Starting phenix.real_space_refine on Sat Jul 4 19:13:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yym_14383/07_2026/7yym_14383.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yym_14383/07_2026/7yym_14383.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7yym_14383/07_2026/7yym_14383.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yym_14383/07_2026/7yym_14383.cif" model { file = "/net/cci-nas-00/data/ceres_data/7yym_14383/07_2026/7yym_14383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yym_14383/07_2026/7yym_14383.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yym_14383/07_2026/7yym_14383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yym_14383/07_2026/7yym_14383.map" } resolution = 4.19 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= 0.001 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 55 5.49 5 S 57 5.16 5 C 7080 2.51 5 N 1945 2.21 5 O 2261 1.98 5 H 10961 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 22359 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 20618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1281, 20618 Classifications: {'peptide': 1281} Link IDs: {'PTRANS': 76, 'TRANS': 1204} Chain breaks: 9 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 1741 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 1741 Classifications: {'RNA': 55} Modifications used: {'3*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 27, 'rna3p_pyr': 27} Link IDs: {'rna3p': 54} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {' U%rna3p_pyr:plan': 2} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 3.67, per 1000 atoms: 0.16 Number of scatterers: 22359 At special positions: 0 Unit cell: (97.704, 105.156, 163.944, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 57 16.00 P 55 15.00 O 2261 8.00 N 1945 7.00 C 7080 6.00 H 10961 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.18 Conformation dependent library (CDL) restraints added in 505.5 milliseconds 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2460 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 9 sheets defined 53.9% alpha, 11.6% beta 18 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 46 through 58 Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 102 through 117 Processing helix chain 'A' and resid 126 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 4.167A pdb=" N GLN A 140 " --> pdb=" O GLU A 136 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU A 141 " --> pdb=" O ARG A 137 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 162 Processing helix chain 'A' and resid 165 through 169 removed outlier: 3.528A pdb=" N ILE A 169 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 184 through 196 removed outlier: 4.241A pdb=" N GLU A 188 " --> pdb=" O HIS A 184 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 231 removed outlier: 4.779A pdb=" N GLU A 220 " --> pdb=" O PRO A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 247 Processing helix chain 'A' and resid 265 through 287 Processing helix chain 'A' and resid 295 through 313 removed outlier: 4.382A pdb=" N SER A 299 " --> pdb=" O SER A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 336 removed outlier: 4.451A pdb=" N ALA A 318 " --> pdb=" O GLY A 314 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLY A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N MET A 324 " --> pdb=" O LYS A 320 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N MET A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLU A 328 " --> pdb=" O MET A 324 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LYS A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 359 Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 374 through 388 removed outlier: 3.784A pdb=" N MET A 378 " --> pdb=" O THR A 374 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR A 387 " --> pdb=" O ILE A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 468 Processing helix chain 'A' and resid 498 through 510 removed outlier: 3.788A pdb=" N GLU A 502 " --> pdb=" O PHE A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 524 Processing helix chain 'A' and resid 542 through 551 Processing helix chain 'A' and resid 568 through 592 removed outlier: 4.041A pdb=" N GLU A 574 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 641 removed outlier: 4.484A pdb=" N GLY A 632 " --> pdb=" O ASN A 628 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 641 " --> pdb=" O TYR A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 706 removed outlier: 3.583A pdb=" N LYS A 701 " --> pdb=" O ILE A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 859 Processing helix chain 'A' and resid 893 through 902 Processing helix chain 'A' and resid 967 through 975 Processing helix chain 'A' and resid 1044 through 1053 removed outlier: 4.113A pdb=" N CYS A1053 " --> pdb=" O ARG A1049 " (cutoff:3.500A) Processing helix chain 'A' and resid 1053 through 1076 Processing helix chain 'A' and resid 1293 through 1302 Processing helix chain 'A' and resid 1303 through 1307 Processing helix chain 'A' and resid 1313 through 1335 Processing helix chain 'A' and resid 1339 through 1351 Processing helix chain 'A' and resid 1352 through 1364 Processing helix chain 'A' and resid 1365 through 1369 removed outlier: 3.721A pdb=" N MET A1369 " --> pdb=" O PRO A1366 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1583 removed outlier: 3.756A pdb=" N GLY A1571 " --> pdb=" O LEU A1567 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N GLU A1572 " --> pdb=" O THR A1568 " (cutoff:3.500A) removed outlier: 9.094A pdb=" N ARG A1573 " --> pdb=" O SER A1569 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ALA A1574 " --> pdb=" O CYS A1570 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LEU A1579 " --> pdb=" O ALA A1575 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N CYS A1580 " --> pdb=" O GLN A1576 " (cutoff:3.500A) Processing helix chain 'A' and resid 1648 through 1657 Processing helix chain 'A' and resid 1660 through 1668 removed outlier: 3.848A pdb=" N LYS A1666 " --> pdb=" O THR A1662 " (cutoff:3.500A) Processing helix chain 'A' and resid 1674 through 1682 removed outlier: 3.792A pdb=" N LEU A1678 " --> pdb=" O LYS A1674 " (cutoff:3.500A) Processing helix chain 'A' and resid 1695 through 1716 removed outlier: 3.753A pdb=" N PHE A1700 " --> pdb=" O GLN A1696 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU A1701 " --> pdb=" O ARG A1697 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A1704 " --> pdb=" O PHE A1700 " (cutoff:3.500A) Processing helix chain 'A' and resid 1722 through 1735 Processing helix chain 'A' and resid 1735 through 1746 Processing helix chain 'A' and resid 1747 through 1751 Processing helix chain 'A' and resid 1756 through 1773 removed outlier: 3.723A pdb=" N LYS A1768 " --> pdb=" O ASP A1764 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS A1773 " --> pdb=" O PHE A1769 " (cutoff:3.500A) Processing helix chain 'A' and resid 1799 through 1817 removed outlier: 4.037A pdb=" N GLY A1803 " --> pdb=" O PRO A1799 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A1810 " --> pdb=" O PHE A1806 " (cutoff:3.500A) Processing helix chain 'A' and resid 1820 through 1842 removed outlier: 3.572A pdb=" N VAL A1824 " --> pdb=" O SER A1820 " (cutoff:3.500A) Proline residue: A1830 - end of helix Proline residue: A1834 - end of helix removed outlier: 3.613A pdb=" N GLU A1837 " --> pdb=" O GLN A1833 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N LYS A1838 " --> pdb=" O PRO A1834 " (cutoff:3.500A) Processing helix chain 'A' and resid 1846 through 1855 Processing helix chain 'A' and resid 1890 through 1910 Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 124 removed outlier: 4.158A pdb=" N THR A 151 " --> pdb=" O TYR A 124 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR A 96 " --> pdb=" O LEU A 148 " (cutoff:3.500A) removed outlier: 8.185A pdb=" N MET A 150 " --> pdb=" O THR A 96 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N PHE A 98 " --> pdb=" O MET A 150 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL A 173 " --> pdb=" O VAL A 97 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU A 99 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP A 175 " --> pdb=" O LEU A 99 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR A 60 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N THR A 206 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N VAL A 62 " --> pdb=" O THR A 206 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ILE A 61 " --> pdb=" O GLU A 235 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 251 through 257 removed outlier: 6.387A pdb=" N CYS A 251 " --> pdb=" O TYR A 560 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N MET A 562 " --> pdb=" O CYS A 251 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE A 253 " --> pdb=" O MET A 562 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ALA A 564 " --> pdb=" O ILE A 253 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL A 255 " --> pdb=" O ALA A 564 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL A 534 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LEU A 563 " --> pdb=" O VAL A 534 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ARG A 536 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N ASP A 565 " --> pdb=" O ARG A 536 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE A 445 " --> pdb=" O VAL A 535 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASN A 477 " --> pdb=" O ILE A 517 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 652 through 656 Processing sheet with id=AA4, first strand: chain 'A' and resid 746 through 750 removed outlier: 3.535A pdb=" N GLN A 747 " --> pdb=" O ILE A1550 