Starting phenix.real_space_refine
on Thu Jun 19 21:22:21 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/7yym_14383/06_2025/7yym_14383.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yym_14383/06_2025/7yym_14383.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yym_14383/06_2025/7yym_14383.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yym_14383/06_2025/7yym_14383.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yym_14383/06_2025/7yym_14383.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yym_14383/06_2025/7yym_14383.cif"
  }
  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
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 12.66, per 1000 atoms: 0.57
  Number of scatterers: 22359
  At special positions: 0
  Unit cell: (97.704, 105.156, 163.944, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      57     16.00
     P      55     15.00
     O    2261      8.00
     N    1945      7.00
     C    7080      6.00
     H   10961      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 6.31
  Conformation dependent library (CDL) restraints added in 1.8 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: 11.60
  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: 10.76

  Time building geometry restraints manager: 7.63 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        0.83 -     1.02: 10923
        1.02 -     1.22: 52
        1.22 -     1.42: 4824
        1.42 -     1.61: 6837
        1.61 -     1.81: 78
  Bond restraints: 22714
  Sorted by residual:
  bond pdb=" N   LYS A 160 "
       pdb=" H   LYS A 160 "
    ideal  model  delta    sigma   weight residual
    0.860  1.037 -0.177 2.00e-02 2.50e+03 7.79e+01
  bond pdb=" CA  LYS A 160 "
       pdb=" HA  LYS A 160 "
    ideal  model  delta    sigma   weight residual
    0.970  1.088 -0.118 2.00e-02 2.50e+03 3.49e+01
  bond pdb=" N   LYS A 160 "
       pdb=" CA  LYS A 160 "
    ideal  model  delta    sigma   weight residual
    1.459  1.484 -0.024 1.19e-02 7.06e+03 4.18e+00
  bond pdb=" NH1 ARG A  86 "
       pdb="HH12 ARG A  86 "
    ideal  model  delta    sigma   weight residual
    0.860  0.826  0.034 2.00e-02 2.50e+03 2.95e+00
  bond pdb=" NE2 GLN A 985 "
       pdb="HE22 GLN A 985 "
    ideal  model  delta    sigma   weight residual
    0.860  0.832  0.028 2.00e-02 2.50e+03 1.92e+00
  ... (remaining 22709 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 39068
        1.56 -     3.11: 1854
        3.11 -     4.67: 202
        4.67 -     6.22: 27
        6.22 -     7.78: 4
  Bond angle restraints: 41155
  Sorted by residual:
  angle pdb=" N   GLN A1826 "
        pdb=" CA  GLN A1826 "
        pdb=" CB  GLN A1826 "
      ideal   model   delta    sigma   weight residual
     110.39  116.43   -6.04 1.66e+00 3.63e-01 1.32e+01
  angle pdb=" N   LYS A 160 "
        pdb=" CA  LYS A 160 "
        pdb=" C   LYS A 160 "
      ideal   model   delta    sigma   weight residual
     111.07  107.29    3.78 1.07e+00 8.73e-01 1.25e+01
  angle pdb=" CA  TRP A 138 "
        pdb=" CB  TRP A 138 "
        pdb=" CG  TRP A 138 "
      ideal   model   delta    sigma   weight residual
     113.60  119.64   -6.04 1.90e+00 2.77e-01 1.01e+01
  angle pdb=" C2'   U B  57 "
        pdb=" C1'   U B  57 "
        pdb=" N1    U B  57 "
      ideal   model   delta    sigma   weight residual
     112.00  116.54   -4.54 1.50e+00 4.44e-01 9.18e+00
  angle pdb=" C2'   A B  13 "
        pdb=" C1'   A B  13 "
        pdb=" N9    A B  13 "
      ideal   model   delta    sigma   weight residual
     112.00  116.42   -4.42 1.50e+00 4.44e-01 8.67e+00
  ... (remaining 41150 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.83: 10461
       35.83 -    71.65: 308
       71.65 -   107.48: 19
      107.48 -   143.30: 0
      143.30 -   179.13: 8
  Dihedral angle restraints: 10796
    sinusoidal: 6381
      harmonic: 4415
  Sorted by residual:
  dihedral pdb=" C5'   A B  59 "
           pdb=" C4'   A B  59 "
           pdb=" C3'   A B  59 "
           pdb=" O3'   A B  59 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   98.94   48.06     1      8.00e+00 1.56e-02 4.97e+01
  dihedral pdb=" O4'   A B  59 "
           pdb=" C4'   A B  59 "
           pdb=" C3'   A B  59 "
           pdb=" C2'   A B  59 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -23.49   47.49     1      8.00e+00 1.56e-02 4.86e+01
  dihedral pdb=" C4'   A B  59 "
           pdb=" C3'   A B  59 "
           pdb=" C2'   A B  59 "
           pdb=" C1'   A B  59 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00    5.77  -40.77     1      8.00e+00 1.56e-02 3.64e+01
  ... (remaining 10793 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 1429
       0.048 -    0.095: 344
       0.095 -    0.143: 105
       0.143 -    0.190: 12
       0.190 -    0.238: 1
  Chirality restraints: 1891
  Sorted by residual:
  chirality pdb=" C1'   A B  13 "
            pdb=" O4'   A B  13 "
            pdb=" C2'   A B  13 "
            pdb=" N9    A B  13 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.22    0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" C1'   G B  51 "
            pdb=" O4'   G B  51 "
            pdb=" C2'   G B  51 "
            pdb=" N9    G B  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.28    0.18 2.00e-01 2.50e+01 7.67e-01
  chirality pdb=" C1'   C B  55 "
            pdb=" O4'   C B  55 "
            pdb=" C2'   C B  55 "
            pdb=" N1    C B  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.29    0.17 2.00e-01 2.50e+01 7.59e-01
  ... (remaining 1888 not shown)

  Planarity restraints: 3090
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  86 "   -0.023 9.50e-02 1.11e+02   7.14e-02 1.13e+02
        pdb=" NE  ARG A  86 "   -0.090 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  86 "    0.088 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  86 "    0.114 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  86 "    0.030 2.00e-02 2.50e+03
        pdb="HH11 ARG A  86 "    0.008 2.00e-02 2.50e+03
        pdb="HH12 ARG A  86 "   -0.121 2.00e-02 2.50e+03
        pdb="HH21 ARG A  86 "   -0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG A  86 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 985 "   -0.057 2.00e-02 2.50e+03   6.86e-02 7.06e+01
        pdb=" CD  GLN A 985 "    0.055 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 985 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 985 "    0.104 2.00e-02 2.50e+03
        pdb="HE21 GLN A 985 "    0.006 2.00e-02 2.50e+03
        pdb="HE22 GLN A 985 "   -0.105 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 187 "   -0.367 9.50e-02 1.11e+02   1.30e-01 6.04e+01
        pdb=" NE  ARG A 187 "   -0.035 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 187 "    0.033 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 187 "    0.046 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 187 "    0.079 2.00e-02 2.50e+03
        pdb="HH11 ARG A 187 "    0.000 2.00e-02 2.50e+03
        pdb="HH12 ARG A 187 "   -0.031 2.00e-02 2.50e+03
        pdb="HH21 ARG A 187 "    0.003 2.00e-02 2.50e+03
        pdb="HH22 ARG A 187 "   -0.080 2.00e-02 2.50e+03
  ... (remaining 3087 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 1305
        2.21 -     2.81: 45824
        2.81 -     3.41: 59671
        3.41 -     4.00: 74844
        4.00 -     4.60: 116099
  Nonbonded interactions: 297743
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 644 "
            pdb=" HG1 THR A 647 "
     model   vdw
     1.613 2.450
  nonbonded pdb=" O   LEU A1678 "
            pdb=" HG1 THR A1682 "
     model   vdw
     1.614 2.450
  nonbonded pdb=" HG1 THR A1867 "
            pdb=" OD1 ASP A1869 "
     model   vdw
     1.622 2.450
  nonbonded pdb=" O   GLU A 542 "
            pdb=" HG  SER A 545 "
     model   vdw
     1.622 2.450
  nonbonded pdb=" H   SER A1862 "
            pdb=" O   THR A1875 "
     model   vdw
     1.635 2.450
  ... (remaining 297738 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.010
  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:             0.390
  Extract box with map and model:          0.980
  Check model and map are aligned:         0.180
  Set scattering table:                    0.210
  Process input model:                     64.190
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.090
  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:3.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   73.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  11753  Z= 0.178
  Angle     :  0.798   7.778  16181  Z= 0.449
  Chirality :  0.046   0.238   1891
  Planarity :  0.011   0.124   1854
  Dihedral  : 15.157 101.222   4817
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 1.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.67 %
    Favored  : 98.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10748 (  564)
  hydrogen bonds       : angle       5.21471 ( 1575)
  covalent geometry    : bond        0.00385 (11753)
  covalent geometry    : angle       0.79809 (16181)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue LYS  160 is missing expected H atoms. Skipping.
Residue TYR  246 is missing expected H atoms. Skipping.
Residue THR  247 is missing expected H atoms. Skipping.
Residue SER  248 is missing expected H atoms. Skipping.
Residue ALA 1807 is missing expected H atoms. Skipping.
Evaluate side-chains
  427 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 425
  time to evaluate  : 1.702 
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: 0.6594
  time to fit residues: 376.7353
Evaluate side-chains
  391 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 391
  time to evaluate  : 1.619 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 55 optimal weight:    6.9990
   chunk 34 optimal weight:    7.9990
   chunk 67 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 104 optimal weight:    0.0370
   chunk 40 optimal weight:    4.9990
   chunk 63 optimal weight:    0.3980
   chunk 77 optimal weight:    5.9990
   chunk 120 optimal weight:    0.0570
   overall best weight:    0.4980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 116 HIS
** A1826 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.127315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.098796 restraints weight = 68849.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.105145 restraints weight = 31042.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.109469 restraints weight = 17288.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021  11753  Z= 0.119
  Angle     :  0.550   6.819  16181  Z= 0.288
  Chirality :  0.038   0.153   1891
  Planarity :  0.005   0.045   1854
  Dihedral  : 15.299  95.988   2263
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.56 (0.20), residues: 635
  sheet: -0.29 (0.41), residues: 153
  loop :  0.04 (0.30), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 138 
 HIS   0.003   0.001   HIS A 703 
 PHE   0.018   0.001   PHE A1671 
 TYR   0.015   0.001   TYR A1891 
 ARG   0.005   0.000   ARG A 788 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05055 (  564)
  hydrogen bonds       : angle       4.64905 ( 1575)
  covalent geometry    : bond        0.00243 (11753)
  covalent geometry    : angle       0.55032 (16181)

