Starting phenix.real_space_refine
on Fri Jun 20 20:25:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zpj_14855/06_2025/7zpj_14855.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zpj_14855/06_2025/7zpj_14855.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zpj_14855/06_2025/7zpj_14855.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zpj_14855/06_2025/7zpj_14855.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zpj_14855/06_2025/7zpj_14855.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zpj_14855/06_2025/7zpj_14855.cif"
  }
  resolution = 3.81
  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=   0.019
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      63      5.16       5
     C    7428      2.51       5
     N    2043      2.21       5
     O    2382      1.98       5
     H   11508      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: 23479
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 20612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1280, 20612
          Classifications: {'peptide': 1280}
          Link IDs: {'PTRANS': 76, 'TRANS': 1203}
          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: 1763
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 1763
          Classifications: {'RNA': 55}
          Modifications used: {'3*END': 1, 'rna3p_pur': 28, 'rna3p_pyr': 27}
          Link IDs: {'rna3p': 54}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 1104
          Classifications: {'peptide': 75}
          Link IDs: {'PCIS': 1, 'TRANS': 73}
  Time building chain proxies: 11.70, per 1000 atoms: 0.50
  Number of scatterers: 23479
  At special positions: 0
  Unit cell: (98.53, 122.745, 163.66, 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      63     16.00
     P      55     15.00
     O    2382      8.00
     N    2043      7.00
     C    7428      6.00
     H   11508      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: 6.71
  Conformation dependent library (CDL) restraints added in 2.0 seconds
  

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2600

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 10 sheets defined
      53.6% alpha, 12.4% beta
      17 base pairs and 24 stacking pairs defined.
    Time for finding SS restraints: 11.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 58
    Processing helix  chain 'A' and resid 66 through 82
      removed outlier: 3.527A  pdb=" N   LYS A  70 " --> pdb=" O   THR A  66 " (cutoff:3.500A)
    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: 4.147A  pdb=" N   GLN A 140 " --> pdb=" O   GLU A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 162
    Processing helix  chain 'A' and resid 177 through 181
    Processing helix  chain 'A' and resid 184 through 196
      removed outlier: 4.292A  pdb=" N   GLU A 188 " --> pdb=" O   HIS A 184 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   CYS A 196 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 231
      removed outlier: 5.037A  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 284
    Processing helix  chain 'A' and resid 294 through 314
    Processing helix  chain 'A' and resid 314 through 334
      removed outlier: 3.855A  pdb=" N   LYS A 331 " --> pdb=" O   ARG A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 361
    Processing helix  chain 'A' and resid 369 through 373
    Processing helix  chain 'A' and resid 374 through 386
      removed outlier: 3.653A  pdb=" N   LYS A 386 " --> pdb=" O   GLU A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 468
    Processing helix  chain 'A' and resid 498 through 510
      removed outlier: 3.661A  pdb=" N   GLU A 502 " --> pdb=" O   PHE A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 513
      No H-bonds generated for 'chain 'A' and resid 511 through 513'
    Processing helix  chain 'A' and resid 520 through 524
    Processing helix  chain 'A' and resid 542 through 551
    Processing helix  chain 'A' and resid 565 through 592
      removed outlier: 3.981A  pdb=" N   LYS A 570 " --> pdb=" O   THR A 566 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   SER A 571 " --> pdb=" O   ASP A 567 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   GLU A 574 " --> pdb=" O   LYS A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 641
      removed outlier: 4.317A  pdb=" N   GLY A 632 " --> pdb=" O   ASN A 628 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU A 641 " --> pdb=" O   TYR A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 706
      removed outlier: 3.565A  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 976
    Processing helix  chain 'A' and resid 1044 through 1053
      removed outlier: 4.085A  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 1363
    Processing helix  chain 'A' and resid 1364 through 1368
    Processing helix  chain 'A' and resid 1552 through 1583
      removed outlier: 3.659A  pdb=" N   GLY A1571 " --> pdb=" O   LEU A1567 " (cutoff:3.500A)
      removed outlier: 7.870A  pdb=" N   GLU A1572 " --> pdb=" O   THR A1568 " (cutoff:3.500A)
      removed outlier: 8.993A  pdb=" N   ARG A1573 " --> pdb=" O   SER A1569 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   ALA A1574 " --> pdb=" O   CYS A1570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1648 through 1657
    Processing helix  chain 'A' and resid 1660 through 1668
      removed outlier: 3.728A  pdb=" N   LYS A1666 " --> pdb=" O   THR A1662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1674 through 1682
      removed outlier: 3.787A  pdb=" N   LEU A1678 " --> pdb=" O   LYS A1674 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1695 through 1716
      removed outlier: 3.616A  pdb=" N   PHE A1700 " --> pdb=" O   GLN A1696 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   LEU A1701 " --> pdb=" O   ARG A1697 " (cutoff:3.500A)
      removed outlier: 3.573A  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 1752
      removed outlier: 4.020A  pdb=" N   TYR A1751 " --> pdb=" O   ASP A1747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1756 through 1773
      removed outlier: 3.590A  pdb=" N   LYS A1768 " --> pdb=" O   ASP A1764 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LYS A1773 " --> pdb=" O   PHE A1769 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1799 through 1817
      removed outlier: 3.868A  pdb=" N   GLY A1803 " --> pdb=" O   PRO A1799 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1820 through 1842
      removed outlier: 3.509A  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: 3.933A  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 helix  chain 'D' and resid 292 through 304
    Processing helix  chain 'D' and resid 342 through 364
    Processing sheet with id=AA1, first strand: chain 'A' and resid 121 through 124
      removed outlier: 3.942A  pdb=" N   THR A 151 " --> pdb=" O   TYR A 124 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   THR A  96 " --> pdb=" O   LEU A 148 " (cutoff:3.500A)
      removed outlier: 7.981A  pdb=" N   MET A 150 " --> pdb=" O   THR A  96 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   PHE A  98 " --> pdb=" O   MET A 150 " (cutoff:3.500A)
      removed outlier: 5.710A  pdb=" N   ARG A  95 " --> pdb=" O   ILE A 169 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   LEU A 171 " --> pdb=" O   ARG A  95 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   VAL A  97 " --> pdb=" O   LEU A 171 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   VAL A 173 " --> pdb=" O   VAL A  97 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ASP A 175 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   THR A  60 " --> pdb=" O   GLY A 204 " (cutoff:3.500A)
      removed outlier: 7.883A  pdb=" N   THR A 206 " --> pdb=" O   THR A  60 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   VAL A  62 " --> pdb=" O   THR A 206 " (cutoff:3.500A)
      removed outlier: 5.977A  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 256
      removed outlier: 6.166A  pdb=" N   CYS A 251 " --> pdb=" O   TYR A 560 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   MET A 562 " --> pdb=" O   CYS A 251 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   ILE A 253 " --> pdb=" O   MET A 562 " (cutoff:3.500A)
      removed outlier: 7.850A  pdb=" N   ALA A 564 " --> pdb=" O   ILE A 253 " (cutoff:3.500A)
      removed outlier: 5.671A  pdb=" N   VAL A 255 " --> pdb=" O   ALA A 564 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   ILE A 445 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 6.616A  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
    Processing sheet with id=AA5, first strand: chain 'A' and resid 816 through 820
      removed outlier: 3.800A  pdb=" N   PHE A 816 " --> pdb=" O   ILE A 827 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   GLU A 824 " --> pdb=" O   THR A 778 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   LYS A 832 " --> pdb=" O   LEU A 770 " (cutoff:3.500A)
      removed outlier: 7.577A  pdb=" N   LEU A 770 " --> pdb=" O   LYS A 832 " (cutoff:3.500A)
      removed outlier: 5.199A  pdb=" N   SER A 834 " --> pdb=" O   CYS A 768 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   CYS A 768 " --> pdb=" O   SER A 834 " (cutoff:3.500A)
      removed outlier: 5.053A  pdb=" N   PHE A 802 " --> pdb=" O   ILE A 773 " (cutoff:3.500A)
      removed outlier: 4.742A  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: 6.176A  pdb=" N   ASP A 991 " --> pdb=" O   VAL A 947 " (cutoff:3.500A)
      removed outlier: 5.718A  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
    Processing sheet with id=AB1, first strand: chain 'D' and resid 308 through 312

    581 hydrogen bonds defined for protein.
