Starting phenix.real_space_refine on Fri Feb 6 04:27:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yym_14383/02_2026/7yym_14383.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yym_14383/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yym_14383/02_2026/7yym_14383.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yym_14383/02_2026/7yym_14383.map" model { file = "/net/cci-nas-00/data/ceres_data/7yym_14383/02_2026/7yym_14383.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yym_14383/02_2026/7yym_14383.cif" } 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-2.0-5952/lib/python3.9/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: 16 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: 3.99, per 1000 atoms: 0.18 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: 1.89 Conformation dependent library (CDL) restraints added in 702.3 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: 4.16 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: 5.84 Time building geometry restraints manager: 2.65 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: 10461 35.83 - 71.65: 308 71.65 - 107.48: 19 107.48 - 143.30: 0 143.30 - 179.13: 8 Dihedral angle restraints: 10796 sinusoidal: 6381 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 10793 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: 4.480 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: 0.140 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 25.490 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 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 : 15.157 101.222 4817 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 covalent geometry : bond 0.00385 (11753) covalent geometry : angle 0.79809 (16181) hydrogen bonds : bond 0.10748 ( 564) hydrogen bonds : angle 5.21471 ( 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 : 0.537 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: 0.2936 time to fit residues: 166.0758 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 : 0.531 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3903 r_free = 0.3903 target = 0.123220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.095221 restraints weight = 70247.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.101382 restraints weight = 31462.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.105554 restraints weight = 17455.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.108337 restraints weight = 10966.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.110194 restraints weight = 7596.879| |-----------------------------------------------------------------------------| r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11753 Z= 0.199 Angle : 0.587 7.009 16181 Z= 0.319 Chirality : 0.039 0.144 1891 Planarity : 0.005 0.044 1854 Dihedral : 15.478 95.959 2263 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % 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: 0.66 (0.24), residues: 1261 helix: 1.22 (0.20), residues: 639 sheet: -0.34 (0.41), residues: 158 loop : -0.23 (0.30), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 790 TYR 0.013 0.001 TYR A1746 PHE 0.027 0.002 PHE A1671 TRP 0.022 0.003 TRP A 138 HIS 0.006 0.001 HIS A1749 Details of bonding type rmsd covalent geometry : bond 0.00357 (11753) covalent geometry : angle 0.58670 (16181) hydrogen bonds : bond 0.05556 ( 564) hydrogen bonds : angle 4.96989 ( 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 410 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 410 time to evaluate : 0.517 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 52 LEU cc_start: 0.8933 (tp) cc_final: 0.8433 (tp) REVERT: A 56 LEU cc_start: 0.8773 (mt) cc_final: 0.8424 (mt) REVERT: A 75 VAL cc_start: 0.8904 (m) cc_final: 0.8675 (m) REVERT: A 79 LYS cc_start: 0.8923 (mttm) cc_final: 0.8451 (mttm) REVERT: A 105 GLN cc_start: 0.8572 (mp10) cc_final: 0.8275 (mp10) REVERT: A 114 ARG cc_start: 0.8941 (ttm110) cc_final: 0.8612 (ttm110) REVERT: A 120 LYS cc_start: 0.8606 (ptpp) cc_final: 0.8264 (ptpp) REVERT: A 141 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8334 (mm-30) REVERT: A 153 TYR cc_start: 0.8538 (m-10) cc_final: 0.8183 (m-10) REVERT: A 171 LEU cc_start: 0.7720 (mm) cc_final: 0.7441 (mm) REVERT: A 221 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8329 (mt-10) REVERT: A 231 ARG cc_start: 0.8897 (tmm-80) cc_final: 0.8254 (ptm-80) REVERT: A 267 TYR cc_start: 0.8689 (t80) cc_final: 0.8142 (t80) REVERT: A 275 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8545 (mt-10) REVERT: A 319 ASP cc_start: 0.8579 (m-30) cc_final: 0.8372 (m-30) REVERT: A 329 LEU cc_start: 0.9234 (tp) cc_final: 0.8981 (tp) REVERT: A 379 LYS cc_start: 0.9376 (mmtm) cc_final: 0.9168 (mmtm) REVERT: A 502 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8565 (mm-30) REVERT: A 503 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8639 (mt-10) REVERT: A 541 THR cc_start: 0.8171 (m) cc_final: 0.7819 (p) REVERT: A 631 ILE cc_start: 0.8123 (pt) cc_final: 0.7595 (mp) REVERT: A 634 ILE cc_start: 0.9043 (mm) cc_final: 0.8799 (mm) REVERT: A 646 PHE cc_start: 0.8707 (m-80) cc_final: 0.8503 (m-80) REVERT: A 648 HIS cc_start: 0.7076 (t-90) cc_final: 0.6739 (t-90) REVERT: A 698 CYS cc_start: 0.9194 (t) cc_final: 0.8766 (m) REVERT: A 749 TYR cc_start: 0.7920 (m-10) cc_final: 0.7692 (m-10) REVERT: A 761 TYR cc_start: 0.8457 (t80) cc_final: 0.8230 (t80) REVERT: A 784 GLU cc_start: 0.8851 (pp20) cc_final: 0.8618 (pm20) REVERT: A 815 HIS cc_start: 0.7504 (p90) cc_final: 0.7123 (p90) REVERT: A 842 MET cc_start: 0.9044 (tpp) cc_final: 0.8495 (tpp) REVERT: A 851 GLN cc_start: 0.9034 (tt0) cc_final: 0.8544 (tt0) REVERT: A 894 PHE cc_start: 0.8116 (m-10) cc_final: 0.7851 (m-10) REVERT: A 901 GLU cc_start: 0.8563 (tm-30) cc_final: 0.8195 (tm-30) REVERT: A 916 LYS cc_start: 0.9535 (tmtt) cc_final: 0.9258 (tptp) REVERT: A 970 GLU cc_start: 0.8786 (tt0) cc_final: 0.8475 (mt-10) REVERT: A 992 HIS cc_start: 0.8179 (m-70) cc_final: 0.7839 (m-70) REVERT: A 996 ARG cc_start: 0.7655 (ptp-170) cc_final: 0.7437 (ptp-170) REVERT: A 1069 GLU cc_start: 0.8583 (tm-30) cc_final: 0.7923 (tm-30) REVERT: A 1070 LEU cc_start: 0.9008 (tp) cc_final: 0.8748 (tp) REVERT: A 1340 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7885 (tm-30) REVERT: A 1346 MET cc_start: 0.8933 (mtp) cc_final: 0.8451 (mtp) REVERT: A 1349 LYS cc_start: 0.8942 (tttt) cc_final: 0.8316 (tmmt) REVERT: A 1350 LYS cc_start: 0.9021 (mmmm) cc_final: 0.8695 (mmmm) REVERT: A 1545 HIS cc_start: 0.8436 (m-70) cc_final: 0.8073 (m-70) REVERT: A 1572 GLU cc_start: 0.8902 (mp0) cc_final: 0.8688 (mp0) REVERT: A 1664 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8296 (mt-10) REVERT: A 1701 LEU cc_start: 0.8193 (tp) cc_final: 0.7931 (tp) REVERT: A 1706 LEU cc_start: 0.8803 (tp) cc_final: 0.8542 (tp) REVERT: A 1716 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7987 (tm-30) REVERT: A 1759 LEU cc_start: 0.9209 (tp) cc_final: 0.8807 (tp) REVERT: A 1764 ASP cc_start: 0.8691 (m-30) cc_final: 0.8377 (m-30) REVERT: A 1809 LEU cc_start: 0.8897 (tp) cc_final: 0.8522 (tp) REVERT: A 1833 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8510 (tm-30) outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.2780 time to fit residues: 150.9448 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 : 0.496 ------------------------------------------------------------------------------- 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: 4.9990 chunk 63 optimal weight: 0.7980 chunk 61 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 116 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.122233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.094618 restraints weight = 70214.