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 816 through 820 removed outlier: 3.788A pdb=" N PHE A 816 " --> pdb=" O ILE A 827 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N GLU A 824 " --> pdb=" O THR A 778 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N THR A 778 " --> pdb=" O GLU A 824 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 832 " --> pdb=" O LEU A 770 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N LEU A 770 " --> pdb=" O LYS A 832 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N SER A 834 " --> pdb=" O CYS A 768 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N CYS A 768 " --> pdb=" O SER A 834 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N PHE A 802 " --> pdb=" O ILE A 773 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N THR A 889 " --> pdb=" O VAL A 884 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 865 through 867 Processing sheet with id=AA7, first strand: chain 'A' and resid 987 through 992 removed outlier: 3.672A pdb=" N LEU A 987 " --> pdb=" O TYR A 951 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ASP A 949 " --> pdb=" O ASP A 989 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ASP A 991 " --> pdb=" O VAL A 947 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N VAL A 947 " --> pdb=" O ASP A 991 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1859 through 1861 Processing sheet with id=AA9, first strand: chain 'A' and resid 1859 through 1861 522 hydrogen bonds defined for protein. 1503 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 72 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 5.54 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.02: 10923 1.02 - 1.22: 52 1.22 - 1.42: 4824 1.42 - 1.61: 6837 1.61 - 1.81: 78 Bond restraints: 22714 Sorted by residual: bond pdb=" N LYS A 160 " pdb=" H LYS A 160 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.79e+01 bond pdb=" CA LYS A 160 " pdb=" HA LYS A 160 " ideal model delta sigma weight residual 0.970 1.088 -0.118 2.00e-02 2.50e+03 3.49e+01 bond pdb=" N LYS A 160 " pdb=" CA LYS A 160 " ideal model delta sigma weight residual 1.459 1.484 -0.024 1.19e-02 7.06e+03 4.18e+00 bond pdb=" NH1 ARG A 86 " pdb="HH12 ARG A 86 " ideal model delta sigma weight residual 0.860 0.826 0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" NE2 GLN A 985 " pdb="HE22 GLN A 985 " ideal model delta sigma weight residual 0.860 0.832 0.028 2.00e-02 2.50e+03 1.92e+00 ... (remaining 22709 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.56: 39068 1.56 - 3.11: 1854 3.11 - 4.67: 202 4.67 - 6.22: 27 6.22 - 7.78: 4 Bond angle restraints: 41155 Sorted by residual: angle pdb=" N GLN A1826 " pdb=" CA GLN A1826 " pdb=" CB GLN A1826 " ideal model delta sigma weight residual 110.39 116.43 -6.04 1.66e+00 3.63e-01 1.32e+01 angle pdb=" N LYS A 160 " pdb=" CA LYS A 160 " pdb=" C LYS A 160 " ideal model delta sigma weight residual 111.07 107.29 3.78 1.07e+00 8.73e-01 1.25e+01 angle pdb=" CA TRP A 138 " pdb=" CB TRP A 138 " pdb=" CG TRP A 138 " ideal model delta sigma weight residual 113.60 119.64 -6.04 1.90e+00 2.77e-01 1.01e+01 angle pdb=" C2' U B 57 " pdb=" C1' U B 57 " pdb=" N1 U B 57 " ideal model delta sigma weight residual 112.00 116.54 -4.54 1.50e+00 4.44e-01 9.18e+00 angle pdb=" C2' A B 13 " pdb=" C1' A B 13 " pdb=" N9 A B 13 " ideal model delta sigma weight residual 112.00 116.42 -4.42 1.50e+00 4.44e-01 8.67e+00 ... (remaining 41150 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 10337 35.83 - 71.65: 209 71.65 - 107.48: 11 107.48 - 143.30: 0 143.30 - 179.13: 8 Dihedral angle restraints: 10565 sinusoidal: 6150 harmonic: 4415 Sorted by residual: dihedral pdb=" C5' A B 59 " pdb=" C4' A B 59 " pdb=" C3' A B 59 " pdb=" O3' A B 59 " ideal model delta sinusoidal sigma weight residual 147.00 98.94 48.06 1 8.00e+00 1.56e-02 4.97e+01 dihedral pdb=" O4' A B 59 " pdb=" C4' A B 59 " pdb=" C3' A B 59 " pdb=" C2' A B 59 " ideal model delta sinusoidal sigma weight residual 24.00 -23.49 47.49 1 8.00e+00 1.56e-02 4.86e+01 dihedral pdb=" C4' A B 59 " pdb=" C3' A B 59 " pdb=" C2' A B 59 " pdb=" C1' A B 59 " ideal model delta sinusoidal sigma weight residual -35.00 5.77 -40.77 1 8.00e+00 1.56e-02 3.64e+01 ... (remaining 10562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1429 0.048 - 0.095: 344 0.095 - 0.143: 105 0.143 - 0.190: 12 0.190 - 0.238: 1 Chirality restraints: 1891 Sorted by residual: chirality pdb=" C1' A B 13 " pdb=" O4' A B 13 " pdb=" C2' A B 13 " pdb=" N9 A B 13 " both_signs ideal model delta sigma weight residual False 2.46 2.22 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C1' G B 51 " pdb=" O4' G B 51 " pdb=" C2' G B 51 " pdb=" N9 G B 51 " both_signs ideal model delta sigma weight residual False 2.46 2.28 0.18 2.00e-01 2.50e+01 7.67e-01 chirality pdb=" C1' C B 55 " pdb=" O4' C B 55 " pdb=" C2' C B 55 " pdb=" N1 C B 55 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.17 2.00e-01 2.50e+01 7.59e-01 ... (remaining 1888 not shown) Planarity restraints: 3090 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 86 " -0.023 9.50e-02 1.11e+02 7.14e-02 1.13e+02 pdb=" NE ARG A 86 " -0.090 2.00e-02 2.50e+03 pdb=" CZ ARG A 86 " 0.088 2.00e-02 2.50e+03 pdb=" NH1 ARG A 86 " 0.114 2.00e-02 2.50e+03 pdb=" NH2 ARG A 86 " 0.030 2.00e-02 2.50e+03 pdb="HH11 ARG A 86 " 0.008 2.00e-02 2.50e+03 pdb="HH12 ARG A 86 " -0.121 2.00e-02 2.50e+03 pdb="HH21 ARG A 86 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG A 86 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 985 " -0.057 2.00e-02 2.50e+03 6.86e-02 7.06e+01 pdb=" CD GLN A 985 " 0.055 2.00e-02 2.50e+03 pdb=" OE1 GLN A 985 " -0.003 2.00e-02 2.50e+03 pdb=" NE2 GLN A 985 " 0.104 2.00e-02 2.50e+03 pdb="HE21 GLN A 985 " 0.006 2.00e-02 2.50e+03 pdb="HE22 GLN A 985 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 187 " -0.367 9.50e-02 1.11e+02 1.30e-01 6.04e+01 pdb=" NE ARG A 187 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG A 187 " 0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG A 187 " 0.046 2.00e-02 2.50e+03 pdb=" NH2 ARG A 187 " 0.079 2.00e-02 2.50e+03 pdb="HH11 ARG A 187 " 0.000 2.00e-02 2.50e+03 pdb="HH12 ARG A 187 " -0.031 2.00e-02 2.50e+03 pdb="HH21 ARG A 187 " 0.003 2.00e-02 2.50e+03 pdb="HH22 ARG A 187 " -0.080 2.00e-02 2.50e+03 ... (remaining 3087 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1305 2.21 - 2.81: 45824 2.81 - 3.41: 59671 3.41 - 4.00: 74844 4.00 - 4.60: 116099 Nonbonded interactions: 297743 Sorted by model distance: nonbonded pdb=" OD1 ASP A 644 " pdb=" HG1 THR A 647 " model vdw 1.613 2.450 nonbonded pdb=" O LEU A1678 " pdb=" HG1 THR A1682 " model vdw 1.614 2.450 nonbonded pdb=" HG1 THR A1867 " pdb=" OD1 ASP A1869 " model vdw 1.622 2.450 nonbonded pdb=" O GLU A 542 " pdb=" HG SER A 545 " model vdw 1.622 2.450 nonbonded pdb=" H SER A1862 " pdb=" O THR A1875 " model vdw 1.635 2.450 ... (remaining 297738 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.370 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: 0.130 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 23.920 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11753 Z= 0.178 Angle : 0.798 7.778 16181 Z= 0.449 Chirality : 0.046 0.238 1891 Planarity : 0.011 0.124 1854 Dihedral : 12.820 101.222 4611 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.18 % Allowed : 1.67 % Favored : 98.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.72 (0.23), residues: 1261 helix: 1.13 (0.20), residues: 632 sheet: -0.07 (0.42), residues: 145 loop : -0.06 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.053 0.005 ARG A 86 TYR 0.030 0.004 TYR A1746 PHE 0.030 0.003 PHE A1660 TRP 0.041 0.005 TRP A 138 HIS 0.012 0.003 HIS A1749 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.18 (11753) covalent geometry : angle 0.79809 / 0.45 (16181) hydrogen bonds : bond 0.10748 / 7.56 ( 564) hydrogen bonds : angle 5.21471 / 3.70 ( 1575) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue ALA 1807 is missing expected H atoms. Skipping. Evaluate side-chains 427 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 425 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8866 (tp) cc_final: 0.8366 (tp) REVERT: A 56 LEU cc_start: 0.8755 (mt) cc_final: 0.8356 (mt) REVERT: A 61 ILE cc_start: 0.8027 (mm) cc_final: 0.7360 (mm) REVERT: A 105 GLN cc_start: 0.8513 (mp10) cc_final: 0.8226 (mp10) REVERT: A 114 ARG cc_start: 0.8903 (ttm110) cc_final: 0.8699 (ttm110) REVERT: A 120 LYS cc_start: 0.8605 (ptpp) cc_final: 0.8235 (ptpp) REVERT: A 141 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8154 (mm-30) REVERT: A 153 TYR cc_start: 0.8413 (m-10) cc_final: 0.8053 (m-10) REVERT: A 161 ASN cc_start: 0.8657 (m110) cc_final: 0.7859 (m-40) REVERT: A 171 LEU cc_start: 0.7759 (mm) cc_final: 0.7408 (mm) REVERT: A 183 ASP cc_start: 0.8434 (m-30) cc_final: 0.8222 (p0) REVERT: A 221 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8259 (mt-10) REVERT: A 222 LYS cc_start: 0.9204 (mmtm) cc_final: 0.9003 (mmtm) REVERT: A 231 ARG cc_start: 0.8941 (tmm-80) cc_final: 0.8400 (ptm-80) REVERT: A 267 TYR cc_start: 0.8555 (t80) cc_final: 0.7940 (t80) REVERT: A 275 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8596 (mt-10) REVERT: A 305 ASP cc_start: 0.7517 (m-30) cc_final: 0.7276 (m-30) REVERT: A 319 ASP cc_start: 0.8513 (m-30) cc_final: 0.8237 (m-30) REVERT: A 329 LEU cc_start: 0.9228 (tp) cc_final: 0.9006 (tp) REVERT: A 343 LYS cc_start: 0.8013 (tptt) cc_final: 0.7571 (tptm) REVERT: A 347 PHE cc_start: 0.8988 (m-80) cc_final: 0.8555 (m-80) REVERT: A 379 LYS cc_start: 0.9398 (mmtm) cc_final: 0.9195 (mmtm) REVERT: A 500 LYS cc_start: 0.9187 (mppt) cc_final: 0.8553 (mppt) REVERT: A 503 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8506 (mt-10) REVERT: A 