    1671 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      42 hydrogen bonds
      68 hydrogen bond angles
      0 basepair planarities
      17 basepair parallelities
      24 stacking parallelities
  Total time for adding SS restraints: 11.05

  Time building geometry restraints manager: 7.50 seconds

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

  Histogram of bond lengths:
        0.82 -     1.02: 11467
        1.02 -     1.22: 49
        1.22 -     1.42: 5060
        1.42 -     1.62: 7181
        1.62 -     1.82: 85
  Bond restraints: 23842
  Sorted by residual:
  bond pdb=" NH1 ARG A  86 "
       pdb="HH12 ARG A  86 "
    ideal  model  delta    sigma   weight residual
    0.860  0.819  0.041 2.00e-02 2.50e+03 4.11e+00
  bond pdb=" NH1 ARG A 800 "
       pdb="HH12 ARG A 800 "
    ideal  model  delta    sigma   weight residual
    0.860  0.826  0.034 2.00e-02 2.50e+03 2.89e+00
  bond pdb=" NE2 GLN A 985 "
       pdb="HE22 GLN A 985 "
    ideal  model  delta    sigma   weight residual
    0.860  0.828  0.032 2.00e-02 2.50e+03 2.59e+00
  bond pdb=" C   ILE A 773 "
       pdb=" N   GLY A 774 "
    ideal  model  delta    sigma   weight residual
    1.330  1.319  0.011 8.80e-03 1.29e+04 1.67e+00
  bond pdb=" NH2 ARG A 640 "
       pdb="HH22 ARG A 640 "
    ideal  model  delta    sigma   weight residual
    0.860  0.835  0.025 2.00e-02 2.50e+03 1.62e+00
  ... (remaining 23837 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.58: 43165
        7.58 -    15.17: 6
       15.17 -    22.75: 0
       22.75 -    30.33: 2
       30.33 -    37.91: 4
  Bond angle restraints: 43177
  Sorted by residual:
  angle pdb=" CB  ALA A 464 "
        pdb=" CA  ALA A 464 "
        pdb=" HA  ALA A 464 "
      ideal   model   delta    sigma   weight residual
     109.00   71.09   37.91 3.00e+00 1.11e-01 1.60e+02
  angle pdb=" N   ALA A 464 "
        pdb=" CA  ALA A 464 "
        pdb=" HA  ALA A 464 "
      ideal   model   delta    sigma   weight residual
     110.00   75.34   34.66 3.00e+00 1.11e-01 1.34e+02
  angle pdb=" O3'   G B  26 "
        pdb=" C3'   G B  26 "
        pdb=" H3'   G B  26 "
      ideal   model   delta    sigma   weight residual
     109.00   76.55   32.45 3.00e+00 1.11e-01 1.17e+02
  angle pdb=" C   ALA A 464 "
        pdb=" CA  ALA A 464 "
        pdb=" HA  ALA A 464 "
      ideal   model   delta    sigma   weight residual
     109.00   77.57   31.43 3.00e+00 1.11e-01 1.10e+02
  angle pdb=" C2'   G B  26 "
        pdb=" C3'   G B  26 "
        pdb=" H3'   G B  26 "
      ideal   model   delta    sigma   weight residual
     109.00   79.64   29.36 3.00e+00 1.11e-01 9.58e+01
  ... (remaining 43172 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.91: 10952
       35.91 -    71.81: 343
       71.81 -   107.72: 23
      107.72 -   143.63: 1
      143.63 -   179.53: 9
  Dihedral angle restraints: 11328
    sinusoidal: 6674
      harmonic: 4654
  Sorted by residual:
  dihedral pdb=" O4'   U B  27 "
           pdb=" C1'   U B  27 "
           pdb=" N1    U B  27 "
           pdb=" C2    U B  27 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   55.37  144.63     1      1.50e+01 4.44e-03 7.75e+01
  dihedral pdb=" O4'   U B  28 "
           pdb=" C1'   U B  28 "
           pdb=" N1    U B  28 "
           pdb=" C2    U B  28 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   60.31  139.69     1      1.50e+01 4.44e-03 7.52e+01
  dihedral pdb=" CG  TRP A 316 "
           pdb=" CD2 TRP A 316 "
           pdb=" CE3 TRP A 316 "
           pdb=" HE3 TRP A 316 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   24.94  -24.94     0      5.00e+00 4.00e-02 2.49e+01
  ... (remaining 11325 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.183: 1970
       0.183 -    0.365: 12
       0.365 -    0.548: 0
       0.548 -    0.730: 0
       0.730 -    0.913: 1
  Chirality restraints: 1983
  Sorted by residual:
  chirality pdb=" C3'   G B  26 "
            pdb=" C4'   G B  26 "
            pdb=" O3'   G B  26 "
            pdb=" C2'   G B  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.56   -0.91 2.00e-01 2.50e+01 2.08e+01
  chirality pdb=" CA  ALA A 464 "
            pdb=" N   ALA A 464 "
            pdb=" C   ALA A 464 "
            pdb=" CB  ALA A 464 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.18    0.31 2.00e-01 2.50e+01 2.40e+00
  chirality pdb=" P     U B  28 "
            pdb=" OP1   U B  28 "
            pdb=" OP2   U B  28 "
            pdb=" O5'   U B  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.71   -0.30 2.00e-01 2.50e+01 2.25e+00
  ... (remaining 1980 not shown)

  Planarity restraints: 3263
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 316 "    0.028 2.00e-02 2.50e+03   6.16e-02 1.52e+02
        pdb=" CG  TRP A 316 "    0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 316 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 316 "   -0.023 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 316 "   -0.055 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 316 "   -0.040 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 316 "    0.120 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 316 "   -0.061 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 316 "   -0.105 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 316 "   -0.077 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 316 "   -0.015 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 316 "    0.046 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 316 "   -0.057 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 316 "    0.063 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 316 "    0.054 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 316 "    0.082 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  86 "   -0.268 9.50e-02 1.11e+02   1.16e-01 1.30e+02
        pdb=" NE  ARG A  86 "   -0.081 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  86 "    0.082 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  86 "    0.126 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  86 "    0.043 2.00e-02 2.50e+03
        pdb="HH11 ARG A  86 "    0.011 2.00e-02 2.50e+03
        pdb="HH12 ARG A  86 "   -0.125 2.00e-02 2.50e+03
        pdb="HH21 ARG A  86 "    0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG A  86 "   -0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 187 "   -0.421 9.50e-02 1.11e+02   1.51e-01 9.05e+01
