Starting phenix.real_space_refine
on Fri Aug  7 23:36:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gw2_51643/08_2026/9gw2_51643.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gw2_51643/08_2026/9gw2_51643.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.84
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gw2_51643/08_2026/9gw2_51643.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gw2_51643/08_2026/9gw2_51643.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gw2_51643/08_2026/9gw2_51643.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gw2_51643/08_2026/9gw2_51643.map"
  }
  resolution = 4.84
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
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     250      5.49       5
     S      32      5.16       5
     C    7442      2.51       5
     N    2440      2.21       5
     O    2950      1.98       5
     H   11011      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 24125
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "N"
      Number of atoms: 3982
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 3982
          Classifications: {'DNA': 125}
          Link IDs: {'rna3p': 124}
    Chain: "O"
      Number of atoms: 3923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 245, 3923
          Classifications: {'peptide': 245}
          Link IDs: {'PTRANS': 7, 'TRANS': 237}
    Chain: "T"
      Number of atoms: 3949
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 125, 3949
          Classifications: {'DNA': 125}
          Link IDs: {'rna3p': 124}
    Chain: "a"
      Number of atoms: 1684
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 1684
          Classifications: {'peptide': 101}
          Link IDs: {'PTRANS': 4, 'TRANS': 96}
    Chain: "b"
      Number of atoms: 1283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 1283
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "c"
      Number of atoms: 1711
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 1711
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "d"
      Number of atoms: 1458
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 1458
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "e"
      Number of atoms: 1601
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 1601
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "f"
      Number of atoms: 1283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 1283
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "g"
      Number of atoms: 1645
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 1645
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "h"
      Number of atoms: 1401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 1401
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 2, 'TRANS': 86}
    Chain: "j"
      Number of atoms: 205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 205
          Classifications: {'peptide': 15}
          Link IDs: {'PTRANS': 1, 'TRANS': 13}
  Time building chain proxies: 4.19, per 1000 atoms: 0.17
  Number of scatterers: 24125
  At special positions: 0
  Unit cell: (84, 119.7, 139.65, 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      32     16.00
     P     250     15.00
     O    2950      8.00
     N    2440      7.00
     C    7442      6.00
     H   11011      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.42
  Conformation dependent library (CDL) restraints added in 512.8 milliseconds
  

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1868

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 16 sheets defined
      61.1% alpha, 6.3% beta
      125 base pairs and 216 stacking pairs defined.
    Time for finding SS restraints: 4.27
  Creating SS restraints...
    Processing helix  chain 'O' and resid 1452 through 1455
    Processing helix  chain 'O' and resid 1456 through 1466
    Processing helix  chain 'O' and resid 1488 through 1491
    Processing helix  chain 'O' and resid 1492 through 1497
    Processing helix  chain 'O' and resid 1505 through 1512
    Processing helix  chain 'O' and resid 1522 through 1526
    Processing helix  chain 'O' and resid 1535 through 1539
      removed outlier: 3.557A  pdb=" N   CYS O1539 " --> pdb=" O   GLY O1536 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1585 through 1599
    Processing helix  chain 'O' and resid 1622 through 1627
    Processing helix  chain 'a' and resid 45 through 58
    Processing helix  chain 'a' and resid 64 through 77
    Processing helix  chain 'a' and resid 86 through 115
      removed outlier: 3.548A  pdb=" N   LEU a 110 " --> pdb=" O   GLU a 106 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 121 through 133
    Processing helix  chain 'b' and resid 24 through 29
    Processing helix  chain 'b' and resid 30 through 41
    Processing helix  chain 'b' and resid 49 through 76
      removed outlier: 3.517A  pdb=" N   GLU b  53 " --> pdb=" O   LEU b  49 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 82 through 94