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.100687 restraints weight = 31485.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.104807 restraints weight = 17456.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.107537 restraints weight = 10974.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.109360 restraints weight = 7587.516| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11753 Z= 0.181 Angle : 0.551 6.504 16181 Z= 0.297 Chirality : 0.038 0.144 1891 Planarity : 0.005 0.046 1854 Dihedral : 15.532 95.123 2263 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.00 % Allowed : 1.84 % 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: 0.57 (0.24), residues: 1261 helix: 1.17 (0.20), residues: 635 sheet: -0.47 (0.41), residues: 156 loop : -0.27 (0.30), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 790 TYR 0.014 0.001 TYR A 771 PHE 0.026 0.002 PHE A1671 TRP 0.033 0.003 TRP A 138 HIS 0.005 0.001 HIS A1713 Details of bonding type rmsd covalent geometry : bond 0.00328 (11753) covalent geometry : angle 0.55063 (16181) hydrogen bonds : bond 0.05123 ( 564) hydrogen bonds : angle 4.86830 ( 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 406 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 406 time to evaluate : 0.368 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 51 LEU cc_start: 0.8696 (mt) cc_final: 0.8473 (mt) REVERT: A 52 LEU cc_start: 0.8921 (tp) cc_final: 0.8361 (tp) REVERT: A 56 LEU cc_start: 0.8776 (mt) cc_final: 0.8347 (mt) REVERT: A 105 GLN cc_start: 0.8631 (mp10) cc_final: 0.8352 (mp10) REVERT: A 120 LYS cc_start: 0.8609 (ptpp) cc_final: 0.8238 (ptpp) REVERT: A 141 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8157 (mm-30) REVERT: A 153 TYR cc_start: 0.8534 (m-10) cc_final: 0.8203 (m-10) REVERT: A 164 LEU cc_start: 0.8651 (tp) cc_final: 0.8417 (tp) REVERT: A 171 LEU cc_start: 0.7721 (mm) cc_final: 0.7426 (mm) REVERT: A 188 GLU cc_start: 0.8817 (mp0) cc_final: 0.8527 (mp0) REVERT: A 221 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8355 (mt-10) REVERT: A 231 ARG cc_start: 0.8882 (tmm-80) cc_final: 0.8169 (ptm-80) REVERT: A 267 TYR cc_start: 0.8683 (t80) cc_final: 0.8126 (t80) REVERT: A 272 MET cc_start: 0.8992 (mpp) cc_final: 0.8563 (mtp) REVERT: A 275 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8539 (mt-10) REVERT: A 329 LEU cc_start: 0.9250 (tp) cc_final: 0.8988 (tp) REVERT: A 502 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8544 (mm-30) REVERT: A 503 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8637 (mt-10) REVERT: A 541 THR cc_start: 0.8147 (m) cc_final: 0.7838 (p) REVERT: A 631 ILE cc_start: 0.8156 (pt) cc_final: 0.7639 (mp) REVERT: A 634 ILE cc_start: 0.9025 (mm) cc_final: 0.8777 (mm) REVERT: A 648 HIS cc_start: 0.7064 (t-90) cc_final: 0.6715 (t-90) REVERT: A 698 CYS cc_start: 0.9166 (t) cc_final: 0.8702 (m) REVERT: A 747 GLN cc_start: 0.8304 (mp-120) cc_final: 0.8071 (mp-120) REVERT: A 761 TYR cc_start: 0.8456 (t80) cc_final: 0.8237 (t80) REVERT: A 784 GLU cc_start: 0.8846 (pp20) cc_final: 0.8625 (pm20) REVERT: A 815 HIS cc_start: 0.7495 (p90) cc_final: 0.7130 (p90) REVERT: A 827 ILE cc_start: 0.9056 (mp) cc_final: 0.8855 (mp) REVERT: A 828 SER cc_start: 0.7954 (m) cc_final: 0.7520 (t) REVERT: A 842 MET cc_start: 0.9020 (tpp) cc_final: 0.8501 (tpp) REVERT: A 851 GLN cc_start: 0.9015 (tt0) cc_final: 0.8528 (tt0) REVERT: A 901 GLU cc_start: 0.8571 (tm-30) cc_final: 0.8225 (tm-30) REVERT: A 916 LYS cc_start: 0.9542 (tmtt) cc_final: 0.9268 (tptp) REVERT: A 970 GLU cc_start: 0.8807 (tt0) cc_final: 0.8420 (mt-10) REVERT: A 992 HIS cc_start: 0.8154 (m-70) cc_final: 0.7827 (m-70) REVERT: A 1069 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8137 (tm-30) REVERT: A 1071 ARG cc_start: 0.8641 (ttp80) cc_final: 0.8179 (tmm-80) REVERT: A 1310 PHE cc_start: 0.6722 (m-80) cc_final: 0.6408 (m-10) REVERT: A 1313 GLU cc_start: 0.7843 (mp0) cc_final: 0.7320 (mp0) REVERT: A 1346 MET cc_start: 0.8929 (mtp) cc_final: 0.8457 (mtp) REVERT: A 1349 LYS cc_start: 0.8947 (tttt) cc_final: 0.8323 (tmmt) REVERT: A 1350 LYS cc_start: 0.9040 (mmmm) cc_final: 0.8761 (mmmm) REVERT: A 1545 HIS cc_start: 0.8464 (m-70) cc_final: 0.8094 (m-70) REVERT: A 1572 GLU cc_start: 0.8898 (mp0) cc_final: 0.8670 (mp0) REVERT: A 1696 GLN cc_start: 0.8386 (mt0) cc_final: 0.8126 (mt0) REVERT: A 1701 LEU cc_start: 0.8115 (tp) cc_final: 0.7844 (tp) REVERT: A 1716 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7998 (tm-30) REVERT: A 1759 LEU cc_start: 0.9170 (tp) cc_final: 0.8813 (tp) REVERT: A 1772 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7855 (tp30) REVERT: A 1802 MET cc_start: 0.8394 (mmp) cc_final: 0.8169 (mmp) REVERT: A 1809 LEU cc_start: 0.8888 (tp) cc_final: 0.8503 (tp) REVERT: A 1815 MET cc_start: 0.8325 (tpt) cc_final: 0.8105 (tpp) REVERT: A 1833 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8512 (tm-30) REVERT: A 1850 GLU cc_start: 0.8200 (tt0) cc_final: 0.7891 (tt0) REVERT: A 1854 MET cc_start: 0.8968 (tpt) cc_final: 0.8703 (tpt) REVERT: A 1895 LYS cc_start: 0.8646 (tttt) cc_final: 0.8317 (mtmm) REVERT: A 1900 ARG cc_start: 0.8635 (ptp-110) cc_final: 0.8404 (ptp90) outliers start: 0 outliers final: 0 residues processed: 406 average time/residue: 0.2682 time to fit residues: 145.4529 Evaluate side-chains 391 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 0.419 ------------------------------------------------------------------------------- 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: 5.9990 chunk 68 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 79 optimal weight: 0.0050 chunk 13 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 66 optimal weight: 0.0170 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 overall best weight: 1.1836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.121667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.093994 restraints weight = 70982.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.100127 restraints weight = 31760.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.104285 restraints weight = 17594.