        pdb=" NE  ARG A 187 "   -0.052 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 187 "    0.053 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 187 "    0.077 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 187 "    0.080 2.00e-02 2.50e+03
        pdb="HH11 ARG A 187 "    0.002 2.00e-02 2.50e+03
        pdb="HH12 ARG A 187 "   -0.062 2.00e-02 2.50e+03
        pdb="HH21 ARG A 187 "    0.003 2.00e-02 2.50e+03
        pdb="HH22 ARG A 187 "   -0.082 2.00e-02 2.50e+03
  ... (remaining 3260 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.18: 1023
        2.18 -     2.78: 46703
        2.78 -     3.39: 65218
        3.39 -     3.99: 81336
        3.99 -     4.60: 127023
  Nonbonded interactions: 321303
  Sorted by model distance:
  nonbonded pdb="HH21 ARG A 935 "
            pdb=" O   GLU A1036 "
     model   vdw
     1.574 2.450
  nonbonded pdb=" HG1 THR A1867 "
            pdb=" OD1 ASP A1869 "
     model   vdw
     1.582 2.450
  nonbonded pdb=" O   LEU A1678 "
            pdb=" HG1 THR A1682 "
     model   vdw
     1.594 2.450
  nonbonded pdb=" O   GLU A 542 "
            pdb=" HG  SER A 545 "
     model   vdw
     1.603 2.450
  nonbonded pdb=" OE1 GLU A 866 "
            pdb=" HZ2 LYS A 868 "
     model   vdw
     1.605 2.450
  ... (remaining 321298 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:             363.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.340
  Extract box with map and model:          0.950
  Check model and map are aligned:         0.170
  Set scattering table:                    0.230
  Process input model:                     62.930
  Find NCS groups from input model:        0.540
  Set up NCS constraints:                  0.150
  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:3.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  432.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3446
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   0.047  12334  Z= 0.229
  Angle     :  0.864  10.310  16970  Z= 0.501
  Chirality :  0.054   0.913   1983
  Planarity :  0.015   0.245   1955
  Dihedral  : 15.404 144.630   5027
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 2.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  :  2.49 %
    Favored  : 96.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.22 (0.22), residues: 1333
  helix:  0.77 (0.18), residues: 672
  sheet: -0.58 (0.37), residues: 180
  loop : -0.28 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.116   0.010   TRP A 316 
 HIS   0.016   0.003   HIS A1749 
 PHE   0.055   0.004   PHE A 537 
 TYR   0.039   0.007   TYR A1676 
 ARG   0.066   0.006   ARG A 459 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13178 (  621)
  hydrogen bonds       : angle       5.40087 ( 1739)
  covalent geometry    : bond        0.00446 (12334)
  covalent geometry    : angle       0.86424 (16970)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
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.
Evaluate side-chains
  216 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 208
  time to evaluate  : 1.973 
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: A  269 ARG cc_start: 0.8394 (ttt180) cc_final: 0.7666 (mtm180)
REVERT: A  272 MET cc_start: 0.7855 (mtp) cc_final: 0.7156 (mtp)
REVERT: A  377 VAL cc_start: 0.8626 (t) cc_final: 0.8384 (m)
REVERT: A  379 LYS cc_start: 0.8641 (mmtt) cc_final: 0.8275 (mmtm)
REVERT: A  503 GLU cc_start: 0.7599 (mt-10) cc_final: 0.7178 (mt-10)
REVERT: A  710 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7582 (tp30)
REVERT: A  940 ASP cc_start: 0.2701 (OUTLIER) cc_final: 0.2303 (m-30)
REVERT: A 1368 ARG cc_start: 0.4125 (mmt90) cc_final: 0.3905 (mpt-90)
REVERT: A 1825 TRP cc_start: 0.2199 (t-100) cc_final: 0.1957 (t60)
  outliers start: 8
  outliers final: 5
  residues processed: 215
  average time/residue: 0.7903
  time to fit residues: 237.0671
Evaluate side-chains
  172 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 166
  time to evaluate  : 2.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 GLU
Chi-restraints excluded: chain A residue  317 CYS
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  940 ASP
Chi-restraints excluded: chain D residue  364 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    0.6980
   chunk 106 optimal weight:    0.4980
   chunk 58 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 56 optimal weight:    8.9990
   chunk 109 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 66 optimal weight:    0.5980
   chunk 81 optimal weight:    1.9990
   chunk 127 optimal weight:    5.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 178 HIS
A 301 GLN
** A1548 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4621 r_free = 0.4621 target = 0.189569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.152479 restraints weight = 67822.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.160397 restraints weight = 30776.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.165490 restraints weight = 16828.327|
|-----------------------------------------------------------------------------|
r_work (final): 0.4335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3946
moved from start:          0.2508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12334  Z= 0.152
  Angle     :  0.598   7.500  16970  Z= 0.317
  Chirality :  0.043   0.767   1983
  Planarity :  0.005   0.099   1955
  Dihedral  : 15.838 152.413   2360
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  6.40 %
    Favored  : 92.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.85 (0.23), residues: 1333
  helix:  1.39 (0.19), residues: 671
  sheet: -0.44 (0.38), residues: 182
  loop : -0.06 (0.29), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.003   TRP A 316 
 HIS   0.005   0.001   HIS A 116 
 PHE   0.052   0.002   PHE A 142 
 TYR   0.017   0.001   TYR A1746 
 ARG   0.008   0.001   ARG A 640 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05264 (  621)
  hydrogen bonds       : angle       4.65976 ( 1739)
  covalent geometry    : bond        0.00324 (12334)
  covalent geometry    : angle       0.59773 (16970)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
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.
