Starting phenix.real_space_refine on Sun Feb 18 14:53:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yym_14383/02_2024/7yym_14383.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yym_14383/02_2024/7yym_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yym_14383/02_2024/7yym_14383.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yym_14383/02_2024/7yym_14383.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yym_14383/02_2024/7yym_14383.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yym_14383/02_2024/7yym_14383.pdb" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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: {'TYR:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 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: 10.28, per 1000 atoms: 0.46 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 - 3.50 Amino acid : False - 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: 18.34 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 9.59 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: 9.03 Time building geometry restraints manager: 19.14 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: 95.71 - 103.37: 213 103.37 - 111.02: 24289 111.02 - 118.67: 6946 118.67 - 126.33: 9376 126.33 - 133.98: 331 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 1.850 nonbonded pdb=" O LEU A1678 " pdb=" HG1 THR A1682 " model vdw 1.614 1.850 nonbonded pdb=" HG1 THR A1867 " pdb=" OD1 ASP A1869 " model vdw 1.622 1.850 nonbonded pdb=" O GLU A 542 " pdb=" HG SER A 545 " model vdw 1.622 1.850 nonbonded pdb=" H SER A1862 " pdb=" O THR A1875 " model vdw 1.635 1.850 ... (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 ========== 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: 3.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.320 Extract box with map and model: 12.710 Check model and map are aligned: 0.330 Set scattering table: 0.220 Process input model: 79.630 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:3.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 99.840 ------------------------------------------------------------------------------- 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= 0.248 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (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 TRP 0.041 0.005 TRP A 138 HIS 0.012 0.003 HIS A1749 PHE 0.030 0.003 PHE A1660 TYR 0.030 0.004 TYR A1746 ARG 0.053 0.005 ARG A 86 *********************** 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 fitting. rotamer outliers: 2 poor density : 425 time to evaluate : 1.783 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: A 52 LEU cc_start: 0.8867 (tp) cc_final: 0.8366 (tp) REVERT: A 56 LEU cc_start: 0.8755 (mt) cc_final: 0.8359 (mt) REVERT: A 61 ILE cc_start: 0.8027 (mm) cc_final: 0.7361 (mm) REVERT: A 105 GLN cc_start: 0.8513 (mp10) cc_final: 0.8223 (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: 0.8232 (ptpp) REVERT: A 141 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8151 (mm-30) REVERT: A 153 TYR cc_start: 0.8413 (m-10) cc_final: 0.8066 (m-10) REVERT: A 161 ASN cc_start: 0.8657 (m110) cc_final: 0.6975 (m-40) REVERT: A 171 LEU cc_start: 0.7759 (mm) cc_final: 0.7407 (mm) REVERT: A 183 ASP cc_start: 0.8434 (m-30) cc_final: 0.8203 (p0) REVERT: A 221 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8274 (mt-10) REVERT: A 231 ARG cc_start: 0.8941 (tmm-80) cc_final: 0.8401 (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: 0.8597 (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: 0.8241 (m-30) REVERT: A 329 LEU cc_start: 0.9228 (tp) cc_final: 0.9008 (tp) REVERT: A 343 LYS cc_start: 0.8013 (tptt) cc_final: 0.7560 (tptm) REVERT: A 347 PHE cc_start: 0.8988 (m-80) cc_final: 0.8554 (m-80) REVERT: A 500 LYS cc_start: 0.9187 (mppt) cc_final: 0.8554 (mppt) REVERT: A 503 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8507 (mt-10) REVERT: A 541 THR cc_start: 0.8189 (m) cc_final: 0.7897 (p) REVERT: A 542 GLU cc_start: 0.8418 (tp30) cc_final: 0.8169 (tp30) REVERT: A 544 ARG cc_start: 0.8917 (ppt170) cc_final: 0.8541 (ppt170) REVERT: A 575 ASP cc_start: 0.8437 (m-30) cc_final: 0.7893 (m-30) REVERT: A 631 ILE cc_start: 0.8072 (pt) cc_final: 0.7674 (mt) REVERT: A 646 PHE cc_start: 0.8592 (m-80) cc_final: 0.8383 (m-80) REVERT: A 648 HIS cc_start: 0.7070 (t-90) cc_final: 0.6743 (t-90) REVERT: A 698 CYS cc_start: 0.9223 (t) cc_final: 0.8844 (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 791 LYS cc_start: 0.9109 (ptmm) cc_final: 0.8836 (pttp) 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: 0.8873 (mp) REVERT: A 831 LEU cc_start: 0.8902 (tt) cc_final: 0.8690 (tt) REVERT: A 851 GLN cc_start: 0.8995 (tt0) cc_final: 0.8477 (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: 0.8195 (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: 0.8128 (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: 0.8883 (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: 0.8694 (mmmm) REVERT: A 1354 CYS cc_start: 0.8759 (p) cc_final: 0.8323 (t) REVERT: A 1545 HIS cc_start: 0.8510 (m-70) cc_final: 0.8217 (m-70) REVERT: A 1585 LYS cc_start: 0.7903 (tmtt) cc_final: 0.7664 (tptt) REVERT: A 1664 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8213 (mt-10) REVERT: A 1698 LEU cc_start: 0.8175 (mt) cc_final: 0.7972 (mt) REVERT: A 1701 LEU cc_start: 0.8243 (tp) cc_final: 0.7915 (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: 0.7871 (tm-30) REVERT: A 1759 LEU cc_start: 0.9174 (tp) cc_final: 0.8747 (tt) REVERT: A 1772 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7749 (tp30) REVERT: A 1809 LEU cc_start: 0.8892 (tp) cc_final: 0.8492 (tp) REVERT: A 1827 VAL cc_start: 0.8753 (t) cc_final: 0.8270 (t) outliers start: 2 outliers final: 0 residues processed: 425 average time/residue: 0.6405 time to fit residues: 363.3658 Evaluate side-chains 391 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 112 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 34 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 104 optimal weight: 1.9990 chunk 40 optimal weight: 0.1980 chunk 63 optimal weight: 0.0270 chunk 77 optimal weight: 4.9990 chunk 120 optimal weight: 0.0050 overall best weight: 0.3652 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11753 Z= 0.143 Angle : 0.535 