*********************** 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
  403 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 403
  time to evaluate  : 1.624 
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: A   52 LEU cc_start: 0.8881 (tp) cc_final: 0.8577 (tp)
REVERT: A  105 GLN cc_start: 0.8504 (mp10) cc_final: 0.8226 (mp10)
REVERT: A  120 LYS cc_start: 0.8602 (ptpp) cc_final: 0.8257 (ptpp)
REVERT: A  141 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8301 (mm-30)
REVERT: A  153 TYR cc_start: 0.8520 (m-10) cc_final: 0.8135 (m-10)
REVERT: A  171 LEU cc_start: 0.7728 (mm) cc_final: 0.7455 (mm)
REVERT: A  188 GLU cc_start: 0.8821 (mp0) cc_final: 0.8543 (mp0)
REVERT: A  217 GLU cc_start: 0.8525 (pm20) cc_final: 0.8315 (pm20)
REVERT: A  221 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8268 (mt-10)
REVERT: A  225 LYS cc_start: 0.8305 (ttpp) cc_final: 0.8096 (tttm)
REVERT: A  231 ARG cc_start: 0.8890 (tmm-80) cc_final: 0.8269 (ptm-80)
REVERT: A  267 TYR cc_start: 0.8625 (t80) cc_final: 0.8053 (t80)
REVERT: A  270 LEU cc_start: 0.9256 (mt) cc_final: 0.9054 (mt)
REVERT: A  275 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8602 (mt-10)
REVERT: A  321 VAL cc_start: 0.8886 (t) cc_final: 0.8181 (t)
REVERT: A  324 MET cc_start: 0.8860 (mpp) cc_final: 0.8576 (mpp)
REVERT: A  329 LEU cc_start: 0.9210 (tp) cc_final: 0.8955 (tp)
REVERT: A  500 LYS cc_start: 0.9226 (mppt) cc_final: 0.8675 (mppt)
REVERT: A  502 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8505 (mm-30)
REVERT: A  503 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8477 (mt-10)
REVERT: A  541 THR cc_start: 0.8194 (m) cc_final: 0.7886 (p)
REVERT: A  544 ARG cc_start: 0.8978 (ppt170) cc_final: 0.8511 (ppt170)
REVERT: A  575 ASP cc_start: 0.8387 (m-30) cc_final: 0.7904 (m-30)
REVERT: A  631 ILE cc_start: 0.8073 (pt) cc_final: 0.7636 (mt)
REVERT: A  634 ILE cc_start: 0.9037 (mm) cc_final: 0.8797 (mm)
REVERT: A  646 PHE cc_start: 0.8672 (m-80) cc_final: 0.8413 (m-80)
REVERT: A  648 HIS cc_start: 0.7074 (t-90) cc_final: 0.6713 (t-90)
REVERT: A  698 CYS cc_start: 0.9189 (t) cc_final: 0.8766 (m)
REVERT: A  749 TYR cc_start: 0.7945 (m-10) cc_final: 0.7655 (m-10)
REVERT: A  761 TYR cc_start: 0.8457 (t80) cc_final: 0.8226 (t80)
REVERT: A  784 GLU cc_start: 0.8843 (pp20) cc_final: 0.8359 (pm20)
REVERT: A  791 LYS cc_start: 0.9038 (ptmm) cc_final: 0.8771 (pttp)
REVERT: A  800 ARG cc_start: 0.8253 (mmt180) cc_final: 0.7877 (mmt90)
REVERT: A  815 HIS cc_start: 0.7403 (p90) cc_final: 0.6986 (p90)
REVERT: A  828 SER cc_start: 0.7957 (m) cc_final: 0.7452 (p)
REVERT: A  842 MET cc_start: 0.9041 (tpp) cc_final: 0.8648 (tpp)
REVERT: A  851 GLN cc_start: 0.8991 (tt0) cc_final: 0.8538 (tt0)
REVERT: A  894 PHE cc_start: 0.8130 (m-10) cc_final: 0.7877 (m-10)
REVERT: A  901 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8207 (tm-30)
REVERT: A  916 LYS cc_start: 0.9534 (tmtt) cc_final: 0.9240 (tptp)
REVERT: A  970 GLU cc_start: 0.8776 (tt0) cc_final: 0.8474 (mt-10)
REVERT: A  973 LYS cc_start: 0.9227 (mmmt) cc_final: 0.8921 (mmmt)
REVERT: A  992 HIS cc_start: 0.8165 (m-70) cc_final: 0.7796 (m-70)
REVERT: A 1069 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8014 (tm-30)
REVERT: A 1070 LEU cc_start: 0.8985 (tp) cc_final: 0.8719 (tp)
REVERT: A 1313 GLU cc_start: 0.6669 (mp0) cc_final: 0.6424 (mp0)
REVERT: A 1340 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7834 (tm-30)
REVERT: A 1346 MET cc_start: 0.8940 (mtp) cc_final: 0.8465 (mtp)
REVERT: A 1349 LYS cc_start: 0.8887 (tttt) cc_final: 0.8234 (tmmt)
REVERT: A 1350 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8666 (mmmm)
REVERT: A 1368 ARG cc_start: 0.8775 (mmm-85) cc_final: 0.8457 (mmm-85)
REVERT: A 1545 HIS cc_start: 0.8409 (m-70) cc_final: 0.8016 (m-70)
REVERT: A 1664 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8201 (mt-10)
REVERT: A 1701 LEU cc_start: 0.8109 (tp) cc_final: 0.7830 (tp)
REVERT: A 1706 LEU cc_start: 0.8793 (tp) cc_final: 0.8529 (tp)
REVERT: A 1716 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7836 (tm-30)
REVERT: A 1759 LEU cc_start: 0.9182 (tp) cc_final: 0.8771 (tt)
REVERT: A 1772 GLU cc_start: 0.8215 (mt-10) cc_final: 0.7763 (tp30)
REVERT: A 1809 LEU cc_start: 0.8851 (tp) cc_final: 0.8448 (tp)
REVERT: A 1833 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8446 (tm-30)
REVERT: A 1895 LYS cc_start: 0.8581 (mtpt) cc_final: 0.8331 (mtmm)
  outliers start: 0
  outliers final: 0
  residues processed: 403
  average time/residue: 0.6825
  time to fit residues: 369.6005
Evaluate side-chains
  390 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 390
  time to evaluate  : 1.767 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 80 optimal weight:    0.8980
   chunk 116 optimal weight:    0.8980
   chunk 87 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 111 optimal weight:    0.0170
   chunk 29 optimal weight:    2.9990
   chunk 98 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 76 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0980
   chunk 68 optimal weight:    0.4980
   overall best weight:    0.4018

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A1826 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.127653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.099279 restraints weight = 69721.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.105581 restraints weight = 31296.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.109825 restraints weight = 17360.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.1924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  11753  Z= 0.103
  Angle     :  0.509   6.253  16181  Z= 0.264
  Chirality :  0.037   0.151   1891
  Planarity :  0.004   0.048   1854
  Dihedral  : 15.191  94.350   2263
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.49 %
    Favored  : 98.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.24), residues: 1261
  helix:  1.73 (0.20), residues: 633
  sheet: -0.22 (0.41), residues: 155
  loop :  0.06 (0.30), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP A 138 
 HIS   0.003   0.001   HIS A 703 
 PHE   0.017   0.001   PHE A 142 
 TYR   0.018   0.001   TYR A 771 
 ARG   0.006   0.000   ARG A 996 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04496 (  564)
  hydrogen bonds       : angle       4.42427 ( 1575)
  covalent geometry    : bond        0.00215 (11753)
  covalent geometry    : angle       0.50906 (16181)