Evaluate side-chains
  190 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 181
  time to evaluate  : 1.679 
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: A   59 ASN cc_start: 0.6365 (m-40) cc_final: 0.5623 (m-40)
REVERT: A  168 ASP cc_start: 0.6500 (m-30) cc_final: 0.5493 (p0)
REVERT: A  272 MET cc_start: 0.7920 (mtp) cc_final: 0.7264 (mtp)
REVERT: A  307 ARG cc_start: 0.7332 (ttt-90) cc_final: 0.7046 (ttp80)
REVERT: A  503 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7263 (mt-10)
REVERT: A 1671 PHE cc_start: 0.4790 (m-10) cc_final: 0.4540 (m-10)
REVERT: A 1800 LYS cc_start: 0.7687 (tttp) cc_final: 0.7286 (tptp)
REVERT: A 1804 ASP cc_start: 0.7008 (m-30) cc_final: 0.6486 (m-30)
REVERT: A 1825 TRP cc_start: 0.1753 (t-100) cc_final: 0.0540 (t-100)
  outliers start: 9
  outliers final: 7
  residues processed: 188
  average time/residue: 0.6315
  time to fit residues: 164.2657
Evaluate side-chains
  171 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 164
  time to evaluate  : 1.651 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  748 CYS
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  958 SER
Chi-restraints excluded: chain A residue 1722 SER
Chi-restraints excluded: chain D residue  321 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 58 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 102 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9980
   chunk 29 optimal weight:    9.9990
   chunk 54 optimal weight:    0.6980
   chunk 119 optimal weight:    0.9990
   chunk 108 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 301 GLN
A 648 HIS
** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1654 ASN
** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4626 r_free = 0.4626 target = 0.189582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.152233 restraints weight = 68594.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.160286 restraints weight = 31446.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.165444 restraints weight = 17296.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.4338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4361
moved from start:          0.4016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072  12334  Z= 0.167
  Angle     :  0.619  15.029  16970  Z= 0.323
  Chirality :  0.044   0.764   1983
  Planarity :  0.005   0.044   1955
  Dihedral  : 15.733 156.074   2353
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  :  7.40 %
    Favored  : 91.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.60 (0.23), residues: 1333
  helix:  1.24 (0.19), residues: 681
  sheet: -1.20 (0.37), residues: 189
  loop :  0.02 (0.30), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 138 
 HIS   0.006   0.001   HIS A1325 
 PHE   0.039   0.002   PHE A 142 
 TYR   0.022   0.002   TYR A1828 
 ARG   0.005   0.001   ARG A  86 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04897 (  621)
  hydrogen bonds       : angle       4.55018 ( 1739)
  covalent geometry    : bond        0.00363 (12334)
  covalent geometry    : angle       0.61854 (16970)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
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.
Evaluate side-chains
  195 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 181
  time to evaluate  : 2.116 
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: A  272 MET cc_start: 0.7984 (mtp) cc_final: 0.7342 (mtp)
REVERT: A  307 ARG cc_start: 0.7817 (ttt-90) cc_final: 0.7235 (ttp80)
REVERT: A  371 LYS cc_start: 0.8506 (mmtm) cc_final: 0.7816 (tttt)
REVERT: A  373 VAL cc_start: 0.3054 (OUTLIER) cc_final: 0.2702 (t)
REVERT: A  503 GLU cc_start: 0.7766 (mt-10) cc_final: 0.7336 (mt-10)
REVERT: A 1036 GLU cc_start: 0.5524 (tp30) cc_final: 0.5048 (tp30)
REVERT: A 1316 GLU cc_start: 0.5330 (tt0) cc_final: 0.4861 (tm-30)
REVERT: A 1363 LYS cc_start: 0.7316 (mmtt) cc_final: 0.6939 (mmtm)
REVERT: A 1369 MET cc_start: 0.5948 (mpp) cc_final: 0.5551 (tpp)
REVERT: A 1661 GLU cc_start: 0.7316 (tp30) cc_final: 0.6947 (tm-30)
REVERT: A 1800 LYS cc_start: 0.7678 (tttp) cc_final: 0.7232 (tptp)
REVERT: A 1804 ASP cc_start: 0.7011 (m-30) cc_final: 0.6599 (m-30)
REVERT: A 1816 ASP cc_start: 0.2825 (OUTLIER) cc_final: 0.1486 (t70)
  outliers start: 14
  outliers final: 12
  residues processed: 191
  average time/residue: 0.7491
  time to fit residues: 202.1067
Evaluate side-chains
  178 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 164
  time to evaluate  : 1.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  377 VAL
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  572 PHE
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  852 TYR
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue 1558 CYS
Chi-restraints excluded: chain A residue 1682 THR
Chi-restraints excluded: chain A residue 1700 PHE
Chi-restraints excluded: chain A residue 1722 SER
Chi-restraints excluded: chain A residue 1816 ASP
Chi-restraints excluded: chain D residue  352 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 132 optimal weight:    6.9990
   chunk 3 optimal weight:    0.8980
   chunk 111 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 120 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 75 optimal weight:    0.7980
   chunk 4 optimal weight:    0.2980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1299 GLN
** D 356 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 = 0.4628 r_free = 0.4628 target = 0.189704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.152444 restraints weight = 69064.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.160633 restraints weight = 31663.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.165867 restraints weight = 17294.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.4345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4596
moved from start:          0.5097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  12334  Z= 0.159
  Angle     :  0.583  10.179  16970  Z= 0.309
  Chirality :  0.042   0.783   1983
  Planarity :  0.005   0.044   1955
  Dihedral  : 15.697 158.384   2353
  Min Nonbonded Distance : 2.280

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  9.48 %
    Favored  : 89.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.23), residues: 1333
  helix:  1.30 (0.20), residues: 679
  sheet: -1.09 (0.36), residues: 199
  loop :  0.12 (0.31), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 316 
 HIS   0.006   0.001   HIS A1325 
 PHE   0.038   0.002   PHE A 142 
 TYR   0.017   0.001   TYR A1828 
 ARG   0.008   0.001   ARG A 789 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04394 (  621)
  hydrogen bonds       : angle       4.44636 ( 1739)
  covalent geometry    : bond        0.00348 (12334)
  covalent geometry    : angle       0.58286 (16970)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
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.
