 ASN A1197 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.134642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.110123 restraints weight = 14363.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.113144 restraints weight = 8245.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.115127 restraints weight = 5881.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.116412 restraints weight = 4762.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.117079 restraints weight = 4165.951| |-----------------------------------------------------------------------------| r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 8411 Z= 0.131 Angle : 0.609 9.751 11661 Z= 0.310 Chirality : 0.039 0.157 1365 Planarity : 0.005 0.054 1263 Dihedral : 9.289 177.159 1672 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.98 % Favored : 90.90 % Rotamer: Outliers : 6.58 % Allowed : 15.00 % Favored : 78.42 % 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 are not related in a simple way. whole: -2.24 (0.28), residues: 846 helix: -0.31 (0.29), residues: 332 sheet: -1.57 (0.47), residues: 112 loop : -2.51 (0.28), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1215 TYR 0.013 0.001 TYR A1181 PHE 0.019 0.001 PHE A 759 TRP 0.013 0.001 TRP A1078 HIS 0.011 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 8407) covalent geometry : angle 0.60720 / 0.31 (11658) hydrogen bonds : bond 0.03768 / 2.48 ( 263) hydrogen bonds : angle 4.02574 / 2.69 ( 767) metal coordination : bond 0.00452 / 0.19 ( 4) metal coordination : angle 2.88538 / 1.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 81 time to evaluate : 0.256 Fit side-chains REVERT: A 624 SER cc_start: 0.8822 (p) cc_final: 0.8522 (t) REVERT: A 731 LYS cc_start: 0.8686 (ptmt) cc_final: 0.8312 (ptmm) REVERT: A 762 LEU cc_start: 0.8378 (OUTLIER) cc_final: 0.8135 (mm) REVERT: A 828 ILE cc_start: 0.1579 (OUTLIER) cc_final: 0.1237 (tp) REVERT: A 843 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8795 (tp) REVERT: A 914 ASP cc_start: 0.8160 (p0) cc_final: 0.7794 (p0) REVERT: A 966 MET cc_start: 0.7977 (mtm) cc_final: 0.7564 (mtp) REVERT: A 983 ASP cc_start: 0.7459 (t70) cc_final: 0.7218 (p0) REVERT: A 1112 THR cc_start: 0.8163 (p) cc_final: 0.7939 (t) REVERT: A 1174 ASN cc_start: 0.6374 (m110) cc_final: 0.6104 (m110) REVERT: A 1175 ARG cc_start: 0.6624 (OUTLIER) cc_final: 0.5904 (mmm160) REVERT: A 1379 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.6878 (p0) REVERT: A 1509 ILE cc_start: 0.6160 (OUTLIER) cc_final: 0.5958 (mp) REVERT: A 1526 THR cc_start: 0.9109 (t) cc_final: 0.8795 (p) outliers start: 50 outliers final: 29 residues processed: 123 average time/residue: 0.0649 time to fit residues: 11.4852 Evaluate side-chains 112 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 77 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 657 PHE Chi-restraints excluded: chain A residue 673 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 843 LEU Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1175 ARG Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1379 ASP Chi-restraints excluded: chain A residue 1403 GLN Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1417 LEU Chi-restraints excluded: chain A residue 1494 THR Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1525 ILE Chi-restraints excluded: chain A residue 1529 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 82 optimal weight: 8.9990 chunk 25 optimal weight: 0.3980 chunk 32 optimal weight: 0.0570 chunk 38 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 2 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 47 optimal weight: 0.8980 overall best weight: 1.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 722 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.135496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110851 restraints weight = 14404.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.113959 restraints weight = 8346.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.116002 restraints weight = 5930.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.117293 restraints weight = 4777.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.117978 restraints weight = 4184.946| |-----------------------------------------------------------------------------| r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8411 Z= 0.120 Angle : 0.595 9.791 11661 Z= 0.303 Chirality : 0.039 0.162 1365 Planarity : 0.004 0.045 1263 Dihedral : 9.034 177.287 1671 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.46 % Favored : 90.43 % Rotamer: Outliers : 6.05 % Allowed : 16.18 % Favored : 77.76 % 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 are not related in a simple way. whole: -1.95 (0.28), residues: 846 helix: -0.02 (0.30), residues: 335 sheet: -1.52 (0.48), residues: 110 loop : -2.37 (0.29), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A1215 TYR 0.011 0.001 TYR A1181 PHE 0.019 0.001 PHE A 759 TRP 0.012 0.001 TRP A1078 HIS 0.011 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 ( 8407) covalent