536 ARG cc_start: 0.8042 (tpt90) cc_final: 0.7821 (tpt90) REVERT: A 541 THR cc_start: 0.8189 (m) cc_final: 0.7891 (p) REVERT: A 542 GLU cc_start: 0.8419 (tp30) cc_final: 0.8170 (tp30) REVERT: A 544 ARG cc_start: 0.8917 (ppt170) cc_final: 0.8540 (ppt170) REVERT: A 575 ASP cc_start: 0.8437 (m-30) cc_final: 0.7889 (m-30) REVERT: A 631 ILE cc_start: 0.8072 (pt) cc_final: 0.7674 (mt) REVERT: A 648 HIS cc_start: 0.7070 (t-90) cc_final: 0.6745 (t-90) REVERT: A 698 CYS cc_start: 0.9223 (t) cc_final: 0.8843 (m) REVERT: A 747 GLN cc_start: 0.8224 (mp-120) cc_final: 0.7753 (mp-120) REVERT: A 761 TYR cc_start: 0.8411 (t80) cc_final: 0.8205 (t80) REVERT: A 800 ARG cc_start: 0.8304 (mmt180) cc_final: 0.7712 (mmt90) REVERT: A 815 HIS cc_start: 0.7441 (p90) cc_final: 0.7025 (p90) REVERT: A 827 ILE cc_start: 0.9103 (mp) cc_final: 0.8876 (mp) REVERT: A 831 LEU cc_start: 0.8903 (tt) cc_final: 0.8689 (tt) REVERT: A 851 GLN cc_start: 0.8995 (tt0) cc_final: 0.8482 (tt0) REVERT: A 894 PHE cc_start: 0.8410 (m-10) cc_final: 0.7993 (m-10) REVERT: A 901 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8194 (tm-30) REVERT: A 902 LYS cc_start: 0.8711 (ptpp) cc_final: 0.8510 (ptmm) REVERT: A 1296 LEU cc_start: 0.8376 (mt) cc_final: 0.8127 (mt) REVERT: A 1313 GLU cc_start: 0.6794 (mp0) cc_final: 0.6503 (mp0) REVERT: A 1340 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7867 (tm-30) REVERT: A 1346 MET cc_start: 0.8884 (mtp) cc_final: 0.8438 (mtp) REVERT: A 1349 LYS cc_start: 0.8909 (tttt) cc_final: 0.8232 (tmmt) REVERT: A 1350 LYS cc_start: 0.8986 (mmmm) cc_final: 0.8693 (mmmm) REVERT: A 1354 CYS cc_start: 0.8759 (p) cc_final: 0.8322 (t) REVERT: A 1386 VAL cc_start: 0.8316 (p) cc_final: 0.7964 (m) REVERT: A 1545 HIS cc_start: 0.8510 (m-70) cc_final: 0.8221 (m-70) REVERT: A 1585 LYS cc_start: 0.7903 (tmtt) cc_final: 0.7665 (tptt) REVERT: A 1664 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8216 (mt-10) REVERT: A 1701 LEU cc_start: 0.8243 (tp) cc_final: 0.7916 (tp) REVERT: A 1706 LEU cc_start: 0.8808 (tp) cc_final: 0.8440 (tp) REVERT: A 1716 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7872 (tm-30) REVERT: A 1759 LEU cc_start: 0.9174 (tp) cc_final: 0.8789 (tt) REVERT: A 1772 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7812 (tp30) REVERT: A 1809 LEU cc_start: 0.8892 (tp) cc_final: 0.8493 (tp) REVERT: A 1827 VAL cc_start: 0.8753 (t) cc_final: 0.8267 (t) REVERT: A 1895 LYS cc_start: 0.8564 (tttt) cc_final: 0.8300 (mtmm) outliers start: 2 outliers final: 0 residues processed: 425 average time/residue: 0.2785 time to fit residues: 160.2054 Evaluate side-chains 389 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.0370 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 overall best weight: 1.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS A1325 HIS ** A1826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.123027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.095040 restraints weight = 70398.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.101189 restraints weight = 31547.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.105358 restraints weight = 17538.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.108145 restraints weight = 11038.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.110023 restraints weight = 7642.606| |-----------------------------------------------------------------------------| r_work (final): 0.3707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11753 Z= 0.201 Angle : 0.589 6.945 16181 Z= 0.320 Chirality : 0.039 0.146 1891 Planarity : 0.005 0.043 1854 Dihedral : 9.718 94.481 2057 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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: 0.63 (0.24), residues: 1261 helix: 1.18 (0.20), residues: 639 sheet: -0.35 (0.41), residues: 158 loop : -0.24 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 790 TYR 0.013 0.001 TYR A1746 PHE 0.028 0.002 PHE A1671 TRP 0.022 0.003 TRP A 138 HIS 0.006 0.001 HIS A1749 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.20 (11753) covalent geometry : angle 0.58873 / 0.32 (16181) hydrogen bonds : bond 0.05474 / 3.80 ( 564) hydrogen bonds : angle 4.99722 / 3.58 ( 1575) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue ALA 1807 is missing expected H atoms. Skipping. Evaluate side-chains 411 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8932 (tp) cc_final: 0.8433 (tp) REVERT: A 56 LEU cc_start: 0.8775 (mt) cc_final: 0.8424 (mt) REVERT: A 75 VAL cc_start: 0.8906 (m) cc_final: 0.8677 (m) REVERT: A 79 LYS cc_start: 0.8924 (mttm) cc_final: 0.8455 (mttm) REVERT: A 105 GLN cc_start: 0.8574 (mp10) cc_final: 0.8280 (mp10) REVERT: A 114 ARG cc_start: 0.8936 (ttm110) cc_final: 0.8612 (ttm110) REVERT: A 120 LYS cc_start: 0.8611 (ptpp) cc_final: 0.8271 (ptpp) REVERT: A 141 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8342 (mm-30) REVERT: A 153 TYR cc_start: 0.8530 (m-10) cc_final: 0.8178 (m-10) REVERT: A 171 LEU cc_start: 0.7723 (mm) cc_final: 0.7434 (mm) REVERT: A 188 GLU cc_start: 0.8825 (mp0) cc_final: 0.8564 (mp0) REVERT: A 221 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8329 (mt-10) REVERT: A 231 ARG cc_start: 0.8888 (tmm-80) cc_final: 0.8242 (ptm-80) REVERT: A 267 TYR cc_start: 0.8682 (t80) cc_final: 0.8129 (t80) REVERT: A 275 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8530 (mt-10) REVERT: A 319 ASP cc_start: 0.8558 (m-30) cc_final: 0.8347 (m-30) REVERT: A 329 LEU cc_start: 0.9233 (tp) cc_final: 0.8980 (tp) REVERT: A 500 LYS cc_start: 0.9283 (mppt) cc_final: 0.9068 (mppt) REVERT: A 502 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8560 (mm-30) REVERT: A 503 GLU cc_start: 0.9073 (mt-10) cc_final: 0.8637 (mt-10) REVERT: A 541 THR cc_start: 0.8172 (m) cc_final: 0.7822 (p) REVERT: A 631 ILE cc_start: 0.8126 (pt) cc_final: 0.7592 (mp) REVERT: A 634 ILE cc_start: 0.9053 (mm) cc_final: 0.8813 (mm) REVERT: A 646 PHE cc_start: 0.8707 (m-80) cc_final: 0.8504 (m-80) REVERT: A 648 HIS cc_start: 0.7069 (t-90) cc_final: 0.6734 (t-90) REVERT: A 698 CYS cc_start: 0.9192 (t) cc_final: 0.8765 (m) REVERT: A 749 TYR cc_start: 0.7885 (m-10) cc_final: 0.7673 (m-10) REVERT: A 761 TYR cc_start: 0.8455 (t80) cc_final: 0.8229 (t80) REVERT: A 784 GLU cc_start: 0.8850 (pp20) cc_final: 0.8619 (pm20) REVERT: A 815 HIS cc_start: 0.7504 (p90) cc_final: 0.7120 (p90) REVERT: A 842 MET cc_start: 0.9041 (tpp) cc_final: 0.8520 (tpp) REVERT: A 851 GLN cc_start: 0.9029 (tt0) cc_final: 0.8543 (tt0) REVERT: A 894 PHE cc_start: 0.8109 (m-10) cc_final: 0.7906 (m-10) REVERT: A 901 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8193 (tm-30) REVERT: A 916 LYS cc_start: 0.9532 (tmtt) cc_final: 0.9255 (tptp) REVERT: A 970 GLU cc_start: 0.8781 (tt0) cc_final: 0.8466 (mt-10) REVERT: A 992 HIS cc_start: 0.8191 (m-70) cc_final: 0.7823 (m-70) REVERT: A 996 ARG cc_start: 0.7661 (ptp-170) cc_final: 0.7444 (ptp-170) REVERT: A 1069 GLU cc_start: 0.8574 (tm-30) cc_final: 0.7919 (tm-30) REVERT: A 1070 LEU cc_start: 0.9010 (tp) cc_final: 0.8734 (tp) REVERT: A 1340 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7889 (tm-30) REVERT: A 1346 MET cc_start: 0.8934 (mtp) cc_final: 0.8427 (mtp) REVERT: A 1349 LYS cc_start: 0.8949 (tttt) cc_final: 0.8332 (tmmt) REVERT: A 1350 LYS cc_start: 0.9020 (mmmm) cc_final: 0.8695 (mmmm) REVERT: A 1545 HIS cc_start: 0.8421 (m-70) cc_final: 0.8056 (m-70) REVERT: A 1572 GLU cc_start: 0.8894 (mp0) cc_final: 0.8692 (mp0) REVERT: A 1664 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8289 (mt-10) REVERT: A 1701 LEU cc_start: 0.8204 (tp) cc_final: 0.7947 (tp) REVERT: A 1706 LEU cc_start: 0.8808 (tp) cc_final: 0.8543 (tp) REVERT: A 1716 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7992 (tm-30) REVERT: A 1759 LEU cc_start: 0.9207 (tp) cc_final: 0.8798 (tp) REVERT: A 1764 ASP cc_start: 0.8702 (m-30) cc_final: 0.8385 (m-30) REVERT: A 1809 LEU cc_start: 0.8899 (tp) cc_final: 0.8508 (tp) REVERT: A 1833 GLN cc_start: 0.8823 (tm-30) cc_final: 0.8514 (tm-30) outliers start: 0 outliers final: 0 residues processed: 411 average time/residue: 0.2929 time to fit residues: 162.0052 Evaluate side-chains 389 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 0.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 110 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.122561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.094813 restraints weight = 70075.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.100978 restraints weight = 31176.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.105157 restraints weight = 17232.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.107893 restraints weight = 10796.