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.107033 restraints weight = 11032.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.108889 restraints weight = 7616.508| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11753 Z= 0.176 Angle : 0.543 6.446 16181 Z= 0.292 Chirality : 0.038 0.154 1891 Planarity : 0.005 0.041 1854 Dihedral : 15.580 93.728 2263 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: 0.44 (0.24), residues: 1261 helix: 1.15 (0.20), residues: 635 sheet: -0.68 (0.39), residues: 173 loop : -0.40 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 790 TYR 0.010 0.001 TYR A 47 PHE 0.030 0.002 PHE A1671 TRP 0.024 0.002 TRP A 138 HIS 0.005 0.001 HIS A1749 Details of bonding type rmsd covalent geometry : bond 0.00319 (11753) covalent geometry : angle 0.54345 (16181) hydrogen bonds : bond 0.04949 ( 564) hydrogen bonds : angle 4.78926 ( 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 407 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.584 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: 0.8929 (tp) cc_final: 0.8468 (tp) REVERT: A 56 LEU cc_start: 0.8756 (mt) cc_final: 0.8414 (mt) REVERT: A 76 LEU cc_start: 0.8731 (tp) cc_final: 0.8435 (tp) REVERT: A 80 GLU cc_start: 0.8546 (mm-30) cc_final: 0.8160 (mm-30) REVERT: A 105 GLN cc_start: 0.8643 (mp10) cc_final: 0.8376 (mp10) REVERT: A 141 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8163 (mm-30) REVERT: A 153 TYR cc_start: 0.8556 (m-10) cc_final: 0.8213 (m-10) REVERT: A 164 LEU cc_start: 0.8662 (tp) cc_final: 0.8451 (tp) REVERT: A 171 LEU cc_start: 0.7736 (mm) cc_final: 0.7510 (mm) REVERT: A 188 GLU cc_start: 0.8829 (mp0) cc_final: 0.8538 (mp0) REVERT: A 221 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8363 (mt-10) REVERT: A 231 ARG cc_start: 0.8847 (tmm-80) cc_final: 0.8523 (ptm-80) REVERT: A 232 SER cc_start: 0.8437 (m) cc_final: 0.7912 (t) REVERT: A 267 TYR cc_start: 0.8699 (t80) cc_final: 0.8105 (t80) REVERT: A 275 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8493 (mt-10) REVERT: A 300 LYS cc_start: 0.9149 (pttm) cc_final: 0.8945 (ptpp) REVERT: A 326 VAL cc_start: 0.9230 (t) cc_final: 0.9004 (t) REVERT: A 327 ARG cc_start: 0.9252 (mmp80) cc_final: 0.9046 (mmp80) REVERT: A 329 LEU cc_start: 0.9262 (tp) cc_final: 0.8997 (tp) REVERT: A 376 LYS cc_start: 0.9017 (mttp) cc_final: 0.8745 (mtpt) REVERT: A 502 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8560 (mm-30) REVERT: A 503 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8604 (mt-10) REVERT: A 541 THR cc_start: 0.8209 (m) cc_final: 0.7843 (p) REVERT: A 631 ILE cc_start: 0.8157 (pt) cc_final: 0.7675 (mp) REVERT: A 648 HIS cc_start: 0.7089 (t-90) cc_final: 0.6734 (t-90) REVERT: A 698 CYS cc_start: 0.9148 (t) cc_final: 0.8676 (m) REVERT: A 749 TYR cc_start: 0.7692 (m-10) cc_final: 0.7474 (m-10) REVERT: A 761 TYR cc_start: 0.8462 (t80) cc_final: 0.8214 (t80) REVERT: A 815 HIS cc_start: 0.7497 (p90) cc_final: 0.7138 (p90) REVERT: A 828 SER cc_start: 0.7922 (m) cc_final: 0.7491 (t) REVERT: A 842 MET cc_start: 0.9036 (tpp) cc_final: 0.8768 (tpt) REVERT: A 845 LEU cc_start: 0.9137 (tp) cc_final: 0.8927 (tp) REVERT: A 851 GLN cc_start: 0.9020 (tt0) cc_final: 0.8527 (tt0) REVERT: A 897 MET cc_start: 0.8712 (mtp) cc_final: 0.8179 (mtp) REVERT: A 901 GLU cc_start: 0.8615 (tm-30) cc_final: 0.8244 (tm-30) REVERT: A 916 LYS cc_start: 0.9542 (tmtt) cc_final: 0.9268 (tptp) REVERT: A 970 GLU cc_start: 0.8825 (tt0) cc_final: 0.8419 (mt-10) REVERT: A 992 HIS cc_start: 0.8169 (m-70) cc_final: 0.7958 (m-70) REVERT: A 1036 GLU cc_start: 0.7414 (mp0) cc_final: 0.6947 (mp0) REVERT: A 1041 HIS cc_start: 0.8031 (t-90) cc_final: 0.7685 (t-90) REVERT: A 1069 GLU cc_start: 0.8549 (tm-30) cc_final: 0.8121 (tm-30) REVERT: A 1071 ARG cc_start: 0.8663 (ttp80) cc_final: 0.8320 (tmm-80) REVERT: A 1310 PHE cc_start: 0.6775 (m-80) cc_final: 0.6485 (m-10) REVERT: A 1313 GLU cc_start: 0.7853 (mp0) cc_final: 0.7299 (mp0) REVERT: A 1346 MET cc_start: 0.8945 (mtp) cc_final: 0.8482 (mtp) REVERT: A 1349 LYS cc_start: 0.8962 (tttt) cc_final: 0.8343 (tmmt) REVERT: A 1350 LYS cc_start: 0.9052 (mmmm) cc_final: 0.8779 (mmmm) REVERT: A 1545 HIS cc_start: 0.8461 (m-70) cc_final: 0.8096 (m-70) REVERT: A 1550 ILE cc_start: 0.7890 (mt) cc_final: 0.7217 (mt) REVERT: A 1572 GLU cc_start: 0.8886 (mp0) cc_final: 0.8668 (mp0) REVERT: A 1701 LEU cc_start: 0.8203 (tp) cc_final: 0.7907 (tp) REVERT: A 1716 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7999 (tm-30) REVERT: A 1759 LEU cc_start: 0.9180 (tp) cc_final: 0.8834 (tp) REVERT: A 1802 MET cc_start: 0.8404 (mmp) cc_final: 0.8187 (mmp) REVERT: A 1809 LEU cc_start: 0.8902 (tp) cc_final: 0.8537 (tp) REVERT: A 1833 GLN cc_start: 0.8838 (tm-30) cc_final: 0.8536 (tm-30) REVERT: A 1850 GLU cc_start: 0.8176 (tt0) cc_final: 0.7856 (tt0) REVERT: A 1854 MET cc_start: 0.8991 (tpt) cc_final: 0.8737 (tpt) outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 0.2751 time to fit residues: 148.5303 Evaluate side-chains 391 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 391 time to evaluate : 0.507 ------------------------------------------------------------------------------- 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: 4.9990 chunk 2 optimal weight: 0.4980 chunk 130 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 0.0670 chunk 115 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 78 optimal weight: 0.0980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.124578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.096685 restraints weight = 69432.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.102892 restraints weight = 31225.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.107091 restraints weight = 17351.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.109871 restraints weight = 10883.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.111739 restraints weight = 7512.062| |-----------------------------------------------------------------------------| r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 11753 Z= 0.107 Angle : 0.508 6.052 16181 Z= 0.263 Chirality : 0.037 0.160 1891 Planarity : 0.004 0.049 1854 Dihedral : 15.423 92.658 2263 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: 0.78 (0.24), residues: 1261 helix: 1.45 (0.20), residues: 635 sheet: -0.67 (0.39), residues: 173 loop : -0.20 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1003 TYR 0.010 0.001 TYR A 819 PHE 0.018 0.001 PHE A 142 TRP 0.017 0.002 TRP A 138 HIS 0.004 0.001 HIS A 703 Details of bonding type rmsd covalent geometry : bond 0.00223 (11753) covalent geometry : angle 0.50758 (16181) hydrogen bonds : bond 0.04426 ( 564) hydrogen bonds : angle 4.43674 ( 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 401 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 0.430 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: A 52 LEU cc_start: 0.8900 (tp) cc_final: 0.8328 (tp) REVERT: A 56 LEU cc_start: 0.8724 (mt) cc_final: 0.8478 (mt) REVERT: A 76 LEU cc_start: 0.8666 (tp) cc_final: 0.8395 (tp) REVERT: A 80 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7984 (mm-30) REVERT: A 105 GLN cc_start: 0.8564 (mp10) cc_final: 0.8339 (mp10) REVERT: A 141 GLU cc_start: 0.8545 (mt-10) cc_final: 0.7994 (mm-30) REVERT: A 153 TYR cc_start: 0.8515 (m-10) cc_final: 0.8161 (m-10) REVERT: A 164 LEU cc_start: 0.8546 (tp) cc_final: 0.8330 (tp) REVERT: A 171 LEU cc_start: 0.7727 (mm) cc_final: 0.7495 (mm) REVERT: A 188 GLU cc_start: 0.8813 (mp0) cc_final: 0.8494 (mp0) REVERT: A 221 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8321 (mt-10) REVERT: A 232 SER cc_start: 0.8378 (m) cc_final: 0.7783 (t) REVERT: A 267 TYR cc_start: 0.8656 (t80) cc_final: 0.8072 (t80) REVERT: A 275 GLU cc_start: 0.8836 (mt-10) cc_final: 0.8444 (mt-10) REVERT: A 326 VAL cc_start: 0.9207 (t) cc_final: 0.8958 (t) REVERT: A 329 LEU cc_start: 0.9251 (tp) cc_final: 0.8993 (tp) REVERT: A 503 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8559 (mt-10) REVERT: A 541 THR cc_start: 0.8183 (m) cc_final: 0.7856 (p) REVERT: A 631 ILE cc_start: 0.8111 (pt) cc_final: 0.7626 (mp) REVERT: A 646 PHE cc_start: 0.8741 (m-80) cc_final: 0.8506 (m-80) REVERT: A 648 HIS cc_start: 0.7068 (t-90) cc_final: 0.6710 (t-90) REVERT: A 698 CYS cc_start: 0.9112 (t) cc_final: 0.8619 (m) REVERT: A 761 TYR cc_start: 0.8433 (t80) cc_final: 0.8201 (t80) REVERT: A 815 HIS cc_start: 0.7402 (p90) cc_final: 0.7044 (p90) REVERT: A 828 SER cc_start: 0.7903 (m) cc_final: 0.7474 (t) REVERT: A 845 LEU cc_start: 0.9091 (tp) cc_final: 0.8875 (tp) REVERT: A 849 LEU cc_start: 0.8881 (tp) cc_final: 0.8666 (tp) REVERT: A 851 GLN cc_start: 0.8979 (tt0) cc_final: 0.8495 (tt0) REVERT: A 854 PHE cc_start: 0.8626 (t80) cc_final: 0.8318 (t80) REVERT: A 897 MET cc_start: 0.8673 (mtp) cc_final: 0.8172 (mtp) REVERT: A 901 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8216 (tm-30) REVERT: A 916 LYS cc_start: 0.9534 (tmtt) cc_final: 0.9249 (tptp) REVERT: A 973 LYS cc_start: 0.9182 (mmmt) cc_final: 0.8826 (mmmt) REVERT: A 992 HIS cc_start: 0.8196 (m-70) cc_final: 0.7874 (m-70) REVERT: A 1036 GLU cc_start: 0.7389 (mp0) cc_final: 0.6858 (mp0) REVERT: A 1041 HIS cc_start: 0.7894 (t-90) cc_final: 0.7604 (t-90) REVERT: A 1069 GLU cc_start: 0.8494 (tm-30) cc_final: 0.7858 (tm-30) REVERT: A 1071 ARG cc_start: 0.8619 (ttp80) cc_final: 0.8230 (tmm-80) REVERT: A 1310 PHE cc_start: 0.6703 (m-80) cc_final: 0.6439 (m-10) REVERT: A 1313 GLU cc_start: 0.7741 (mp0) cc_final: 0.7228 (mp0) REVERT: A 1346 MET cc_start: 0.8920 (mtp) cc_final: 0.8469 (mtp) REVERT: A 1349 LYS cc_start: 0.8913 (tttt) cc_final: 0.8275 (tmmt) REVERT: A 1350 LYS cc_start: 0.9012 (mmmm) cc_final: 0.8734 (mmmm) REVERT: A 1545 HIS cc_start: 0.8420 (m-70) cc_final: 0.8066 (m-70) REVERT: A 1572 GLU cc_start: 0.8868 (mp0) cc_final: 0.8643 (mp0) REVERT: A 1688 TYR cc_start: 0.7552 (m-10) cc_final: 0.7291 (m-10) REVERT: A 1701 LEU cc_start: 0.8095 (tp) cc_final: 0.7806 (tp) REVERT: A 1759 LEU cc_start: 0.9155 (tp) cc_final: 0.8722 (tp) REVERT: A 1809 LEU cc_start: 0.8874 (tp) cc_final: 0.8477 (tp) REVERT: A 1815 MET cc_start: 0.8236 (tpt) cc_final: 0.7986 (tpp) REVERT: A 1833 GLN cc_start: 0.8799 (tm-30) cc_final: 0.8478 (tm-30) REVERT: A 1850 GLU cc_start: 0.8185 (tt0) cc_final: 0.7850 (tt0) REVERT: A 1854 MET cc_start: 0.8973 (tpt) cc_final: 0.8720 (tpt) REVERT: A 1895 LYS cc_start: 0.8612 (tttt) cc_final: 0.8311 (mtmm) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.2674 time to fit residues: 142.2090 Evaluate side-chains 384 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 384 time to evaluate : 0.552 ------------------------------------------------------------------------------- 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: 0.1980 chunk 107 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.123035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.095317 restraints weight = 71173.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.101530 restraints weight = 31614.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.105691 restraints weight = 17449.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.108428 restraints weight = 10979.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.110243 restraints weight = 7612.618| |-----------------------------------------------------------------------------| r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11753 Z= 0.134 Angle : 0.520 5.999 16181 Z= 0.273 Chirality : 0.037 0.157 1891 Planarity : 0.004 0.045 1854 Dihedral : 15.402 91.524 2263 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % 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: 0.82 (0.24), residues: 1261 helix: 1.44 (0.20), residues: 635 sheet: -0.55 (0.40), residues: 168 loop : -0.18 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 996 TYR 0.018 0.001 TYR A 124 PHE 0.030 0.001 PHE A1671 TRP 0.052 0.003 TRP A 138 HIS 0.004 0.001 HIS A1687 Details of bonding type rmsd covalent geometry : bond 0.00259 (11753) covalent geometry : angle 0.51954 (16181) hydrogen bonds : bond 0.04487 ( 564) hydrogen bonds : angle 4.48959 ( 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 402 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 402 time to evaluate : 0.536 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 52 LEU cc_start: 0.8905 (tp) cc_final: 0.8347 (tp) REVERT: A 56 LEU cc_start: 0.8775 (mt) cc_final: 0.8529 (mt) REVERT: A 76 LEU cc_start: 0.8589 (tp) cc_final: 0.8333 (tp) REVERT: A 80 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8151 (mm-30) REVERT: A 94 LYS cc_start: 0.7597 (tttt) cc_final: 0.7378 (tttm) REVERT: A 105 GLN cc_start: 0.8584 (mp10) cc_final: 0.8376 (mp10) REVERT: A 141 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8039 (mm-30) REVERT: A 153 TYR cc_start: 0.8537 (m-10) cc_final: 0.8181 (m-10) REVERT: A 161 ASN cc_start: 0.8904 (m-40) cc_final: 0.8532 (m110) REVERT: A 171 LEU cc_start: 0.7733 (mm) cc_final: 0.7497 (mm) REVERT: A 188 GLU cc_start: 0.8831 (mp0) cc_final: 0.8502 (mp0) REVERT: A 221 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8344 (mt-10) REVERT: A 232 SER cc_start: 0.8131 (m) cc_final: 0.7654 (t) REVERT: A 267 TYR cc_start: 0.8656 (t80) cc_final: 0.8196 (t80) REVERT: A 268 GLU cc_start: 0.8846 (mp0) cc_final: 0.8522 (mp0) REVERT: A 272 MET cc_start: 0.8956 (mpp) cc_final: 0.8493 (mtp) REVERT: A 275 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8485 (mt-10) REVERT: A 329 LEU cc_start: 0.9249 (tp) cc_final: 0.8987 (tp) REVERT: A 503 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8573 (mt-10) REVERT: A 541 THR cc_start: 0.8122 (m) cc_final: 0.7793 (p) REVERT: A 631 ILE cc_start: 0.8142 (pt) cc_final: 0.7658 (mp) REVERT: A 646 PHE cc_start: 0.8738 (m-80) cc_final: 0.8500 (m-80) REVERT: A 648 HIS cc_start: 0.7053 (t-90) cc_final: 0.6712 (t-90) REVERT: A 698 CYS cc_start: 0.9101 (t) cc_final: 0.8611 (m) REVERT: A 749 TYR cc_start: 0.7824 (m-10) cc_final: 0.7584 (m-10) REVERT: A 761 TYR cc_start: 0.8439 (t80) cc_final: 0.8199 (t80) REVERT: A 815 HIS cc_start: 0.7429 (p90) cc_final: 0.7050 (p90) REVERT: A 827 ILE cc_start: 0.8945 (mp) cc_final: 0.8715 (mp) REVERT: A 828 SER cc_start: 0.7870 (m) cc_final: 0.7432 (t) REVERT: A 842 MET cc_start: 0.9309 (tpt) cc_final: 0.8936 (tpp) REVERT: A 849 LEU cc_start: 0.8928 (tp) cc_final: 0.8726 (tp) REVERT: A 851 GLN cc_start: 0.9008 (tt0) cc_final: 0.8505 (tt0) REVERT: A 897 MET cc_start: 0.8695 (mtp) cc_final: 0.8210 (mtp) REVERT: A 901 GLU cc_start: 0.8603 (tm-30) cc_final: 0.8237 (tm-30) REVERT: A 902 LYS cc_start: 0.9067 (ptmm) cc_final: 0.8717 (ptmm) REVERT: A 916 LYS cc_start: 0.9540 (tmtt) cc_final: 0.9254 (tptp) REVERT: A 970 GLU cc_start: 0.8774 (tt0) cc_final: 0.8491 (tt0) REVERT: A 992 HIS cc_start: 0.8198 (m-70) cc_final: 0.7883 (m-70) REVERT: A 1041 HIS cc_start: 0.7915 (t-90) cc_final: 0.7654 (t-90) REVERT: A 1043 ILE cc_start: 0.8277 (mt) cc_final: 0.8076 (mm) REVERT: A 1069 GLU cc_start: 0.8514 (tm-30) cc_final: 0.7978 (tm-30) REVERT: A 1071 ARG cc_start: 0.8634 (ttp80) cc_final: 0.8273 (tmm-80) REVERT: A 1310 PHE cc_start: 0.6748 (m-80) cc_final: 0.6454 (m-10) REVERT: A 1313 GLU cc_start: 0.7772 (mp0) cc_final: 0.7234 (mp0) REVERT: A 1346 MET cc_start: 0.8935 (mtp) cc_final: 0.8489 (mtp) REVERT: A 1349 LYS cc_start: 0.8922 (tttt) cc_final: 0.8291 (tmmt) REVERT: A 1350 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8668 (mmmm) REVERT: A 1545 HIS cc_start: 0.8451 (m-70) cc_final: 0.8114 (m-70) REVERT: A 1572 GLU cc_start: 0.8883 (mp0) cc_final: 0.8675 (mp0) REVERT: A 1674 LYS cc_start: 0.9114 (mmtp) cc_final: 0.8749 (mmpt) REVERT: A 1696 GLN cc_start: 0.7685 (mm-40) cc_final: 0.7344 (mm-40) REVERT: A 1701 LEU cc_start: 0.8106 (tp) cc_final: 0.7808 (tp) REVERT: A 1759 LEU cc_start: 0.9170 (tp) cc_final: 0.8737 (tp) REVERT: A 1809 LEU cc_start: 0.8905 (tp) cc_final: 0.8503 (tp) REVERT: A 1833 GLN cc_start: 0.8794 (tm-30) cc_final: 0.8485 (tm-30) REVERT: A 1850 GLU cc_start: 0.8169 (tt0) cc_final: 0.7813 (tt0) REVERT: A 1854 MET cc_start: 0.8979 (tpt) cc_final: 0.8722 (tpt) REVERT: A 1895 LYS cc_start: 0.8627 (tttt) cc_final: 0.8329 (mtmm) REVERT: A 1900 ARG cc_start: 0.8628 (ptp-110) cc_final: 0.8314 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 402 average time/residue: 0.2825 time to fit residues: 150.2976 Evaluate side-chains 387 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 387 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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: 2.9990 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 4 optimal weight: 0.3980 chunk 127 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 15 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.121353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.093877 restraints weight = 71706.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.100018 restraints weight = 31889.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.104133 restraints weight = 17628.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.106821 restraints weight = 11103.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.108666 restraints weight = 7719.522| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11753 Z= 0.166 Angle : 0.535 6.117 16181 Z= 0.286 Chirality : 0.038 0.155 1891 Planarity : 0.004 0.039 1854 Dihedral : 15.509 90.892 2263 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.53 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: 0.60 (0.24), residues: 1261 helix: 1.28 (0.20), residues: 635 sheet: -0.56 (0.40), residues: 168 loop : -0.34 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 187 TYR 0.016 0.001 TYR A 124 PHE 0.029 0.002 PHE A1671 TRP 0.034 0.003 TRP A 138 HIS 0.006 0.001 HIS A1687 Details of bonding type rmsd covalent geometry : bond 0.00304 (11753) covalent geometry : angle 0.53476 (16181) hydrogen bonds : bond 0.04651 ( 564) hydrogen bonds : angle 4.60806 ( 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 399 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 0.399 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: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.8727 (mt) cc_final: 0.8527 (mt) REVERT: A 52 LEU cc_start: 0.8944 (tp) cc_final: 0.8517 (tp) REVERT: A 56 LEU cc_start: 0.8785 (mt) cc_final: 0.8414 (mt) REVERT: A 76 LEU cc_start: 0.8570 (tp) cc_final: 0.8342 (tp) REVERT: A 80 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8259 (mm-30) REVERT: A 153 TYR cc_start: 0.8556 (m-10) cc_final: 0.8198 (m-10) REVERT: A 164 LEU cc_start: 0.8682 (tp) cc_final: 0.8479 (tp) REVERT: A 171 LEU cc_start: 0.7749 (mm) cc_final: 0.7506 (mm) REVERT: A 188 GLU cc_start: 0.8824 (mp0) cc_final: 0.8493 (mp0) REVERT: A 221 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8341 (mt-10) REVERT: A 232 SER cc_start: 0.8143 (m) cc_final: 0.7652 (t) REVERT: A 267 TYR cc_start: 0.8691 (t80) cc_final: 0.8231 (t80) REVERT: A 268 GLU cc_start: 0.8858 (mp0) cc_final: 0.8514 (mp0) REVERT: A 272 MET cc_start: 0.9002 (mpp) cc_final: 0.8520 (mtp) REVERT: A 275 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8494 (mt-10) REVERT: A 329 LEU cc_start: 0.9258 (tp) cc_final: 0.9009 (tp) REVERT: A 382 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8722 (mt-10) REVERT: A 503 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8587 (mt-10) REVERT: A 541 THR cc_start: 0.8128 (m) cc_final: 0.7746 (p) REVERT: A 631 ILE cc_start: 0.8162 (pt) cc_final: 0.7629 (mp) REVERT: A 648 HIS cc_start: 0.7052 (t-90) cc_final: 0.6722 (t-90) REVERT: A 698 CYS cc_start: 0.9088 (t) cc_final: 0.8592 (m) REVERT: A 758 ARG cc_start: 0.8542 (mtm-85) cc_final: 0.8213 (ttp-110) REVERT: A 761 TYR cc_start: 0.8446 (t80) cc_final: 0.8189 (t80) REVERT: A 800 ARG cc_start: 0.8488 (mmt90) cc_final: 0.8011 (mmt180) REVERT: A 815 HIS cc_start: 0.7467 (p90) cc_final: 0.7087 (p90) REVERT: A 827 ILE cc_start: 0.8891 (mp) cc_final: 0.8647 (mp) REVERT: A 828 SER cc_start: 0.7871 (m) cc_final: 0.7452 (t) REVERT: A 842 MET cc_start: 0.9271 (tpt) cc_final: 0.8682 (tpp) REVERT: A 851 GLN cc_start: 0.9019 (tt0) cc_final: 0.8535 (tt0) REVERT: A 891 ASP cc_start: 0.8564 (t0) cc_final: 0.8234 (m-30) REVERT: A 897 MET cc_start: 0.8644 (mtp) cc_final: 0.8063 (mtp) REVERT: A 901 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8279 (tm-30) REVERT: A 902 LYS cc_start: 0.9064 (ptmm) cc_final: 0.8722 (ptmm) REVERT: A 916 LYS cc_start: 0.9543 (tmtt) cc_final: 0.9264 (tptp) REVERT: A 992 HIS cc_start: 0.8204 (m-70) cc_final: 0.7894 (m-70) REVERT: A 1001 THR cc_start: 0.8713 (p) cc_final: 0.8294 (m) REVERT: A 1041 HIS cc_start: 0.7950 (t-90) cc_final: 0.7685 (t-90) REVERT: A 1043 ILE cc_start: 0.8292 (mt) cc_final: 0.8070 (mm) REVERT: A 1069 