    Processing helix  chain 'c' and resid 17 through 23
    Processing helix  chain 'c' and resid 28 through 37
    Processing helix  chain 'c' and resid 47 through 74
      removed outlier: 3.639A  pdb=" N   LEU c  66 " --> pdb=" O   GLU c  62 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 80 through 91
    Processing helix  chain 'c' and resid 91 through 98
    Processing helix  chain 'd' and resid 37 through 49
    Processing helix  chain 'd' and resid 55 through 84
    Processing helix  chain 'd' and resid 90 through 102
    Processing helix  chain 'd' and resid 104 through 123
      removed outlier: 4.092A  pdb=" N   LYS d 108 " --> pdb=" O   GLY d 104 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 45 through 58
    Processing helix  chain 'e' and resid 64 through 78
      removed outlier: 3.530A  pdb=" N   PHE e  68 " --> pdb=" O   ARG e  64 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ASP e  78 " --> pdb=" O   GLU e  74 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 86 through 115
    Processing helix  chain 'e' and resid 121 through 133
    Processing helix  chain 'f' and resid 25 through 29
    Processing helix  chain 'f' and resid 30 through 41
    Processing helix  chain 'f' and resid 49 through 76
      removed outlier: 3.761A  pdb=" N   GLU f  53 " --> pdb=" O   LEU f  49 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 82 through 93
      removed outlier: 3.520A  pdb=" N   VAL f  86 " --> pdb=" O   THR f  82 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 17 through 23
    Processing helix  chain 'g' and resid 28 through 38
    Processing helix  chain 'g' and resid 46 through 74
      removed outlier: 4.439A  pdb=" N   VAL g  50 " --> pdb=" O   ALA g  46 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 80 through 90
    Processing helix  chain 'g' and resid 91 through 98
      removed outlier: 3.640A  pdb=" N   LYS g  96 " --> pdb=" O   GLU g  92 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 37 through 49
      removed outlier: 3.630A  pdb=" N   LYS h  43 " --> pdb=" O   VAL h  39 " (cutoff:3.500A)
    Processing helix  chain 'h' and resid 55 through 84
    Processing helix  chain 'h' and resid 90 through 102
    Processing helix  chain 'h' and resid 103 through 123
    Processing helix  chain 'j' and resid 940 through 945
      removed outlier: 3.737A  pdb=" N   GLU j 944 " --> pdb=" O   GLU j 940 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'O' and resid 1474 through 1475
      removed outlier: 5.751A  pdb=" N   ASP O1474 " --> pdb=" O   GLY O1621 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'O' and resid 1480 through 1481
      removed outlier: 7.323A  pdb=" N   VAL O1480 " --> pdb=" O   VAL O1583 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   GLU O1613 " --> pdb=" O   LEU O1609 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'O' and resid 1552 through 1556
    Processing sheet with id=AA4, first strand: chain 'O' and resid 1575 through 1578
      removed outlier: 6.651A  pdb=" N   PHE O1650 " --> pdb=" O   VAL O1576 " (cutoff:3.500A)
      removed outlier: 4.763A  pdb=" N   GLU O1578 " --> pdb=" O   VAL O1648 " (cutoff:3.500A)
      removed outlier: 7.421A  pdb=" N   VAL O1648 " --> pdb=" O   GLU O1578 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'O' and resid 1628 through 1629
      removed outlier: 6.462A  pdb=" N   ASN O1628 " --> pdb=" O   PHE O1664 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'O' and resid 1669 through 1670
    Processing sheet with id=AA7, first strand: chain 'a' and resid 84 through 85
      removed outlier: 7.151A  pdb=" N   ARG a  84 " --> pdb=" O   VAL b  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'a' and resid 119 through 120
    Processing sheet with id=AA9, first strand: chain 'b' and resid 96 through 98
      removed outlier: 6.297A  pdb=" N   THR b  96 " --> pdb=" O   THR g 102 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'c' and resid 43 through 44
      removed outlier: 7.079A  pdb=" N   ARG c  43 " --> pdb=" O   ILE d  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'c' and resid 78 through 79
    Processing sheet with id=AB3, first strand: chain 'c' and resid 102 through 103
      removed outlier: 6.726A  pdb=" N   THR c 102 " --> pdb=" O   TYR f  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'e' and resid 84 through 85
      removed outlier: 6.984A  pdb=" N   ARG e  84 " --> pdb=" O   VAL f  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'e' and resid 119 through 120
    Processing sheet with id=AB6, first strand: chain 'g' and resid 43 through 44
      removed outlier: 7.250A  pdb=" N   ARG g  43 " --> pdb=" O   ILE h  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB6
    Processing sheet with id=AB7, first strand: chain 'g' and resid 78 through 79

    457 hydrogen bonds defined for protein.