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.109686 restraints weight = 7459.635| |-----------------------------------------------------------------------------| r_work (final): 0.3702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11753 Z= 0.173 Angle : 0.548 6.370 16181 Z= 0.294 Chirality : 0.038 0.145 1891 Planarity : 0.005 0.042 1854 Dihedral : 9.719 93.371 2057 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: 0.61 (0.24), residues: 1261 helix: 1.18 (0.20), residues: 635 sheet: -0.47 (0.41), residues: 156 loop : -0.22 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1697 TYR 0.014 0.001 TYR A 771 PHE 0.024 0.001 PHE A1671 TRP 0.041 0.003 TRP A 138 HIS 0.005 0.001 HIS A1713 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.17 (11753) covalent geometry : angle 0.54759 / 0.29 (16181) hydrogen bonds : bond 0.05033 / 3.49 ( 564) hydrogen bonds : angle 4.82204 / 3.46 ( 1575) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue ALA 1807 is missing expected H atoms. Skipping. Evaluate side-chains 407 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8754 (mt) cc_final: 0.8522 (mt) REVERT: A 52 LEU cc_start: 0.8919 (tp) cc_final: 0.8347 (tp) REVERT: A 56 LEU cc_start: 0.8763 (mt) cc_final: 0.8337 (mt) REVERT: A 105 GLN cc_start: 0.8630 (mp10) cc_final: 0.8357 (mp10) REVERT: A 120 LYS cc_start: 0.8581 (ptpp) cc_final: 0.8204 (ptpp) REVERT: A 135 LYS cc_start: 0.9593 (tmtt) cc_final: 0.9392 (tptp) REVERT: A 141 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8156 (mm-30) REVERT: A 153 TYR cc_start: 0.8551 (m-10) cc_final: 0.8200 (m-10) REVERT: A 164 LEU cc_start: 0.8643 (tp) cc_final: 0.8411 (tp) REVERT: A 171 LEU cc_start: 0.7721 (mm) cc_final: 0.7432 (mm) REVERT: A 188 GLU cc_start: 0.8820 (mp0) cc_final: 0.8537 (mp0) REVERT: A 221 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8366 (mt-10) REVERT: A 227 GLU cc_start: 0.8261 (pt0) cc_final: 0.8056 (pt0) REVERT: A 231 ARG cc_start: 0.8884 (tmm-80) cc_final: 0.8166 (ptm-80) REVERT: A 267 TYR cc_start: 0.8694 (t80) cc_final: 0.8136 (t80) REVERT: A 272 MET cc_start: 0.9001 (mpp) cc_final: 0.8566 (mtp) REVERT: A 275 GLU cc_start: 0.8889 (mt-10) cc_final: 0.8533 (mt-10) REVERT: A 329 LEU cc_start: 0.9255 (tp) cc_final: 0.8991 (tp) REVERT: A 500 LYS cc_start: 0.9278 (mppt) cc_final: 0.8736 (mppt) REVERT: A 502 GLU cc_start: 0.8918 (mm-30) cc_final: 0.8557 (mm-30) REVERT: A 503 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8532 (mt-10) REVERT: A 541 THR cc_start: 0.8146 (m) cc_final: 0.7832 (p) REVERT: A 631 ILE cc_start: 0.8146 (pt) cc_final: 0.7634 (mp) REVERT: A 634 ILE cc_start: 0.9031 (mm) cc_final: 0.8787 (mm) REVERT: A 646 PHE cc_start: 0.8728 (m-80) cc_final: 0.8518 (m-80) REVERT: A 648 HIS cc_start: 0.7070 (t-90) cc_final: 0.6718 (t-90) REVERT: A 698 CYS cc_start: 0.9168 (t) cc_final: 0.8699 (m) REVERT: A 747 GLN cc_start: 0.8320 (mp-120) cc_final: 0.8071 (mp-120) REVERT: A 761 TYR cc_start: 0.8455 (t80) cc_final: 0.8222 (t80) REVERT: A 815 HIS cc_start: 0.7501 (p90) cc_final: 0.7136 (p90) REVERT: A 827 ILE cc_start: 0.9042 (mp) cc_final: 0.8834 (mp) REVERT: A 828 SER cc_start: 0.7915 (m) cc_final: 0.7492 (t) REVERT: A 842 MET cc_start: 0.9015 (tpp) cc_final: 0.8482 (tpp) REVERT: A 851 GLN cc_start: 0.9007 (tt0) cc_final: 0.8513 (tt0) REVERT: A 894 PHE cc_start: 0.8156 (m-10) cc_final: 0.7896 (m-10) REVERT: A 901 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8232 (tm-30) REVERT: A 916 LYS cc_start: 0.9550 (tmtt) cc_final: 0.9275 (tptp) REVERT: A 970 GLU cc_start: 0.8816 (tt0) cc_final: 0.8427 (mt-10) REVERT: A 992 HIS cc_start: 0.8192 (m-70) cc_final: 0.7847 (m-70) REVERT: A 1069 GLU cc_start: 0.8563 (tm-30) cc_final: 0.7913 (tm-30) REVERT: A 1070 LEU cc_start: 0.8992 (tp) cc_final: 0.8714 (tp) REVERT: A 1310 PHE cc_start: 0.6738 (m-80) cc_final: 0.6427 (m-10) REVERT: A 1313 GLU cc_start: 0.7824 (mp0) cc_final: 0.7290 (mp0) REVERT: A 1346 MET cc_start: 0.8898 (mtp) cc_final: 0.8428 (mtp) REVERT: A 1349 LYS cc_start: 0.8945 (tttt) cc_final: 0.8325 (tmmt) REVERT: A 1350 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8762 (mmmm) REVERT: A 1369 MET cc_start: 0.8219 (mpp) cc_final: 0.7990 (mpp) REVERT: A 1545 HIS cc_start: 0.8451 (m-70) cc_final: 0.8098 (m-70) REVERT: A 1572 GLU cc_start: 0.8904 (mp0) cc_final: 0.8678 (mp0) REVERT: A 1696 GLN cc_start: 0.8391 (mt0) cc_final: 0.8122 (mt0) REVERT: A 1701 LEU cc_start: 0.8110 (tp) cc_final: 0.7836 (tp) REVERT: A 1716 GLU cc_start: 0.8211 (mt-10) cc_final: 0.8009 (tm-30) REVERT: A 1759 LEU cc_start: 0.9168 (tp) cc_final: 0.8763 (tp) REVERT: A 1802 MET cc_start: 0.8402 (mmp) cc_final: 0.8177 (mmp) REVERT: A 1809 LEU cc_start: 0.8882 (tp) cc_final: 0.8505 (tp) REVERT: A 1815 MET cc_start: 0.8330 (tpt) cc_final: 0.8111 (tpp) REVERT: A 1833 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8517 (tm-30) REVERT: A 1854 MET cc_start: 0.8901 (tpt) cc_final: 0.8665 (tpt) REVERT: A 1895 LYS cc_start: 0.8638 (tttt) cc_final: 0.8331 (mtmm) outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 0.2927 time to fit residues: 160.8006 Evaluate side-chains 390 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 91 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 79 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 66 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 92 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.119829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.092413 restraints weight = 71251.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.098461 restraints weight = 31876.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.102564 restraints weight = 17678.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.105253 restraints weight = 11066.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.107052 restraints weight = 7648.830| |-----------------------------------------------------------------------------| r_work (final): 0.3661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11753 Z= 0.228 Angle : 0.572 6.566 16181 Z= 0.315 Chirality : 0.038 0.143 1891 Planarity : 0.005 0.089 1854 Dihedral : 9.987 92.474 2057 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % 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: 0.13 (0.23), residues: 1261 helix: 0.83 (0.20), residues: 635 sheet: -0.65 (0.40), residues: 168 loop : -0.53 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1845 TYR 0.011 0.001 TYR A 47 PHE 0.026 0.002 PHE A1671 TRP 0.021 0.002 TRP A 138 HIS 0.006 0.001 HIS A1713 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.23 (11753) covalent geometry : angle 0.57203 / 0.32 (16181) hydrogen bonds : bond 0.05367 / 3.71 ( 564) hydrogen bonds : angle 5.03995 / 3.62 ( 1575) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue ALA 1807 is missing expected H atoms. Skipping. Evaluate side-chains 408 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8759 (mt) cc_final: 0.8540 (mt) REVERT: A 52 LEU cc_start: 0.8946 (tp) cc_final: 0.8505 (tp) REVERT: A 56 LEU cc_start: 0.8785 (mt) cc_final: 0.8441 (mt) REVERT: A 76 LEU cc_start: 0.8739 (tp) cc_final: 0.8480 (tp) REVERT: A 80 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8185 (mm-30) REVERT: A 105 GLN cc_start: 0.8669 (mp10) cc_final: 0.8410 (mp10) REVERT: A 141 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8151 (mm-30) REVERT: A 153 TYR cc_start: 0.8600 (m-10) cc_final: 0.8260 (m-10) REVERT: A 164 LEU cc_start: 0.8732 (tp) cc_final: 0.8503 (tp) REVERT: A 171 LEU cc_start: 0.7728 (mm) cc_final: 0.7478 (mm) REVERT: A 188 GLU cc_start: 0.8836 (mp0) cc_final: 0.8544 (mp0) REVERT: A 221 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8376 (mt-10) REVERT: A 231 ARG cc_start: 0.8870 (tmm-80) cc_final: 0.8523 (ptm-80) REVERT: A 232 SER cc_start: 0.8464 (m) cc_final: 0.7950 (t) REVERT: A 267 TYR cc_start: 0.8724 (t80) cc_final: 0.8264 (t80) REVERT: A 268 GLU cc_start: 0.8900 (mp0) cc_final: 0.8524 (mp0) REVERT: A 272 MET cc_start: 0.9043 (mpp) cc_final: 0.8433 (mtt) REVERT: A 275 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8565 (mt-10) REVERT: A 300 LYS cc_start: 0.9138 (pttm) cc_final: 0.8935 (ptpp) REVERT: A 329 LEU cc_start: 0.9269 (tp) cc_final: 0.9013 (tp) REVERT: A 502 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8585 (mm-30) REVERT: A 503 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8655 (mt-10) REVERT: A 541 THR cc_start: 0.8108 (m) cc_final: 0.7732 (p) REVERT: A 575 ASP cc_start: 0.8439 (m-30) cc_final: 0.8197 (m-30) REVERT: A 631 ILE cc_start: 0.8174 (pt) cc_final: 0.7662 (mp) REVERT: A 634 ILE cc_start: 0.9016 (mm) cc_final: 0.8774 (mm) REVERT: A 648 HIS cc_start: 0.7100 (t-90) cc_final: 0.6749 (t-90) REVERT: A 698 CYS cc_start: 0.9177 (t) cc_final: 0.8687 (m) REVERT: A 749 TYR cc_start: 0.7708 (m-10) cc_final: 0.7503 (m-10) REVERT: A 761 TYR cc_start: 0.8469 (t80) cc_final: 0.8213 (t80) REVERT: A 815 HIS cc_start: 0.7544 (p90) cc_final: 0.7190 (p90) REVERT: A 830 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7631 (tm-30) REVERT: A 842 MET cc_start: 0.9004 (tpp) cc_final: 0.8522 (tpp) REVERT: A 851 GLN cc_start: 0.9033 (tt0) cc_final: 0.8540 (tt0) REVERT: A 894 PHE cc_start: 0.8141 (m-10) cc_final: 0.7933 (m-10) REVERT: A 901 GLU cc_start: 0.8643 (tm-30) cc_final: 0.8273 (tm-30) REVERT: A 916 LYS cc_start: 0.9545 (tmtt) cc_final: 0.9275 (tptp) REVERT: A 970 GLU cc_start: 0.8821 (tt0) cc_final: 0.8426 (mt-10) REVERT: A 992 HIS cc_start: 0.8201 (m-70) cc_final: 0.7991 (m-70) REVERT: A 1036 GLU cc_start: 0.7475 (mp0) cc_final: 0.7050 (mp0) REVERT: A 1069 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8166 (tm-30) REVERT: A 1310 PHE cc_start: 0.6839 (m-80) cc_final: 0.6542 (m-10) REVERT: A 1313 GLU cc_start: 0.7906 (mp0) cc_final: 0.7342 (mp0) REVERT: A 1346 MET cc_start: 0.8931 (mtp) cc_final: 0.8482 (mtp) REVERT: A 1349 LYS cc_start: 0.8968 (tttt) cc_final: 0.8374 (tmmt) REVERT: A 1350 LYS cc_start: 0.9055 (mmmm) cc_final: 0.8782 (mmmm) REVERT: A 1369 MET cc_start: 0.8187 (mpp) cc_final: 0.7943 (mpp) REVERT: A 1545 HIS cc_start: 0.8461 (m-70) cc_final: 0.8116 (m-70) REVERT: A 1550 ILE cc_start: 0.7937 (mt) cc_final: 0.7263 (mt) REVERT: A 1572 GLU cc_start: 0.8918 (mp0) cc_final: 0.8689 (mp0) REVERT: A 1654 ASN cc_start: 0.8983 (m-40) cc_final: 0.8719 (m110) REVERT: A 1701 LEU cc_start: 0.8246 (tp) cc_final: 0.7969 (tp) REVERT: A 1716 GLU cc_start: 0.8241 (mt-10) cc_final: 0.8024 (tm-30) REVERT: A 1726 LEU cc_start: 0.8681 (mp) cc_final: 0.8371 (mt) REVERT: A 1748 TYR cc_start: 0.8349 (m-10) cc_final: 0.8043 (m-10) REVERT: A 1759 LEU cc_start: 0.9183 (tp) cc_final: 0.8841 (tp) REVERT: A 1772 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7812 (tp30) REVERT: A 1802 MET cc_start: 0.8447 (mmp) cc_final: 0.8205 (mmp) REVERT: A 1833 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8572 (tm-30) REVERT: A 1847 PRO cc_start: 0.8646 (Cg_exo) cc_final: 0.8365 (Cg_endo) REVERT: A 1895 LYS cc_start: 0.8656 (tttt) cc_final: 0.8372 (mtmm) outliers start: 0 outliers final: 0 residues processed: 408 average time/residue: 0.2776 time to fit residues: 152.9573 Evaluate side-chains 388 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 34 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1299 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 = 0.3826 r_free = 0.3826 target = 0.117316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.090268 restraints weight = 72237.