6.937 16181 Z= 0.277 Chirality : 0.038 0.150 1891 Planarity : 0.004 0.045 1854 Dihedral : 15.277 95.774 2263 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.24), residues: 1261 helix: 1.64 (0.20), residues: 635 sheet: 0.05 (0.43), residues: 146 loop : 0.07 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 138 HIS 0.004 0.001 HIS A 145 PHE 0.018 0.001 PHE A1671 TYR 0.016 0.001 TYR A1891 ARG 0.004 0.000 ARG A1368 *********************** 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 405 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 405 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8855 (tp) cc_final: 0.8351 (tp) REVERT: A 56 LEU cc_start: 0.8767 (mt) cc_final: 0.8405 (mt) REVERT: A 105 GLN cc_start: 0.8539 (mp10) cc_final: 0.8189 (mp10) REVERT: A 120 LYS cc_start: 0.8652 (ptpp) cc_final: 0.8317 (ptpp) REVERT: A 141 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8154 (mm-30) REVERT: A 153 TYR cc_start: 0.8421 (m-10) cc_final: 0.8037 (m-10) REVERT: A 164 LEU cc_start: 0.8368 (tp) cc_final: 0.8150 (tp) REVERT: A 171 LEU cc_start: 0.7705 (mm) cc_final: 0.7457 (mm) REVERT: A 221 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8226 (mt-10) REVERT: A 231 ARG cc_start: 0.8825 (tmm-80) cc_final: 0.8207 (ptm-80) REVERT: A 267 TYR cc_start: 0.8542 (t80) cc_final: 0.7969 (t80) REVERT: A 275 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8541 (mt-10) REVERT: A 319 ASP cc_start: 0.8549 (m-30) cc_final: 0.8318 (m-30) REVERT: A 321 VAL cc_start: 0.8870 (t) cc_final: 0.8141 (t) REVERT: A 324 MET cc_start: 0.8801 (mpp) cc_final: 0.8548 (mpp) REVERT: A 329 LEU cc_start: 0.9213 (tp) cc_final: 0.8945 (tp) REVERT: A 500 LYS cc_start: 0.9229 (mppt) cc_final: 0.8964 (mppt) REVERT: A 502 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8476 (mm-30) REVERT: A 503 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8563 (mt-10) REVERT: A 541 THR cc_start: 0.8144 (m) cc_final: 0.7853 (p) REVERT: A 544 ARG cc_start: 0.8929 (ppt170) cc_final: 0.8475 (ppt170) REVERT: A 631 ILE cc_start: 0.8065 (pt) cc_final: 0.7616 (mt) REVERT: A 634 ILE cc_start: 0.9024 (mm) cc_final: 0.8782 (mm) REVERT: A 648 HIS cc_start: 0.7084 (t-90) cc_final: 0.6752 (t-90) REVERT: A 698 CYS cc_start: 0.9161 (t) cc_final: 0.8729 (m) REVERT: A 761 TYR cc_start: 0.8417 (t80) cc_final: 0.8211 (t80) REVERT: A 784 GLU cc_start: 0.8827 (pp20) cc_final: 0.8568 (pm20) REVERT: A 800 ARG cc_start: 0.8214 (mmt180) cc_final: 0.7846 (mmt90) REVERT: A 815 HIS cc_start: 0.7376 (p90) cc_final: 0.6956 (p90) REVERT: A 824 GLU cc_start: 0.7160 (tm-30) cc_final: 0.6547 (tm-30) REVERT: A 828 SER cc_start: 0.8040 (m) cc_final: 0.7543 (p) REVERT: A 842 MET cc_start: 0.9005 (tpp) cc_final: 0.8626 (tpp) REVERT: A 849 LEU cc_start: 0.8935 (tp) cc_final: 0.8718 (tp) REVERT: A 851 GLN cc_start: 0.8975 (tt0) cc_final: 0.8517 (tt0) REVERT: A 894 PHE cc_start: 0.8122 (m-10) cc_final: 0.7874 (m-10) REVERT: A 901 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8242 (tm-30) REVERT: A 916 LYS cc_start: 0.9549 (tmtt) cc_final: 0.9267 (tptp) REVERT: A 970 GLU cc_start: 0.8727 (tt0) cc_final: 0.8486 (mt-10) REVERT: A 992 HIS cc_start: 0.8142 (m-70) cc_final: 0.7868 (m-70) REVERT: A 1069 GLU cc_start: 0.8524 (tm-30) cc_final: 0.7965 (tm-30) REVERT: A 1313 GLU cc_start: 0.6574 (mp0) cc_final: 0.6331 (mp0) REVERT: A 1340 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7811 (tm-30) REVERT: A 1346 MET cc_start: 0.8920 (mtp) cc_final: 0.8449 (mtp) REVERT: A 1349 LYS cc_start: 0.8903 (tttt) cc_final: 0.8237 (tmmt) REVERT: A 1350 LYS cc_start: 0.8995 (mmmm) cc_final: 0.8666 (mmmm) REVERT: A 1368 ARG cc_start: 0.8704 (mmm-85) cc_final: 0.8388 (mmm-85) REVERT: A 1545 HIS cc_start: 0.8464 (m-70) cc_final: 0.8101 (m-70) REVERT: A 1664 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8254 (mt-10) REVERT: A 1701 LEU cc_start: 0.8129 (tp) cc_final: 0.7848 (tp) REVERT: A 1706 LEU cc_start: 0.8785 (tp) cc_final: 0.8497 (tp) REVERT: A 1716 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7742 (tm-30) REVERT: A 1759 LEU cc_start: 0.9145 (tp) cc_final: 0.8699 (tt) REVERT: A 1772 GLU cc_start: 0.8168 (mt-10) cc_final: 0.7714 (tp30) REVERT: A 1809 LEU cc_start: 0.8878 (tp) cc_final: 0.8442 (tp) REVERT: A 1833 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8375 (tm-30) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.6707 time to fit residues: 362.7417 Evaluate side-chains 388 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 388 time to evaluate : 2.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 67 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 120 optimal weight: 0.5980 chunk 130 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 145 HIS ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1325 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11753 Z= 0.239 Angle : 0.562 6.912 16181 Z= 0.309 Chirality : 0.038 0.141 1891 Planarity : 0.005 0.046 1854 Dihedral : 15.426 94.397 2263 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.24), residues: 1261 helix: 1.20 (0.20), residues: 635 sheet: -0.01 (0.42), residues: 158 loop : -0.27 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP A 138 HIS 0.006 0.001 HIS A1713 PHE 0.018 0.002 PHE A 142 TYR 0.014 0.001 TYR A 47 ARG 0.006 0.001 ARG A 996 *********************** 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 410 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 410 time to evaluate : 1.637 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: 0.8917 (tp) cc_final: 0.8411 (tp) REVERT: A 56 LEU cc_start: 0.8895 (mt) cc_final: 0.8539 (mt) REVERT: A 75 VAL cc_start: 0.8974 (m) cc_final: 0.8712 (m) REVERT: A 79 LYS cc_start: 0.8936 (mttm) cc_final: 0.8466 (mttm) REVERT: A 84 GLN cc_start: 0.8619 (tm-30) cc_final: 0.8197 (tm-30) REVERT: A 105 GLN cc_start: 0.8691 (mp10) cc_final: 0.8322 (mp10) REVERT: A 114 ARG cc_start: 0.8962 (ttm110) cc_final: 0.8633 (ttm110) REVERT: A 120 LYS cc_start: 0.8654 (ptpp) cc_final: 0.8273 (ptpp) REVERT: A 141 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8219 (mm-30) REVERT: A 153 TYR cc_start: 0.8513 (m-10) cc_final: 0.8115 (m-10) REVERT: A 164 LEU cc_start: 0.8632 (tp) cc_final: 0.8410 (tp) REVERT: A 171 LEU cc_start: 0.7659 (mm) cc_final: 0.7416 (mm) REVERT: A 221 