geometry : angle 0.59346 / 0.30 (11658) hydrogen bonds : bond 0.03586 / 2.36 ( 263) hydrogen bonds : angle 3.87585 / 2.59 ( 767) metal coordination : bond 0.00415 / 0.15 ( 4) metal coordination : angle 2.66814 / 0.96 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 81 time to evaluate : 0.179 Fit side-chains REVERT: A 624 SER cc_start: 0.8846 (p) cc_final: 0.8570 (t) REVERT: A 630 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8464 (mt) REVERT: A 731 LYS cc_start: 0.8655 (ptmt) cc_final: 0.8289 (ptmm) REVERT: A 762 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8123 (mm) REVERT: A 828 ILE cc_start: 0.1753 (OUTLIER) cc_final: 0.1440 (tp) REVERT: A 914 ASP cc_start: 0.8139 (p0) cc_final: 0.7765 (p0) REVERT: A 966 MET cc_start: 0.7958 (mtm) cc_final: 0.7518 (mtp) REVERT: A 983 ASP cc_start: 0.7440 (t70) cc_final: 0.7205 (p0) REVERT: A 1112 THR cc_start: 0.8133 (p) cc_final: 0.7904 (t) REVERT: A 1174 ASN cc_start: 0.6288 (m110) cc_final: 0.6066 (m110) REVERT: A 1379 ASP cc_start: 0.7779 (OUTLIER) cc_final: 0.6955 (p0) REVERT: A 1509 ILE cc_start: 0.6096 (OUTLIER) cc_final: 0.5880 (mp) REVERT: A 1526 THR cc_start: 0.9113 (t) cc_final: 0.8781 (p) REVERT: A 1542 ARG cc_start: 0.6902 (OUTLIER) cc_final: 0.6147 (ptp-170) outliers start: 46 outliers final: 25 residues processed: 119 average time/residue: 0.0802 time to fit residues: 13.3305 Evaluate side-chains 108 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 77 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 657 PHE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1379 ASP Chi-restraints excluded: chain A residue 1403 GLN Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1494 THR Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1525 ILE Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1542 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 61 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 66 optimal weight: 0.0170 chunk 40 optimal weight: 7.9990 chunk 34 optimal weight: 0.3980 chunk 62 optimal weight: 5.9990 chunk 82 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 10.0000 overall best weight: 3.0824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.131142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.105905 restraints weight = 14266.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.108920 restraints weight = 8449.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.110832 restraints weight = 6090.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.112103 restraints weight = 4989.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.112890 restraints weight = 4378.703| |-----------------------------------------------------------------------------| r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 8411 Z= 0.202 Angle : 0.668 10.011 11661 Z= 0.338 Chirality : 0.041 0.173 1365 Planarity : 0.005 0.041 1263 Dihedral : 9.076 175.840 1665 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.64 % Favored : 89.24 % Rotamer: Outliers : 5.79 % Allowed : 17.11 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.29), residues: 846 helix: 0.18 (0.30), residues: 331 sheet: -1.74 (0.48), residues: 113 loop : -2.44 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1193 TYR 0.015 0.002 TYR A1358 PHE 0.022 0.002 PHE A 759 TRP 0.012 0.002 TRP A1078 HIS 0.012 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.20 ( 8407) covalent geometry : angle 0.66552 / 0.34 (11658) hydrogen bonds : bond 0.04401 / 2.91 ( 263) hydrogen bonds : angle 4.07778 / 2.70 ( 767) metal coordination : bond 0.00686 / 0.32 ( 4) metal coordination : angle 3.59781 / 1.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 77 time to evaluate : 0.302 Fit side-chains REVERT: A 630 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8547 (mt) REVERT: A 731 LYS cc_start: 0.8684 (ptmt) cc_final: 0.8292 (ptmm) REVERT: A 762 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8259 (mm) REVERT: A 828 ILE cc_start: 0.1752 (OUTLIER) cc_final: 0.1429 (tp) REVERT: A 914 ASP cc_start: 0.8148 (p0) cc_final: 0.7736 (p0) REVERT: A 966 MET cc_start: 0.8004 (mtm) cc_final: 0.7568 (mtp) REVERT: A 1112 THR cc_start: 0.8125 (p) cc_final: 0.7891 (t) REVERT: A 1174 ASN cc_start: 0.6404 (m110) cc_final: 0.6161 (m110) REVERT: A 1175 ARG cc_start: 0.6787 (OUTLIER) cc_final: 0.5955 (mtp85) REVERT: A 1379 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.6970 (p0) REVERT: A 1509 ILE cc_start: 0.6152 (OUTLIER) cc_final: 0.5734 (mp) REVERT: A 1542 ARG cc_start: 0.6917 (OUTLIER) cc_final: 0.6245 (ptp-170) outliers start: 44 outliers final: 30 residues processed: 109 average time/residue: 0.0760 time to fit residues: 11.7420 Evaluate side-chains 109 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 72 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 657 PHE Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 828 ILE Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 986 ILE Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1175 ARG Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1379 ASP Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1459 ILE Chi-restraints excluded: chain A residue 1494 THR Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1525 ILE Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1542 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 73 optimal weight: 0.0770 chunk 43 optimal weight: 8.9990 chunk 62 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 85 optimal weight: 9.9990 chunk 35 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 overall best weight: 1.3744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.134592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.109549 restraints weight = 14442.