*********************** 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
  403 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 402
  time to evaluate  : 1.978 
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: A   52 LEU cc_start: 0.8870 (tp) cc_final: 0.8363 (tp)
REVERT: A   56 LEU cc_start: 0.8691 (mt) cc_final: 0.8309 (mt)
REVERT: A  105 GLN cc_start: 0.8479 (mp10) cc_final: 0.8245 (mp10)
REVERT: A  120 LYS cc_start: 0.8600 (ptpp) cc_final: 0.8254 (ptpp)
REVERT: A  141 GLU cc_start: 0.8625 (mt-10) cc_final: 0.8088 (mm-30)
REVERT: A  153 TYR cc_start: 0.8489 (m-10) cc_final: 0.8068 (m-10)
REVERT: A  164 LEU cc_start: 0.8436 (tp) cc_final: 0.8208 (tp)
REVERT: A  171 LEU cc_start: 0.7717 (mm) cc_final: 0.7449 (mm)
REVERT: A  188 GLU cc_start: 0.8840 (mp0) cc_final: 0.8552 (mp0)
REVERT: A  221 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8258 (mt-10)
REVERT: A  231 ARG cc_start: 0.8888 (tmm-80) cc_final: 0.8199 (ptm-80)
REVERT: A  267 TYR cc_start: 0.8616 (t80) cc_final: 0.8043 (t80)
REVERT: A  272 MET cc_start: 0.8936 (mpp) cc_final: 0.8503 (mtp)
REVERT: A  275 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8527 (mt-10)
REVERT: A  321 VAL cc_start: 0.8872 (t) cc_final: 0.8159 (t)
REVERT: A  324 MET cc_start: 0.8865 (mpp) cc_final: 0.8663 (mpp)
REVERT: A  326 VAL cc_start: 0.9215 (t) cc_final: 0.8964 (t)
REVERT: A  327 ARG cc_start: 0.9226 (mmp80) cc_final: 0.9010 (mmp80)
REVERT: A  329 LEU cc_start: 0.9241 (tp) cc_final: 0.8970 (tp)
REVERT: A  500 LYS cc_start: 0.9247 (mppt) cc_final: 0.8710 (mppt)
REVERT: A  502 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8513 (mm-30)
REVERT: A  503 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8472 (mt-10)
REVERT: A  541 THR cc_start: 0.8173 (m) cc_final: 0.7876 (p)
REVERT: A  631 ILE cc_start: 0.8047 (pt) cc_final: 0.7596 (mt)
REVERT: A  634 ILE cc_start: 0.9047 (mm) cc_final: 0.8787 (mm)
REVERT: A  646 PHE cc_start: 0.8653 (m-80) cc_final: 0.8397 (m-80)
REVERT: A  648 HIS cc_start: 0.7065 (t-90) cc_final: 0.6717 (t-90)
REVERT: A  698 CYS cc_start: 0.9157 (t) cc_final: 0.8700 (m)
REVERT: A  749 TYR cc_start: 0.7825 (m-10) cc_final: 0.7516 (m-10)
REVERT: A  761 TYR cc_start: 0.8451 (t80) cc_final: 0.8235 (t80)
REVERT: A  784 GLU cc_start: 0.8840 (pp20) cc_final: 0.8596 (pm20)
REVERT: A  800 ARG cc_start: 0.8306 (mmt180) cc_final: 0.7880 (mmt90)
REVERT: A  815 HIS cc_start: 0.7432 (p90) cc_final: 0.7024 (p90)
REVERT: A  818 VAL cc_start: 0.7643 (p) cc_final: 0.7422 (p)
REVERT: A  828 SER cc_start: 0.7920 (m) cc_final: 0.7500 (t)
REVERT: A  842 MET cc_start: 0.9013 (tpp) cc_final: 0.8430 (tpp)
REVERT: A  849 LEU cc_start: 0.8937 (tp) cc_final: 0.8734 (tp)
REVERT: A  851 GLN cc_start: 0.8935 (tt0) cc_final: 0.8429 (tt0)
REVERT: A  901 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8248 (tm-30)
REVERT: A  916 LYS cc_start: 0.9538 (tmtt) cc_final: 0.9236 (tptp)
REVERT: A  970 GLU cc_start: 0.8823 (tt0) cc_final: 0.8434 (mt-10)
REVERT: A  973 LYS cc_start: 0.9223 (mmmt) cc_final: 0.8881 (mmmt)
REVERT: A  992 HIS cc_start: 0.8165 (m-70) cc_final: 0.7794 (m-70)
REVERT: A  996 ARG cc_start: 0.8141 (ptp-170) cc_final: 0.7795 (ptp-170)
REVERT: A 1060 ARG cc_start: 0.8600 (tpp80) cc_final: 0.8369 (tpp80)
REVERT: A 1069 GLU cc_start: 0.8534 (tm-30) cc_final: 0.7981 (tm-30)
REVERT: A 1310 PHE cc_start: 0.6625 (m-80) cc_final: 0.6262 (m-10)
REVERT: A 1340 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7834 (tm-30)
REVERT: A 1346 MET cc_start: 0.8938 (mtp) cc_final: 0.8462 (mtp)
REVERT: A 1349 LYS cc_start: 0.8871 (tttt) cc_final: 0.8218 (tmmt)
REVERT: A 1350 LYS cc_start: 0.9004 (mmmm) cc_final: 0.8665 (mmmm)
REVERT: A 1368 ARG cc_start: 0.8778 (mmm-85) cc_final: 0.8559 (mmm-85)
REVERT: A 1369 MET cc_start: 0.8144 (mpp) cc_final: 0.7846 (mpp)
REVERT: A 1386 VAL cc_start: 0.8281 (t) cc_final: 0.7943 (m)
REVERT: A 1545 HIS cc_start: 0.8399 (m-70) cc_final: 0.8001 (m-70)
REVERT: A 1696 GLN cc_start: 0.8253 (mt0) cc_final: 0.7976 (mt0)
REVERT: A 1701 LEU cc_start: 0.8089 (tp) cc_final: 0.7798 (tp)
REVERT: A 1716 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7809 (tm-30)
REVERT: A 1759 LEU cc_start: 0.9132 (tp) cc_final: 0.8703 (tt)
REVERT: A 1772 GLU cc_start: 0.8189 (mt-10) cc_final: 0.7768 (tp30)
REVERT: A 1802 MET cc_start: 0.8360 (mmp) cc_final: 0.8149 (mmp)
REVERT: A 1809 LEU cc_start: 0.8849 (tp) cc_final: 0.8417 (tp)
REVERT: A 1827 VAL cc_start: 0.8659 (t) cc_final: 0.8407 (t)
REVERT: A 1833 GLN cc_start: 0.8797 (tm-30) cc_final: 0.8458 (tm-30)
REVERT: A 1854 MET cc_start: 0.8907 (tpt) cc_final: 0.8666 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 402
  average time/residue: 0.6604
  time to fit residues: 353.7859
Evaluate side-chains
  383 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 383
  time to evaluate  : 1.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 89 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 29 optimal weight:    5.9990
   chunk 94 optimal weight:    1.9990
   chunk 95 optimal weight:    0.5980
   chunk 74 optimal weight:    0.5980
   chunk 93 optimal weight:    0.4980
   chunk 18 optimal weight:    3.9990
   chunk 96 optimal weight:    0.4980
   chunk 0 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A1325 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.126765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.098408 restraints weight = 69745.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.104780 restraints weight = 31313.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.109058 restraints weight = 17314.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  11753  Z= 0.113
  Angle     :  0.503   6.130  16181  Z= 0.261
  Chirality :  0.037   0.148   1891
  Planarity :  0.004   0.046   1854
  Dihedral  : 15.141  92.878   2263
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.96 %
    Favored  : 99.04 %
  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:  1.16 (0.24), residues: 1261
  helix:  1.72 (0.20), residues: 635
  sheet: -0.43 (0.40), residues: 167
  loop : -0.01 (0.31), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 138 
 HIS   0.003   0.001   HIS A1713 
 PHE   0.018   0.001   PHE A 142 
 TYR   0.010   0.001   TYR A 819 
 ARG   0.003   0.000   ARG A 996 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04331 (  564)
  hydrogen bonds       : angle       4.36207 ( 1575)
  covalent geometry    : bond        0.00229 (11753)
  covalent geometry    : angle       0.50309 (16181)