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8317 (mt-10) REVERT: A 231 ARG cc_start: 0.8848 (tmm-80) cc_final: 0.8147 (ptm-80) REVERT: A 267 TYR cc_start: 0.8609 (t80) cc_final: 0.8165 (t80) REVERT: A 272 MET cc_start: 0.8957 (mpp) cc_final: 0.8506 (mtp) REVERT: A 275 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8551 (mt-10) REVERT: A 319 ASP cc_start: 0.8611 (m-30) cc_final: 0.8394 (m-30) REVERT: A 329 LEU cc_start: 0.9274 (tp) cc_final: 0.9013 (tp) REVERT: A 498 PHE cc_start: 0.8137 (m-80) cc_final: 0.7125 (m-10) REVERT: A 500 LYS cc_start: 0.9277 (mppt) cc_final: 0.8712 (mppt) REVERT: A 502 GLU cc_start: 0.8901 (mm-30) cc_final: 0.8548 (mm-30) REVERT: A 503 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8524 (mt-10) REVERT: A 541 THR cc_start: 0.8182 (m) cc_final: 0.7863 (p) REVERT: A 570 LYS cc_start: 0.9150 (mmpt) cc_final: 0.8912 (mmmt) REVERT: A 573 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8752 (mt-10) REVERT: A 631 ILE cc_start: 0.8151 (pt) cc_final: 0.7699 (mt) REVERT: A 634 ILE cc_start: 0.9053 (mm) cc_final: 0.8818 (mm) REVERT: A 648 HIS cc_start: 0.7092 (t-90) cc_final: 0.6759 (t-90) REVERT: A 698 CYS cc_start: 0.9199 (t) cc_final: 0.8746 (m) REVERT: A 761 TYR cc_start: 0.8472 (t80) cc_final: 0.8226 (t80) REVERT: A 779 THR cc_start: 0.8563 (m) cc_final: 0.8110 (m) REVERT: A 815 HIS cc_start: 0.7489 (p90) cc_final: 0.7124 (p90) REVERT: A 824 GLU cc_start: 0.7072 (tm-30) cc_final: 0.6556 (tm-30) REVERT: A 828 SER cc_start: 0.8022 (m) cc_final: 0.7604 (t) REVERT: A 842 MET cc_start: 0.9023 (tpp) cc_final: 0.8530 (tpp) REVERT: A 851 GLN cc_start: 0.9035 (tt0) cc_final: 0.8554 (tt0) REVERT: A 901 GLU cc_start: 0.8648 (tm-30) cc_final: 0.8351 (tm-30) REVERT: A 916 LYS cc_start: 0.9569 (tmtt) cc_final: 0.9301 (tptp) REVERT: A 970 GLU cc_start: 0.8729 (tt0) cc_final: 0.8484 (mt-10) REVERT: A 973 LYS cc_start: 0.9068 (mmmt) cc_final: 0.8834 (mmmt) REVERT: A 992 HIS cc_start: 0.8187 (m-70) cc_final: 0.7945 (m-70) REVERT: A 1069 GLU cc_start: 0.8564 (tm-30) cc_final: 0.7875 (tm-30) REVERT: A 1346 MET cc_start: 0.8939 (mtp) cc_final: 0.8493 (mtp) REVERT: A 1349 LYS cc_start: 0.8940 (tttt) cc_final: 0.8323 (tmmt) REVERT: A 1350 LYS cc_start: 0.8978 (mmmm) cc_final: 0.8718 (mmmm) REVERT: A 1386 VAL cc_start: 0.8364 (t) cc_final: 0.8003 (m) REVERT: A 1545 HIS cc_start: 0.8419 (m-70) cc_final: 0.8192 (m-70) REVERT: A 1696 GLN cc_start: 0.8290 (mt0) cc_final: 0.8040 (mt0) REVERT: A 1701 LEU cc_start: 0.8206 (tp) cc_final: 0.7934 (tp) REVERT: A 1716 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7977 (tm-30) REVERT: A 1759 LEU cc_start: 0.9197 (tp) cc_final: 0.8805 (tp) REVERT: A 1764 ASP cc_start: 0.8491 (m-30) cc_final: 0.8284 (m-30) REVERT: A 1772 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7789 (tp30) REVERT: A 1802 MET cc_start: 0.8399 (mmp) cc_final: 0.8189 (mmp) REVERT: A 1809 LEU cc_start: 0.8926 (tp) cc_final: 0.8580 (tp) REVERT: A 1813 ILE cc_start: 0.8520 (mm) cc_final: 0.8315 (mm) REVERT: A 1833 GLN cc_start: 0.8781 (tm-30) cc_final: 0.8474 (tm-30) REVERT: A 1850 GLU cc_start: 0.8217 (tt0) cc_final: 0.7901 (tt0) REVERT: A 1854 MET cc_start: 0.8991 (tpt) cc_final: 0.8729 (tpt) REVERT: A 1900 ARG cc_start: 0.8648 (ptp-110) cc_final: 0.8409 (ptp90) outliers start: 0 outliers final: 0 residues processed: 410 average time/residue: 0.6638 time to fit residues: 362.2478 Evaluate side-chains 393 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 393 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 119 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 57 optimal weight: 0.0050 chunk 81 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 63 optimal weight: 0.0670 chunk 115 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 overall best weight: 0.5536 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11753 Z= 0.142 Angle : 0.509 6.554 16181 Z= 0.264 Chirality : 0.037 0.147 1891 Planarity : 0.004 0.044 1854 Dihedral : 15.336 93.631 2263 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.24), residues: 1261 helix: 1.51 (0.20), residues: 635 sheet: 0.11 (0.43), residues: 151 loop : -0.03 (0.30), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 138 HIS 0.007 0.001 HIS A 116 PHE 0.020 0.001 PHE A1671 TYR 0.015 0.001 TYR A 793 ARG 0.007 0.000 ARG A 788 *********************** 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 fitting. rotamer outliers: 0 poor density : 407 time to evaluate : 1.747 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: 0.8863 (tp) cc_final: 0.8349 (tp) REVERT: A 56 LEU cc_start: 0.8807 (mt) cc_final: 0.8425 (mt) REVERT: A 79 LYS cc_start: 0.8909 (mttm) cc_final: 0.8444 (mttm) REVERT: A 84 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8336 (tm-30) REVERT: A 105 GLN cc_start: 0.8666 (mp10) cc_final: 0.8277 (mp10) REVERT: A 116 HIS cc_start: 0.8100 (t-170) cc_final: 0.7703 (t-170) REVERT: A 120 LYS cc_start: 0.8625 (ptpp) cc_final: 0.8226 (ptpp) REVERT: A 141 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8162 (mm-30) REVERT: A 153 TYR cc_start: 0.8439 (m-10) cc_final: 0.8018 (m-10) REVERT: A 161 ASN cc_start: 0.8015 (m-40) cc_final: 0.7787 (m-40) REVERT: A 164 LEU cc_start: 0.8499 (tp) cc_final: 0.8274 (tp) REVERT: A 171 LEU cc_start: 0.7706 (mm) cc_final: 0.7333 (mm) REVERT: A 217 GLU cc_start: 0.8604 (pm20) cc_final: 0.8318 (pm20) REVERT: A 221 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8262 (mt-10) REVERT: A 225 LYS cc_start: 0.8237 (ttpt) cc_final: 0.7980 (tttm) REVERT: A 231 ARG cc_start: 0.8824 (tmm-80) cc_final: 0.8194 (ptm-80) REVERT: A 267 TYR cc_start: 0.8621 (t80) cc_final: 0.8111 (t80) REVERT: A 275 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8465 (mt-10) REVERT: A 329 LEU cc_start: 0.9262 (tp) cc_final: 0.9006 (tp) REVERT: A 382 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8639 (mt-10) REVERT: A 500 LYS cc_start: 0.9249 (mppt) cc_final: 0.8682 (mppt) REVERT: A 502 GLU cc_start: 0.8846 (mm-30) cc_final: 0.8495 (mm-30) REVERT: A 503 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8464 (mt-10) REVERT: A 541 THR cc_start: 0.8180 (m) cc_final: 0.7838 (p) REVERT: A 631 ILE cc_start: 0.8080 (pt) cc_final: 0.7628 (mt) REVERT: A 634 ILE cc_start: 0.9042 (mm) cc_final: 0.8782 (mm) REVERT: A 648 HIS cc_start: 0.7088 (t-90) cc_final: 0.6747 (t-90) REVERT: A 698 CYS cc_start: 0.9137 (t) cc_final: 0.8635 (m) REVERT: A 761 TYR cc_start: 0.8427 (t80) cc_final: 0.8208 (t80) REVERT: A 815 HIS cc_start: 0.7382 (p90) cc_final: 0.7008 (p90) REVERT: A 824 GLU cc_start: 0.7218 (tm-30) cc_final: 0.6788 (tm-30) REVERT: A 828 SER cc_start: 0.7996 (m) cc_final: 0.7563 (t) REVERT: A 842 MET cc_start: 0.9010 (tpp) cc_final: 0.8768 (tpt) REVERT: A 845 LEU cc_start: 0.9095 (tp) cc_final: 0.8886 (tp) REVERT: A 849 LEU cc_start: 0.8896 (tp) cc_final: 0.8685 (tp) REVERT: A 851 GLN cc_start: 0.8992 (tt0) cc_final: 0.8461 (tt0) REVERT: A 897 MET cc_start: 0.8678 (mtp) cc_final: 0.8177 (mtp) REVERT: A 901 GLU cc_start: 0.8609 (tm-30) cc_final: 0.8331 (tm-30) REVERT: A 916 LYS cc_start: 0.9573 (tmtt) cc_final: 0.9299 (tptp) REVERT: A 970 GLU cc_start: 0.8719 (tt0) cc_final: 0.8413 (mt-10) REVERT: A 992 HIS cc_start: 0.8141 (m-70) cc_final: 0.7921 (m-70) REVERT: A 1310 PHE cc_start: 0.6527 (m-80) cc_final: 0.6287 (m-10) REVERT: A 1313 GLU cc_start: 0.7666 (mp0) cc_final: 0.7221 (mp0) REVERT: A 1346 MET cc_start: 0.8930 (mtp) cc_final: 0.8469 (mtp) REVERT: A 1349 LYS cc_start: 0.8909 (tttt) cc_final: 0.8274 (tmmt) REVERT: A 1350 LYS cc_start: 0.9012 (mmmm) cc_final: 0.8745 (mmmm) REVERT: A 1386 VAL cc_start: 0.8364 (t) cc_final: 0.7982 (m) REVERT: A 1545 HIS cc_start: 0.8348 (m-70) cc_final: 0.8075 (m-70) REVERT: A 1696 GLN cc_start: 0.8325 (mt0) cc_final: 0.8037 (mt0) REVERT: A 1701 LEU cc_start: 0.8138 (tp) cc_final: 0.7843 (tp) REVERT: A 1716 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7894 (tm-30) REVERT: A 1759 LEU cc_start: 0.9136 (tp) cc_final: 0.8733 (tp) REVERT: A 1763 ILE cc_start: 0.9133 (mt) cc_final: 0.8927 (mt) REVERT: A 1772 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7692 (tp30) REVERT: A 1809 LEU cc_start: 0.8956 (tp) cc_final: 0.8669 (tp) REVERT: A 1833 GLN cc_start: 0.8769 (tm-30) cc_final: 0.8461 (tm-30) REVERT: A 1850 GLU cc_start: 0.8167 (tt0) cc_final: 0.7858 (tt0) REVERT: A 1854 MET cc_start: 0.8989 (tpt) cc_final: 0.8726 (tpt) outliers start: 0 outliers final: 0 residues processed: 407 average time/residue: 0.6620 time to fit residues: 356.6117 Evaluate side-chains 389 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 389 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 107 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 chunk 95 optimal weight: 0.0980 chunk 53 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11753 Z= 0.141 Angle : 0.494 6.224 16181 Z= 0.257 Chirality : 0.037 0.144 1891 Planarity : 0.004 0.046 1854 Dihedral : 15.239 91.793 2263 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.24), residues: 1261 helix: 1.60 (0.20), residues: 641 sheet: 0.10 (0.43), residues: 151 loop : 0.07 (0.31), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 138 HIS 0.003 0.001 HIS A1749 PHE 0.020 0.001 PHE A 142 TYR 0.009 0.001 TYR A 819 ARG 0.002 0.000 ARG A 307 *********************** 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 395 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8865 (tp) cc_final: 0.8358 (tp) REVERT: A 56 LEU cc_start: 0.8828 (mt) cc_final: 0.8462 (mt) REVERT: A 84 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8270 (tm-30) REVERT: A 105 GLN cc_start: 0.8662 (mp10) cc_final: 0.8293 (mp10) REVERT: A 120 LYS cc_start: 0.8613 (ptpp) cc_final: 0.8209 (ptpp) REVERT: A 141 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8088 (mm-30) REVERT: A 153 TYR cc_start: 0.8466 (m-10) cc_final: 0.8058 (m-10) REVERT: A 164 LEU cc_start: 0.8504 (tp) cc_final: 0.8283 (tp) REVERT: A 171 LEU cc_start: 0.7664 (mm) cc_final: 0.7351 (mm) REVERT: A 217 GLU cc_start: 0.8599 (pm20) cc_final: 0.8381 (pm20) REVERT: A 221 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8273 (mt-10) REVERT: A 231 ARG cc_start: 0.8804 (tmm-80) cc_final: 0.8511 (ptm-80) REVERT: A 267 TYR cc_start: 0.8615 (t80) cc_final: 0.8114 (t80) REVERT: A 275 GLU cc_start: 0.8845 (mt-10) cc_final: 0.8444 (mt-10) REVERT: A 326 VAL cc_start: 0.9234 (t) cc_final: 0.8965 (t) REVERT: A 329 LEU cc_start: 0.9263 (tp) cc_final: 0.8997 (tp) REVERT: A 382 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8626 (mt-10) REVERT: A 503 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8550 (mt-10) REVERT: A 541 THR cc_start: 0.8197 (m) cc_final: 0.7854 (p) REVERT: A 631 ILE cc_start: 0.8105 (pt) cc_final: 0.7653 (mt) REVERT: A 634 ILE cc_start: 0.9032 (mm) cc_final: 0.8783 (mm) REVERT: A 648 HIS cc_start: 0.7089 (t-90) cc_final: 0.6749 (t-90) REVERT: A 698 CYS cc_start: 0.9115 (t) cc_final: 0.8605 (m) REVERT: A 761 TYR cc_start: 0.8427 (t80) cc_final: 0.8207 (t80) REVERT: A 824 GLU cc_start: 0.7303 (tm-30) cc_final: 0.6851 (tm-30) REVERT: A 828 SER cc_start: 0.7969 (m) cc_final: 0.7514 (t) REVERT: A 851 GLN cc_start: 0.8998 (tt0) cc_final: 0.8477 (tt0) REVERT: A 897 MET cc_start: 0.8661 (mtp) cc_final: 0.8229 (mtp) REVERT: A 901 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8342 (tm-30) REVERT: A 916 LYS cc_start: 0.9570 (tmtt) cc_final: 0.9293 (tptp) REVERT: A 970 GLU cc_start: 0.8721 (tt0) cc_final: 0.8375 (mt-10) REVERT: A 992 HIS cc_start: 0.8149 (m-70) cc_final: 0.7912 (m-70) REVERT: A 1069 GLU cc_start: 0.8491 (tm-30) cc_final: 0.7988 (tm-30) REVERT: A 1310 PHE cc_start: 0.6575 (m-80) cc_final: 0.6325 (m-10) REVERT: A 1313 GLU cc_start: 0.7646 (mp0) cc_final: 0.7213 (mp0) REVERT: A 1346 MET cc_start: 0.8935 (mtp) cc_final: 0.8506 (mtp) REVERT: A 1349 LYS cc_start: 0.8901 (tttt) cc_final: 0.8279 (tmmt) REVERT: A 1350 LYS cc_start: 0.9044 (mmmm) cc_final: 0.8772 (mmmm) REVERT: A 1386 VAL cc_start: 0.8354 (t) cc_final: 0.7985 (m) REVERT: A 1545 HIS cc_start: 0.8341 (m-70) cc_final: 0.8051 (m-70) REVERT: A 1696 GLN cc_start: 0.8276 (mt0) cc_final: 0.8028 (mt0) REVERT: A 1701 LEU cc_start: 0.8181 (tp) cc_final: 0.7895 (tp) REVERT: A 1716 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7874 (tm-30) REVERT: A 1728 ASP cc_start: 0.8056 (m-30) cc_final: 0.7851 (m-30) REVERT: A 1730 ARG cc_start: 0.8182 (ttt-90) cc_final: 0.7981 (ttt180) REVERT: A 1759 LEU cc_start: 0.9104 (tp) cc_final: 0.8704 (tp) REVERT: A 1763 ILE cc_start: 0.9129 (mt) cc_final: 0.8920 (mt) REVERT: A 1772 GLU cc_start: 0.8248 (mt-10) cc_final: 0.7683 (tp30) REVERT: A 1809 LEU cc_start: 0.8937 (tp) cc_final: 0.8696 (tp) REVERT: A 1833 GLN cc_start: 0.8764 (tm-30) cc_final: 0.8428 (tm-30) REVERT: A 1850 GLU cc_start: 0.8165 (tt0) cc_final: 0.7855 (tt0) REVERT: A 1854 MET cc_start: 0.8988 (tpt) cc_final: 0.8727 (tpt) REVERT: A 1900 ARG cc_start: 0.8596 (ptp-110) cc_final: 0.8313 (ptp90) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.6449 time to fit residues: 337.5585 Evaluate side-chains 384 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 384 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 43 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1299 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11753 Z= 0.231 Angle : 0.548 6.600 16181 Z= 0.300 Chirality : 0.037 0.145 1891 Planarity : 0.005 0.045 1854 Dihedral : 15.452 90.765 2263 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.24), residues: 1261 helix: 1.13 (0.20), residues: 642 sheet: -0.04 (0.42), residues: 158 loop : -0.30 (0.31), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.004 TRP A 138 HIS 0.008 0.001 HIS A 116 PHE 0.019 0.002 PHE A1671 TYR 0.017 0.001 TYR A 124 ARG 0.005 0.000 ARG A 788 *********************** 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 411 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 411 time to evaluate : 1.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8895 (tp) cc_final: 0.8401 (tp) REVERT: A 56 LEU cc_start: 0.8897 (mt) cc_final: 0.8528 (mt) REVERT: A 84 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8050 (tm-30) REVERT: A 105 GLN cc_start: 0.8763 (mp10) cc_final: 0.8430 (mp10) REVERT: A 120 LYS cc_start: 0.8599 (ptpp) cc_final: 0.8187 (ptpp) REVERT: A 141 GLU cc_start: 0.8764 (mt-10) cc_final: 0.8120 (mm-30) REVERT: A 171 LEU cc_start: 0.7604 (mm) cc_final: 0.7355 (mm) REVERT: A 221 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8269 (mt-10) REVERT: A 232 SER cc_start: 0.8476 (m) cc_final: 0.7924 (t) REVERT: A 235 GLU cc_start: 0.8097 (pm20) cc_final: 0.7885 (pm20) REVERT: A 267 TYR cc_start: 0.8667 (t80) cc_final: 0.8177 (t80) REVERT: A 272 MET cc_start: 0.8956 (mpp) cc_final: 0.8460 (mtp) REVERT: A 275 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8542 (mt-10) REVERT: A 329 LEU cc_start: 0.9282 (tp) cc_final: 0.9017 (tp) REVERT: A 354 LYS cc_start: 0.9224 (mmtm) cc_final: 0.9020 (mptt) REVERT: A 382 GLU cc_start: 0.8998 (mt-10) cc_final: 0.8740 (mt-10) REVERT: A 503 GLU cc_start: 0.9024 (mt-10) cc_final: 0.8572 (mt-10) REVERT: A 541 THR cc_start: 0.8183 (m) cc_final: 0.7799 (p) REVERT: A 631 ILE cc_start: 0.8150 (pt) cc_final: 0.7696 (mt) REVERT: A 634 ILE cc_start: 0.9055 (mm) cc_final: 0.8796 (mm) REVERT: A 648 HIS cc_start: 0.7099 (t-90) cc_final: 0.6764 (t-90) REVERT: A 698 CYS cc_start: 0.9144 (t) cc_final: 0.8626 (m) REVERT: A 761 TYR cc_start: 0.8445 (t80) cc_final: 0.8201 (t80) REVERT: A 775 MET cc_start: 0.8125 (mtp) cc_final: 0.7657 (mtp) REVERT: A 824 GLU cc_start: 0.7319 (tm-30) cc_final: 0.6856 (tm-30) REVERT: A 828 SER cc_start: 0.7985 (m) cc_final: 0.7538 (t) REVERT: A 842 MET cc_start: 0.9314 (tpt) cc_final: 0.9018 (tpp) REVERT: A 849 LEU cc_start: 0.8950 (tp) cc_final: 0.8748 (tp) REVERT: A 851 GLN cc_start: 0.9064 (tt0) cc_final: 0.8491 (tt0) REVERT: A 897 MET cc_start: 0.8683 (mtp) cc_final: 0.8215 (mtp) REVERT: A 901 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8411 (tm-30) REVERT: A 916 LYS cc_start: 0.9574 (tmtt) cc_final: 0.9301 (tptp) REVERT: A 1041 HIS cc_start: 0.8125 (t-90) cc_final: 0.7820 (t-90) REVERT: A 1069 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8041 (tm-30) REVERT: A 1305 ASN cc_start: 0.8490 (t0) cc_final: 0.8118 (t0) REVERT: A 1310 PHE cc_start: 0.6711 (m-80) cc_final: 0.6405 (m-10) REVERT: A 1313 GLU cc_start: 0.7711 (mp0) cc_final: 0.7260 (mp0) REVERT: A 1346 MET cc_start: 0.8963 (mtp) cc_final: 0.8551 (mtp) REVERT: A 1349 LYS cc_start: 0.8941 (tttt) cc_final: 0.8342 (tmmt) REVERT: A 1350 LYS cc_start: 0.9002 (mmmm) cc_final: 0.8737 (mmmm) REVERT: A 1386 VAL cc_start: 0.8388 (t) cc_final: 0.8000 (m) REVERT: A 1545 HIS cc_start: 0.8366 (m-70) cc_final: 0.8114 (m-70) REVERT: A 1674 LYS cc_start: 0.9187 (mmtp) cc_final: 0.8856 (mmpt) REVERT: A 1701 LEU cc_start: 0.8301 (tp) cc_final: 0.8038 (tp) REVERT: A 1706 LEU cc_start: 0.8937 (tp) cc_final: 0.8650 (mt) REVERT: A 1716 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7993 (tm-30) REVERT: A 1728 ASP cc_start: 0.8097 (m-30) cc_final: 0.7868 (m-30) REVERT: A 1730 ARG cc_start: 0.8222 (ttt-90) cc_final: 0.8016 (ttt180) REVERT: A 1759 LEU cc_start: 0.9154 (tp) cc_final: 0.8820 (tp) REVERT: A 1772 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7761 (tp30) REVERT: A 1802 MET cc_start: 0.8408 (mmp) cc_final: 0.8182 (mmp) REVERT: A 1809 LEU cc_start: 0.9060 (tp) cc_final: 0.8815 (tp) REVERT: A 1813 ILE cc_start: 0.8657 (tp) cc_final: 0.8439 (tp) REVERT: A 1833 GLN cc_start: 0.8807 (tm-30) cc_final: 0.8485 (tm-30) REVERT: A 1850 GLU cc_start: 0.8156 (tt0) cc_final: 0.7837 (tt0) REVERT: A 1854 MET cc_start: 0.9003 (tpt) cc_final: 0.8756 (tpt) outliers start: 0 outliers final: 0 residues processed: 411 average time/residue: 0.6424 time to fit residues: 353.4382 Evaluate side-chains 385 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 124 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 80 optimal weight: 0.0870 chunk 78 optimal weight: 0.0970 chunk 59 optimal weight: 2.9990 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2766 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= 0.141 Angle : 0.507 6.800 16181 Z= 0.262 Chirality : 0.037 0.149 1891 Planarity : 0.004 0.042 1854 Dihedral : 15.347 90.233 2263 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.24), residues: 1261 helix: 1.57 (0.20), residues: 640 sheet: 0.02 (0.43), residues: 158 loop : -0.03 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP A 138 HIS 0.004 0.001 HIS A 116 PHE 0.029 0.001 PHE A1671 TYR 0.016 0.001 TYR A 124 ARG 0.004 0.000 ARG A 788 *********************** 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 395 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 395 time to evaluate : 1.924 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: A 52 LEU cc_start: 0.8823 (tp) cc_final: 0.8279 (tp) REVERT: A 56 LEU cc_start: 0.8818 (mt) cc_final: 0.8416 (mt) REVERT: A 79 LYS cc_start: 0.8888 (mttm) cc_final: 