    1323 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      319 hydrogen bonds
      638 hydrogen bond angles
      0 basepair planarities
      125 basepair parallelities
      216 stacking parallelities
  Total time for adding SS restraints: 5.87

  Time building geometry restraints manager: 3.27 seconds

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

  Histogram of bond lengths:
        0.83 -     1.02: 10995
        1.02 -     1.22: 73
        1.22 -     1.42: 6039
        1.42 -     1.62: 7711
        1.62 -     1.82: 49
  Bond restraints: 24867
  Sorted by residual:
  bond pdb=" C3'  DC N  48 "
       pdb=" O3'  DC N  48 "
    ideal  model  delta    sigma   weight residual
    1.435  1.543 -0.108 1.30e-02 5.92e+03 6.87e+01
  bond pdb=" C1'  DT N  78 "
       pdb=" N1   DT N  78 "
    ideal  model  delta    sigma   weight residual
    1.468  1.535 -0.067 1.40e-02 5.10e+03 2.32e+01
  bond pdb=" C5'  DT N   6 "
       pdb=" C4'  DT N   6 "
    ideal  model  delta    sigma   weight residual
    1.512  1.546 -0.034 7.00e-03 2.04e+04 2.31e+01
  bond pdb=" C5'  DC N 110 "
       pdb=" C4'  DC N 110 "
    ideal  model  delta    sigma   weight residual
    1.512  1.544 -0.032 7.00e-03 2.04e+04 2.07e+01
  bond pdb=" C3'  DC T 116 "
       pdb=" O3'  DC T 116 "
    ideal  model  delta    sigma   weight residual
    1.435  1.377  0.058 1.30e-02 5.92e+03 2.01e+01
  ... (remaining 24862 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    15.92: 44988
       15.92 -    31.83: 0
       31.83 -    47.75: 0
       47.75 -    63.66: 0
       63.66 -    79.58: 1
  Bond angle restraints: 44989
  Sorted by residual:
  angle pdb=" O3'  DC N  48 "
        pdb=" P    DT N  49 "
        pdb=" OP1  DT N  49 "
      ideal   model   delta    sigma   weight residual
     108.00   28.42   79.58 3.00e+00 1.11e-01 7.04e+02
  angle pdb=" O4'  DC N   3 "
        pdb=" C1'  DC N   3 "
        pdb=" N1   DC N   3 "
      ideal   model   delta    sigma   weight residual
     108.00  116.07   -8.07 7.00e-01 2.04e+00 1.33e+02
  angle pdb=" C3'  DC N  48 "
        pdb=" O3'  DC N  48 "
        pdb=" P    DT N  49 "
      ideal   model   delta    sigma   weight residual
     119.70  132.89  -13.19 1.20e+00 6.94e-01 1.21e+02
  angle pdb=" O4'  DC T 179 "
        pdb=" C1'  DC T 179 "
        pdb=" N1   DC T 179 "
      ideal   model   delta    sigma   weight residual
     108.00  113.67   -5.67 7.00e-01 2.04e+00 6.57e+01
  angle pdb=" O4'  DC N 114 "
        pdb=" C1'  DC N 114 "
        pdb=" N1   DC N 114 "
      ideal   model   delta    sigma   weight residual
     108.00  113.54   -5.54 7.00e-01 2.04e+00 6.27e+01
  ... (remaining 44984 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.14: 9236
       35.14 -    70.27: 1372
       70.27 -   105.41: 17
      105.41 -   140.54: 2
      140.54 -   175.68: 1
  Dihedral angle restraints: 10628
    sinusoidal: 7331
      harmonic: 3297
  Sorted by residual:
  dihedral pdb=" C4'  DG T 130 "
           pdb=" C3'  DG T 130 "
           pdb=" O3'  DG T 130 "
           pdb=" P    DC T 131 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   44.32  175.68     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" CD  ARG c  82 "
           pdb=" NE  ARG c  82 "