Evaluate side-chains
  187 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 170
  time to evaluate  : 1.750 
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: A  269 ARG cc_start: 0.8436 (ttt180) cc_final: 0.7943 (mtt180)
REVERT: A  272 MET cc_start: 0.8063 (mtp) cc_final: 0.7444 (mtp)
REVERT: A  307 ARG cc_start: 0.7572 (ttt-90) cc_final: 0.7323 (ttp80)
REVERT: A  360 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.6834 (mm-30)
REVERT: A  371 LYS cc_start: 0.8637 (mmtm) cc_final: 0.8005 (tttt)
REVERT: A  379 LYS cc_start: 0.8699 (mmtt) cc_final: 0.8205 (mmtt)
REVERT: A  503 GLU cc_start: 0.7810 (mt-10) cc_final: 0.7403 (mt-10)
REVERT: A 1036 GLU cc_start: 0.5931 (tp30) cc_final: 0.5215 (tp30)
REVERT: A 1316 GLU cc_start: 0.5444 (tt0) cc_final: 0.4962 (tm-30)
REVERT: A 1354 CYS cc_start: 0.6490 (OUTLIER) cc_final: 0.6152 (m)
REVERT: A 1369 MET cc_start: 0.6468 (mpp) cc_final: 0.5858 (tpp)
REVERT: A 1661 GLU cc_start: 0.7394 (tp30) cc_final: 0.7135 (tm-30)
REVERT: A 1816 ASP cc_start: 0.2621 (OUTLIER) cc_final: 0.1980 (t70)
  outliers start: 17
  outliers final: 12
  residues processed: 180
  average time/residue: 0.9246
  time to fit residues: 242.5708
Evaluate side-chains
  183 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 168
  time to evaluate  : 2.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 VAL
Chi-restraints excluded: chain A residue  271 LEU
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  572 PHE
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  789 ARG
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  852 TYR
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1354 CYS
Chi-restraints excluded: chain A residue 1682 THR
Chi-restraints excluded: chain A residue 1816 ASP
Chi-restraints excluded: chain D residue  352 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 88 optimal weight:    0.3980
   chunk 22 optimal weight:    0.6980
   chunk 30 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 131 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   chunk 3 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 301 GLN
** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 943 HIS
** A1545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.189393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.152603 restraints weight = 68950.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.160545 restraints weight = 31423.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.165801 restraints weight = 17332.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.4351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4784
moved from start:          0.5926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12334  Z= 0.135
  Angle     :  0.546   9.567  16970  Z= 0.289
  Chirality :  0.042   0.779   1983
  Planarity :  0.004   0.048   1955
  Dihedral  : 15.654 159.487   2353
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 7.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 10.06 %
    Favored  : 88.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.75 (0.23), residues: 1333
  helix:  1.45 (0.20), residues: 682
  sheet: -1.13 (0.36), residues: 199
  loop : -0.01 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 316 
 HIS   0.006   0.001   HIS A1325 
 PHE   0.029   0.002   PHE A 142 
 TYR   0.021   0.001   TYR A1828 
 ARG   0.004   0.000   ARG A 459 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04228 (  621)
  hydrogen bonds       : angle       4.35025 ( 1739)
  covalent geometry    : bond        0.00292 (12334)
  covalent geometry    : angle       0.54632 (16970)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
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.
Evaluate side-chains
  210 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 192
  time to evaluate  : 1.684 
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: A   70 LYS cc_start: 0.7974 (mtpt) cc_final: 0.7577 (tttp)
REVERT: A  168 ASP cc_start: 0.7249 (m-30) cc_final: 0.6455 (p0)
REVERT: A  272 MET cc_start: 0.8057 (mtp) cc_final: 0.7442 (mtp)
REVERT: A  307 ARG cc_start: 0.7680 (ttt-90) cc_final: 0.7442 (ttp80)
REVERT: A  371 LYS cc_start: 0.8710 (mmtm) cc_final: 0.8018 (tttp)
REVERT: A  379 LYS cc_start: 0.8688 (mmtt) cc_final: 0.8229 (mmtt)
REVERT: A  503 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7458 (mt-10)
REVERT: A 1036 GLU cc_start: 0.6109 (tp30) cc_final: 0.5402 (tp30)
REVERT: A 1058 LEU cc_start: 0.4683 (OUTLIER) cc_final: 0.2764 (pp)
REVERT: A 1316 GLU cc_start: 0.5439 (tt0) cc_final: 0.4934 (tm-30)
REVERT: A 1354 CYS cc_start: 0.6801 (t) cc_final: 0.6354 (m)
REVERT: A 1816 ASP cc_start: 0.3213 (OUTLIER) cc_final: 0.1983 (t70)
REVERT: A 1854 MET cc_start: 0.6855 (mmm) cc_final: 0.6598 (mmm)
  outliers start: 18
  outliers final: 15
  residues processed: 203
  average time/residue: 0.6072
  time to fit residues: 170.1711
Evaluate side-chains
  199 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 182
  time to evaluate  : 1.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 CYS
Chi-restraints excluded: chain A residue  177 CYS
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  460 LEU
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  572 PHE
Chi-restraints excluded: chain A residue  771 TYR
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  852 TYR
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1558 CYS
Chi-restraints excluded: chain A residue 1682 THR
Chi-restraints excluded: chain A residue 1700 PHE
Chi-restraints excluded: chain A residue 1816 ASP
Chi-restraints excluded: chain D residue  352 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 119 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9980
   chunk 75 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 37 optimal weight:    7.9990
   chunk 84 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0770
   chunk 80 optimal weight:    0.0370
   overall best weight:    0.6016

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

Flipped N/Q/H residues before XYZ refinement:
** D 356 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 = 0.4626 r_free = 0.4626 target = 0.189377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.152622 restraints weight = 69084.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.160707 restraints weight = 31722.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.165940 restraints weight = 17434.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.4355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4910
moved from start:          0.6617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  12334  Z= 0.127
  Angle     :  0.549   9.305  16970  Z= 0.288
  Chirality :  0.042   0.783   1983
  Planarity :  0.004   0.048   1955
  Dihedral  : 15.645 160.135   2353
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 11.14 %
    Favored  : 86.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.82 (0.23), residues: 1333
  helix:  1.50 (0.20), residues: 681
  sheet: -1.01 (0.36), residues: 199
  loop : -0.03 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 316 
 HIS   0.010   0.001   HIS A 184 
 PHE   0.031   0.002   PHE A 894 
 TYR   0.016   0.001   TYR A1686 
 ARG   0.006   0.000   ARG A1573 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04070 (  621)
  hydrogen bonds       : angle       4.27816 ( 1739)
  covalent geometry    : bond        0.00277 (12334)
  covalent geometry    : angle       0.54894 (16970)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
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.