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.112638 restraints weight = 8481.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.114675 restraints weight = 6072.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.115830 restraints weight = 4922.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.116720 restraints weight = 4357.405| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8411 Z= 0.125 Angle : 0.629 11.750 11661 Z= 0.314 Chirality : 0.039 0.192 1365 Planarity : 0.005 0.047 1263 Dihedral : 8.892 177.067 1665 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.10 % Favored : 90.90 % Rotamer: Outliers : 5.39 % Allowed : 18.16 % Favored : 76.45 % 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 are not related in a simple way. whole: -1.73 (0.29), residues: 846 helix: 0.31 (0.30), residues: 339 sheet: -1.63 (0.49), residues: 111 loop : -2.35 (0.29), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1532 TYR 0.010 0.001 TYR A1181 PHE 0.015 0.001 PHE A 759 TRP 0.014 0.001 TRP A1078 HIS 0.010 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 ( 8407) covalent geometry : angle 0.62780 / 0.31 (11658) hydrogen bonds : bond 0.03654 / 2.40 ( 263) hydrogen bonds : angle 3.85672 / 2.57 ( 767) metal coordination : bond 0.00476 / 0.23 ( 4) metal coordination : angle 2.40437 / 0.92 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 75 time to evaluate : 0.292 Fit side-chains REVERT: A 624 SER cc_start: 0.8870 (p) cc_final: 0.8602 (t) REVERT: A 630 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8480 (mt) REVERT: A 731 LYS cc_start: 0.8615 (ptmt) cc_final: 0.8249 (ptmm) REVERT: A 914 ASP cc_start: 0.8124 (p0) cc_final: 0.7717 (p0) REVERT: A 966 MET cc_start: 0.8011 (mtm) cc_final: 0.7341 (mtm) REVERT: A 1112 THR cc_start: 0.8114 (p) cc_final: 0.7886 (t) REVERT: A 1175 ARG cc_start: 0.6716 (OUTLIER) cc_final: 0.5971 (mtp85) REVERT: A 1379 ASP cc_start: 0.7751 (OUTLIER) cc_final: 0.6930 (p0) REVERT: A 1509 ILE cc_start: 0.6149 (OUTLIER) cc_final: 0.5749 (mp) outliers start: 41 outliers final: 30 residues processed: 104 average time/residue: 0.0664 time to fit residues: 9.9324 Evaluate side-chains 107 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 73 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1175 ARG Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1221 GLU Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1333 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1379 ASP Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1494 THR Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1525 ILE Chi-restraints excluded: chain A residue 1526 THR Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1542 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 4 optimal weight: 0.9990 chunk 76 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 7.9990 chunk 80 optimal weight: 20.0000 chunk 9 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.132240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.107041 restraints weight = 14333.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.110065 restraints weight = 8472.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.112020 restraints weight = 6115.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.113198 restraints weight = 4990.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.114025 restraints weight = 4407.628| |-----------------------------------------------------------------------------| r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8411 Z= 0.161 Angle : 0.655 11.390 11661 Z= 0.326 Chirality : 0.040 0.151 1365 Planarity : 0.005 0.047 1263 Dihedral : 8.909 176.351 1665 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.64 % Favored : 89.36 % Rotamer: Outliers : 5.13 % Allowed : 18.82 % Favored : 76.05 % 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 are not related in a simple way. whole: -1.60 (0.29), residues: 846 helix: 0.45 (0.30), residues: 338 sheet: -1.58 (0.49), residues: 110 loop : -2.30 (0.29), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1215 TYR 0.012 0.001 TYR A1358 PHE 0.019 0.002 PHE A 759 TRP 0.012 0.002 TRP A1078 HIS 0.011 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 ( 8407) covalent geometry : angle 0.65397 / 0.33 (11658) hydrogen bonds : bond 0.04000 / 2.62 ( 263) hydrogen bonds : angle 3.91756 / 2.59 ( 767) metal coordination : bond 0.00511 / 0.25 ( 4) metal