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.096236 restraints weight = 32174.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.100266 restraints weight = 17802.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.102907 restraints weight = 11171.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.104708 restraints weight = 7743.332| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11753 Z= 0.280 Angle : 0.608 6.591 16181 Z= 0.343 Chirality : 0.039 0.147 1891 Planarity : 0.005 0.048 1854 Dihedral : 10.411 92.265 2057 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: -0.42 (0.23), residues: 1261 helix: 0.32 (0.19), residues: 635 sheet: -0.65 (0.41), residues: 162 loop : -0.81 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 996 TYR 0.014 0.001 TYR A 124 PHE 0.019 0.002 PHE A1671 TRP 0.016 0.003 TRP A 138 HIS 0.008 0.001 HIS A1713 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.28 (11753) covalent geometry : angle 0.60804 / 0.34 (16181) hydrogen bonds : bond 0.05787 / 3.99 ( 564) hydrogen bonds : angle 5.31790 / 3.82 ( 1575) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue ALA 1807 is missing expected H atoms. Skipping. Evaluate side-chains 404 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8832 (mt) cc_final: 0.8604 (mt) REVERT: A 52 LEU cc_start: 0.8961 (tp) cc_final: 0.8521 (tp) REVERT: A 56 LEU cc_start: 0.8809 (mt) cc_final: 0.8450 (mt) REVERT: A 76 LEU cc_start: 0.8755 (tp) cc_final: 0.8512 (tp) REVERT: A 80 GLU cc_start: 0.8527 (mm-30) cc_final: 0.8160 (mm-30) REVERT: A 114 ARG cc_start: 0.9010 (ttm110) cc_final: 0.8704 (ttm110) REVERT: A 141 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8250 (mm-30) REVERT: A 153 TYR cc_start: 0.8636 (m-10) cc_final: 0.8310 (m-10) REVERT: A 164 LEU cc_start: 0.8772 (tp) cc_final: 0.8556 (tp) REVERT: A 171 LEU cc_start: 0.7679 (mm) cc_final: 0.7456 (mm) REVERT: A 188 GLU cc_start: 0.8830 (mp0) cc_final: 0.8533 (mp0) REVERT: A 221 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8356 (mt-10) REVERT: A 232 SER cc_start: 0.8530 (m) cc_final: 0.7974 (t) REVERT: A 267 TYR cc_start: 0.8725 (t80) cc_final: 0.8262 (t80) REVERT: A 268 GLU cc_start: 0.8906 (mp0) cc_final: 0.8509 (mp0) REVERT: A 272 MET cc_start: 0.9037 (mpp) cc_final: 0.8707 (mtp) REVERT: A 275 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8639 (mt-10) REVERT: A 329 LEU cc_start: 0.9280 (tp) cc_final: 0.9025 (tp) REVERT: A 503 GLU cc_start: 0.9086 (mt-10) cc_final: 0.8653 (mt-10) REVERT: A 541 THR cc_start: 0.8160 (m) cc_final: 0.7808 (p) REVERT: A 575 ASP cc_start: 0.8649 (m-30) cc_final: 0.8272 (m-30) REVERT: A 631 ILE cc_start: 0.8246 (pt) cc_final: 0.7757 (mp) REVERT: A 648 HIS cc_start: 0.7076 (t-90) cc_final: 0.6711 (t-90) REVERT: A 698 CYS cc_start: 0.9180 (t) cc_final: 0.8666 (m) REVERT: A 761 TYR cc_start: 0.8466 (t80) cc_final: 0.8200 (t80) REVERT: A 775 MET cc_start: 0.8126 (mtp) cc_final: 0.7671 (mtp) REVERT: A 800 ARG cc_start: 0.8538 (mmt90) cc_final: 0.8076 (mmt180) REVERT: A 815 HIS cc_start: 0.7569 (p90) cc_final: 0.7250 (p90) REVERT: A 842 MET cc_start: 0.8984 (tpp) cc_final: 0.8502 (tpp) REVERT: A 851 GLN cc_start: 0.9079 (tt0) cc_final: 0.8551 (tt0) REVERT: A 901 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8344 (tm-30) REVERT: A 916 LYS cc_start: 0.9550 (tmtt) cc_final: 0.9285 (tptp) REVERT: A 970 GLU cc_start: 0.8777 (tt0) cc_final: 0.8386 (mt-10) REVERT: A 992 HIS cc_start: 0.8239 (m-70) cc_final: 0.7929 (m-70) REVERT: A 1001 THR cc_start: 0.8729 (p) cc_final: 0.8287 (m) REVERT: A 1069 GLU cc_start: 0.8570 (tm-30) cc_final: 0.7996 (tm-30) REVERT: A 1313 GLU cc_start: 0.7926 (mp0) cc_final: 0.7379 (mp0) REVERT: A 1346 MET cc_start: 0.8913 (mtp) cc_final: 0.8534 (mtp) REVERT: A 1350 LYS cc_start: 0.9010 (mmmm) cc_final: 0.8803 (mmmm) REVERT: A 1545 HIS cc_start: 0.8500 (m-70) cc_final: 0.8222 (m-70) REVERT: A 1572 GLU cc_start: 0.8902 (mp0) cc_final: 0.8650 (mp0) REVERT: A 1674 LYS cc_start: 0.9156 (mmtp) cc_final: 0.8834 (mmpt) REVERT: A 1696 GLN cc_start: 0.8397 (mt0) cc_final: 0.7898 (mm110) REVERT: A 1701 LEU cc_start: 0.8257 (tp) cc_final: 0.8010 (tp) REVERT: A 1748 TYR cc_start: 0.8350 (m-10) cc_final: 0.8087 (m-10) REVERT: A 1759 LEU cc_start: 0.9201 (tp) cc_final: 0.8880 (tp) REVERT: A 1802 MET cc_start: 0.8483 (mmp) cc_final: 0.8231 (mmp) REVERT: A 1833 GLN cc_start: 0.8892 (tm-30) cc_final: 0.8593 (tm-30) REVERT: A 1850 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8263 (tm-30) REVERT: A 1895 LYS cc_start: 0.8695 (tttt) cc_final: 0.8421 (mtmm) outliers start: 0 outliers final: 0 residues processed: 404 average time/residue: 0.2910 time to fit residues: 158.4005 Evaluate side-chains 386 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 386 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 121 optimal weight: 2.9990 chunk 62 optimal weight: 0.0470 chunk 107 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.9480 ------------------------------------------------------------------------------- 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 = 0.3874 r_free = 0.3874 target = 0.120814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.093475 restraints weight = 71293.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.099597 restraints weight = 31551.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.103711 restraints weight = 17337.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.106425 restraints weight = 10878.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.108267 restraints weight = 7506.026| |-----------------------------------------------------------------------------| r_work (final): 0.3693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11753 Z= 0.151 Angle : 0.539 5.913 16181 Z= 0.288 Chirality : 0.038 0.155 1891 Planarity : 0.005 0.042 1854 Dihedral : 10.195 91.902 2057 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: 0.05 (0.24), residues: 1261 helix: 0.80 (0.20), residues: 635 sheet: -0.73 (0.41), residues: 168 loop : -0.60 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 996 TYR 0.013 0.001 TYR A1330 PHE 0.031 0.002 PHE A1671 TRP 0.055 0.003 TRP A 138 HIS 0.005 0.001 HIS A1687 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.15 (11753) covalent geometry : angle 0.53904 / 0.29 (16181) hydrogen bonds : bond 0.04906 / 3.42 ( 564) hydrogen bonds : angle 4.78375 / 3.43 ( 1575) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue ALA 1807 is missing expected H atoms. Skipping. Evaluate side-chains 406 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 0.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8781 (mt) cc_final: 0.8562 (mt) REVERT: A 52 LEU cc_start: 0.8885 (tp) cc_final: 0.8404 (tp) REVERT: A 56 LEU cc_start: 0.8713 (mt) cc_final: 0.8342 (mt) REVERT: A 76 LEU cc_start: 0.8734 (tp) cc_final: 0.8465 (tp) REVERT: A 80 GLU cc_start: 0.8528 (mm-30) cc_final: 0.8117 (mm-30) REVERT: A 94 LYS cc_start: 0.7588 (tttt) cc_final: 0.7364 (tttm) REVERT: A 114 ARG cc_start: 0.8978 (ttm110) cc_final: 0.8686 (ttm110) REVERT: A 141 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8143 (mm-30) REVERT: A 153 TYR cc_start: 0.8566 (m-10) cc_final: 0.8239 (m-10) REVERT: A 160 LYS cc_start: 0.9085 (pttp) cc_final: 0.8858 (ptmm) REVERT: A 164 LEU cc_start: 0.8686 (tp) cc_final: 0.8458 (tp) REVERT: A 171 LEU cc_start: 0.7722 (mm) cc_final: 0.7484 (mm) REVERT: A 188 GLU cc_start: 0.8825 (mp0) cc_final: 0.8514 (mp0) REVERT: A 217 GLU cc_start: 0.8610 (pm20) cc_final: 0.8252 (pm20) REVERT: A 221 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8325 (mt-10) REVERT: A 232 SER cc_start: 0.8164 (m) cc_final: 0.7734 (t) REVERT: A 267 TYR cc_start: 0.8700 (t80) cc_final: 0.8229 (t80) REVERT: A 268 GLU cc_start: 0.8882 (mp0) cc_final: 0.8516 (mp0) REVERT: A 272 MET cc_start: 0.8989 (mpp) cc_final: 0.8530 (mtp) REVERT: A 275 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8496 (mt-10) REVERT: A 300 LYS cc_start: 0.9206 (pttm) cc_final: 0.8960 (ptpp) REVERT: A 329 LEU cc_start: 0.9250 (tp) cc_final: 0.9005 (tp) REVERT: A 503 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8590 (mt-10) REVERT: A 541 THR cc_start: 0.8211 (m) cc_final: 0.7836 (p) REVERT: A 575 ASP cc_start: 0.8458 (m-30) cc_final: 0.8200 (m-30) REVERT: A 631 ILE cc_start: 0.8146 (pt) cc_final: 0.7650 (mp) REVERT: A 648 HIS cc_start: 0.7065 (t-90) cc_final: 0.6698 (t-90) REVERT: A 698 CYS cc_start: 0.9114 (t) cc_final: 0.8611 (m) REVERT: A 761 TYR cc_start: 0.8446 (t80) cc_final: 0.8187 (t80) REVERT: A 800 ARG cc_start: 0.8630 (mmt90) cc_final: 0.8022 (mmt180) REVERT: A 815 HIS cc_start: 0.7517 (p90) cc_final: 0.7197 (p90) REVERT: A 827 ILE cc_start: 0.8957 (mp) cc_final: 0.8722 (mp) REVERT: A 828 SER cc_start: 0.7908 (m) cc_final: 0.7472 (t) REVERT: A 842 MET cc_start: 0.8951 (tpp) cc_final: 0.8451 (tpp) REVERT: A 849 LEU cc_start: 0.8933 (tp) cc_final: 0.8711 (tp) REVERT: A 851 GLN cc_start: 0.9018 (tt0) cc_final: 0.8517 (tt0) REVERT: A 853 ILE cc_start: 0.8983 (mt) cc_final: 0.8691 (mt) REVERT: A 891 ASP cc_start: 0.8576 (t0) cc_final: 0.8232 (m-30) REVERT: A 901 GLU cc_start: 0.8649 (tm-30) cc_final: 0.8309 (tm-30) REVERT: A 902 LYS