GLU cc_start: 0.8553 (tm-30) cc_final: 0.7992 (tm-30) REVERT: A 1071 ARG cc_start: 0.8668 (ttp80) cc_final: 0.8257 (tmm-80) REVERT: A 1305 ASN cc_start: 0.8512 (t0) cc_final: 0.8116 (t0) REVERT: A 1313 GLU cc_start: 0.7800 (mp0) cc_final: 0.7264 (mp0) REVERT: A 1346 MET cc_start: 0.8951 (mtp) cc_final: 0.8506 (mtp) REVERT: A 1349 LYS cc_start: 0.8947 (tttt) cc_final: 0.8333 (tmmt) REVERT: A 1350 LYS cc_start: 0.8991 (mmmm) cc_final: 0.8702 (mmmm) REVERT: A 1545 HIS cc_start: 0.8476 (m-70) cc_final: 0.8205 (m-70) REVERT: A 1572 GLU cc_start: 0.8903 (mp0) cc_final: 0.8689 (mp0) REVERT: A 1674 LYS cc_start: 0.9127 (mmtp) cc_final: 0.8766 (mmpt) REVERT: A 1696 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7411 (mm-40) REVERT: A 1701 LEU cc_start: 0.8122 (tp) cc_final: 0.7808 (tp) REVERT: A 1716 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7705 (tm-30) REVERT: A 1748 TYR cc_start: 0.8288 (m-10) cc_final: 0.7990 (m-10) REVERT: A 1759 LEU cc_start: 0.9177 (tp) cc_final: 0.8822 (tp) REVERT: A 1802 MET cc_start: 0.8419 (mmp) cc_final: 0.8217 (mmp) REVERT: A 1815 MET cc_start: 0.8307 (tpt) cc_final: 0.8093 (tpt) REVERT: A 1833 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8504 (tm-30) REVERT: A 1850 GLU cc_start: 0.8170 (tt0) cc_final: 0.7795 (tt0) REVERT: A 1854 MET cc_start: 0.8973 (tpt) cc_final: 0.8713 (tpt) REVERT: A 1895 LYS cc_start: 0.8636 (tttt) cc_final: 0.8371 (mtmm) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.2698 time to fit residues: 142.5116 Evaluate side-chains 383 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 0.528 ------------------------------------------------------------------------------- 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: 6.9990 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 76 optimal weight: 0.0870 chunk 111 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1299 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.123571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.095912 restraints weight = 70646.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.102120 restraints weight = 31616.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.106305 restraints weight = 17484.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.109090 restraints weight = 10982.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.110948 restraints weight = 7585.332| |-----------------------------------------------------------------------------| r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 11753 Z= 0.115 Angle : 0.514 5.691 16181 Z= 0.268 Chirality : 0.037 0.157 1891 Planarity : 0.004 0.043 1854 Dihedral : 15.432 90.822 2263 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % 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: 0.85 (0.24), residues: 1261 helix: 1.47 (0.20), residues: 635 sheet: -0.52 (0.41), residues: 168 loop : -0.16 (0.31), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1071 TYR 0.014 0.001 TYR A 124 PHE 0.029 0.001 PHE A1671 TRP 0.030 0.002 TRP A 138 HIS 0.004 0.001 HIS A 703 Details of bonding type rmsd covalent geometry : bond 0.00238 (11753) covalent geometry : angle 0.51441 (16181) hydrogen bonds : bond 0.04322 ( 564) hydrogen bonds : angle 4.37759 ( 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 399 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 399 time to evaluate : 0.360 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 52 LEU cc_start: 0.8889 (tp) cc_final: 0.8459 (tp) REVERT: A 56 LEU cc_start: 0.8722 (mt) cc_final: 0.8343 (mt) REVERT: A 59 ASN cc_start: 0.7159 (m-40) cc_final: 0.6949 (m-40) REVERT: A 80 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8189 (mm-30) REVERT: A 120 LYS cc_start: 0.8456 (ptpp) cc_final: 0.8105 (ptpp) REVERT: A 141 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8067 (mm-30) REVERT: A 153 TYR cc_start: 0.8547 (m-10) cc_final: 0.8183 (m-10) REVERT: A 171 LEU cc_start: 0.7745 (mm) cc_final: 0.7495 (mm) REVERT: A 186 TYR cc_start: 0.8586 (m-10) cc_final: 0.8105 (m-10) REVERT: A 188 GLU cc_start: 0.8828 (mp0) cc_final: 0.8503 (mp0) REVERT: A 217 GLU cc_start: 0.8616 (pm20) cc_final: 0.8372 (pm20) REVERT: A 221 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8309 (mt-10) REVERT: A 231 ARG cc_start: 0.8870 (ttm170) cc_final: 0.8482 (ptp-170) REVERT: A 232 SER cc_start: 0.8144 (m) cc_final: 0.7629 (t) REVERT: A 267 TYR cc_start: 0.8662 (t80) cc_final: 0.8079 (t80) REVERT: A 272 MET cc_start: 0.8971 (mpp) cc_final: 0.8471 (mtp) REVERT: A 275 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8459 (mt-10) REVERT: A 329 LEU cc_start: 0.9250 (tp) cc_final: 0.9011 (tp) REVERT: A 382 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8656 (mt-10) REVERT: A 503 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8568 (mt-10) REVERT: A 541 THR cc_start: 0.8099 (m) cc_final: 0.7729 (p) REVERT: A 631 ILE cc_start: 0.8132 (pt) cc_final: 0.7635 (mp) REVERT: A 646 PHE cc_start: 0.8739 (m-80) cc_final: 0.8476 (m-80) REVERT: A 648 HIS cc_start: 0.7062 (t-90) cc_final: 0.6713 (t-90) REVERT: A 698 CYS cc_start: 0.9078 (t) cc_final: 0.8567 (m) REVERT: A 758 ARG cc_start: 0.8572 (mtm-85) cc_final: 0.8251 (ttp-110) REVERT: A 761 TYR cc_start: 0.8431 (t80) cc_final: 0.8181 (t80) REVERT: A 815 HIS cc_start: 0.7416 (p90) cc_final: 0.7038 (p90) REVERT: A 828 SER cc_start: 0.7845 (m) cc_final: 0.7371 (p) REVERT: A 832 LYS cc_start: 0.8830 (tmtt) cc_final: 0.8623 (tmtt) REVERT: A 842 MET cc_start: 0.9200 (tpt) cc_final: 0.8917 (tpp) REVERT: A 851 GLN cc_start: 0.8978 (tt0) cc_final: 0.8485 (tt0) REVERT: A 891 ASP cc_start: 0.8624 (t0) cc_final: 0.8218 (m-30) REVERT: A 897 MET cc_start: 0.8667 (mtp) cc_final: 0.8199 (mtp) REVERT: A 901 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8260 (tm-30) REVERT: A 902 LYS cc_start: 0.9045 (ptmm) cc_final: 0.8699 (ptmm) REVERT: A 916 LYS cc_start: 0.9539 (tmtt) cc_final: 0.9255 (tptp) REVERT: A 970 GLU cc_start: 0.8781 (tt0) cc_final: 0.8555 (tt0) REVERT: A 992 HIS cc_start: 0.8199 (m-70) cc_final: 0.7877 (m-70) REVERT: A 1041 HIS cc_start: 0.7904 (t-90) cc_final: 0.7603 (t-90) REVERT: A 1043 ILE cc_start: 0.8268 (mt) cc_final: 0.8041 (mm) REVERT: A 1069 GLU cc_start: 0.8518 (tm-30) cc_final: 0.7951 (tm-30) REVERT: A 1071 ARG cc_start: 0.8655 (ttp80) cc_final: 0.8261 (tmm-80) REVERT: A 1310 PHE cc_start: 0.6763 (m-80) cc_final: 0.6534 (m-10) REVERT: A 1313 GLU cc_start: 0.7756 (mp0) cc_final: 0.7229 (mp0) REVERT: A 1346 MET cc_start: 0.8948 (mtp) cc_final: 0.8492 (mtp) REVERT: A 1349 LYS cc_start: 0.8915 (tttt) cc_final: 0.8276 (tmmt) REVERT: A 1350 LYS cc_start: 0.8962 (mmmm) cc_final: 0.8652 (mmmm) REVERT: A 1545 HIS cc_start: 0.8442 (m-70) cc_final: 0.8121 (m-70) REVERT: A 1572 GLU cc_start: 0.8877 (mp0) cc_final: 0.8660 (mp0) REVERT: A 1654 ASN cc_start: 0.8923 (m-40) cc_final: 0.8664 (m110) REVERT: A 1664 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8185 (mt-10) REVERT: A 1674 LYS cc_start: 0.9109 (mmtp) cc_final: 0.8729 (mmpt) REVERT: A 1696 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7448 (mm-40) REVERT: A 1701 LEU cc_start: 0.8113 (tp) cc_final: 0.7798 (tp) REVERT: A 1710 ILE cc_start: 0.9085 (tp) cc_final: 0.8855 (tp) REVERT: A 1716 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7649 (tm-30) REVERT: A 1748 TYR cc_start: 0.8221 (m-10) cc_final: 0.7868 (m-10) REVERT: A 1759 LEU cc_start: 0.9143 (tp) cc_final: 0.8716 (tp) REVERT: A 1833 GLN cc_start: 0.8796 (tm-30) cc_final: 0.8479 (tm-30) REVERT: A 1854 MET cc_start: 0.8966 (tpt) cc_final: 0.8701 (tpt) REVERT: A 1895 LYS cc_start: 0.8612 (tttt) cc_final: 0.8333 (mtmm) outliers start: 0 outliers final: 0 residues processed: 399 average time/residue: 0.2607 time to fit residues: 138.6140 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 : 0.467 ------------------------------------------------------------------------------- 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: 1.9990 chunk 103 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.121190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.093875 restraints weight = 71324.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.099960 restraints weight = 31818.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.104030 restraints weight = 17629.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.106740 restraints weight = 11124.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.108596 restraints weight = 7732.806| |-----------------------------------------------------------------------------| r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11753 Z= 0.171 Angle : 0.546 5.814 16181 Z= 0.293 Chirality : 0.038 0.155 1891 Planarity : 0.005 0.074 1854 Dihedral : 15.508 90.914 2263 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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: 0.56 (0.24), residues: 1261 helix: 1.22 (0.20), residues: 635 sheet: -0.56 (0.41), residues: 168 loop : -0.32 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1845 TYR 0.014 0.001 TYR A 124 PHE 0.027 0.002 PHE A1671 TRP 0.028 0.002 TRP A 138 HIS 0.006 0.001 HIS A1687 Details of bonding type rmsd covalent geometry : bond 0.00316 (11753) covalent geometry : angle 0.54610 (16181) hydrogen bonds : bond 0.04646 ( 564) hydrogen bonds : angle 4.62154 ( 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 : 0.533 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 51 LEU cc_start: 0.8760 (mt) cc_final: 0.8560 (mt) REVERT: A 52 LEU cc_start: 0.8920 (tp) cc_final: 0.8417 (tp) REVERT: A 56 LEU cc_start: 0.8769 (mt) cc_final: 0.8527 (mt) REVERT: A 80 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8197 (mm-30) REVERT: A 120 LYS cc_start: 0.8448 (ptpp) cc_final: 0.8086 (ptpp) REVERT: A 141 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8136 (mm-30) REVERT: A 153 TYR cc_start: 0.8571 (m-10) cc_final: 0.8211 (m-10) REVERT: A 171 LEU cc_start: 0.7749 (mm) cc_final: 0.7497 (mm) REVERT: A 188 GLU cc_start: 0.8829 (mp0) cc_final: 0.8498 (mp0) REVERT: A 217 GLU cc_start: 0.8616 (pm20) cc_final: 0.8257 (pm20) REVERT: A 221 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8340 (mt-10) REVERT: A 232 SER cc_start: 0.8148 (m) cc_final: 0.7630 (t) REVERT: A 267 TYR cc_start: 0.8721 (t80) cc_final: 0.8247 (t80) REVERT: A 268 GLU cc_start: 0.8882 (mp0) cc_final: 0.8504 (mp0) REVERT: A 329 LEU cc_start: 0.9279 (tp) cc_final: 0.9041 (tp) REVERT: A 382 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8699 (mt-10) REVERT: A 503 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8584 (mt-10) REVERT: A 541 THR cc_start: 0.8116 (m) cc_final: 0.7738 (p) REVERT: A 631 ILE cc_start: 0.8162 (pt) cc_final: 0.7633 (mp) REVERT: A 648 HIS cc_start: 0.7052 (t-90) cc_final: 0.6700 (t-90) REVERT: A 698 CYS cc_start: 0.9090 (t) cc_final: 0.8582 (m) REVERT: A 758 ARG cc_start: 0.8553 (mtm-85) cc_final: 0.8253 (ttp-110) REVERT: A 761 TYR cc_start: 0.8430 (t80) cc_final: 0.8176 (t80) REVERT: A 815 HIS cc_start: 0.7463 (p90) cc_final: 0.7080 (p90) REVERT: A 827 ILE cc_start: 0.8866 (mp) cc_final: 0.8622 (mp) REVERT: A 828 SER cc_start: 0.7834 (m) cc_final: 0.7401 (t) REVERT: A 832 LYS cc_start: 0.8827 (tmtt) cc_final: 0.8624 (tmtt) REVERT: A 842 MET cc_start: 0.9236 (tpt) cc_final: 0.8684 (tpp) REVERT: A 851 GLN cc_start: 0.9011 (tt0) cc_final: 0.8537 (tt0) REVERT: A 891 ASP cc_start: 0.8626 (t0) cc_final: 0.8212 (m-30) REVERT: A 897 MET cc_start: 0.8628 (mtp) cc_final: 0.8086 (mtp) REVERT: A 901 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8291 (tm-30) REVERT: A 902 LYS cc_start: 0.9071 (ptmm) cc_final: 0.8752 (ptmm) REVERT: A 916 LYS cc_start: 0.9543 (tmtt) cc_final: 0.9266 (tptp) REVERT: A 992 HIS cc_start: 0.8213 (m-70) cc_final: 0.7892 (m-70) REVERT: A 1041 HIS cc_start: 0.7954 (t-90) cc_final: 0.7681 (t-90) REVERT: A 1043 ILE cc_start: 0.8272 (mt) cc_final: 0.8035 (mm) REVERT: A 1069 GLU cc_start: 0.8579 (tm-30) cc_final: 0.7996 (tm-30) REVERT: A 1071 ARG cc_start: 0.8679 (ttp80) cc_final: 0.8297 (tmm-80) REVERT: A 1313 GLU cc_start: 0.7808 (mp0) cc_final: 0.7266 (mp0) REVERT: A 1346 MET cc_start: 0.8986 (mtp) cc_final: 0.8538 (mtp) REVERT: A 1349 LYS cc_start: 0.8927 (tttt) cc_final: 0.8311 (tmmt) REVERT: A 1350 LYS cc_start: 0.8987 (mmmm) cc_final: 0.8698 (mmmm) REVERT: A 1545 HIS cc_start: 0.8459 (m-70) cc_final: 0.8182 (m-70) REVERT: A 1572 GLU cc_start: 0.8903 (mp0) cc_final: 0.8684 (mp0) REVERT: A 1654 ASN cc_start: 0.8951 (m-40) cc_final: 0.8694 (m110) REVERT: A 1674 LYS cc_start: 0.9114 (mmtp) cc_final: 0.8744 (mmpt) REVERT: A 1696 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7503 (mm110) REVERT: A 1701 LEU cc_start: 0.8142 (tp) cc_final: 0.7856 (tp) REVERT: A 1716 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7683 (tm-30) REVERT: A 1748 TYR cc_start: 0.8250 (m-10) cc_final: 0.7981 (m-10) REVERT: A 1833 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8509 (tm-30) REVERT: A 1895 LYS cc_start: 0.8662 (tttt) cc_final: 0.8390 (mtmm) outliers start: 0 outliers final: 0 residues processed: 400 average time/residue: 0.2741 time to fit residues: 146.1742 Evaluate side-chains 383 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 383 time to evaluate : 0.489 ------------------------------------------------------------------------------- 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: 4.9990 chunk 4 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 113 optimal weight: 0.5980 chunk 82 optimal weight: 8.9990 chunk 25 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 11 optimal weight: 0.0970 chunk 60 optimal weight: 1.9990 chunk 84 optimal weight: 0.0980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.124058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.096547 restraints weight = 70392.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.102653 restraints weight = 31594.