coordination : angle 2.84200 / 1.19 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 72 time to evaluate : 0.306 Fit side-chains REVERT: A 630 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8486 (mt) REVERT: A 731 LYS cc_start: 0.8638 (ptmt) cc_final: 0.8267 (ptmm) REVERT: A 762 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8217 (mm) REVERT: A 914 ASP cc_start: 0.8114 (p0) cc_final: 0.7844 (p0) REVERT: A 966 MET cc_start: 0.8030 (mtm) cc_final: 0.7376 (mtm) REVERT: A 1112 THR cc_start: 0.8130 (p) cc_final: 0.7903 (t) REVERT: A 1175 ARG cc_start: 0.6832 (OUTLIER) cc_final: 0.6127 (mtp85) REVERT: A 1379 ASP cc_start: 0.7638 (m-30) cc_final: 0.6970 (p0) REVERT: A 1509 ILE cc_start: 0.6180 (OUTLIER) cc_final: 0.5763 (mp) REVERT: A 1542 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6132 (ptp-170) outliers start: 39 outliers final: 28 residues processed: 99 average time/residue: 0.0650 time to fit residues: 9.3044 Evaluate side-chains 102 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 69 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 630 LEU Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 789 VAL Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 857 VAL Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 987 ASP Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1175 ARG Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1333 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1397 THR Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1494 THR Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1525 ILE Chi-restraints excluded: chain A residue 1526 THR Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1542 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 79 optimal weight: 6.9990 chunk 40 optimal weight: 0.0070 chunk 15 optimal weight: 9.9990 chunk 29 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 22 optimal weight: 8.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.136673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.111945 restraints weight = 14212.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.115026 restraints weight = 8387.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.116878 restraints weight = 6017.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.118249 restraints weight = 4924.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.118987 restraints weight = 4320.770| |-----------------------------------------------------------------------------| r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 8411 Z= 0.111 Angle : 0.625 11.706 11661 Z= 0.309 Chirality : 0.038 0.144 1365 Planarity : 0.004 0.050 1263 Dihedral : 8.735 177.708 1665 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 4.74 % Allowed : 19.08 % Favored : 76.18 % 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 are not related in a simple way. whole: -1.41 (0.29), residues: 846 helix: 0.60 (0.30), residues: 334 sheet: -1.36 (0.50), residues: 109 loop : -2.20 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1215 TYR 0.009 0.001 TYR A1181 PHE 0.014 0.001 PHE A 759 TRP 0.015 0.001 TRP A1078 HIS 0.010 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 8407) covalent geometry : angle 0.62475 / 0.31 (11658) hydrogen bonds : bond 0.03338 / 2.18 ( 263) hydrogen bonds : angle 3.71536 / 2.48 ( 767) metal coordination : bond 0.00292 / 0.14 ( 4) metal coordination : angle 1.77912 / 0.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 81 time to evaluate : 0.287 Fit side-chains REVERT: A 624 SER cc_start: 0.8849 (p) cc_final: 0.8570 (t) REVERT: A 731 LYS cc_start: 0.8594 (ptmt) cc_final: 0.8236 (ptmm) REVERT: A 914 ASP cc_start: 0.8093 (p0) cc_final: 0.7833 (p0) REVERT: A 1112 THR cc_start: 0.8090 (p) cc_final: 0.7832 (t) REVERT: A 1175 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6046 (mtp85) REVERT: A 1333 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8584 (tt) REVERT: A 1363 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7393 (mt-10) REVERT: A 1379 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7052 (p0) REVERT: A 1509 ILE cc_start: 0.6187 (OUTLIER) cc_final: 0.5805 (mp) REVERT: A 1542 ARG cc_start: 0.6810 (OUTLIER) cc_final: 0.5870 (ptp-170) outliers start: 36 outliers final: 24 residues processed: 105 average time/residue: 0.0804 time to fit residues: 11.9224 Evaluate side-chains 104 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1175 ARG Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1333 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1379 ASP Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1494 THR Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1525 ILE Chi-restraints excluded: chain A residue 1526 THR Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1542 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 68 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 91 optimal weight: 10.0000 chunk 9 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 0.0070 chunk 40 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.131099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.105868 restraints weight = 14417.