cc_start: 0.9051 (ptmm) cc_final: 0.8711 (ptmm) REVERT: A 916 LYS cc_start: 0.9542 (tmtt) cc_final: 0.9268 (tptp) REVERT: A 973 LYS cc_start: 0.9247 (mmmt) cc_final: 0.8842 (mmmt) REVERT: A 992 HIS cc_start: 0.8251 (m-70) cc_final: 0.7940 (m-70) REVERT: A 1041 HIS cc_start: 0.8040 (t-90) cc_final: 0.7681 (t-90) REVERT: A 1069 GLU cc_start: 0.8534 (tm-30) cc_final: 0.7894 (tm-30) REVERT: A 1310 PHE cc_start: 0.6847 (m-80) cc_final: 0.6595 (m-10) REVERT: A 1313 GLU cc_start: 0.7839 (mp0) cc_final: 0.7295 (mp0) REVERT: A 1346 MET cc_start: 0.8898 (mtp) cc_final: 0.8493 (mtp) REVERT: A 1350 LYS cc_start: 0.8973 (mmmm) cc_final: 0.8692 (tppt) REVERT: A 1545 HIS cc_start: 0.8488 (m-70) cc_final: 0.8183 (m-70) REVERT: A 1572 GLU cc_start: 0.8868 (mp0) cc_final: 0.8631 (mp0) REVERT: A 1661 GLU cc_start: 0.8188 (mp0) cc_final: 0.7505 (mp0) REVERT: A 1664 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8223 (mt-10) REVERT: A 1674 LYS cc_start: 0.9138 (mmtp) cc_final: 0.8720 (mmpt) REVERT: A 1696 GLN cc_start: 0.8384 (mt0) cc_final: 0.7903 (mm110) REVERT: A 1701 LEU cc_start: 0.8106 (tp) cc_final: 0.7830 (tp) REVERT: A 1716 GLU cc_start: 0.8326 (mt-10) cc_final: 0.8063 (tm-30) REVERT: A 1748 TYR cc_start: 0.8329 (m-10) cc_final: 0.8000 (m-10) REVERT: A 1759 LEU cc_start: 0.9155 (tp) cc_final: 0.8805 (tp) REVERT: A 1772 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7815 (tp30) REVERT: A 1802 MET cc_start: 0.8405 (mmp) cc_final: 0.8157 (mmp) REVERT: A 1833 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8546 (tm-30) REVERT: A 1850 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8212 (tm-30) REVERT: A 1854 MET cc_start: 0.8917 (tpt) cc_final: 0.8682 (tpt) REVERT: A 1895 LYS cc_start: 0.8690 (tttt) cc_final: 0.8412 (mtmm) outliers start: 0 outliers final: 0 residues processed: 406 average time/residue: 0.2891 time to fit residues: 159.0727 Evaluate side-chains 389 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 115 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 127 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 62 optimal weight: 0.1980 chunk 15 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.122992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.095447 restraints weight = 70694.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.101561 restraints weight = 31368.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.105760 restraints weight = 17354.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.108476 restraints weight = 10830.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.110310 restraints weight = 7491.712| |-----------------------------------------------------------------------------| r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7033 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11753 Z= 0.110 Angle : 0.515 5.591 16181 Z= 0.268 Chirality : 0.037 0.160 1891 Planarity : 0.004 0.039 1854 Dihedral : 9.940 90.980 2057 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: 0.55 (0.24), residues: 1261 helix: 1.26 (0.20), residues: 635 sheet: -0.65 (0.41), residues: 168 loop : -0.38 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 788 TYR 0.011 0.001 TYR A1746 PHE 0.021 0.001 PHE A 142 TRP 0.036 0.002 TRP A 138 HIS 0.004 0.001 HIS A 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (11753) covalent geometry : angle 0.51479 / 0.27 (16181) hydrogen bonds : bond 0.04455 / 3.13 ( 564) hydrogen bonds : angle 4.45627 / 3.20 ( 1575) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue ALA 1807 is missing expected H atoms. Skipping. Evaluate side-chains 402 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8732 (mt) cc_final: 0.8521 (mt) REVERT: A 52 LEU cc_start: 0.8863 (tp) cc_final: 0.8260 (tp) REVERT: A 56 LEU cc_start: 0.8673 (mt) cc_final: 0.8413 (mt) REVERT: A 76 LEU cc_start: 0.8713 (tp) cc_final: 0.8413 (tp) REVERT: A 80 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8003 (mm-30) REVERT: A 94 LYS cc_start: 0.7579 (tttt) cc_final: 0.7326 (tttm) REVERT: A 114 ARG cc_start: 0.8968 (ttm110) cc_final: 0.8653 (ttm110) REVERT: A 141 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8115 (mm-30) REVERT: A 153 TYR cc_start: 0.8571 (m-10) cc_final: 0.8223 (m-10) REVERT: A 160 LYS cc_start: 0.9047 (pttp) cc_final: 0.8816 (ptmm) REVERT: A 164 LEU cc_start: 0.8627 (tp) cc_final: 0.8406 (tp) REVERT: A 171 LEU cc_start: 0.7731 (mm) cc_final: 0.7492 (mm) REVERT: A 182 LEU cc_start: 0.8985 (tp) cc_final: 0.8736 (tt) REVERT: A 188 GLU cc_start: 0.8831 (mp0) cc_final: 0.8520 (mp0) REVERT: A 217 GLU cc_start: 0.8605 (pm20) cc_final: 0.8241 (pm20) REVERT: A 221 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8312 (mt-10) REVERT: A 232 SER cc_start: 0.8179 (m) cc_final: 0.7688 (t) REVERT: A 267 TYR cc_start: 0.8702 (t80) cc_final: 0.8099 (t80) REVERT: A 272 MET cc_start: 0.8968 (mpp) cc_final: 0.8525 (mtp) REVERT: A 275 GLU cc_start: 0.8827 (mt-10) cc_final: 0.8471 (mt-10) REVERT: A 300 LYS cc_start: 0.9180 (pttm) cc_final: 0.8934 (ptpp) REVERT: A 329 LEU cc_start: 0.9261 (tp) cc_final: 0.9029 (tp) REVERT: A 346 LEU cc_start: 0.9109 (mt) cc_final: 0.8897 (mt) REVERT: A 503 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8576 (mt-10) REVERT: A 541 THR cc_start: 0.8167 (m) cc_final: 0.7806 (p) REVERT: A 631 ILE cc_start: 0.8131 (pt) cc_final: 0.7642 (mp) REVERT: A 646 PHE cc_start: 0.8760 (m-80) cc_final: 0.8513 (m-80) REVERT: A 648 HIS cc_start: 0.7069 (t-90) cc_final: 0.6694 (t-90) REVERT: A 698 CYS cc_start: 0.9096 (t) cc_final: 0.8548 (m) REVERT: A 761 TYR cc_start: 0.8435 (t80) cc_final: 0.8184 (t80) REVERT: A 800 ARG cc_start: 0.8629 (mmt90) cc_final: 0.8007 (mmt180) REVERT: A 815 HIS cc_start: 0.7454 (p90) cc_final: 0.7111 (p90) REVERT: A 828 SER cc_start: 0.7823 (m) cc_final: 0.7347 (p) REVERT: A 830 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7551 (tm-30) REVERT: A 842 MET cc_start: 0.8961 (tpp) cc_final: 0.8509 (tpp) REVERT: A 849 LEU cc_start: 0.8901 (tp) cc_final: 0.8678 (tp) REVERT: A 851 GLN cc_start: 0.9003 (tt0) cc_final: 0.8487 (tt0) REVERT: A 891 ASP cc_start: 0.8619 (t0) cc_final: 0.8244 (m-30) REVERT: A 894 PHE cc_start: 0.7962 (m-10) cc_final: 0.7743 (m-10) REVERT: A 901 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8276 (tm-30) REVERT: A 902 LYS cc_start: 0.9022 (ptmm) cc_final: 0.8692 (ptmm) REVERT: A 916 LYS cc_start: 0.9552 (tmtt) cc_final: 0.9273 (tptp) REVERT: A 973 LYS cc_start: 0.9196 (mmmt) cc_final: 0.8758 (mmmt) REVERT: A 992 HIS cc_start: 0.8244 (m-70) cc_final: 0.7934 (m-70) REVERT: A 1041 HIS cc_start: 0.7944 (t-90) cc_final: 0.7637 (t-90) REVERT: A 1069 GLU cc_start: 0.8524 (tm-30) cc_final: 0.7993 (tm-30) REVERT: A 1310 PHE cc_start: 0.6820 (m-80) cc_final: 0.6601 (m-10) REVERT: A 1313 GLU cc_start: 0.7732 (mp0) cc_final: 0.7202 (mp0) REVERT: A 1339 HIS cc_start: 0.8390 (p90) cc_final: 0.7964 (p90) REVERT: A 1346 MET cc_start: 0.8911 (mtp) cc_final: 0.8515 (mtp) REVERT: A 1350 LYS cc_start: 0.8968 (mmmm) cc_final: 0.8685 (tppt) REVERT: A 1545 HIS cc_start: 0.8480 (m-70) cc_final: 0.8259 (m-70) REVERT: A 1572 GLU cc_start: 0.8878 (mp0) cc_final: 0.8659 (mp0) REVERT: A 1664 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8170 (mt-10) REVERT: A 1674 LYS cc_start: 0.9115 (mmtp) cc_final: 0.8721 (mmpt) REVERT: A 1688 TYR cc_start: 0.7660 (m-10) cc_final: 0.7324 (m-10) REVERT: A 1696 GLN cc_start: 0.8363 (mt0) cc_final: 0.7854 (mm110) REVERT: A 1701 LEU cc_start: 0.8074 (tp) cc_final: 0.7776 (tp) REVERT: A 1716 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7955 (tm-30) REVERT: A 1748 TYR cc_start: 0.8302 (m-10) cc_final: 0.7981 (m-10) REVERT: A 1759 LEU cc_start: 0.9153 (tp) cc_final: 0.8746 (tp) REVERT: A 1772 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7754 (tp30) REVERT: A 1802 MET cc_start: 0.8381 (mmp) cc_final: 0.8173 (mmp) REVERT: A 1833 GLN cc_start: 0.8822 (tm-30) cc_final: 0.8514 (tm-30) REVERT: A 1850 GLU cc_start: 0.8611 (tm-30) cc_final: 0.8172 (tm-30) REVERT: A 1854 MET cc_start: 0.8886 (tpt) cc_final: 0.8645 (tpp) REVERT: A 1895 LYS cc_start: 0.8671 (tttt) cc_final: 0.8370 (mtmm) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.2895 time to fit residues: 156.2750 Evaluate side-chains 388 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 388 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 54 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 120 optimal weight: 0.0970 chunk 83 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 72 optimal weight: 0.3980 chunk 76 optimal weight: 0.6980 chunk 111 optimal weight: 0.5980 chunk 98 optimal weight: 0.0670 chunk 40 optimal weight: 5.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.123991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.096389 restraints weight = 70018.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.102568 restraints weight = 31112.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.106742 restraints weight = 17167.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.109495 restraints weight = 10748.