*********************** 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
  400 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 400
  time to evaluate  : 1.880 
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: 0.8877 (tp) cc_final: 0.8372 (tp)
REVERT: A   56 LEU cc_start: 0.8729 (mt) cc_final: 0.8351 (mt)
REVERT: A  105 GLN cc_start: 0.8524 (mp10) cc_final: 0.8301 (mp10)
REVERT: A  113 VAL cc_start: 0.9040 (m) cc_final: 0.8838 (p)
REVERT: A  141 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8118 (mm-30)
REVERT: A  153 TYR cc_start: 0.8465 (m-10) cc_final: 0.8085 (m-10)
REVERT: A  164 LEU cc_start: 0.8507 (tp) cc_final: 0.8288 (tp)
REVERT: A  171 LEU cc_start: 0.7731 (mm) cc_final: 0.7522 (mm)
REVERT: A  188 GLU cc_start: 0.8856 (mp0) cc_final: 0.8526 (mp0)
REVERT: A  221 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8286 (mt-10)
REVERT: A  231 ARG cc_start: 0.8869 (tmm-80) cc_final: 0.8145 (ptm-80)
REVERT: A  267 TYR cc_start: 0.8613 (t80) cc_final: 0.8046 (t80)
REVERT: A  275 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8481 (mt-10)
REVERT: A  321 VAL cc_start: 0.8906 (t) cc_final: 0.8187 (t)
REVERT: A  324 MET cc_start: 0.8855 (mpp) cc_final: 0.8651 (mpp)
REVERT: A  326 VAL cc_start: 0.9224 (t) cc_final: 0.8945 (t)
REVERT: A  329 LEU cc_start: 0.9252 (tp) cc_final: 0.8996 (tp)
REVERT: A  382 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8633 (mt-10)
REVERT: A  502 GLU cc_start: 0.8876 (mm-30) cc_final: 0.8516 (mm-30)
REVERT: A  503 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8558 (mt-10)
REVERT: A  541 THR cc_start: 0.8195 (m) cc_final: 0.7886 (p)
REVERT: A  580 LYS cc_start: 0.9463 (pttp) cc_final: 0.9180 (pttt)
REVERT: A  631 ILE cc_start: 0.8080 (pt) cc_final: 0.7632 (mt)
REVERT: A  634 ILE cc_start: 0.9046 (mm) cc_final: 0.8793 (mm)
REVERT: A  646 PHE cc_start: 0.8694 (m-80) cc_final: 0.8477 (m-80)
REVERT: A  648 HIS cc_start: 0.7068 (t-90) cc_final: 0.6723 (t-90)
REVERT: A  698 CYS cc_start: 0.9152 (t) cc_final: 0.8651 (m)
REVERT: A  749 TYR cc_start: 0.7899 (m-10) cc_final: 0.7579 (m-10)
REVERT: A  761 TYR cc_start: 0.8457 (t80) cc_final: 0.8247 (t80)
REVERT: A  784 GLU cc_start: 0.8833 (pp20) cc_final: 0.8613 (pm20)
REVERT: A  818 VAL cc_start: 0.7633 (p) cc_final: 0.7373 (p)
REVERT: A  827 ILE cc_start: 0.9007 (mp) cc_final: 0.8800 (mp)
REVERT: A  828 SER cc_start: 0.7907 (m) cc_final: 0.7445 (t)
REVERT: A  842 MET cc_start: 0.9028 (tpp) cc_final: 0.8733 (tpt)
REVERT: A  845 LEU cc_start: 0.9116 (tp) cc_final: 0.8913 (tp)
REVERT: A  851 GLN cc_start: 0.8965 (tt0) cc_final: 0.8476 (tt0)
REVERT: A  897 MET cc_start: 0.8754 (mtp) cc_final: 0.8226 (mtp)
REVERT: A  901 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8285 (tm-30)
REVERT: A  916 LYS cc_start: 0.9541 (tmtt) cc_final: 0.9243 (tptp)
REVERT: A  970 GLU cc_start: 0.8865 (tt0) cc_final: 0.8413 (mt-10)
REVERT: A  973 LYS cc_start: 0.9196 (mmmt) cc_final: 0.8847 (mmmt)
REVERT: A  992 HIS cc_start: 0.8177 (m-70) cc_final: 0.7808 (m-70)
REVERT: A 1069 GLU cc_start: 0.8540 (tm-30) cc_final: 0.7995 (tm-30)
REVERT: A 1070 LEU cc_start: 0.8964 (tp) cc_final: 0.8705 (tp)
REVERT: A 1310 PHE cc_start: 0.6645 (m-80) cc_final: 0.6389 (m-10)
REVERT: A 1313 GLU cc_start: 0.7704 (mp0) cc_final: 0.7228 (mp0)
REVERT: A 1340 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7829 (tm-30)
REVERT: A 1346 MET cc_start: 0.8950 (mtp) cc_final: 0.8488 (mtp)
REVERT: A 1349 LYS cc_start: 0.8873 (tttt) cc_final: 0.8232 (tmmt)
REVERT: A 1350 LYS cc_start: 0.9028 (mmmm) cc_final: 0.8688 (mmmm)
REVERT: A 1368 ARG cc_start: 0.8797 (mmm-85) cc_final: 0.8478 (mmm-85)
REVERT: A 1386 VAL cc_start: 0.8299 (t) cc_final: 0.7960 (m)
REVERT: A 1545 HIS cc_start: 0.8447 (m-70) cc_final: 0.8072 (m-70)
REVERT: A 1696 GLN cc_start: 0.8287 (mt0) cc_final: 0.8021 (mt0)
REVERT: A 1701 LEU cc_start: 0.8103 (tp) cc_final: 0.7807 (tp)
REVERT: A 1716 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7911 (tm-30)
REVERT: A 1759 LEU cc_start: 0.9151 (tp) cc_final: 0.8705 (tp)
REVERT: A 1772 GLU cc_start: 0.8236 (mt-10) cc_final: 0.7794 (tp30)
REVERT: A 1802 MET cc_start: 0.8384 (mmp) cc_final: 0.8150 (mmp)
REVERT: A 1809 LEU cc_start: 0.8850 (tp) cc_final: 0.8421 (tp)
REVERT: A 1833 GLN cc_start: 0.8810 (tm-30) cc_final: 0.8465 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 400
  average time/residue: 0.6798
  time to fit residues: 362.1725
Evaluate side-chains
  383 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 383
  time to evaluate  : 1.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 132 optimal weight:    5.9990
   chunk 92 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 121 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 124 optimal weight:    7.9990
   chunk 22 optimal weight:    0.7980
   chunk 119 optimal weight:    0.8980
   overall best weight:    1.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.122590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.094843 restraints weight = 71046.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.100998 restraints weight = 31490.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.105097 restraints weight = 17375.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7407
moved from start:          0.2483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11753  Z= 0.194
  Angle     :  0.542   6.252  16181  Z= 0.294
  Chirality :  0.037   0.141   1891
  Planarity :  0.005   0.079   1854
  Dihedral  : 15.299  92.134   2263
  Min Nonbonded Distance : 2.239

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  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:  0.77 (0.24), residues: 1261
  helix:  1.38 (0.20), residues: 636
  sheet: -0.52 (0.40), residues: 173
  loop : -0.18 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 138 
 HIS   0.006   0.001   HIS A1713 
 PHE   0.017   0.001   PHE A 142 
 TYR   0.009   0.001   TYR A 124 
 ARG   0.010   0.000   ARG A1845 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04793 (  564)
  hydrogen bonds       : angle       4.66251 ( 1575)
  covalent geometry    : bond        0.00345 (11753)
  covalent geometry    : angle       0.54227 (16181)

*********************** 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
  412 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 412
  time to evaluate  : 1.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 LEU cc_start: 0.8912 (tp) cc_final: 0.8346 (tp)
REVERT: A   56 LEU cc_start: 0.8799 (mt) cc_final: 0.8359 (mt)
REVERT: A  105 GLN cc_start: 0.8618 (mp10) cc_final: 0.8402 (mp10)
REVERT: A  141 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8149 (mm-30)
REVERT: A  171 LEU cc_start: 0.7723 (mm) cc_final: 0.7505 (mm)
REVERT: A  188 GLU cc_start: 0.8863 (mp0) cc_final: 0.8545 (mp0)
REVERT: A  221 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8338 (mt-10)
REVERT: A  267 TYR cc_start: 0.8659 (t80) cc_final: 0.8010 (t80)
REVERT: A  268 GLU cc_start: 0.8869 (mp0) cc_final: 0.8451 (mp0)
REVERT: A  275 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8534 (mt-10)
REVERT: A  329 LEU cc_start: 0.9266 (tp) cc_final: 0.9014 (tp)
REVERT: A  382 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8733 (mt-10)
REVERT: A  502 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8528 (mm-30)
REVERT: A  503 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8591 (mt-10)
REVERT: A  541 THR cc_start: 0.8214 (m) cc_final: 0.7895 (p)
REVERT: A  631 ILE cc_start: 0.8167 (pt) cc_final: 0.7719 (mt)
REVERT: A  634 ILE cc_start: 0.9086 (mm) cc_final: 0.8834 (mm)
REVERT: A  648 HIS cc_start: 0.7057 (t-90) cc_final: 0.6714 (t-90)
REVERT: A  698 CYS cc_start: 0.9170 (t) cc_final: 0.8669 (m)
REVERT: A  761 TYR cc_start: 0.8481 (t80) cc_final: 0.8244 (t80)
REVERT: A  818 VAL cc_start: 0.7666 (p) cc_final: 0.7369 (p)
REVERT: A  827 ILE cc_start: 0.9023 (mp) cc_final: 0.8799 (mp)
REVERT: A  828 SER cc_start: 0.7921 (m) cc_final: 0.7484 (t)
REVERT: A  851 GLN cc_start: 0.9010 (tt0) cc_final: 0.8518 (tt0)
REVERT: A  897 MET cc_start: 0.8673 (mtp) cc_final: 0.8172 (mtp)
REVERT: A  901 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8305 (tm-30)
REVERT: A  916 LYS cc_start: 0.9555 (tmtt) cc_final: 0.9264 (tptp)
REVERT: A  970 GLU cc_start: 0.8850 (tt0) cc_final: 0.8405 (mt-10)
REVERT: A  992 HIS cc_start: 0.8181 (m-70) cc_final: 0.7821 (m-70)
REVERT: A 1305 ASN cc_start: 0.8333 (t0) cc_final: 0.8023 (t0)
REVERT: A 1310 PHE cc_start: 0.6776 (m-80) cc_final: 0.6498 (m-10)
REVERT: A 1313 GLU cc_start: 0.7811 (mp0) cc_final: 0.7298 (mp0)
REVERT: A 1340 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7955 (tm-30)
REVERT: A 1346 MET cc_start: 0.8982 (mtp) cc_final: 0.8539 (mtp)
REVERT: A 1349 LYS cc_start: 0.8935 (tttt) cc_final: 0.8309 (tmmt)
REVERT: A 1350 LYS cc_start: 0.9036 (mmmm) cc_final: 0.8789 (mmmm)
REVERT: A 1386 VAL cc_start: 0.8335 (t) cc_final: 0.7987 (m)
REVERT: A 1545 HIS cc_start: 0.8481 (m-70) cc_final: 0.8106 (m-70)
REVERT: A 1701 LEU cc_start: 0.8133 (tp) cc_final: 0.7860 (tp)
REVERT: A 1759 LEU cc_start: 0.9167 (tp) cc_final: 0.8802 (tp)
REVERT: A 1802 MET cc_start: 0.8450 (mmp) cc_final: 0.8233 (mmp)
REVERT: A 1809 LEU cc_start: 0.8873 (tp) cc_final: 0.8474 (tp)
REVERT: A 1833 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8514 (tm-30)
REVERT: A 1900 ARG cc_start: 0.8643 (ptp-110) cc_final: 0.8358 (ptp90)
  outliers start: 0
  outliers final: 0
  residues processed: 412
  average time/residue: 0.6624
  time to fit residues: 359.9117
Evaluate side-chains
  391 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 391
  time to evaluate  : 1.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 24 optimal weight:    0.0770
   chunk 94 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 28 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 12 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   overall best weight:    0.7342