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.108921 restraints weight = 8453.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.110929 restraints weight = 6078.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.111971 restraints weight = 4937.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.112908 restraints weight = 4379.856| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 8411 Z= 0.192 Angle : 0.693 10.839 11661 Z= 0.346 Chirality : 0.041 0.155 1365 Planarity : 0.005 0.051 1263 Dihedral : 8.940 175.712 1665 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.76 % Favored : 89.24 % Rotamer: Outliers : 4.08 % Allowed : 20.13 % Favored : 75.79 % 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 are not related in a simple way. whole: -1.47 (0.29), residues: 846 helix: 0.60 (0.30), residues: 338 sheet: -1.60 (0.48), residues: 112 loop : -2.25 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1215 TYR 0.014 0.001 TYR A1358 PHE 0.020 0.002 PHE A 759 TRP 0.009 0.002 TRP A 643 HIS 0.012 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.19 ( 8407) covalent geometry : angle 0.69163 / 0.35 (11658) hydrogen bonds : bond 0.04263 / 2.80 ( 263) hydrogen bonds : angle 3.96716 / 2.61 ( 767) metal coordination : bond 0.00488 / 0.23 ( 4) metal coordination : angle 3.00146 / 1.36 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1692 Ramachandran restraints generated. 846 Oldfield, 0 Emsley, 846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 68 time to evaluate : 0.214 Fit side-chains REVERT: A 762 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8326 (mm) REVERT: A 914 ASP cc_start: 0.8096 (p0) cc_final: 0.7794 (p0) REVERT: A 1175 ARG cc_start: 0.6852 (OUTLIER) cc_final: 0.6177 (mtp85) REVERT: A 1379 ASP cc_start: 0.7653 (m-30) cc_final: 0.7044 (p0) REVERT: A 1509 ILE cc_start: 0.6108 (OUTLIER) cc_final: 0.5687 (mp) REVERT: A 1542 ARG cc_start: 0.6867 (OUTLIER) cc_final: 0.6370 (ptp-170) outliers start: 31 outliers final: 23 residues processed: 91 average time/residue: 0.0698 time to fit residues: 8.9991 Evaluate side-chains 91 residues out of total 760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 639 LEU Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 734 VAL Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 836 ASP Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 848 ILE Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 969 LEU Chi-restraints excluded: chain A residue 980 GLU Chi-restraints excluded: chain A residue 1003 LEU Chi-restraints excluded: chain A residue 1089 VAL Chi-restraints excluded: chain A residue 1175 ARG Chi-restraints excluded: chain A residue 1199 PHE Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1210 THR Chi-restraints excluded: chain A residue 1271 ASN Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1353 LEU Chi-restraints excluded: chain A residue 1405 ASN Chi-restraints excluded: chain A residue 1494 THR Chi-restraints excluded: chain A residue 1509 ILE Chi-restraints excluded: chain A residue 1522 THR Chi-restraints excluded: chain A residue 1525 ILE Chi-restraints excluded: chain A residue 1526 THR Chi-restraints excluded: chain A residue 1529 ILE Chi-restraints excluded: chain A residue 1542 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 75 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 12 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 706 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.132282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.107183 restraints weight = 14483.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.110235 restraints weight = 8467.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112246 restraints weight = 6074.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.113302 restraints weight = 4933.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.114280 restraints weight = 4372.565| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8411 Z= 0.162 Angle : 0.680 11.122 11661 Z= 0.338 Chirality : 0.040 0.190 1365 Planarity : 0.004 0.053 1263 Dihedral : 8.895 176.341 1665 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 3.82 % Allowed : 20.53 % Favored : 75.66 % 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 are not related in a simple way. whole: -1.50 (0.29), residues: 846 helix: 0.58 (0.30), residues: 339 sheet: -1.68 (0.49), residues: 110 loop : -2.26 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A1215 TYR 0.008 0.001 TYR A1181 PHE 0.020 0.001 PHE A 759 TRP 0.012 0.001 TRP A1078 HIS 0.011 0.001 HIS A 756 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.16 ( 8407) covalent geometry : angle 0.67918 / 0.34 (11658) hydrogen bonds : bond 0.04019 / 2.63 ( 263) hydrogen bonds : angle 3.92152 / 2.59 ( 767) metal coordination : bond 0.00409 / 0.19 ( 4) metal coordination : angle 2.56228 / 1.06 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1202.13 seconds wall clock time: 21 minutes 26.31 seconds (1286.31 seconds total)