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.111329 restraints weight = 7392.489| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7007 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11753 Z= 0.102 Angle : 0.509 5.431 16181 Z= 0.264 Chirality : 0.037 0.160 1891 Planarity : 0.004 0.044 1854 Dihedral : 9.732 90.120 2057 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: 0.83 (0.24), residues: 1261 helix: 1.47 (0.20), residues: 634 sheet: -0.65 (0.41), residues: 168 loop : -0.14 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1071 TYR 0.010 0.001 TYR A1751 PHE 0.029 0.001 PHE A1671 TRP 0.031 0.002 TRP A 138 HIS 0.004 0.001 HIS A 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.10 (11753) covalent geometry : angle 0.50931 / 0.26 (16181) hydrogen bonds : bond 0.04260 / 3.00 ( 564) hydrogen bonds : angle 4.32436 / 3.10 ( 1575) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue ALA 1807 is missing expected H atoms. Skipping. Evaluate side-chains 398 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 398 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8842 (tp) cc_final: 0.8260 (tp) REVERT: A 56 LEU cc_start: 0.8675 (mt) cc_final: 0.8207 (mt) REVERT: A 76 LEU cc_start: 0.8657 (tp) cc_final: 0.8456 (tp) REVERT: A 80 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8069 (mm-30) REVERT: A 94 LYS cc_start: 0.7572 (tttt) cc_final: 0.7305 (tttm) REVERT: A 141 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8092 (mm-30) REVERT: A 153 TYR cc_start: 0.8531 (m-10) cc_final: 0.8179 (m-10) REVERT: A 164 LEU cc_start: 0.8550 (tp) cc_final: 0.8347 (tp) REVERT: A 171 LEU cc_start: 0.7739 (mm) cc_final: 0.7512 (mm) REVERT: A 188 GLU cc_start: 0.8830 (mp0) cc_final: 0.8565 (mp0) REVERT: A 217 GLU cc_start: 0.8600 (pm20) cc_final: 0.8251 (pm20) REVERT: A 221 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8292 (mt-10) REVERT: A 232 SER cc_start: 0.8153 (m) cc_final: 0.7679 (t) REVERT: A 267 TYR cc_start: 0.8652 (t80) cc_final: 0.8003 (t80) REVERT: A 268 GLU cc_start: 0.8840 (mp0) cc_final: 0.8487 (mp0) REVERT: A 272 MET cc_start: 0.8964 (mpp) cc_final: 0.8476 (mtp) REVERT: A 275 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8440 (mt-10) REVERT: A 300 LYS cc_start: 0.9179 (pttm) cc_final: 0.8917 (ptpp) REVERT: A 307 ARG cc_start: 0.9082 (ptp-110) cc_final: 0.8817 (ptp90) REVERT: A 329 LEU cc_start: 0.9262 (tp) cc_final: 0.9031 (tp) REVERT: A 346 LEU cc_start: 0.9102 (mt) cc_final: 0.8898 (mt) REVERT: A 354 LYS cc_start: 0.9167 (mmtm) cc_final: 0.8935 (mptt) REVERT: A 503 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8548 (mt-10) REVERT: A 541 THR cc_start: 0.8149 (m) cc_final: 0.7806 (p) REVERT: A 631 ILE cc_start: 0.8117 (pt) cc_final: 0.7621 (mp) REVERT: A 646 PHE cc_start: 0.8721 (m-80) cc_final: 0.8496 (m-80) REVERT: A 648 HIS cc_start: 0.7054 (t-90) cc_final: 0.6682 (t-90) REVERT: A 698 CYS cc_start: 0.9077 (t) cc_final: 0.8559 (m) REVERT: A 747 GLN cc_start: 0.8334 (mp-120) cc_final: 0.8000 (mp-120) REVERT: A 749 TYR cc_start: 0.8158 (m-10) cc_final: 0.7876 (m-10) REVERT: A 761 TYR cc_start: 0.8417 (t80) cc_final: 0.8171 (t80) REVERT: A 779 THR cc_start: 0.8679 (m) cc_final: 0.8269 (m) REVERT: A 800 ARG cc_start: 0.8606 (mmt90) cc_final: 0.7984 (mmt180) REVERT: A 815 HIS cc_start: 0.7381 (p90) cc_final: 0.7016 (p90) REVERT: A 824 GLU cc_start: 0.7545 (tm-30) cc_final: 0.7274 (tm-30) REVERT: A 827 ILE cc_start: 0.8877 (mp) cc_final: 0.8635 (mp) REVERT: A 828 SER cc_start: 0.7820 (m) cc_final: 0.7357 (t) REVERT: A 842 MET cc_start: 0.8921 (tpp) cc_final: 0.8463 (tpp) REVERT: A 849 LEU cc_start: 0.8888 (tp) cc_final: 0.8660 (tp) REVERT: A 851 GLN cc_start: 0.8939 (tt0) cc_final: 0.8434 (tt0) REVERT: A 891 ASP cc_start: 0.8634 (t0) cc_final: 0.8276 (m-30) REVERT: A 894 PHE cc_start: 0.7943 (m-10) cc_final: 0.7730 (m-10) REVERT: A 901 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8248 (tm-30) REVERT: A 902 LYS cc_start: 0.9023 (ptmm) cc_final: 0.8686 (ptmm) REVERT: A 916 LYS cc_start: 0.9537 (tmtt) cc_final: 0.9253 (tptp) REVERT: A 992 HIS cc_start: 0.8219 (m-70) cc_final: 0.7908 (m-70) REVERT: A 1069 GLU cc_start: 0.8536 (tm-30) cc_final: 0.7960 (tm-30) REVERT: A 1071 ARG cc_start: 0.8588 (ttp80) cc_final: 0.8262 (tmm-80) REVERT: A 1313 GLU cc_start: 0.7684 (mp0) cc_final: 0.7187 (mp0) REVERT: A 1346 MET cc_start: 0.8936 (mtp) cc_final: 0.8475 (mtp) REVERT: A 1349 LYS cc_start: 0.8906 (tttt) cc_final: 0.8277 (tmmt) REVERT: A 1350 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8646 (mmmm) REVERT: A 1545 HIS cc_start: 0.8481 (m-70) cc_final: 0.8222 (m-70) REVERT: A 1572 GLU cc_start: 0.8861 (mp0) cc_final: 0.8639 (mp0) REVERT: A 1654 ASN cc_start: 0.8914 (m-40) cc_final: 0.8654 (m110) REVERT: A 1664 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8146 (mt-10) REVERT: A 1674 LYS cc_start: 0.9101 (mmtp) cc_final: 0.8693 (mmpt) REVERT: A 1696 GLN cc_start: 0.8347 (mt0) cc_final: 0.7831 (mm110) REVERT: A 1701 LEU cc_start: 0.8102 (tp) cc_final: 0.7787 (tp) REVERT: A 1710 ILE cc_start: 0.9056 (tp) cc_final: 0.8816 (tp) REVERT: A 1716 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7953 (tm-30) REVERT: A 1748 TYR cc_start: 0.8265 (m-10) cc_final: 0.7907 (m-10) REVERT: A 1759 LEU cc_start: 0.9139 (tp) cc_final: 0.8718 (tp) REVERT: A 1772 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7698 (tp30) REVERT: A 1815 MET cc_start: 0.8261 (tpt) cc_final: 0.8023 (tpt) REVERT: A 1833 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8485 (tm-30) REVERT: A 1850 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8179 (tm-30) REVERT: A 1851 LEU cc_start: 0.8615 (mm) cc_final: 0.8284 (mm) REVERT: A 1854 MET cc_start: 0.8885 (tpt) cc_final: 0.8648 (tpp) REVERT: A 1895 LYS cc_start: 0.8692 (tttt) cc_final: 0.8392 (mtmm) outliers start: 0 outliers final: 0 residues processed: 398 average time/residue: 0.2642 time to fit residues: 142.1956 Evaluate side-chains 381 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 101 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 58 optimal weight: 0.0770 chunk 26 optimal weight: 0.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- 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 = 0.3859 r_free = 0.3859 target = 0.119568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.092401 restraints weight = 71833.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.098442 restraints weight = 31930.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.102512 restraints weight = 17632.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.105197 restraints weight = 11065.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.106989 restraints weight = 7660.042| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 11753 Z= 0.201 Angle : 0.554 5.958 16181 Z= 0.302 Chirality : 0.038 0.153 1891 Planarity : 0.005 0.046 1854 Dihedral : 10.027 89.499 2057 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: 0.35 (0.24), residues: 1261 helix: 1.09 (0.20), residues: 635 sheet: -0.75 (0.40), residues: 168 loop : -0.46 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1003 TYR 0.012 0.001 TYR A 47 PHE 0.027 0.002 PHE A1671 TRP 0.029 0.003 TRP A 138 HIS 0.005 0.001 HIS A1713 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.20 (11753) covalent geometry : angle 0.55359 / 0.30 (16181) hydrogen bonds : bond 0.04832 / 3.35 ( 564) hydrogen bonds : angle 4.75899 / 3.42 ( 1575) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue ALA 1807 is missing expected H atoms. Skipping. Evaluate side-chains 400 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8902 (tp) cc_final: 0.8290 (tp) REVERT: A 56 LEU cc_start: 0.8785 (mt) cc_final: 0.8455 (mt) REVERT: A 76 LEU cc_start: 0.8731 (tp) cc_final: 0.8486 (tp) REVERT: A 80 GLU cc_start: 0.8507 (mm-30) cc_final: 0.8033 (mm-30) REVERT: A 98 PHE cc_start: 0.8678 (m-80) cc_final: 0.8368 (m-10) REVERT: A 120 LYS cc_start: 0.8440 (ptpp) cc_final: 0.8058 (ptpp) REVERT: A 141 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8164 (mm-30) REVERT: A 153 TYR cc_start: 0.8581 (m-10) cc_final: 0.8226 (m-10) REVERT: A 171 LEU cc_start: 0.7748 (mm) cc_final: 0.7495 (mm) REVERT: A 188 GLU cc_start: 0.8835 (mp0) cc_final: 0.8530 (mp0) REVERT: A 217 GLU cc_start: 0.8618 (pm20) cc_final: 0.8295 (pm20) REVERT: A 221 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8345 (mt-10) REVERT: A 231 ARG cc_start: 0.8890 (ttm170) cc_final: 0.8531 (ptp-170) REVERT: A 232 SER cc_start: 0.8197 (m) cc_final: 0.7641 (t) REVERT: A 267 TYR cc_start: 0.8744 (t80) cc_final: 0.8269 (t80) REVERT: A 268 GLU cc_start: 0.8919 (mp0) cc_final: 0.8544 (mp0) REVERT: A 275 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8561 (mt-10) REVERT: A 329 LEU cc_start: 0.9256 (tp) cc_final: 0.9025 (tp) REVERT: A 354 LYS cc_start: 0.9201 (mmtm) cc_final: 0.8993 (mptt) REVERT: A 503 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8588 (mt-10) REVERT: A 541 THR cc_start: 0.8198 (m) cc_final: 0.7816 (p) REVERT: A 631 ILE cc_start: 0.8170 (pt) cc_final: 0.7669 (mp) REVERT: A 648 HIS cc_start: 0.7047 (t-90) cc_final: 0.6695 (t-90) REVERT: A 698 CYS cc_start: 0.9108 (t) cc_final: 0.8564 (m) REVERT: A 747 GLN cc_start: 0.8355 (mp-120) cc_final: 0.8118 (mp-120) REVERT: A 749 TYR cc_start: 0.8191 (m-10) cc_final: 0.7906 (m-10) REVERT: A 761 TYR cc_start: 0.8446 (t80) cc_final: 0.8185 (t80) REVERT: A 800 ARG cc_start: 0.8670 (mmt90) cc_final: 0.7986 (mmt180) REVERT: A 815 HIS cc_start: 0.7476 (p90) cc_final: 0.7143 (p90) REVERT: A 827 ILE cc_start: 0.8847 (mp) cc_final: 0.8598 (mp) REVERT: A 828 SER cc_start: 0.7856 (m) cc_final: 0.7416 (t) REVERT: A 842 MET cc_start: 0.8972 (tpp) cc_final: 0.8513 (tpp) REVERT: A 851 GLN cc_start: 0.9027 (tt0) cc_final: 0.8549 (tt0) REVERT: A 891 ASP cc_start: 0.8649 (t0) cc_final: 0.8278 (m-30) REVERT: A 901 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8384 (tm-30) REVERT: A 902 LYS cc_start: 0.9040 (ptmm) cc_final: 0.8716 (ptmm) REVERT: A 916 LYS cc_start: 0.9548 (tmtt) cc_final: 0.9276 (tptp) REVERT: A 960 PHE cc_start: 0.6787 (t80) cc_final: 0.6548 (t80) REVERT: A 992 HIS cc_start: 0.8247 (m-70) cc_final: 0.7929 (m-70) REVERT: A 1001 THR cc_start: 0.8691 (p) cc_final: 0.8301 (m) REVERT: A 1041 HIS cc_start: 0.8027 (t-90) cc_final: 0.7634 (t-90) REVERT: A 1069 GLU cc_start: 0.8588 (tm-30) cc_final: 0.7978 (tm-30) REVERT: A 1299 GLN cc_start: 0.8721 (mm110) cc_final: 0.8122 (mm110) REVERT: A 1313 GLU