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A  92 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.124383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.096545 restraints weight = 70557.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.102742 restraints weight = 31183.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.106964 restraints weight = 17181.330|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  11753  Z= 0.125
  Angle     :  0.509   6.013  16181  Z= 0.267
  Chirality :  0.037   0.150   1891
  Planarity :  0.004   0.045   1854
  Dihedral  : 15.275  91.431   2263
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  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:  0.97 (0.24), residues: 1261
  helix:  1.58 (0.20), residues: 636
  sheet: -0.55 (0.39), residues: 173
  loop : -0.07 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.003   TRP A 138 
 HIS   0.003   0.001   HIS A1713 
 PHE   0.013   0.001   PHE A 142 
 TYR   0.015   0.001   TYR A 793 
 ARG   0.003   0.000   ARG A1697 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04364 (  564)
  hydrogen bonds       : angle       4.40778 ( 1575)
  covalent geometry    : bond        0.00246 (11753)
  covalent geometry    : angle       0.50891 (16181)

*********************** 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
  407 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 407
  time to evaluate  : 1.710 
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: A   52 LEU cc_start: 0.8899 (tp) cc_final: 0.8344 (tp)
REVERT: A   56 LEU cc_start: 0.8762 (mt) cc_final: 0.8507 (mt)
REVERT: A   76 LEU cc_start: 0.8652 (tp) cc_final: 0.8374 (tp)
REVERT: A   80 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8035 (mm-30)
REVERT: A  105 GLN cc_start: 0.8574 (mp10) cc_final: 0.8361 (mp10)
REVERT: A  141 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8051 (mm-30)
REVERT: A  171 LEU cc_start: 0.7732 (mm) cc_final: 0.7480 (mm)
REVERT: A  188 GLU cc_start: 0.8854 (mp0) cc_final: 0.8517 (mp0)
REVERT: A  221 GLU cc_start: 0.8785 (mt-10) cc_final: 0.8279 (mt-10)
REVERT: A  231 ARG cc_start: 0.8943 (ptm160) cc_final: 0.8397 (ptp-170)
REVERT: A  232 SER cc_start: 0.8461 (m) cc_final: 0.7921 (t)
REVERT: A  267 TYR cc_start: 0.8631 (t80) cc_final: 0.7983 (t80)
REVERT: A  268 GLU cc_start: 0.8845 (mp0) cc_final: 0.8478 (mp0)
REVERT: A  272 MET cc_start: 0.8969 (mpp) cc_final: 0.8617 (mtp)
REVERT: A  275 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8599 (mt-10)
REVERT: A  321 VAL cc_start: 0.8904 (t) cc_final: 0.8223 (t)
REVERT: A  324 MET cc_start: 0.8948 (mpp) cc_final: 0.8693 (mpp)
REVERT: A  329 LEU cc_start: 0.9243 (tp) cc_final: 0.8987 (tp)
REVERT: A  382 GLU cc_start: 0.8979 (mt-10) cc_final: 0.8654 (mt-10)
REVERT: A  503 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8560 (mt-10)
REVERT: A  541 THR cc_start: 0.8177 (m) cc_final: 0.7872 (p)
REVERT: A  631 ILE cc_start: 0.8127 (pt) cc_final: 0.7685 (mt)
REVERT: A  634 ILE cc_start: 0.9048 (mm) cc_final: 0.8788 (mm)
REVERT: A  648 HIS cc_start: 0.7081 (t-90) cc_final: 0.6714 (t-90)
REVERT: A  698 CYS cc_start: 0.9149 (t) cc_final: 0.8631 (m)
REVERT: A  748 CYS cc_start: 0.8212 (p) cc_final: 0.7931 (p)
REVERT: A  761 TYR cc_start: 0.8463 (t80) cc_final: 0.8228 (t80)
REVERT: A  818 VAL cc_start: 0.7674 (p) cc_final: 0.7350 (p)
REVERT: A  827 ILE cc_start: 0.8999 (mp) cc_final: 0.8775 (mp)
REVERT: A  828 SER cc_start: 0.7904 (m) cc_final: 0.7478 (t)
REVERT: A  842 MET cc_start: 0.9362 (tpt) cc_final: 0.8940 (tpp)
REVERT: A  851 GLN cc_start: 0.8985 (tt0) cc_final: 0.8467 (tt0)
REVERT: A  897 MET cc_start: 0.8665 (mtp) cc_final: 0.8184 (mtp)
REVERT: A  901 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8324 (tm-30)
REVERT: A  916 LYS cc_start: 0.9553 (tmtt) cc_final: 0.9260 (tptp)
REVERT: A  992 HIS cc_start: 0.8187 (m-70) cc_final: 0.7825 (m-70)
REVERT: A 1041 HIS cc_start: 0.7934 (t-90) cc_final: 0.7668 (t-90)
REVERT: A 1069 GLU cc_start: 0.8542 (tm-30) cc_final: 0.7973 (tm-30)
REVERT: A 1305 ASN cc_start: 0.8318 (t0) cc_final: 0.7975 (t0)
REVERT: A 1310 PHE cc_start: 0.6750 (m-80) cc_final: 0.6478 (m-10)
REVERT: A 1313 GLU cc_start: 0.7734 (mp0) cc_final: 0.7213 (mp0)
REVERT: A 1340 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7883 (tm-30)
REVERT: A 1346 MET cc_start: 0.8953 (mtp) cc_final: 0.8483 (mtp)
REVERT: A 1349 LYS cc_start: 0.8886 (tttt) cc_final: 0.8265 (tmmt)
REVERT: A 1350 LYS cc_start: 0.9047 (mmmm) cc_final: 0.8710 (mmmm)
REVERT: A 1386 VAL cc_start: 0.8310 (t) cc_final: 0.7971 (m)
REVERT: A 1545 HIS cc_start: 0.8468 (m-70) cc_final: 0.8168 (m-70)
REVERT: A 1688 TYR cc_start: 0.7519 (m-10) cc_final: 0.7299 (m-10)
REVERT: A 1701 LEU cc_start: 0.8122 (tp) cc_final: 0.7837 (tp)
REVERT: A 1759 LEU cc_start: 0.9151 (tp) cc_final: 0.8783 (tp)
REVERT: A 1772 GLU cc_start: 0.8276 (mt-10) cc_final: 0.7824 (tp30)
REVERT: A 1802 MET cc_start: 0.8424 (mmp) cc_final: 0.8202 (mmp)
REVERT: A 1809 LEU cc_start: 0.8840 (tp) cc_final: 0.8428 (tp)
REVERT: A 1833 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8436 (tm-30)
REVERT: A 1838 LYS cc_start: 0.9054 (ptpp) cc_final: 0.8846 (ptpp)
REVERT: A 1850 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8091 (tm-30)
REVERT: A 1854 MET cc_start: 0.8950 (tpt) cc_final: 0.8742 (tpt)
REVERT: A 1900 ARG cc_start: 0.8596 (ptp-110) cc_final: 0.8247 (ptp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 407
  average time/residue: 0.6529
  time to fit residues: 352.3870
Evaluate side-chains
  386 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 386
  time to evaluate  : 1.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 129 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 9 optimal weight:    0.0980
   chunk 107 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.122507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.094927 restraints weight = 70654.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.101034 restraints weight = 31429.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.105158 restraints weight = 17405.869|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.2836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11753  Z= 0.170
  Angle     :  0.533   6.027  16181  Z= 0.286
  Chirality :  0.037   0.151   1891
  Planarity :  0.004   0.040   1854
  Dihedral  : 15.384  90.476   2263
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.70 (0.24), residues: 1261
  helix:  1.35 (0.20), residues: 636
  sheet: -0.48 (0.41), residues: 168
  loop : -0.29 (0.30), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP A 138 
 HIS   0.005   0.001   HIS A1713 
 PHE   0.012   0.001   PHE A1839 
 TYR   0.009   0.001   TYR A 819 
 ARG   0.003   0.000   ARG A1697 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04667 (  564)
  hydrogen bonds       : angle       4.54165 ( 1575)
  covalent geometry    : bond        0.00310 (11753)
  covalent geometry    : angle       0.53314 (16181)