Evaluate side-chains
  213 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 188
  time to evaluate  : 1.585 
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: A   70 LYS cc_start: 0.8134 (mtpt) cc_final: 0.7752 (tttp)
REVERT: A  140 GLN cc_start: 0.6547 (OUTLIER) cc_final: 0.6140 (pm20)
REVERT: A  168 ASP cc_start: 0.7366 (m-30) cc_final: 0.6653 (p0)
REVERT: A  269 ARG cc_start: 0.8493 (ttt180) cc_final: 0.8111 (mtt180)
REVERT: A  272 MET cc_start: 0.8110 (mtp) cc_final: 0.7548 (mtp)
REVERT: A  307 ARG cc_start: 0.7747 (ttt-90) cc_final: 0.7522 (ttp80)
REVERT: A  360 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7486 (mm-30)
REVERT: A  371 LYS cc_start: 0.8749 (mmtm) cc_final: 0.8114 (tttp)
REVERT: A  379 LYS cc_start: 0.8746 (mmtt) cc_final: 0.8297 (mmtt)
REVERT: A  503 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7483 (mt-10)
REVERT: A  684 MET cc_start: 0.5943 (mpp) cc_final: 0.5705 (mmp)
REVERT: A  747 GLN cc_start: 0.7349 (tp40) cc_final: 0.6701 (tm-30)
REVERT: A 1058 LEU cc_start: 0.4915 (OUTLIER) cc_final: 0.3133 (pp)
REVERT: A 1316 GLU cc_start: 0.5493 (tt0) cc_final: 0.4980 (tm-30)
REVERT: A 1354 CYS cc_start: 0.6877 (t) cc_final: 0.6484 (m)
REVERT: A 1800 LYS cc_start: 0.7526 (tmtt) cc_final: 0.7224 (tmtt)
REVERT: A 1802 MET cc_start: 0.6210 (mmp) cc_final: 0.5973 (mmp)
REVERT: A 1816 ASP cc_start: 0.2889 (OUTLIER) cc_final: 0.2413 (t70)
REVERT: A 1854 MET cc_start: 0.6757 (mmm) cc_final: 0.6531 (mmm)
  outliers start: 25
  outliers final: 18
  residues processed: 203
  average time/residue: 0.6317
  time to fit residues: 178.6333
Evaluate side-chains
  206 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 184
  time to evaluate  : 1.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 HIS
Chi-restraints excluded: chain A residue  140 GLN
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  177 CYS
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  572 PHE
Chi-restraints excluded: chain A residue  771 TYR
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  790 ARG
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  852 TYR
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue 1036 GLU
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1558 CYS
Chi-restraints excluded: chain A residue 1682 THR
Chi-restraints excluded: chain A residue 1700 PHE
Chi-restraints excluded: chain A residue 1816 ASP
Chi-restraints excluded: chain D residue  352 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 79 optimal weight:    0.0870
   chunk 22 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 134 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 119 optimal weight:    0.9990
   chunk 138 optimal weight:    9.9990
   chunk 18 optimal weight:    0.7980
   chunk 130 optimal weight:   10.0000
   chunk 121 optimal weight:    3.9990
   overall best weight:    0.9764

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1299 GLN
** D 356 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 = 0.4611 r_free = 0.4611 target = 0.188404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.151305 restraints weight = 69955.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.159201 restraints weight = 32326.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.164407 restraints weight = 17956.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.4337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5284
moved from start:          0.8021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.093  12334  Z= 0.180
  Angle     :  0.608   9.968  16970  Z= 0.324
  Chirality :  0.043   0.789   1983
  Planarity :  0.005   0.062   1955
  Dihedral  : 15.757 160.096   2351
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.73 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 11.72 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.34 (0.23), residues: 1333
  helix:  1.14 (0.20), residues: 681
  sheet: -1.04 (0.36), residues: 199
  loop : -0.41 (0.31), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP A1380 
 HIS   0.008   0.001   HIS A1683 
 PHE   0.015   0.002   PHE A 142 
 TYR   0.031   0.002   TYR A1828 
 ARG   0.006   0.001   ARG A 459 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04493 (  621)
  hydrogen bonds       : angle       4.59003 ( 1739)
  covalent geometry    : bond        0.00384 (12334)
  covalent geometry    : angle       0.60803 (16970)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
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.
Evaluate side-chains
  222 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 194
  time to evaluate  : 1.846 
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: A  140 GLN cc_start: 0.6882 (OUTLIER) cc_final: 0.6530 (pm20)
REVERT: A  268 GLU cc_start: 0.8541 (mm-30) cc_final: 0.7925 (tm-30)
REVERT: A  316 TRP cc_start: 0.6212 (t60) cc_final: 0.4846 (t60)
REVERT: A  317 CYS cc_start: 0.6246 (m) cc_final: 0.5571 (m)
REVERT: A  360 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7365 (mm-30)
REVERT: A  371 LYS cc_start: 0.8856 (mmtm) cc_final: 0.8364 (tttt)
REVERT: A  503 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7580 (mt-10)
REVERT: A  537 PHE cc_start: 0.6990 (OUTLIER) cc_final: 0.6759 (m-80)
REVERT: A  771 TYR cc_start: 0.3946 (OUTLIER) cc_final: 0.1563 (m-10)
REVERT: A 1354 CYS cc_start: 0.7320 (t) cc_final: 0.7023 (m)
REVERT: A 1356 LEU cc_start: 0.8685 (mt) cc_final: 0.8458 (mt)
REVERT: A 1587 LEU cc_start: 0.6655 (mm) cc_final: 0.6360 (mm)
REVERT: A 1661 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7377 (tm-30)
REVERT: A 1800 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.7188 (tmtt)
REVERT: A 1802 MET cc_start: 0.6654 (mmp) cc_final: 0.6454 (mmp)
REVERT: A 1816 ASP cc_start: 0.3547 (OUTLIER) cc_final: 0.3072 (t70)
  outliers start: 28
  outliers final: 22
  residues processed: 210
  average time/residue: 0.5899
  time to fit residues: 173.3344
Evaluate side-chains
  215 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 187
  time to evaluate  : 1.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 THR
Chi-restraints excluded: chain A residue  140 GLN
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  177 CYS
Chi-restraints excluded: chain A residue  302 ILE
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  387 TYR
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  537 PHE
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  572 PHE
Chi-restraints excluded: chain A residue  771 TYR
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  790 ARG
Chi-restraints excluded: chain A residue  791 LYS
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  852 TYR
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1558 CYS
Chi-restraints excluded: chain A residue 1586 VAL
Chi-restraints excluded: chain A residue 1653 LEU
Chi-restraints excluded: chain A residue 1682 THR
Chi-restraints excluded: chain A residue 1700 PHE
Chi-restraints excluded: chain A residue 1800 LYS
Chi-restraints excluded: chain A residue 1816 ASP
Chi-restraints excluded: chain D residue  352 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 138 optimal weight:    9.9990
   chunk 97 optimal weight:    0.8980
   chunk 116 optimal weight:    0.0870
   chunk 104 optimal weight:    0.3980
   chunk 117 optimal weight:    0.6980
   chunk 77 optimal weight:    0.6980
   chunk 92 optimal weight:    2.9990
   chunk 86 optimal weight:    0.4980
   chunk 132 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
** A 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4626 r_free = 0.4626 target = 0.189594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.152142 restraints weight = 71013.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.160342 restraints weight = 33043.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.165603 restraints weight = 18221.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.4348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5258
moved from start:          0.8378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.112  12334  Z= 0.114
  Angle     :  0.544   9.457  16970  Z= 0.282
  Chirality :  0.041   0.785   1983
  Planarity :  0.005   0.072   1955
  Dihedral  : 15.670 160.574   2351
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 7.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 13.55 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.73 (0.24), residues: 1333
  helix:  1.47 (0.20), residues: 682
  sheet: -0.91 (0.37), residues: 194
  loop : -0.25 (0.31), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 316 
 HIS   0.004   0.001   HIS A 178 
 PHE   0.034   0.001   PHE A 894 
 TYR   0.014   0.001   TYR A1746 
 ARG   0.006   0.000   ARG A 307 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03888 (  621)
  hydrogen bonds       : angle       4.30862 ( 1739)
  covalent geometry    : bond        0.00265 (12334)
  covalent geometry    : angle       0.54392 (16970)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
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.