0.8516 (mttm) REVERT: A 84 GLN cc_start: 0.8548 (tm-30) cc_final: 0.7955 (tm-30) REVERT: A 120 LYS cc_start: 0.8593 (ptpp) cc_final: 0.8168 (ptpp) REVERT: A 141 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8022 (mm-30) REVERT: A 171 LEU cc_start: 0.7631 (mm) cc_final: 0.7388 (mm) REVERT: A 217 GLU cc_start: 0.8577 (pm20) cc_final: 0.8322 (pm20) REVERT: A 221 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8199 (mt-10) REVERT: A 235 GLU cc_start: 0.8166 (pm20) cc_final: 0.7912 (pm20) REVERT: A 267 TYR cc_start: 0.8620 (t80) cc_final: 0.8101 (t80) REVERT: A 272 MET cc_start: 0.8886 (mpp) cc_final: 0.8390 (mtp) REVERT: A 275 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8470 (mt-10) REVERT: A 329 LEU cc_start: 0.9253 (tp) cc_final: 0.8978 (tp) REVERT: A 382 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8638 (mt-10) REVERT: A 503 GLU cc_start: 0.8995 (mt-10) cc_final: 0.8536 (mt-10) REVERT: A 541 THR cc_start: 0.8213 (m) cc_final: 0.7857 (p) REVERT: A 631 ILE cc_start: 0.8079 (pt) cc_final: 0.7631 (mt) REVERT: A 634 ILE cc_start: 0.9011 (mm) cc_final: 0.8746 (mm) REVERT: A 648 HIS cc_start: 0.7057 (t-90) cc_final: 0.6709 (t-90) REVERT: A 698 CYS cc_start: 0.9106 (t) cc_final: 0.8578 (m) REVERT: A 761 TYR cc_start: 0.8418 (t80) cc_final: 0.8195 (t80) REVERT: A 775 MET cc_start: 0.8071 (mtp) cc_final: 0.7633 (mtp) REVERT: A 824 GLU cc_start: 0.7363 (tm-30) cc_final: 0.6921 (tm-30) REVERT: A 828 SER cc_start: 0.7960 (m) cc_final: 0.7508 (t) REVERT: A 842 MET cc_start: 0.9266 (tpt) cc_final: 0.8960 (tpp) REVERT: A 851 GLN cc_start: 0.9010 (tt0) cc_final: 0.8408 (tt0) REVERT: A 897 MET cc_start: 0.8694 (mtp) cc_final: 0.8146 (mtp) REVERT: A 901 GLU cc_start: 0.8654 (tm-30) cc_final: 0.8365 (tm-30) REVERT: A 916 LYS cc_start: 0.9568 (tmtt) cc_final: 0.9292 (tptp) REVERT: A 1041 HIS cc_start: 0.7934 (t-90) cc_final: 0.7587 (t-90) REVERT: A 1305 ASN cc_start: 0.8440 (t0) cc_final: 0.8053 (t0) REVERT: A 1313 GLU cc_start: 0.7589 (mp0) cc_final: 0.7177 (mp0) REVERT: A 1339 HIS cc_start: 0.8416 (p90) cc_final: 0.8005 (p90) REVERT: A 1346 MET cc_start: 0.8930 (mtp) cc_final: 0.8501 (mtp) REVERT: A 1349 LYS cc_start: 0.8890 (tttt) cc_final: 0.8263 (tmmt) REVERT: A 1350 LYS cc_start: 0.8992 (mmmm) cc_final: 0.8706 (mmmm) REVERT: A 1375 ASP cc_start: 0.8450 (t0) cc_final: 0.8233 (t0) REVERT: A 1386 VAL cc_start: 0.8347 (t) cc_final: 0.7972 (m) REVERT: A 1545 HIS cc_start: 0.8259 (m-70) cc_final: 0.7972 (m-70) REVERT: A 1651 LYS cc_start: 0.9094 (ptmm) cc_final: 0.8891 (ptmm) REVERT: A 1674 LYS cc_start: 0.9163 (mmtp) cc_final: 0.8794 (mmpt) REVERT: A 1701 LEU cc_start: 0.8195 (tp) cc_final: 0.7910 (tp) REVERT: A 1716 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7920 (mt-10) REVERT: A 1728 ASP cc_start: 0.8064 (m-30) cc_final: 0.7840 (m-30) REVERT: A 1730 ARG cc_start: 0.8179 (ttt-90) cc_final: 0.7973 (ttt180) REVERT: A 1759 LEU cc_start: 0.9098 (tp) cc_final: 0.8730 (tp) REVERT: A 1772 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7740 (tp30) REVERT: A 1809 LEU cc_start: 0.9064 (tp) cc_final: 0.8808 (tp) REVERT: A 1833 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8419 (tm-30) REVERT: A 1850 GLU cc_start: 0.8079 (tt0) cc_final: 0.7751 (tt0) REVERT: A 1854 MET cc_start: 0.8996 (tpt) cc_final: 0.8744 (tpt) outliers start: 0 outliers final: 0 residues processed: 395 average time/residue: 0.6570 time to fit residues: 345.2871 Evaluate side-chains 376 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 79 optimal weight: 0.0020 chunk 51 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 81 optimal weight: 0.1980 chunk 87 optimal weight: 0.6980 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11753 Z= 0.144 Angle : 0.500 6.146 16181 Z= 0.260 Chirality : 0.037 0.152 1891 Planarity : 0.004 0.040 1854 Dihedral : 15.276 89.409 2263 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.25), residues: 1261 helix: 1.68 (0.20), residues: 640 sheet: 0.03 (0.43), residues: 158 loop : 0.01 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 138 HIS 0.003 0.001 HIS A 703 PHE 0.022 0.001 PHE A 142 TYR 0.012 0.001 TYR A 124 ARG 0.003 0.000 ARG A 327 *********************** 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 400 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 400 time to evaluate : 1.712 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: A 52 LEU cc_start: 0.8829 (tp) cc_final: 0.8224 (tp) REVERT: A 56 LEU cc_start: 0.8827 (mt) cc_final: 0.8352 (mt) REVERT: A 79 LYS cc_start: 0.8878 (mttm) cc_final: 0.8503 (mttm) REVERT: A 84 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8284 (tm-30) REVERT: A 114 ARG cc_start: 0.8900 (ttm110) cc_final: 0.8584 (ttm110) REVERT: A 120 LYS cc_start: 0.8574 (ptpp) cc_final: 0.8167 (ptpp) REVERT: A 141 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8055 (mm-30) REVERT: A 171 LEU cc_start: 0.7610 (mm) cc_final: 0.7379 (mm) REVERT: A 217 GLU cc_start: 0.8564 (pm20) cc_final: 0.8337 (pm20) REVERT: A 221 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8204 (mt-10) REVERT: A 235 GLU cc_start: 0.8185 (pm20) cc_final: 0.7928 (pm20) REVERT: A 267 TYR cc_start: 0.8619 (t80) cc_final: 0.8112 (t80) REVERT: A 272 MET cc_start: 0.8902 (mpp) cc_final: 0.8390 (mtp) REVERT: A 275 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8472 (mt-10) REVERT: A 329 LEU cc_start: 0.9249 (tp) cc_final: 0.8999 (tp) REVERT: A 382 GLU cc_start: 0.8942 (mt-10) cc_final: 0.8670 (mt-10) REVERT: A 503 GLU cc_start: 0.8999 (mt-10) cc_final: 0.8544 (mt-10) REVERT: A 631 ILE cc_start: 0.8103 (pt) cc_final: 0.7652 (mt) REVERT: A 634 ILE cc_start: 0.9015 (mm) cc_final: 0.8751 (mm) REVERT: A 648 HIS cc_start: 0.7062 (t-90) cc_final: 0.6711 (t-90) REVERT: A 698 CYS cc_start: 0.9104 (t) cc_final: 0.8560 (m) REVERT: A 761 TYR cc_start: 0.8419 (t80) cc_final: 0.8186 (t80) REVERT: A 775 MET cc_start: 0.8081 (mtp) cc_final: 0.7639 (mtp) REVERT: A 800 ARG cc_start: 0.8403 (mmt90) cc_final: 0.7968 (mmt180) REVERT: A 824 GLU cc_start: 0.7413 (tm-30) cc_final: 0.6977 (tm-30) REVERT: A 827 ILE cc_start: 0.8922 (mp) cc_final: 0.8711 (mp) REVERT: A 828 SER cc_start: 0.7922 (m) cc_final: 0.7447 (t) REVERT: A 842 MET cc_start: 0.9260 (tpt) cc_final: 0.8964 (tpp) REVERT: A 851 GLN cc_start: 0.9003 (tt0) cc_final: 0.8505 (tt0) REVERT: A 897 MET cc_start: 0.8740 (mtp) cc_final: 0.8317 (mtp) REVERT: A 901 GLU cc_start: 0.8656 (tm-30) cc_final: 0.8364 (tm-30) REVERT: A 916 LYS cc_start: 0.9566 (tmtt) cc_final: 0.9284 (tptp) REVERT: A 1069 GLU cc_start: 0.8513 (tm-30) cc_final: 0.7814 (tm-30) REVERT: A 1313 GLU cc_start: 0.7573 (mp0) cc_final: 0.7257 (mp0) REVERT: A 1339 HIS cc_start: 0.8395 (p90) cc_final: 0.7998 (p90) REVERT: A 1346 MET cc_start: 0.8952 (mtp) cc_final: 0.8524 (mtp) REVERT: A 1349 LYS cc_start: 0.8890 (tttt) cc_final: 0.8268 (tmmt) REVERT: A 1350 LYS cc_start: 0.8992 (mmmm) cc_final: 0.8708 (mmmm) REVERT: A 1386 VAL cc_start: 0.8357 (t) cc_final: 0.7980 (m) REVERT: A 1545 HIS cc_start: 0.8265 (m-70) cc_final: 0.7980 (m-70) REVERT: A 1585 LYS cc_start: 0.7900 (tptt) cc_final: 0.7555 (tptp) REVERT: A 1651 LYS cc_start: 0.9089 (ptmm) cc_final: 0.8887 (ptmm) REVERT: A 1674 LYS cc_start: 0.9158 (mmtp) cc_final: 0.8792 (mmpt) REVERT: A 1701 LEU cc_start: 0.8214 (tp) cc_final: 0.7923 (tp) REVERT: A 1710 ILE cc_start: 0.9089 (tp) cc_final: 0.8853 (tp) REVERT: A 1716 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7585 (mt-10) REVERT: A 1728 ASP cc_start: 0.8085 (m-30) cc_final: 0.7869 (m-30) REVERT: A 1730 ARG cc_start: 0.8177 (ttt-90) cc_final: 0.7945 (ttt180) REVERT: A 1748 TYR cc_start: 0.8135 (m-10) cc_final: 0.7752 (m-10) REVERT: A 1759 LEU cc_start: 0.9086 (tp) cc_final: 0.8705 (tp) REVERT: A 1772 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7682 (tp30) REVERT: A 1809 LEU cc_start: 0.9059 (tp) cc_final: 0.8525 (tp) REVERT: A 1833 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8410 (tm-30) REVERT: A 1850 GLU cc_start: 0.8113 (tt0) cc_final: 0.7805 (tt0) REVERT: A 1854 MET cc_start: 0.8994 (tpt) cc_final: 0.8743 (tpt) REVERT: A 1900 ARG cc_start: 0.8617 (ptp-110) cc_final: 0.8289 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 400 average time/residue: 0.6412 time to fit residues: 342.8501 Evaluate side-chains 379 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 116 optimal weight: 0.6980 chunk 122 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 119 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 93 optimal weight: 0.8980 chunk 36 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11753 Z= 0.183 Angle : 0.525 6.373 16181 Z= 0.279 Chirality : 0.037 0.149 1891 Planarity : 0.004 0.037 1854 Dihedral : 15.365 89.659 2263 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.24), residues: 1261 helix: 1.47 (0.20), residues: 640 sheet: 0.01 (0.43), residues: 158 loop : -0.16 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 138 HIS 0.006 0.001 HIS A1687 PHE 0.021 0.002 PHE A1671 TYR 0.011 0.001 TYR A 47 ARG 0.003 0.000 ARG A1697 *********************** 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 398 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 398 time to evaluate : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8854 (tp) cc_final: 0.8286 (tp) REVERT: A 56 LEU cc_start: 0.8862 (mt) cc_final: 0.8387 (mt) REVERT: A 79 LYS cc_start: 0.8893 (mttm) cc_final: 0.8505 (mttm) REVERT: A 84 GLN cc_start: 0.8583 (tm-30) cc_final: 0.8315 (tm-30) REVERT: A 116 HIS cc_start: 0.8228 (t-170) cc_final: 0.7940 (t-170) REVERT: A 120 LYS cc_start: 0.8554 (ptpp) cc_final: 0.8124 (ptpp) REVERT: A 141 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8120 (mm-30) REVERT: A 171 LEU cc_start: 0.7619 (mm) cc_final: 0.7393 (mm) REVERT: A 217 GLU cc_start: 0.8606 (pm20) cc_final: 0.8328 (pm20) REVERT: A 221 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8252 (mt-10) REVERT: A 235 GLU cc_start: 0.8190 (pm20) cc_final: 0.7972 (pm20) REVERT: A 267 TYR cc_start: 0.8678 (t80) cc_final: 0.8150 (t80) REVERT: A 329 LEU cc_start: 0.9256 (tp) cc_final: 0.9006 (tp) REVERT: A 382 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8673 (mt-10) REVERT: A 503 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8561 (mt-10) REVERT: A 541 THR cc_start: 0.8164 (m) cc_final: 0.7846 (p) REVERT: A 631 ILE cc_start: 0.8135 (pt) cc_final: 0.7679 (mt) REVERT: A 634 ILE cc_start: 0.9032 (mm) cc_final: 0.8772 (mm) REVERT: A 648 HIS cc_start: 0.7038 (t-90) cc_final: 0.6699 (t-90) REVERT: A 698 CYS cc_start: 0.9107 (t) cc_final: 0.8568 (m) REVERT: A 761 TYR cc_start: 0.8428 (t80) cc_final: 0.8199 (t80) REVERT: A 775 MET cc_start: 0.8091 (mtp) cc_final: 0.7656 (mtp) REVERT: A 779 THR cc_start: 0.8730 (m) cc_final: 0.8288 (m) REVERT: A 824 GLU cc_start: 0.7402 (tm-30) cc_final: 0.6994 (tm-30) REVERT: A 842 MET cc_start: 0.9249 (tpt) cc_final: 0.9030 (tpp) REVERT: A 851 GLN cc_start: 0.9030 (tt0) cc_final: 0.8454 (tt0) REVERT: A 897 MET cc_start: 0.8682 (mtp) cc_final: 0.8240 (mtp) REVERT: A 901 GLU cc_start: 0.8699 (tm-30) cc_final: 0.8398 (tm-30) REVERT: A 916 LYS cc_start: 0.9567 (tmtt) cc_final: 0.9295 (tptp) REVERT: A 1069 GLU cc_start: 0.8514 (tm-30) cc_final: 0.7827 (tm-30) REVERT: A 1305 ASN cc_start: 0.8495 (t0) cc_final: 0.8101 (t0) REVERT: A 1313 GLU cc_start: 0.7628 (mp0) cc_final: 0.7215 (mp0) REVERT: A 1346 MET cc_start: 0.8958 (mtp) cc_final: 0.8539 (mtp) REVERT: A 1349 LYS cc_start: 0.8930 (tttt) cc_final: 0.8330 (tmmt) REVERT: A 1350 LYS cc_start: 0.9000 (mmmm) cc_final: 0.8741 (mmmm) REVERT: A 1386 VAL cc_start: 0.8405 (t) cc_final: 0.8000 (m) REVERT: A 1545 HIS cc_start: 0.8273 (m-70) cc_final: 0.8014 (m-70) REVERT: A 1651 LYS cc_start: 0.9088 (ptmm) cc_final: 0.8888 (ptmm) REVERT: A 1674 LYS cc_start: 0.9163 (mmtp) cc_final: 0.8807 (mmpt) REVERT: A 1701 LEU cc_start: 0.8237 (tp) cc_final: 0.7951 (tp) REVERT: A 1710 ILE cc_start: 0.9099 (tp) cc_final: 0.8884 (tp) REVERT: A 1728 ASP cc_start: 0.8090 (m-30) cc_final: 0.7868 (m-30) REVERT: A 1730 ARG cc_start: 0.8211 (ttt-90) cc_final: 0.7984 (ttt180) REVERT: A 1748 TYR cc_start: 0.8146 (m-10) cc_final: 0.7813 (m-10) REVERT: A 1750 LYS cc_start: 0.8915 (mttt) cc_final: 0.8630 (mttt) REVERT: A 1759 LEU cc_start: 0.9108 (tp) cc_final: 0.8752 (tp) REVERT: A 1772 GLU cc_start: 0.8265 (mt-10) cc_final: 0.7704 (tp30) REVERT: A 1802 MET cc_start: 0.8377 (mmp) cc_final: 0.8169 (mmp) REVERT: A 1809 LEU cc_start: 0.9056 (tp) cc_final: 0.8695 (tp) REVERT: A 1833 GLN cc_start: 0.8736 (tm-30) cc_final: 0.8385 (tm-30) REVERT: A 1850 GLU cc_start: 0.8126 (tt0) cc_final: 0.7792 (tt0) REVERT: A 1854 MET cc_start: 