*********************** 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
  413 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 413
  time to evaluate  : 1.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 LEU cc_start: 0.8911 (tp) cc_final: 0.8354 (tp)
REVERT: A   56 LEU cc_start: 0.8781 (mt) cc_final: 0.8515 (mt)
REVERT: A   76 LEU cc_start: 0.8682 (tp) cc_final: 0.8411 (tp)
REVERT: A   80 GLU cc_start: 0.8462 (mm-30) cc_final: 0.8007 (mm-30)
REVERT: A  105 GLN cc_start: 0.8616 (mp10) cc_final: 0.8330 (mp10)
REVERT: A  141 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8043 (mm-30)
REVERT: A  164 LEU cc_start: 0.8687 (tp) cc_final: 0.8484 (tp)
REVERT: A  171 LEU cc_start: 0.7743 (mm) cc_final: 0.7499 (mm)
REVERT: A  188 GLU cc_start: 0.8861 (mp0) cc_final: 0.8517 (mp0)
REVERT: A  221 GLU cc_start: 0.8804 (mt-10) cc_final: 0.8293 (mt-10)
REVERT: A  231 ARG cc_start: 0.8970 (ptm160) cc_final: 0.8438 (ptp-170)
REVERT: A  232 SER cc_start: 0.8517 (m) cc_final: 0.7990 (t)
REVERT: A  267 TYR cc_start: 0.8650 (t80) cc_final: 0.8184 (t80)
REVERT: A  268 GLU cc_start: 0.8849 (mp0) cc_final: 0.8507 (mp0)
REVERT: A  272 MET cc_start: 0.8993 (mpp) cc_final: 0.8509 (mtp)
REVERT: A  275 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8560 (mt-10)
REVERT: A  321 VAL cc_start: 0.8918 (t) cc_final: 0.8354 (t)
REVERT: A  324 MET cc_start: 0.8958 (mpp) cc_final: 0.8728 (mpp)
REVERT: A  329 LEU cc_start: 0.9254 (tp) cc_final: 0.9007 (tp)
REVERT: A  350 THR cc_start: 0.8864 (m) cc_final: 0.8661 (p)
REVERT: A  382 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8730 (mt-10)
REVERT: A  503 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8590 (mt-10)
REVERT: A  541 THR cc_start: 0.8153 (m) cc_final: 0.7775 (p)
REVERT: A  631 ILE cc_start: 0.8126 (pt) cc_final: 0.7677 (mt)
REVERT: A  634 ILE cc_start: 0.9072 (mm) cc_final: 0.8811 (mm)
REVERT: A  648 HIS cc_start: 0.7069 (t-90) cc_final: 0.6724 (t-90)
REVERT: A  698 CYS cc_start: 0.9143 (t) cc_final: 0.8626 (m)
REVERT: A  748 CYS cc_start: 0.8243 (p) cc_final: 0.7928 (p)
REVERT: A  761 TYR cc_start: 0.8465 (t80) cc_final: 0.8218 (t80)
REVERT: A  818 VAL cc_start: 0.7715 (p) cc_final: 0.7491 (p)
REVERT: A  828 SER cc_start: 0.7932 (m) cc_final: 0.7583 (t)
REVERT: A  842 MET cc_start: 0.9326 (tpt) cc_final: 0.8726 (tpp)
REVERT: A  851 GLN cc_start: 0.9028 (tt0) cc_final: 0.8533 (tt0)
REVERT: A  897 MET cc_start: 0.8656 (mtp) cc_final: 0.8070 (mtp)
REVERT: A  901 GLU cc_start: 0.8689 (tm-30) cc_final: 0.8334 (tm-30)
REVERT: A  916 LYS cc_start: 0.9553 (tmtt) cc_final: 0.9266 (tptp)
REVERT: A  992 HIS cc_start: 0.8190 (m-70) cc_final: 0.7835 (m-70)
REVERT: A 1069 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8139 (tm-30)
REVERT: A 1305 ASN cc_start: 0.8396 (t0) cc_final: 0.8061 (t0)
REVERT: A 1310 PHE cc_start: 0.6789 (m-80) cc_final: 0.6478 (m-10)
REVERT: A 1313 GLU cc_start: 0.7794 (mp0) cc_final: 0.7252 (mp0)
REVERT: A 1346 MET cc_start: 0.8958 (mtp) cc_final: 0.8523 (mtp)
REVERT: A 1349 LYS cc_start: 0.8939 (tttt) cc_final: 0.8327 (tmmt)
REVERT: A 1350 LYS cc_start: 0.8998 (mmmm) cc_final: 0.8727 (mmmm)
REVERT: A 1386 VAL cc_start: 0.8317 (t) cc_final: 0.7971 (m)
REVERT: A 1545 HIS cc_start: 0.8498 (m-70) cc_final: 0.8187 (m-70)
REVERT: A 1669 TYR cc_start: 0.7736 (t80) cc_final: 0.7115 (t80)
REVERT: A 1674 LYS cc_start: 0.9159 (mmtp) cc_final: 0.8817 (mmpt)
REVERT: A 1688 TYR cc_start: 0.7593 (m-10) cc_final: 0.7349 (m-10)
REVERT: A 1695 TYR cc_start: 0.7230 (p90) cc_final: 0.6910 (p90)
REVERT: A 1696 GLN cc_start: 0.7746 (mm-40) cc_final: 0.7361 (mm-40)
REVERT: A 1701 LEU cc_start: 0.8209 (tp) cc_final: 0.7948 (tp)
REVERT: A 1716 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7730 (tm-30)
REVERT: A 1759 LEU cc_start: 0.9168 (tp) cc_final: 0.8806 (tp)
REVERT: A 1772 GLU cc_start: 0.8283 (mt-10) cc_final: 0.7787 (tp30)
REVERT: A 1802 MET cc_start: 0.8447 (mmp) cc_final: 0.8219 (mmp)
REVERT: A 1809 LEU cc_start: 0.8878 (tp) cc_final: 0.8461 (tp)
REVERT: A 1816 ASP cc_start: 0.7281 (p0) cc_final: 0.6826 (p0)
REVERT: A 1833 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8422 (tm-30)
REVERT: A 1838 LYS cc_start: 0.9024 (ptpp) cc_final: 0.8824 (ptpp)
REVERT: A 1850 GLU cc_start: 0.8569 (tm-30) cc_final: 0.8143 (tm-30)
REVERT: A 1854 MET cc_start: 0.8951 (tpt) cc_final: 0.8703 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 413
  average time/residue: 0.7357
  time to fit residues: 412.3073
Evaluate side-chains
  388 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 388
  time to evaluate  : 1.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 131 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 64 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 118 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 122 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   overall best weight:    1.7588

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.119437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.092098 restraints weight = 71830.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.098140 restraints weight = 31963.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.102226 restraints weight = 17730.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7473
moved from start:          0.3157

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= 0.247
  Angle     :  0.577   6.082  16181  Z= 0.320
  Chirality :  0.038   0.143   1891
  Planarity :  0.005   0.044   1854
  Dihedral  : 15.643  90.420   2263
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.60 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.70 %
    Favored  : 99.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.17 (0.24), residues: 1261
  helix:  0.88 (0.20), residues: 636
  sheet: -0.66 (0.40), residues: 168
  loop : -0.53 (0.31), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.003   TRP A 138 
 HIS   0.007   0.001   HIS A1713 
 PHE   0.025   0.002   PHE A 142 
 TYR   0.017   0.001   TYR A 124 
 ARG   0.007   0.001   ARG A 996 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05217 (  564)
  hydrogen bonds       : angle       4.95493 ( 1575)
  covalent geometry    : bond        0.00426 (11753)
  covalent geometry    : angle       0.57683 (16181)

*********************** 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
  404 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 404
  time to evaluate  : 1.633 
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: 0.8921 (tp) cc_final: 0.8477 (tp)
REVERT: A   56 LEU cc_start: 0.8802 (mt) cc_final: 0.8449 (mt)
REVERT: A   76 LEU cc_start: 0.8704 (tp) cc_final: 0.8483 (tp)
REVERT: A   80 GLU cc_start: 0.8494 (mm-30) cc_final: 0.8125 (mm-30)
REVERT: A   98 PHE cc_start: 0.8651 (m-80) cc_final: 0.8335 (m-10)
REVERT: A  105 GLN cc_start: 0.8668 (mp10) cc_final: 0.8383 (mp10)
REVERT: A  141 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8135 (mm-30)
REVERT: A  171 LEU cc_start: 0.7715 (mm) cc_final: 0.7459 (mm)
REVERT: A  188 GLU cc_start: 0.8858 (mp0) cc_final: 0.8536 (mp0)
REVERT: A  217 GLU cc_start: 0.8650 (pm20) cc_final: 0.8358 (pm20)
REVERT: A  221 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8311 (mt-10)
REVERT: A  231 ARG cc_start: 0.8986 (ptm160) cc_final: 0.8455 (ptp-170)
REVERT: A  232 SER cc_start: 0.8525 (m) cc_final: 0.8017 (t)
REVERT: A  267 TYR cc_start: 0.8698 (t80) cc_final: 0.8217 (t80)
REVERT: A  268 GLU cc_start: 0.8887 (mp0) cc_final: 0.8444 (mp0)
REVERT: A  329 LEU cc_start: 0.9275 (tp) cc_final: 0.9030 (tp)
REVERT: A  354 LYS cc_start: 0.9232 (mmtm) cc_final: 0.9023 (mptt)
REVERT: A  382 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8771 (mt-10)
REVERT: A  503 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8607 (mt-10)
REVERT: A  541 THR cc_start: 0.8175 (m) cc_final: 0.7769 (p)
REVERT: A  631 ILE cc_start: 0.8150 (pt) cc_final: 0.7702 (mt)
REVERT: A  634 ILE cc_start: 0.9093 (mm) cc_final: 0.8838 (mm)
REVERT: A  648 HIS cc_start: 0.7032 (t-90) cc_final: 0.6698 (t-90)
REVERT: A  698 CYS cc_start: 0.9143 (t) cc_final: 0.8624 (m)
REVERT: A  748 CYS cc_start: 0.8254 (p) cc_final: 0.7974 (p)
REVERT: A  761 TYR cc_start: 0.8481 (t80) cc_final: 0.8223 (t80)
REVERT: A  815 HIS cc_start: 0.7556 (p90) cc_final: 0.7230 (p90)
REVERT: A  818 VAL cc_start: 0.7750 (p) cc_final: 0.7429 (p)
REVERT: A  828 SER cc_start: 0.7988 (m) cc_final: 0.7640 (t)
REVERT: A  842 MET cc_start: 0.9326 (tpt) cc_final: 0.8794 (tpp)
REVERT: A  851 GLN cc_start: 0.9062 (tt0) cc_final: 0.8585 (tt0)
REVERT: A  891 ASP cc_start: 0.8756 (t0) cc_final: 0.8234 (m-30)
REVERT: A  897 MET cc_start: 0.8666 (mtp) cc_final: 0.8097 (mtp)
REVERT: A  901 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8401 (tm-30)
REVERT: A  916 LYS cc_start: 0.9557 (tmtt) cc_final: 0.9282 (tptp)
REVERT: A  992 HIS cc_start: 0.8198 (m-70) cc_final: 0.7968 (m-70)
REVERT: A 1001 THR cc_start: 0.8743 (p) cc_final: 0.8342 (m)
REVERT: A 1069 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8146 (tm-30)
REVERT: A 1305 ASN cc_start: 0.8481 (t0) cc_final: 0.8154 (t0)
REVERT: A 1310 PHE cc_start: 0.6861 (m-80) cc_final: 0.6523 (m-10)
REVERT: A 1313 GLU cc_start: 0.7876 (mp0) cc_final: 0.7314 (mp0)
REVERT: A 1346 MET cc_start: 0.8965 (mtp) cc_final: 0.8539 (mtp)
REVERT: A 1349 LYS cc_start: 0.8969 (tttt) cc_final: 0.8370 (tmmt)
REVERT: A 1350 LYS cc_start: 0.9017 (mmmm) cc_final: 0.8737 (mmmm)
REVERT: A 1386 VAL cc_start: 0.8347 (t) cc_final: 0.7974 (m)
REVERT: A 1545 HIS cc_start: 0.8460 (m-70) cc_final: 0.8172 (m-70)
REVERT: A 1674 LYS cc_start: 0.9175 (mmtp) cc_final: 0.8831 (mmpt)
REVERT: A 1696 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7485 (mm-40)
REVERT: A 1701 LEU cc_start: 0.8317 (tp) cc_final: 0.8032 (tp)
REVERT: A 1716 GLU cc_start: 0.8134 (tm-30) cc_final: 0.7739 (tm-30)
REVERT: A 1748 TYR cc_start: 0.8340 (m-10) cc_final: 0.8036 (m-10)
REVERT: A 1759 LEU cc_start: 0.9192 (tp) cc_final: 0.8843 (tp)
REVERT: A 1772 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7810 (tp30)
REVERT: A 1802 MET cc_start: 0.8508 (mmp) cc_final: 0.8247 (mmp)
REVERT: A 1833 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8431 (tm-30)
REVERT: A 1850 GLU cc_start: 0.8543 (tm-30) cc_final: 0.8111 (tm-30)
REVERT: A 1854 MET cc_start: 0.8956 (tpt) cc_final: 0.8706 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 404
  average time/residue: 0.6398
  time to fit residues: 342.8024
Evaluate side-chains
  385 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 385
  time to evaluate  : 1.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 7 optimal weight:    4.9990
   chunk 89 optimal weight:    0.0010
   chunk 84 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 112 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 91 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.9190