Evaluate side-chains
  215 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 190
  time to evaluate  : 1.833 
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: A   70 LYS cc_start: 0.8346 (mtpt) cc_final: 0.7820 (ttpp)
REVERT: A   83 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.7164 (p90)
REVERT: A  140 GLN cc_start: 0.6776 (OUTLIER) cc_final: 0.6363 (pm20)
REVERT: A  272 MET cc_start: 0.8253 (mtp) cc_final: 0.7681 (mtp)
REVERT: A  371 LYS cc_start: 0.8850 (mmtm) cc_final: 0.8272 (tttp)
REVERT: A  379 LYS cc_start: 0.8778 (mmtt) cc_final: 0.8329 (mmtt)
REVERT: A  503 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7593 (mt-10)
REVERT: A  537 PHE cc_start: 0.6906 (OUTLIER) cc_final: 0.6665 (m-80)
REVERT: A  771 TYR cc_start: 0.3863 (OUTLIER) cc_final: 0.1479 (m-10)
REVERT: A 1036 GLU cc_start: 0.6634 (tp30) cc_final: 0.5988 (tp30)
REVERT: A 1354 CYS cc_start: 0.7326 (t) cc_final: 0.7019 (m)
REVERT: A 1587 LEU cc_start: 0.6661 (mm) cc_final: 0.6373 (mm)
REVERT: A 1661 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7349 (tm-30)
REVERT: A 1800 LYS cc_start: 0.7407 (OUTLIER) cc_final: 0.7062 (tmtt)
REVERT: A 1816 ASP cc_start: 0.3061 (OUTLIER) cc_final: 0.2661 (t70)
  outliers start: 25
  outliers final: 19
  residues processed: 203
  average time/residue: 0.5955
  time to fit residues: 169.7839
Evaluate side-chains
  206 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 181
  time to evaluate  : 1.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 HIS
Chi-restraints excluded: chain A residue  140 GLN
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  177 CYS
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  537 PHE
Chi-restraints excluded: chain A residue  544 ARG
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  572 PHE
Chi-restraints excluded: chain A residue  771 TYR
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  790 ARG
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  852 TYR
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1558 CYS
Chi-restraints excluded: chain A residue 1682 THR
Chi-restraints excluded: chain A residue 1687 HIS
Chi-restraints excluded: chain A residue 1700 PHE
Chi-restraints excluded: chain A residue 1761 HIS
Chi-restraints excluded: chain A residue 1800 LYS
Chi-restraints excluded: chain A residue 1816 ASP
Chi-restraints excluded: chain D residue  352 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 102 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 124 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 121 optimal weight:    0.8980
   chunk 71 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 23 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 109 GLN
A 301 GLN
** A 841 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4613 r_free = 0.4613 target = 0.188288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.150603 restraints weight = 70811.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.158773 restraints weight = 33271.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4356 r_free = 0.4356 target = 0.164016 restraints weight = 18432.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.4332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5486
moved from start:          0.9295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.118  12334  Z= 0.151
  Angle     :  0.590  10.566  16970  Z= 0.311
  Chirality :  0.043   0.789   1983
  Planarity :  0.005   0.059   1955
  Dihedral  : 15.713 160.324   2351
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.95 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 14.05 %
    Favored  : 83.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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: 1333
  helix:  1.35 (0.20), residues: 683
  sheet: -0.91 (0.37), residues: 194
  loop : -0.36 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A1380 
 HIS   0.006   0.001   HIS A1545 
 PHE   0.013   0.002   PHE A 142 
 TYR   0.022   0.001   TYR A1828 
 ARG   0.006   0.001   ARG A1573 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04207 (  621)
  hydrogen bonds       : angle       4.50862 ( 1739)
  covalent geometry    : bond        0.00327 (12334)
  covalent geometry    : angle       0.58991 (16970)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
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.
Evaluate side-chains
  223 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 198
  time to evaluate  : 1.622 
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: A   70 LYS cc_start: 0.8447 (mtpt) cc_final: 0.7978 (ttpp)
REVERT: A  109 GLN cc_start: 0.7505 (OUTLIER) cc_final: 0.6934 (tp40)
REVERT: A  140 GLN cc_start: 0.6966 (OUTLIER) cc_final: 0.6568 (pm20)
REVERT: A  268 GLU cc_start: 0.8547 (mm-30) cc_final: 0.7936 (tm-30)
REVERT: A  316 TRP cc_start: 0.6506 (t60) cc_final: 0.5128 (t60)
REVERT: A  317 CYS cc_start: 0.6805 (m) cc_final: 0.6299 (m)
REVERT: A  356 HIS cc_start: 0.8840 (t70) cc_final: 0.8639 (t70)
REVERT: A  360 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7075 (mm-30)
REVERT: A  371 LYS cc_start: 0.8893 (mmtm) cc_final: 0.8422 (tttp)
REVERT: A  503 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7636 (mt-10)
REVERT: A  537 PHE cc_start: 0.6983 (OUTLIER) cc_final: 0.6740 (m-80)
REVERT: A  640 ARG cc_start: 0.4203 (ttp80) cc_final: 0.3868 (ttp80)
REVERT: A  771 TYR cc_start: 0.4450 (OUTLIER) cc_final: 0.2185 (m-10)
REVERT: A  834 SER cc_start: 0.6924 (p) cc_final: 0.6722 (m)
REVERT: A 1354 CYS cc_start: 0.7611 (t) cc_final: 0.6915 (m)
REVERT: A 1356 LEU cc_start: 0.8685 (mt) cc_final: 0.8387 (mt)
REVERT: A 1587 LEU cc_start: 0.7048 (mm) cc_final: 0.6718 (mm)
REVERT: A 1661 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7497 (tm-30)
REVERT: A 1751 TYR cc_start: 0.6061 (m-80) cc_final: 0.5775 (m-80)
REVERT: A 1816 ASP cc_start: 0.3565 (OUTLIER) cc_final: 0.3230 (t70)
  outliers start: 25
  outliers final: 18
  residues processed: 215
  average time/residue: 0.7141
  time to fit residues: 222.7258
Evaluate side-chains
  217 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 193
  time to evaluate  : 2.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 HIS
Chi-restraints excluded: chain A residue  109 GLN
Chi-restraints excluded: chain A residue  140 GLN
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  232 SER
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  537 PHE
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  572 PHE
Chi-restraints excluded: chain A residue  771 TYR
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  790 ARG
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  852 TYR
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1545 HIS
Chi-restraints excluded: chain A residue 1558 CYS
Chi-restraints excluded: chain A residue 1700 PHE
Chi-restraints excluded: chain A residue 1800 LYS
Chi-restraints excluded: chain A residue 1816 ASP
Chi-restraints excluded: chain D residue  352 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 60 optimal weight:    0.3980
   chunk 1 optimal weight:    0.9980
   chunk 25 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 11 optimal weight:    2.9990
   chunk 101 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 841 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 = 0.4611 r_free = 0.4611 target = 0.188333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.150660 restraints weight = 70713.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.158766 restraints weight = 33289.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4352 r_free = 0.4352 target = 0.164012 restraints weight = 18475.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.4327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5493
moved from start:          0.9389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.159  12334  Z= 0.196
  Angle     :  0.815  59.148  16970  Z= 0.469
  Chirality :  0.043   0.789   1983
  Planarity :  0.005   0.057   1955
  Dihedral  : 15.710 160.326   2351
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 13.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.63 %
    Favored  : 83.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.57 (0.24), residues: 1333
  helix:  1.34 (0.20), residues: 683
  sheet: -0.91 (0.37), residues: 194
  loop : -0.37 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A1380 
 HIS   0.006   0.001   HIS A1545 
 PHE   0.013   0.002   PHE A 142 
 TYR   0.020   0.001   TYR A1828 
 ARG   0.005   0.000   ARG A1573 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04225 (  621)
  hydrogen bonds       : angle       4.51014 ( 1739)
  covalent geometry    : bond        0.00425 (12334)
  covalent geometry    : angle       0.81454 (16970)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
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.