0.9004 (tpt) cc_final: 0.8751 (tpt) REVERT: A 1900 ARG cc_start: 0.8635 (ptp-110) cc_final: 0.8305 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 398 average time/residue: 0.6466 time to fit residues: 343.3025 Evaluate side-chains 383 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 383 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 87 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 105 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 chunk 112 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.3049 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= 0.169 Angle : 0.521 6.431 16181 Z= 0.273 Chirality : 0.037 0.151 1891 Planarity : 0.004 0.037 1854 Dihedral : 15.373 90.085 2263 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.24), residues: 1261 helix: 1.47 (0.20), residues: 640 sheet: 0.03 (0.43), residues: 158 loop : -0.12 (0.31), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 138 HIS 0.004 0.001 HIS A1687 PHE 0.024 0.001 PHE A1671 TYR 0.021 0.001 TYR A 793 ARG 0.005 0.000 ARG A1003 ********************** 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 396 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 1.749 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: 0.8821 (tp) cc_final: 0.8224 (tp) REVERT: A 56 LEU cc_start: 0.8832 (mt) cc_final: 0.8350 (mt) REVERT: A 79 LYS cc_start: 0.8875 (mttm) cc_final: 0.8505 (mttm) REVERT: A 84 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8286 (tm-30) REVERT: A 105 GLN cc_start: 0.8628 (mp10) cc_final: 0.8235 (mp10) REVERT: A 116 HIS cc_start: 0.8233 (t-170) cc_final: 0.7924 (t-170) REVERT: A 120 LYS cc_start: 0.8549 (ptpp) cc_final: 0.8107 (ptpp) REVERT: A 141 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8065 (mm-30) REVERT: A 171 LEU cc_start: 0.7607 (mm) cc_final: 0.7383 (mm) REVERT: A 217 GLU cc_start: 0.8600 (pm20) cc_final: 0.8292 (pm20) REVERT: A 221 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8238 (mt-10) REVERT: A 267 TYR cc_start: 0.8678 (t80) cc_final: 0.8077 (t80) REVERT: A 329 LEU cc_start: 0.9232 (tp) cc_final: 0.8999 (tp) REVERT: A 382 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8668 (mt-10) REVERT: A 503 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8551 (mt-10) REVERT: A 631 ILE cc_start: 0.8118 (pt) cc_final: 0.7664 (mt) REVERT: A 634 ILE cc_start: 0.9022 (mm) cc_final: 0.8767 (mm) REVERT: A 648 HIS cc_start: 0.7023 (t-90) cc_final: 0.6676 (t-90) REVERT: A 698 CYS cc_start: 0.9085 (t) cc_final: 0.8551 (m) REVERT: A 761 TYR cc_start: 0.8426 (t80) cc_final: 0.8193 (t80) REVERT: A 775 MET cc_start: 0.8066 (mtp) cc_final: 0.7640 (mtp) REVERT: A 779 THR cc_start: 0.8736 (m) cc_final: 0.8289 (m) REVERT: A 800 ARG cc_start: 0.8428 (mmt90) cc_final: 0.7981 (mmt180) REVERT: A 824 GLU cc_start: 0.7420 (tm-30) cc_final: 0.7005 (tm-30) REVERT: A 830 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7555 (tm-30) REVERT: A 842 MET cc_start: 0.9247 (tpt) cc_final: 0.9030 (tpp) REVERT: A 851 GLN cc_start: 0.9020 (tt0) cc_final: 0.8441 (tt0) REVERT: A 897 MET cc_start: 0.8672 (mtp) cc_final: 0.8237 (mtp) REVERT: A 901 GLU cc_start: 0.8679 (tm-30) cc_final: 0.8383 (tm-30) REVERT: A 916 LYS cc_start: 0.9567 (tmtt) cc_final: 0.9296 (tptp) REVERT: A 1001 THR cc_start: 0.8705 (p) cc_final: 0.8269 (m) REVERT: A 1069 GLU cc_start: 0.8492 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 1305 ASN cc_start: 0.8504 (t0) cc_final: 0.8111 (t0) REVERT: A 1311 ASN cc_start: 0.8180 (m110) cc_final: 0.7733 (m110) REVERT: A 1313 GLU cc_start: 0.7598 (mp0) cc_final: 0.7237 (mp0) REVERT: A 1346 MET cc_start: 0.8956 (mtp) cc_final: 0.8533 (mtp) REVERT: A 1349 LYS cc_start: 0.8911 (tttt) cc_final: 0.8304 (tmmt) REVERT: A 1350 LYS cc_start: 0.8994 (mmmm) cc_final: 0.8734 (mmmm) REVERT: A 1386 VAL cc_start: 0.8406 (t) cc_final: 0.8002 (m) REVERT: A 1545 HIS cc_start: 0.8264 (m-70) cc_final: 0.8007 (m-70) REVERT: A 1651 LYS cc_start: 0.9091 (ptmm) cc_final: 0.8882 (ptmm) REVERT: A 1674 LYS cc_start: 0.9162 (mmtp) cc_final: 0.8802 (mmpt) REVERT: A 1701 LEU cc_start: 0.8235 (tp) cc_final: 0.7948 (tp) REVERT: A 1710 ILE cc_start: 0.9108 (tp) cc_final: 0.8884 (tp) REVERT: A 1730 ARG cc_start: 0.8187 (ttt-90) cc_final: 0.7955 (ttt180) REVERT: A 1748 TYR cc_start: 0.8106 (m-10) cc_final: 0.7794 (m-10) REVERT: A 1750 LYS cc_start: 0.8890 (mttt) cc_final: 0.8647 (mttt) REVERT: A 1759 LEU cc_start: 0.9104 (tp) cc_final: 0.8748 (tp) REVERT: A 1772 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7742 (tp30) REVERT: A 1802 MET cc_start: 0.8369 (mmp) cc_final: 0.8160 (mmp) REVERT: A 1809 LEU cc_start: 0.9067 (tp) cc_final: 0.8716 (tp) REVERT: A 1833 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8355 (tm-30) REVERT: A 1850 GLU cc_start: 0.8103 (tt0) cc_final: 0.7778 (tt0) REVERT: A 1854 MET cc_start: 0.9000 (tpt) cc_final: 0.8750 (tpt) REVERT: A 1900 ARG cc_start: 0.8623 (ptp-110) cc_final: 0.8304 (ptp-170) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.6390 time to fit residues: 337.2249 Evaluate side-chains 376 residues out of total 1146 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 376 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 133 random chunks: chunk 32 optimal weight: 0.7980 chunk 97 optimal weight: 0.0870 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 211 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.122069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.094718 restraints weight = 70676.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.100915 restraints weight = 31862.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.105055 restraints weight = 17717.202| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11753 Z= 0.177 Angle : 0.526 6.006 16181 Z= 0.279 Chirality : 0.037 0.150 1891 Planarity : 0.004 0.037 1854 Dihedral : 15.416 90.601 2263 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.24), residues: 1261 helix: 1.38 (0.20), residues: 641 sheet: 0.04 (0.43), residues: 155 loop : -0.18 (0.31), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 138 HIS 0.004 0.001 HIS A1713 PHE 0.023 0.001 PHE A1671 TYR 0.017 0.001 TYR A 793 ARG 0.004 0.000 ARG A 996 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7534.06 seconds wall clock time: 132 minutes 57.59 seconds (7977.59 seconds total)