           pdb=" CZ  ARG c  82 "
           pdb=" NH1 ARG c  82 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   32.61  -32.61     1      1.00e+01 1.00e-02 1.51e+01
  dihedral pdb=" C4'  DC T 118 "
           pdb=" C3'  DC T 118 "
           pdb=" O3'  DC T 118 "
           pdb=" P    DG T 119 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   81.57  138.43     1      3.50e+01 8.16e-04 1.37e+01
  ... (remaining 10625 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.103: 1656
       0.103 -    0.206: 305
       0.206 -    0.309: 161
       0.309 -    0.412: 72
       0.412 -    0.515: 19
  Chirality restraints: 2213
  Sorted by residual:
  chirality pdb=" P    DT N  49 "
            pdb=" OP1  DT N  49 "
            pdb=" OP2  DT N  49 "
            pdb=" O5'  DT N  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34    1.82    0.51 2.00e-01 2.50e+01 6.62e+00
  chirality pdb=" P    DT T 165 "
            pdb=" OP1  DT T 165 "
            pdb=" OP2  DT T 165 "
            pdb=" O5'  DT T 165 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.83   -0.49 2.00e-01 2.50e+01 6.04e+00
  chirality pdb=" P    DT N   6 "
            pdb=" OP1  DT N   6 "
            pdb=" OP2  DT N   6 "
            pdb=" O5'  DT N   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.81   -0.48 2.00e-01 2.50e+01 5.71e+00
  ... (remaining 2210 not shown)

  Planarity restraints: 2813
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG c  82 "    0.492 9.50e-02 1.11e+02   1.65e-01 3.42e+01
        pdb=" NE  ARG c  82 "   -0.033 2.00e-02 2.50e+03
        pdb=" CZ  ARG c  82 "    0.027 2.00e-02 2.50e+03
        pdb=" NH1 ARG c  82 "   -0.031 2.00e-02 2.50e+03
        pdb=" NH2 ARG c  82 "    0.001 2.00e-02 2.50e+03
        pdb="HH11 ARG c  82 "   -0.001 2.00e-02 2.50e+03
        pdb="HH12 ARG c  82 "    0.014 2.00e-02 2.50e+03
        pdb="HH21 ARG c  82 "   -0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG c  82 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG c  33 "    0.375 9.50e-02 1.11e+02   1.28e-01 3.02e+01
        pdb=" NE  ARG c  33 "   -0.031 2.00e-02 2.50e+03
        pdb=" CZ  ARG c  33 "    0.026 2.00e-02 2.50e+03
        pdb=" NH1 ARG c  33 "   -0.043 2.00e-02 2.50e+03
        pdb=" NH2 ARG c  33 "    0.027 2.00e-02 2.50e+03
        pdb="HH11 ARG c  33 "   -0.000 2.00e-02 2.50e+03
        pdb="HH12 ARG c  33 "    0.030 2.00e-02 2.50e+03
        pdb="HH21 ARG c  33 "    0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG c  33 "   -0.027 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG g  18 "    0.134 9.50e-02 1.11e+02   5.63e-02 2.85e+01
        pdb=" NE  ARG g  18 "    0.042 2.00e-02 2.50e+03
        pdb=" CZ  ARG g  18 "   -0.046 2.00e-02 2.50e+03
        pdb=" NH1 ARG g  18 "   -0.049 2.00e-02 2.50e+03
        pdb=" NH2 ARG g  18 "   -0.034 2.00e-02 2.50e+03
        pdb="HH11 ARG g  18 "    0.000 2.00e-02 2.50e+03
        pdb="HH12 ARG g  18 "    0.045 2.00e-02 2.50e+03
        pdb="HH21 ARG g  18 "   -0.000 2.00e-02 2.50e+03
        pdb="HH22 ARG g  18 "    0.036 2.00e-02 2.50e+03
  ... (remaining 2810 not shown)

  Histogram of nonbonded interaction distances:
        1.88 -     2.42: 10006
        2.42 -     2.97: 49680
        2.97 -     3.51: 59693
        3.51 -     4.06: 84909