Evaluate side-chains
  218 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 192
  time to evaluate  : 1.662 
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: A   70 LYS cc_start: 0.8449 (mtpt) cc_final: 0.7993 (ttpp)
REVERT: A  140 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6568 (pm20)
REVERT: A  268 GLU cc_start: 0.8558 (mm-30) cc_final: 0.7949 (tm-30)
REVERT: A  316 TRP cc_start: 0.6498 (t60) cc_final: 0.5118 (t60)
REVERT: A  317 CYS cc_start: 0.6785 (m) cc_final: 0.6282 (m)
REVERT: A  356 HIS cc_start: 0.8824 (t70) cc_final: 0.8623 (t70)
REVERT: A  360 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7076 (mm-30)
REVERT: A  371 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8409 (tttp)
REVERT: A  503 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7638 (mt-10)
REVERT: A  537 PHE cc_start: 0.6980 (OUTLIER) cc_final: 0.6744 (m-80)
REVERT: A  548 GLN cc_start: 0.6596 (mp10) cc_final: 0.6396 (mt0)
REVERT: A  640 ARG cc_start: 0.4202 (ttp80) cc_final: 0.3891 (ttp80)
REVERT: A  771 TYR cc_start: 0.4444 (OUTLIER) cc_final: 0.2172 (m-10)
REVERT: A  834 SER cc_start: 0.6931 (p) cc_final: 0.6730 (m)
REVERT: A 1354 CYS cc_start: 0.7318 (t) cc_final: 0.6903 (m)
REVERT: A 1356 LEU cc_start: 0.8684 (mt) cc_final: 0.8388 (mt)
REVERT: A 1587 LEU cc_start: 0.7024 (mm) cc_final: 0.6726 (mm)
REVERT: A 1661 GLU cc_start: 0.7785 (tm-30) cc_final: 0.7505 (tm-30)
REVERT: A 1751 TYR cc_start: 0.6063 (m-80) cc_final: 0.5779 (m-80)
REVERT: A 1816 ASP cc_start: 0.3490 (OUTLIER) cc_final: 0.3071 (t70)
  outliers start: 26
  outliers final: 21
  residues processed: 210
  average time/residue: 0.5894
  time to fit residues: 171.0675
Evaluate side-chains
  218 residues out of total 1208 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 192
  time to evaluate  : 1.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 HIS
Chi-restraints excluded: chain A residue  140 GLN
Chi-restraints excluded: chain A residue  174 PHE
Chi-restraints excluded: chain A residue  232 SER
Chi-restraints excluded: chain A residue  359 CYS
Chi-restraints excluded: chain A residue  360 GLU
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  537 PHE
Chi-restraints excluded: chain A residue  569 ILE
Chi-restraints excluded: chain A residue  572 PHE
Chi-restraints excluded: chain A residue  771 TYR
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  790 ARG
Chi-restraints excluded: chain A residue  791 LYS
Chi-restraints excluded: chain A residue  846 ILE
Chi-restraints excluded: chain A residue  852 TYR
Chi-restraints excluded: chain A residue  938 ASN
Chi-restraints excluded: chain A residue  975 LYS
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1545 HIS
Chi-restraints excluded: chain A residue 1558 CYS
Chi-restraints excluded: chain A residue 1687 HIS
Chi-restraints excluded: chain A residue 1700 PHE
Chi-restraints excluded: chain A residue 1800 LYS
Chi-restraints excluded: chain A residue 1816 ASP
Chi-restraints excluded: chain D residue  352 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 44 optimal weight:    0.6980
   chunk 130 optimal weight:   10.0000
   chunk 50 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0040
   chunk 76 optimal weight:    0.3980
   chunk 79 optimal weight:    0.7980
   chunk 70 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 112 optimal weight:    0.7980
   overall best weight:    0.5392

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

Flipped N/Q/H residues before XYZ refinement:
** A  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 841 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 = 0.4609 r_free = 0.4609 target = 0.187931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.150451 restraints weight = 70648.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.158481 restraints weight = 33122.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.163745 restraints weight = 18495.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.4326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5495
moved from start:          0.9392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.159  12334  Z= 0.196
  Angle     :  0.815  59.197  16970  Z= 0.469
  Chirality :  0.043   0.789   1983
  Planarity :  0.005   0.059   1955
  Dihedral  : 15.710 160.326   2351
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 13.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 14.71 %
    Favored  : 83.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.33 %
    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:  0.57 (0.24), residues: 1333
  helix:  1.34 (0.20), residues: 683
  sheet: -0.91 (0.37), residues: 194
  loop : -0.37 (0.31), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A1380 
 HIS   0.006   0.001   HIS A1545 
 PHE   0.013   0.002   PHE A 142 
 TYR   0.020   0.001   TYR A1828 
 ARG   0.005   0.000   ARG A1573 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04225 (  621)
  hydrogen bonds       : angle       4.51013 ( 1739)
  covalent geometry    : bond        0.00425 (12334)
  covalent geometry    : angle       0.81464 (16970)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8951.73 seconds
wall clock time: 157 minutes 7.18 seconds (9427.18 seconds total)