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.106769 restraints weight = 17573.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.109491 restraints weight = 11080.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.111326 restraints weight = 7692.875| |-----------------------------------------------------------------------------| r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11753 Z= 0.106 Angle : 0.531 5.491 16181 Z= 0.273 Chirality : 0.038 0.158 1891 Planarity : 0.004 0.046 1854 Dihedral : 15.392 91.599 2263 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.88 (0.24), residues: 1261 helix: 1.50 (0.21), residues: 634 sheet: -0.51 (0.41), residues: 168 loop : -0.17 (0.31), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1845 TYR 0.013 0.001 TYR A 124 PHE 0.026 0.001 PHE A1671 TRP 0.025 0.002 TRP A 138 HIS 0.003 0.001 HIS A 703 Details of bonding type rmsd covalent geometry : bond 0.00231 (11753) covalent geometry : angle 0.53050 (16181) hydrogen bonds : bond 0.04129 ( 564) hydrogen bonds : angle 4.27536 ( 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 401 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8885 (tp) cc_final: 0.8362 (tp) REVERT: A 56 LEU cc_start: 0.8684 (mt) cc_final: 0.8457 (mt) REVERT: A 80 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8133 (mm-30) REVERT: A 141 GLU cc_start: 0.8469 (mt-10) cc_final: 0.7997 (mm-30) REVERT: A 153 TYR cc_start: 0.8509 (m-10) cc_final: 0.8149 (m-10) REVERT: A 171 LEU cc_start: 0.7746 (mm) cc_final: 0.7499 (mm) REVERT: A 186 TYR cc_start: 0.8583 (m-10) cc_final: 0.8096 (m-10) REVERT: A 188 GLU cc_start: 0.8827 (mp0) cc_final: 0.8506 (mp0) REVERT: A 217 GLU cc_start: 0.8604 (pm20) cc_final: 0.8268 (pm20) REVERT: A 221 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8308 (mt-10) REVERT: A 232 SER cc_start: 0.8215 (m) cc_final: 0.7689 (t) REVERT: A 267 TYR cc_start: 0.8694 (t80) cc_final: 0.8215 (t80) REVERT: A 268 GLU cc_start: 0.8889 (mp0) cc_final: 0.8539 (mp0) REVERT: A 269 ARG cc_start: 0.9268 (tpm170) cc_final: 0.9032 (mmm160) REVERT: A 307 ARG cc_start: 0.9079 (ptp-110) cc_final: 0.8863 (ptp90) REVERT: A 329 LEU cc_start: 0.9268 (tp) cc_final: 0.9035 (tp) REVERT: A 382 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8648 (mt-10) REVERT: A 503 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8538 (mt-10) REVERT: A 541 THR cc_start: 0.8067 (m) cc_final: 0.7704 (p) REVERT: A 631 ILE cc_start: 0.8108 (pt) cc_final: 0.7678 (mt) REVERT: A 648 HIS cc_start: 0.7046 (t-90) cc_final: 0.6690 (t-90) REVERT: A 761 TYR cc_start: 0.8402 (t80) cc_final: 0.8166 (t80) REVERT: A 800 ARG cc_start: 0.8414 (mmt90) cc_final: 0.7985 (mmt180) REVERT: A 827 ILE cc_start: 0.8815 (mp) cc_final: 0.8600 (mp) REVERT: A 828 SER cc_start: 0.7793 (m) cc_final: 0.7301 (p) REVERT: A 830 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7474 (tm-30) REVERT: A 832 LYS cc_start: 0.8814 (tmtt) cc_final: 0.8566 (tmtt) REVERT: A 842 MET cc_start: 0.9258 (tpt) cc_final: 0.8695 (tpp) REVERT: A 851 GLN cc_start: 0.8964 (tt0) cc_final: 0.8489 (tt0) REVERT: A 891 ASP cc_start: 0.8621 (t0) cc_final: 0.8217 (m-30) REVERT: A 897 MET cc_start: 0.8639 (mtp) cc_final: 0.8197 (mtp) REVERT: A 901 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8271 (tm-30) REVERT: A 902 LYS cc_start: 0.9048 (ptmm) cc_final: 0.8730 (ptmm) REVERT: A 916 LYS cc_start: 0.9542 (tmtt) cc_final: 0.9254 (tptp) REVERT: A 992 HIS cc_start: 0.8207 (m-70) cc_final: 0.7877 (m-70) REVERT: A 1069 GLU cc_start: 0.8539 (tm-30) cc_final: 0.7916 (tm-30) REVERT: A 1071 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8262 (tmm-80) REVERT: A 1299 GLN cc_start: 0.8853 (mm110) cc_final: 0.8339 (mm110) REVERT: A 1313 GLU cc_start: 0.7694 (mp0) cc_final: 0.7182 (mp0) REVERT: A 1339 HIS cc_start: 0.8436 (p90) cc_final: 0.8008 (p90) REVERT: A 1346 MET cc_start: 0.8959 (mtp) cc_final: 0.8488 (mtp) REVERT: A 1349 LYS cc_start: 0.8910 (tttt) cc_final: 0.8268 (tmmt) REVERT: A 1350 LYS cc_start: 0.8969 (mmmm) cc_final: 0.8633 (mmmm) REVERT: A 1545 HIS cc_start: 0.8445 (m-70) cc_final: 0.8152 (m-70) REVERT: A 1572 GLU cc_start: 0.8891 (mp0) cc_final: 0.8661 (mp0) REVERT: A 1664 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8138 (mt-10) REVERT: A 1674 LYS cc_start: 0.9084 (mmtp) cc_final: 0.8670 (mmpt) REVERT: A 1696 GLN cc_start: 0.7859 (mm-40) cc_final: 0.7521 (mm110) REVERT: A 1701 LEU cc_start: 0.8060 (tp) cc_final: 0.7755 (tp) REVERT: A 1710 ILE cc_start: 0.9044 (tp) cc_final: 0.8809 (tp) REVERT: A 1712 LYS cc_start: 0.8929 (tttp) cc_final: 0.8620 (mtpp) REVERT: A 1716 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7665 (tm-30) REVERT: A 1748 TYR cc_start: 0.8254 (m-10) cc_final: 0.7926 (m-10) REVERT: A 1832 MET cc_start: 0.8950 (mtp) cc_final: 0.8741 (mtp) REVERT: A 1833 GLN cc_start: 0.8784 (tm-30) cc_final: 0.8498 (tm-30) REVERT: A 1850 GLU cc_start: 0.8459 (tm-30) cc_final: 0.8098 (tm-30) REVERT: A 1895 LYS cc_start: 0.8619 (tttt) cc_final: 0.8350 (mtmm) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.2955 time to fit residues: 157.0663 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 : 0.500 ------------------------------------------------------------------------------- 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: 2.9990 chunk 32 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 17 optimal weight: 0.0670 chunk 77 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 overall best weight: 1.3922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.119882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.092644 restraints weight = 71718.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.098677 restraints weight = 32115.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.102731 restraints weight = 17843.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.105466 restraints weight = 11259.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.107228 restraints weight = 7800.766| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 11753 Z= 0.198 Angle : 0.564 5.832 16181 Z= 0.306 Chirality : 0.038 0.152 1891 Planarity : 0.005 0.047 1854 Dihedral : 15.566 91.910 2263 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % 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: 0.45 (0.24), residues: 1261 helix: 1.14 (0.20), residues: 633 sheet: -0.56 (0.41), residues: 163 loop : -0.42 (0.30), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 800 TYR 0.014 0.001 TYR A 47 PHE 0.024 0.002 PHE A1671 TRP 0.024 0.003 TRP A 138 HIS 0.006 0.001 HIS A1713 Details of bonding type rmsd covalent geometry : bond 0.00356 (11753) covalent geometry : angle 0.56393 (16181) hydrogen bonds : bond 0.04820 ( 564) hydrogen bonds : angle 4.68656 ( 1575) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4425.19 seconds wall clock time: 76 minutes 0.36 seconds (4560.36 seconds total)