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A1299 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.122203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.094423 restraints weight = 70875.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.100592 restraints weight = 31661.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.104793 restraints weight = 17621.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.3642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.3191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11753  Z= 0.149
  Angle     :  0.541   6.205  16181  Z= 0.287
  Chirality :  0.038   0.147   1891
  Planarity :  0.005   0.052   1854
  Dihedral  : 15.580  90.791   2263
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  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:  0.43 (0.24), residues: 1261
  helix:  1.13 (0.20), residues: 635
  sheet: -0.66 (0.40), residues: 168
  loop : -0.40 (0.31), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 138 
 HIS   0.004   0.001   HIS A1687 
 PHE   0.019   0.002   PHE A 142 
 TYR   0.012   0.001   TYR A 124 
 ARG   0.005   0.000   ARG A 790 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04637 (  564)
  hydrogen bonds       : angle       4.58989 ( 1575)
  covalent geometry    : bond        0.00285 (11753)
  covalent geometry    : angle       0.54116 (16181)

*********************** 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
  399 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 399
  time to evaluate  : 1.787 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   51 LEU cc_start: 0.8775 (mt) cc_final: 0.8525 (mt)
REVERT: A   52 LEU cc_start: 0.8883 (tp) cc_final: 0.8326 (tp)
REVERT: A   56 LEU cc_start: 0.8766 (mt) cc_final: 0.8515 (mt)
REVERT: A   76 LEU cc_start: 0.8607 (tp) cc_final: 0.8380 (tp)
REVERT: A   80 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8117 (mm-30)
REVERT: A   94 LYS cc_start: 0.7628 (tttm) cc_final: 0.7396 (tmtt)
REVERT: A   98 PHE cc_start: 0.8631 (m-80) cc_final: 0.8308 (m-10)
REVERT: A  105 GLN cc_start: 0.8608 (mp10) cc_final: 0.8347 (mp10)
REVERT: A  141 GLU cc_start: 0.8648 (mt-10) cc_final: 0.8069 (mm-30)
REVERT: A  171 LEU cc_start: 0.7749 (mm) cc_final: 0.7480 (mm)
REVERT: A  188 GLU cc_start: 0.8844 (mp0) cc_final: 0.8432 (mp0)
REVERT: A  217 GLU cc_start: 0.8608 (pm20) cc_final: 0.8245 (pm20)
REVERT: A  221 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8280 (mt-10)
REVERT: A  231 ARG cc_start: 0.8982 (ptm160) cc_final: 0.8452 (ptp-170)
REVERT: A  232 SER cc_start: 0.8533 (m) cc_final: 0.8057 (t)
REVERT: A  267 TYR cc_start: 0.8687 (t80) cc_final: 0.8027 (t80)
REVERT: A  268 GLU cc_start: 0.8886 (mp0) cc_final: 0.8482 (mp0)
REVERT: A  307 ARG cc_start: 0.9095 (ptp-110) cc_final: 0.8834 (ptp90)
REVERT: A  329 LEU cc_start: 0.9269 (tp) cc_final: 0.9020 (tp)
REVERT: A  354 LYS cc_start: 0.9165 (mmtm) cc_final: 0.8951 (mptt)
REVERT: A  382 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8743 (mt-10)
REVERT: A  503 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8580 (mt-10)
REVERT: A  541 THR cc_start: 0.8128 (m) cc_final: 0.7743 (p)
REVERT: A  631 ILE cc_start: 0.8098 (pt) cc_final: 0.7654 (mt)
REVERT: A  634 ILE cc_start: 0.9060 (mm) cc_final: 0.8850 (mm)
REVERT: A  636 ARG cc_start: 0.8695 (tmt170) cc_final: 0.8373 (tmt170)
REVERT: A  648 HIS cc_start: 0.7011 (t-90) cc_final: 0.6660 (t-90)
REVERT: A  748 CYS cc_start: 0.8244 (p) cc_final: 0.7917 (p)
REVERT: A  761 TYR cc_start: 0.8466 (t80) cc_final: 0.8226 (t80)
REVERT: A  815 HIS cc_start: 0.7523 (p90) cc_final: 0.7204 (p90)
REVERT: A  818 VAL cc_start: 0.7721 (p) cc_final: 0.7186 (p)
REVERT: A  828 SER cc_start: 0.7954 (m) cc_final: 0.7499 (t)
REVERT: A  842 MET cc_start: 0.9284 (tpt) cc_final: 0.9053 (tpp)
REVERT: A  851 GLN cc_start: 0.9006 (tt0) cc_final: 0.8507 (tt0)
REVERT: A  891 ASP cc_start: 0.8658 (t0) cc_final: 0.8111 (m-30)
REVERT: A  897 MET cc_start: 0.8722 (mtp) cc_final: 0.8234 (mtp)
REVERT: A  901 GLU cc_start: 0.8716 (tm-30) cc_final: 0.8377 (tm-30)
REVERT: A  916 LYS cc_start: 0.9556 (tmtt) cc_final: 0.9278 (tptp)
REVERT: A  992 HIS cc_start: 0.8254 (m-70) cc_final: 0.7961 (m-70)
REVERT: A  996 ARG cc_start: 0.7954 (ptp-170) cc_final: 0.7718 (ptp90)
REVERT: A 1001 THR cc_start: 0.8729 (p) cc_final: 0.8294 (m)
REVERT: A 1069 GLU cc_start: 0.8562 (tm-30) cc_final: 0.7950 (tm-30)
REVERT: A 1305 ASN cc_start: 0.8466 (t0) cc_final: 0.8130 (t0)
REVERT: A 1313 GLU cc_start: 0.7771 (mp0) cc_final: 0.7243 (mp0)
REVERT: A 1346 MET cc_start: 0.8952 (mtp) cc_final: 0.8483 (mtp)
REVERT: A 1349 LYS cc_start: 0.8963 (tttt) cc_final: 0.8348 (tmmt)
REVERT: A 1350 LYS cc_start: 0.9025 (mmmm) cc_final: 0.8731 (mmmm)
REVERT: A 1386 VAL cc_start: 0.8321 (t) cc_final: 0.7925 (m)
REVERT: A 1545 HIS cc_start: 0.8499 (m-70) cc_final: 0.8212 (m-70)
REVERT: A 1664 GLU cc_start: 0.8774 (mt-10) cc_final: 0.8230 (mt-10)
REVERT: A 1674 LYS cc_start: 0.9167 (mmtp) cc_final: 0.8805 (mmpt)
REVERT: A 1688 TYR cc_start: 0.7625 (m-10) cc_final: 0.7423 (m-10)
REVERT: A 1696 GLN cc_start: 0.7854 (mm-40) cc_final: 0.7575 (mm110)
REVERT: A 1701 LEU cc_start: 0.8201 (tp) cc_final: 0.7926 (tp)
REVERT: A 1716 GLU cc_start: 0.8162 (tm-30) cc_final: 0.7781 (tm-30)
REVERT: A 1748 TYR cc_start: 0.8319 (m-10) cc_final: 0.8041 (m-10)
REVERT: A 1759 LEU cc_start: 0.9161 (tp) cc_final: 0.8801 (tp)
REVERT: A 1772 GLU cc_start: 0.8266 (mt-10) cc_final: 0.7770 (tp30)
REVERT: A 1802 MET cc_start: 0.8455 (mmp) cc_final: 0.8206 (mmp)
REVERT: A 1833 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8402 (tm-30)
REVERT: A 1850 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8087 (tm-30)
REVERT: A 1854 MET cc_start: 0.8948 (tpt) cc_final: 0.8703 (tpp)
REVERT: A 1900 ARG cc_start: 0.8640 (ptp-110) cc_final: 0.8305 (ptp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 399
  average time/residue: 0.6558
  time to fit residues: 348.4583
Evaluate side-chains
  385 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 385
  time to evaluate  : 1.781 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 2 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 22 optimal weight:    0.8980
   chunk 122 optimal weight:    0.7980
   chunk 132 optimal weight:    5.9990
   chunk 108 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9980
   chunk 92 optimal weight:    3.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A1299 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.122581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.095041 restraints weight = 71380.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.101210 restraints weight = 31617.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.105335 restraints weight = 17466.435|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7411
moved from start:          0.3326