        4.06 -     4.60: 121696
  Nonbonded interactions: 325984
  Sorted by model distance:
  nonbonded pdb=" O   TYR c  40 "
            pdb=" HG  SER d  78 "
     model   vdw
     1.877 2.450
  nonbonded pdb=" HG1 THR d  90 "
            pdb=" OE1 GLU d  93 "
     model   vdw
     1.878 2.450
  nonbonded pdb=" H2'  DC N  46 "
            pdb=" H6   DC N  46 "
     model   vdw
     1.887 2.270
  nonbonded pdb="HD12 LEU a  62 "
            pdb="HH21 ARG b  40 "
     model   vdw
     1.891 2.270
  nonbonded pdb=" O   LEU e 104 "
            pdb=" HG1 THR e 108 "
     model   vdw
     1.897 2.450
  ... (remaining 325979 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
Found NCS groups:
ncs_group {
  reference = (chain 'a' and resid 40 through 134)
  selection = chain 'e'
}
ncs_group {
  reference = chain 'b'
  selection = chain 'f'
}
ncs_group {
  reference = (chain 'c' and resid 16 through 118)
  selection = chain 'g'
}
ncs_group {
  reference = (chain 'd' and resid 35 through 123)
  selection = chain 'h'
}

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:             1.660
  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:             0.160
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.070
  Process input model:                     26.740
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.040
  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:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7135
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      :  0.008   0.108  13856  Z= 0.642
  Angle     :  1.878  79.578  19760  Z= 1.060
  Chirality :  0.125   0.515   2213
  Planarity :  0.017   0.217   1657
  Dihedral  : 23.821 175.677   5850
  Min Nonbonded Distance : 2.077

Molprobity Statistics.
  All-atom Clashscore : 1.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  2.00 %
    Favored  : 97.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.05 (0.25), residues: 983
  helix:  0.69 (0.20), residues: 592
  sheet: -1.64 (0.89), residues: 28
  loop : -1.00 (0.29), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.036   0.005   ARG c  82 
 TYR   0.037   0.007   TYR O1604 
 PHE   0.041   0.005   PHE j 948 
 TRP   0.037   0.006   TRP O1562 
 HIS   0.021   0.004   HIS b  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00751 /  0.64 (13856)
  covalent geometry    : angle       1.87838 /  1.06 (19760)
  hydrogen bonds       : bond        0.12309 / 13.44 (  776)
  hydrogen bonds       : angle       4.81830 /  6.27 ( 1961)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  473 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 467
  time to evaluate  : 0.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1452 ASP cc_start: 0.5855 (m-30) cc_final: 0.5063 (m-30)
REVERT: O 1478 GLU cc_start: 0.7814 (pt0) cc_final: 0.7537 (pt0)
REVERT: O 1482 LEU cc_start: 0.8103 (mp) cc_final: 0.6729 (tt)
REVERT: O 1498 GLN cc_start: 0.8642 (tp40) cc_final: 0.8305 (tp40)
REVERT: O 1526 MET cc_start: 0.8541 (mtm) cc_final: 0.7989 (mtm)
REVERT: O 1574 THR cc_start: 0.7955 (m) cc_final: 0.7450 (m)
REVERT: O 1587 LYS cc_start: 0.7549 (tttt) cc_final: 0.7272 (mttt)
REVERT: O 1589 PHE cc_start: 0.7321 (t80) cc_final: 0.6967 (t80)
REVERT: O 1595 GLU cc_start: 0.8620 (tt0) cc_final: 0.8212 (tt0)