cc_start: 0.7838 (mp0) cc_final: 0.7316 (mp0) REVERT: A 1346 MET cc_start: 0.8945 (mtp) cc_final: 0.8485 (mtp) REVERT: A 1349 LYS cc_start: 0.8955 (tttt) cc_final: 0.8355 (tmmt) REVERT: A 1350 LYS cc_start: 0.9014 (mmmm) cc_final: 0.8741 (mmmm) REVERT: A 1545 HIS cc_start: 0.8458 (m-70) cc_final: 0.8205 (m-70) REVERT: A 1572 GLU cc_start: 0.8917 (mp0) cc_final: 0.8685 (mp0) REVERT: A 1664 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8202 (mt-10) REVERT: A 1674 LYS cc_start: 0.9135 (mmtp) cc_final: 0.8749 (mmpt) REVERT: A 1679 GLN cc_start: 0.7952 (mm-40) cc_final: 0.7373 (tp-100) REVERT: A 1688 TYR cc_start: 0.7746 (m-10) cc_final: 0.7499 (m-10) REVERT: A 1701 LEU cc_start: 0.8179 (tp) cc_final: 0.7881 (tp) REVERT: A 1716 GLU cc_start: 0.8310 (mt-10) cc_final: 0.8011 (tm-30) REVERT: A 1748 TYR cc_start: 0.8264 (m-10) cc_final: 0.7975 (m-10) REVERT: A 1772 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7799 (tp30) REVERT: A 1802 MET cc_start: 0.8409 (mmp) cc_final: 0.8166 (mmp) REVERT: A 1815 MET cc_start: 0.8320 (tpt) cc_final: 0.8056 (tpt) REVERT: A 1833 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8525 (tm-30) REVERT: A 1843 VAL cc_start: 0.8125 (p) cc_final: 0.7759 (p) REVERT: A 1850 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8244 (tm-30) REVERT: A 1851 LEU cc_start: 0.8666 (mm) cc_final: 0.8308 (mm) REVERT: A 1854 MET cc_start: 0.8884 (tpt) cc_final: 0.8626 (tpp) REVERT: A 1895 LYS cc_start: 0.8699 (tttt) cc_final: 0.8432 (mtmm) outliers start: 0 outliers final: 0 residues processed: 400 average time/residue: 0.2834 time to fit residues: 153.9785 Evaluate side-chains 389 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 389 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 101 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 114 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.3889 r_free = 0.3889 target = 0.121922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.094355 restraints weight = 70699.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.100503 restraints weight = 31505.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.104643 restraints weight = 17436.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.107396 restraints weight = 10935.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.109231 restraints weight = 7548.974| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11753 Z= 0.124 Angle : 0.524 5.733 16181 Z= 0.275 Chirality : 0.038 0.158 1891 Planarity : 0.004 0.040 1854 Dihedral : 9.898 89.357 2057 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.24), residues: 1261 helix: 1.26 (0.20), residues: 633 sheet: -0.73 (0.40), residues: 168 loop : -0.31 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1071 TYR 0.010 0.001 TYR A 819 PHE 0.028 0.001 PHE A1671 TRP 0.026 0.002 TRP A 138 HIS 0.004 0.001 HIS A 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (11753) covalent geometry : angle 0.52364 / 0.27 (16181) hydrogen bonds : bond 0.04360 / 3.08 ( 564) hydrogen bonds : angle 4.47900 / 3.20 ( 1575) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 160 is missing expected H atoms. Skipping. Residue TYR 246 is missing expected H atoms. Skipping. Residue THR 247 is missing expected H atoms. Skipping. Residue SER 248 is missing expected H atoms. Skipping. Residue ALA 1807 is missing expected H atoms. Skipping. Evaluate side-chains 405 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.8446 (mm-30) cc_final: 0.7958 (mm-30) REVERT: A 98 PHE cc_start: 0.8666 (m-80) cc_final: 0.8327 (m-10) REVERT: A 120 LYS cc_start: 0.8432 (ptpp) cc_final: 0.8059 (ptpp) REVERT: A 141 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8091 (mm-30) REVERT: A 153 TYR cc_start: 0.8568 (m-10) cc_final: 0.8217 (m-10) REVERT: A 171 LEU cc_start: 0.7760 (mm) cc_final: 0.7501 (mm) REVERT: A 188 GLU cc_start: 0.8834 (mp0) cc_final: 0.8495 (mp0) REVERT: A 217 GLU cc_start: 0.8597 (pm20) cc_final: 0.8247 (pm20) REVERT: A 221 GLU cc_start: 0.8830 (mt-10) cc_final: 0.8328 (mt-10) REVERT: A 232 SER cc_start: 0.8160 (m) cc_final: 0.7698 (t) REVERT: A 267 TYR cc_start: 0.8712 (t80) cc_final: 0.8230 (t80) REVERT: A 268 GLU cc_start: 0.8887 (mp0) cc_final: 0.8532 (mp0) REVERT: A 269 ARG cc_start: 0.9272 (tpm170) cc_final: 0.9044 (mmm160) REVERT: A 300 LYS cc_start: 0.9215 (pttm) cc_final: 0.8947 (ptpp) REVERT: A 319 ASP cc_start: 0.8621 (m-30) cc_final: 0.8401 (m-30) REVERT: A 329 LEU cc_start: 0.9275 (tp) cc_final: 0.9046 (tp) REVERT: A 503 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8561 (mt-10) REVERT: A 541 THR cc_start: 0.8171 (m) cc_final: 0.7805 (p) REVERT: A 631 ILE cc_start: 0.8139 (pt) cc_final: 0.7606 (mp) REVERT: A 648 HIS cc_start: 0.7037 (t-90) cc_final: 0.6667 (t-90) REVERT: A 698 CYS cc_start: 0.9072 (t) cc_final: 0.8553 (m) REVERT: A 747 GLN cc_start: 0.8363 (mp-120) cc_final: 0.8051 (mp-120) REVERT: A 749 TYR cc_start: 0.8163 (m-10) cc_final: 0.7892 (m-10) REVERT: A 761 TYR cc_start: 0.8427 (t80) cc_final: 0.8170 (t80) REVERT: A 779 THR cc_start: 0.8691 (m) cc_final: 0.8274 (m) REVERT: A 800 ARG cc_start: 0.8649 (mmt90) cc_final: 0.7973 (mmt180) REVERT: A 815 HIS cc_start: 0.7414 (p90) cc_final: 0.7054 (p90) REVERT: A 824 GLU cc_start: 0.7526 (tm-30) cc_final: 0.7257 (tm-30) REVERT: A 827 ILE cc_start: 0.8809 (mp) cc_final: 0.8578 (mp) REVERT: A 828 SER cc_start: 0.7839 (m) cc_final: 0.7357 (p) REVERT: A 830 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7483 (tm-30) REVERT: A 842 MET cc_start: 0.8977 (tpp) cc_final: 0.8550 (tpp) REVERT: A 851 GLN cc_start: 0.8983 (tt0) cc_final: 0.8491 (tt0) REVERT: A 891 ASP cc_start: 0.8646 (t0) cc_final: 0.8282 (m-30) REVERT: A 894 PHE cc_start: 0.7895 (m-10) cc_final: 0.7683 (m-10) REVERT: A 901 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8343 (tm-30) REVERT: A 902 LYS cc_start: 0.9009 (ptmm) cc_final: 0.8689 (ptmm) REVERT: A 916 LYS cc_start: 0.9542 (tmtt) cc_final: 0.9264 (tptp) REVERT: A 992 HIS cc_start: 0.8228 (m-70) cc_final: 0.7889 (m-70) REVERT: A 1001 THR cc_start: 0.8679 (p) cc_final: 0.8262 (m) REVERT: A 1069 GLU cc_start: 0.8543 (tm-30) cc_final: 0.7913 (tm-30) REVERT: A 1071 ARG cc_start: 0.8656 (ttp80) cc_final: 0.8155 (tmm-80) REVERT: A 1298 LEU cc_start: 0.8720 (tp) cc_final: 0.8519 (tp) REVERT: A 1313 GLU cc_start: 0.7751 (mp0) cc_final: 0.7229 (mp0) REVERT: A 1342 ARG cc_start: 0.8687 (mmm160) cc_final: 0.8411 (mmm-85) REVERT: A 1346 MET cc_start: 0.8932 (mtp) cc_final: 0.8448 (mtp) REVERT: A 1349 LYS cc_start: 0.8933 (tttt) cc_final: 0.8312 (tmmt) REVERT: A 1350 LYS cc_start: 0.8984 (mmmm) cc_final: 0.8712 (mmmm) REVERT: A 1545 HIS cc_start: 0.8452 (m-70) cc_final: 0.8190 (m-70) REVERT: A 1572 GLU cc_start: 0.8890 (mp0) cc_final: 0.8665 (mp0) REVERT: A 1664 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8260 (mt-10) REVERT: A 1674 LYS cc_start: 0.9108 (mmtp) cc_final: 0.8577 (mmpt) REVERT: A 1696 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7514 (mm110) REVERT: A 1701 LEU cc_start: 0.8117 (tp) cc_final: 0.7805 (tp) REVERT: A 1710 ILE cc_start: 0.9068 (tp) cc_final: 0.8812 (tp) REVERT: A 1716 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7954 (tm-30) REVERT: A 1748 TYR cc_start: 0.8255 (m-10) cc_final: 0.7979 (m-10) REVERT: A 1772 GLU cc_start: 0.8268 (mt-10) cc_final: 0.7738 (tp30) REVERT: A 1802 MET cc_start: 0.8353 (mmp) cc_final: 0.8136 (mmp) REVERT: A 1815 MET cc_start: 0.8283 (tpt) cc_final: 0.8001 (tpt) REVERT: A 1832 MET cc_start: 0.8972 (mtp) cc_final: 0.8664 (mtp) REVERT: A 1833 GLN cc_start: 0.8816 (tm-30) cc_final: 0.8505 (tm-30) REVERT: A 1843 VAL cc_start: 0.8237 (p) cc_final: 0.7926 (p) REVERT: A 1850 GLU cc_start: 0.8655 (tm-30) cc_final: 0.8230 (tm-30) REVERT: A 1851 LEU cc_start: 0.8656 (mm) cc_final: 0.8277 (mm) REVERT: A 1854 MET cc_start: 0.8868 (tpt) cc_final: 0.8613 (tpp) REVERT: A 1895 LYS cc_start: 0.8666 (tttt) cc_final: 0.8381 (mtmm) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.2702 time to fit residues: 148.0215 Evaluate side-chains 390 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 73 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 107 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 70 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 77 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A1299 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 = 0.3882 r_free = 0.3882 target = 0.121321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.093952 restraints weight = 70813.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.100068 restraints weight = 31556.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.104146 restraints weight = 17417.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.106834 restraints weight = 10948.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.108643 restraints weight = 7579.903| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11753 Z= 0.135 Angle : 0.524 5.703 16181 Z= 0.277 Chirality : 0.038 0.158 1891 Planarity : 0.004 0.060 1854 Dihedral : 9.883 88.859 2057 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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: 0.58 (0.24), residues: 1261 helix: 1.26 (0.20), residues: 633 sheet: -0.71 (0.41), residues: 163 loop : -0.30 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 758 TYR 0.016 0.001 TYR A1688 PHE 0.025 0.001 PHE A1671 TRP 0.027 0.002 TRP A 138 HIS 0.004 0.001 HIS A1687 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.14 (11753) covalent geometry : angle 0.52408 / 0.28 (16181) hydrogen bonds : bond 0.04423 / 3.11 ( 564) hydrogen bonds : angle 4.49834 / 3.22 ( 1575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4615.98 seconds wall clock time: 79 minutes 20.56 seconds (4760.56 seconds total)