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11753  Z= 0.136
  Angle     :  0.529   5.701  16181  Z= 0.280
  Chirality :  0.038   0.156   1891
  Planarity :  0.004   0.041   1854
  Dihedral  : 15.514  91.134   2263
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.58 (0.24), residues: 1261
  helix:  1.28 (0.20), residues: 635
  sheet: -0.68 (0.40), residues: 168
  loop : -0.33 (0.31), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 138 
 HIS   0.004   0.001   HIS A1713 
 PHE   0.018   0.001   PHE A 142 
 TYR   0.011   0.001   TYR A 819 
 ARG   0.004   0.000   ARG A 789 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04470 (  564)
  hydrogen bonds       : angle       4.48028 ( 1575)
  covalent geometry    : bond        0.00264 (11753)
  covalent geometry    : angle       0.52903 (16181)

********************** 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
  399 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 399
  time to evaluate  : 1.607 
Fit side-chains
   revert: symmetry clash
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   revert: symmetry clash
   revert: symmetry clash
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   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
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REVERT: A   51 LEU cc_start: 0.8745 (mt) cc_final: 0.8536 (mt)
REVERT: A   52 LEU cc_start: 0.8864 (tp) cc_final: 0.8372 (tp)
REVERT: A   56 LEU cc_start: 0.8759 (mt) cc_final: 0.8387 (mt)
REVERT: A   80 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8271 (mm-30)
REVERT: A   98 PHE cc_start: 0.8612 (m-80) cc_final: 0.8291 (m-10)
REVERT: A  105 GLN cc_start: 0.8611 (mp10) cc_final: 0.8352 (mp10)
REVERT: A  141 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8056 (mm-30)
REVERT: A  171 LEU cc_start: 0.7762 (mm) cc_final: 0.7509 (mm)
REVERT: A  182 LEU cc_start: 0.9025 (tp) cc_final: 0.8812 (tt)
REVERT: A  188 GLU cc_start: 0.8865 (mp0) cc_final: 0.8652 (mp0)
REVERT: A  217 GLU cc_start: 0.8616 (pm20) cc_final: 0.8268 (pm20)
REVERT: A  221 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8275 (mt-10)
REVERT: A  231 ARG cc_start: 0.8996 (ptm160) cc_final: 0.8475 (ptp-170)
REVERT: A  232 SER cc_start: 0.8556 (m) cc_final: 0.8026 (t)
REVERT: A  267 TYR cc_start: 0.8672 (t80) cc_final: 0.8183 (t80)
REVERT: A  268 GLU cc_start: 0.8871 (mp0) cc_final: 0.8443 (mp0)
REVERT: A  275 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8659 (mt-10)
REVERT: A  329 LEU cc_start: 0.9277 (tp) cc_final: 0.9041 (tp)
REVERT: A  382 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8731 (mt-10)
REVERT: A  503 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8566 (mt-10)
REVERT: A  541 THR cc_start: 0.8134 (m) cc_final: 0.7757 (p)
REVERT: A  631 ILE cc_start: 0.8085 (pt) cc_final: 0.7638 (mt)
REVERT: A  634 ILE cc_start: 0.9059 (mm) cc_final: 0.8857 (mm)
REVERT: A  636 ARG cc_start: 0.8686 (tmt170) cc_final: 0.8386 (tmt170)
REVERT: A  648 HIS cc_start: 0.6991 (t-90) cc_final: 0.6647 (t-90)
REVERT: A  684 MET cc_start: 0.6433 (mpp) cc_final: 0.5871 (mpp)
REVERT: A  748 CYS cc_start: 0.8250 (p) cc_final: 0.7917 (p)
REVERT: A  779 THR cc_start: 0.8691 (m) cc_final: 0.8277 (m)
REVERT: A  815 HIS cc_start: 0.7489 (p90) cc_final: 0.7157 (p90)
REVERT: A  824 GLU cc_start: 0.7530 (tm-30) cc_final: 0.7271 (tm-30)
REVERT: A  827 ILE cc_start: 0.8906 (mp) cc_final: 0.8691 (mp)
REVERT: A  828 SER cc_start: 0.7894 (m) cc_final: 0.7481 (t)
REVERT: A  842 MET cc_start: 0.9286 (tpt) cc_final: 0.9067 (tpp)
REVERT: A  851 GLN cc_start: 0.9004 (tt0) cc_final: 0.8506 (tt0)
REVERT: A  853 ILE cc_start: 0.8959 (mt) cc_final: 0.8730 (mt)
REVERT: A  897 MET cc_start: 0.8680 (mtp) cc_final: 0.8210 (mtp)
REVERT: A  901 GLU cc_start: 0.8692 (tm-30) cc_final: 0.8352 (tm-30)
REVERT: A  916 LYS cc_start: 0.9558 (tmtt) cc_final: 0.9282 (tptp)
REVERT: A  992 HIS cc_start: 0.8255 (m-70) cc_final: 0.7959 (m-70)
REVERT: A  996 ARG cc_start: 0.7939 (ptp-170) cc_final: 0.7656 (ptp90)
REVERT: A 1001 THR cc_start: 0.8743 (p) cc_final: 0.8326 (m)
REVERT: A 1069 GLU cc_start: 0.8559 (tm-30) cc_final: 0.7947 (tm-30)
REVERT: A 1299 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8026 (mm110)
REVERT: A 1301 LEU cc_start: 0.8579 (mt) cc_final: 0.8178 (mt)
REVERT: A 1305 ASN cc_start: 0.8480 (t0) cc_final: 0.8162 (t0)
REVERT: A 1313 GLU cc_start: 0.7757 (mp0) cc_final: 0.7230 (mp0)
REVERT: A 1346 MET cc_start: 0.8958 (mtp) cc_final: 0.8526 (mtp)
REVERT: A 1349 LYS cc_start: 0.8944 (tttt) cc_final: 0.8328 (tmmt)
REVERT: A 1350 LYS cc_start: 0.9019 (mmmm) cc_final: 0.8745 (mmmm)
REVERT: A 1386 VAL cc_start: 0.8339 (t) cc_final: 0.7947 (m)
REVERT: A 1545 HIS cc_start: 0.8515 (m-70) cc_final: 0.8232 (m-70)
REVERT: A 1585 LYS cc_start: 0.7872 (tptt) cc_final: 0.7540 (tptt)
REVERT: A 1664 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8158 (mt-10)
REVERT: A 1674 LYS cc_start: 0.9160 (mmtp) cc_final: 0.8790 (mmpt)
REVERT: A 1696 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7465 (mm-40)
REVERT: A 1701 LEU cc_start: 0.8188 (tp) cc_final: 0.7902 (tp)
REVERT: A 1716 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7740 (tm-30)
REVERT: A 1748 TYR cc_start: 0.8306 (m-10) cc_final: 0.8012 (m-10)
REVERT: A 1759 LEU cc_start: 0.9154 (tp) cc_final: 0.8792 (tp)
REVERT: A 1772 GLU cc_start: 0.8249 (mt-10) cc_final: 0.7758 (tp30)
REVERT: A 1802 MET cc_start: 0.8468 (mmp) cc_final: 0.8221 (mmp)
REVERT: A 1833 GLN cc_start: 0.8743 (tm-30) cc_final: 0.8388 (tm-30)
REVERT: A 1850 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8086 (tm-30)
REVERT: A 1854 MET cc_start: 0.8941 (tpt) cc_final: 0.8696 (tpp)
REVERT: A 1900 ARG cc_start: 0.8630 (ptp-110) cc_final: 0.8315 (ptp-170)
  outliers start: 0
  outliers final: 0
  residues processed: 399
  average time/residue: 0.6680
  time to fit residues: 354.4750
Evaluate side-chains
  386 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 386
  time to evaluate  : 1.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 128 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 114 optimal weight:    0.7980
   chunk 59 optimal weight:    0.2980
   chunk 9 optimal weight:    1.9990
   chunk 103 optimal weight:    0.3980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A1299 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.123681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.096122 restraints weight = 70763.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.102278 restraints weight = 31744.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.106431 restraints weight = 17645.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.3384

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= 0.116
  Angle     :  0.513   5.720  16181  Z= 0.268
  Chirality :  0.037   0.153   1891
  Planarity :  0.004   0.044   1854
  Dihedral  : 15.435  91.812   2263
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  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:  0.76 (0.24), residues: 1261
  helix:  1.44 (0.20), residues: 634
  sheet: -0.64 (0.40), residues: 168
  loop : -0.25 (0.31), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 138 
 HIS   0.003   0.001   HIS A 703 
 PHE   0.021   0.001   PHE A 142 
 TYR   0.012   0.001   TYR A1686 
 ARG   0.004   0.000   ARG A 789 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04264 (  564)
  hydrogen bonds       : angle       4.36449 ( 1575)
  covalent geometry    : bond        0.00236 (11753)
  covalent geometry    : angle       0.51299 (16181)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9918.71 seconds
wall clock time: 171 minutes 0.68 seconds (10260.68 seconds total)