REVERT: O 1596 TYR cc_start: 0.5565 (m-10) cc_final: 0.5123 (m-10)
REVERT: O 1612 ASP cc_start: 0.7656 (t0) cc_final: 0.7139 (t0)
REVERT: O 1616 ASP cc_start: 0.5625 (t0) cc_final: 0.4501 (t0)
REVERT: a   38 LYS cc_start: 0.7218 (pttp) cc_final: 0.6955 (pttt)
REVERT: a   40 HIS cc_start: 0.7298 (t70) cc_final: 0.7050 (t70)
REVERT: a   60 GLU cc_start: 0.8121 (pt0) cc_final: 0.7845 (pt0)
REVERT: a   63 ILE cc_start: 0.8521 (mt) cc_final: 0.8308 (mm)
REVERT: a  100 TYR cc_start: 0.7888 (t80) cc_final: 0.7624 (t80)
REVERT: a  104 LEU cc_start: 0.8074 (tp) cc_final: 0.7807 (tt)
REVERT: a  108 THR cc_start: 0.8578 (m) cc_final: 0.8081 (m)
REVERT: a  130 ARG cc_start: 0.8479 (tpt90) cc_final: 0.8155 (tpt90)
REVERT: b   25 ASN cc_start: 0.8854 (m-40) cc_final: 0.8629 (m110)
REVERT: b   26 ILE cc_start: 0.8678 (tp) cc_final: 0.8197 (mt)
REVERT: b   43 VAL cc_start: 0.8488 (t) cc_final: 0.8098 (m)
REVERT: b   68 ASP cc_start: 0.8293 (m-30) cc_final: 0.7849 (m-30)
REVERT: c   44 VAL cc_start: 0.8882 (t) cc_final: 0.8449 (p)
REVERT: c   57 GLU cc_start: 0.7773 (tt0) cc_final: 0.7355 (tm-30)
REVERT: c   62 GLU cc_start: 0.8210 (tp30) cc_final: 0.7681 (tp30)
REVERT: c   85 GLN cc_start: 0.7580 (tp40) cc_final: 0.7300 (tp40)
REVERT: d   41 VAL cc_start: 0.8124 (t) cc_final: 0.7755 (t)
REVERT: d   45 LEU cc_start: 0.8766 (tp) cc_final: 0.8520 (tp)
REVERT: d   52 THR cc_start: 0.8072 (m) cc_final: 0.7864 (m)
REVERT: d   71 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7394 (tm-30)
REVERT: d   85 LYS cc_start: 0.8248 (mttp) cc_final: 0.7671 (mtpt)
REVERT: d   87 SER cc_start: 0.8571 (m) cc_final: 0.8154 (p)
REVERT: d  120 LYS cc_start: 0.8391 (mttt) cc_final: 0.7977 (tptp)
REVERT: e   43 ARG cc_start: 0.7582 (ttm170) cc_final: 0.7298 (ttp80)
REVERT: e   56 GLN cc_start: 0.8499 (mt0) cc_final: 0.8203 (mt0)
REVERT: e   57 LYS cc_start: 0.8330 (ttpp) cc_final: 0.8064 (tmtt)
REVERT: e   63 ILE cc_start: 0.8614 (mt) cc_final: 0.8265 (mt)
REVERT: e   74 GLU cc_start: 0.7622 (tt0) cc_final: 0.7324 (tt0)
REVERT: e   94 GLN cc_start: 0.8312 (tt0) cc_final: 0.7809 (tt0)
REVERT: e  126 GLN cc_start: 0.8457 (mt0) cc_final: 0.8252 (mm-40)
REVERT: f   25 ASN cc_start: 0.8455 (m-40) cc_final: 0.8223 (m-40)
REVERT: f   74 GLU cc_start: 0.8861 (mt-10) cc_final: 0.8390 (mm-30)
REVERT: g   25 GLN cc_start: 0.9199 (mm-40) cc_final: 0.8960 (mm-40)
REVERT: g   36 ARG cc_start: 0.8646 (mtm110) cc_final: 0.8258 (ttp-110)
REVERT: g   43 ARG cc_start: 0.7691 (mtt180) cc_final: 0.7470 (mtm180)
REVERT: g   56 LEU cc_start: 0.8325 (mt) cc_final: 0.8061 (mt)
REVERT: g   60 THR cc_start: 0.8978 (m) cc_final: 0.8777 (p)
REVERT: g   62 GLU cc_start: 0.8861 (tp30) cc_final: 0.8646 (tp30)
REVERT: g   85 GLN cc_start: 0.7287 (tp40) cc_final: 0.6977 (tp40)
REVERT: g   93 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7230 (mt-10)
REVERT: g   96 LYS cc_start: 0.8927 (ttmt) cc_final: 0.8194 (tptt)
REVERT: g   97 LEU cc_start: 0.9099 (tp) cc_final: 0.8892 (tt)
REVERT: g  105 GLN cc_start: 0.7144 (mm-40) cc_final: 0.5904 (tp-100)
REVERT: h   62 MET cc_start: 0.6944 (mmm) cc_final: 0.6693 (mmm)
REVERT: h   85 LYS cc_start: 0.8493 (mtmm) cc_final: 0.8058 (mptt)
REVERT: h   90 THR cc_start: 0.8349 (p) cc_final: 0.8134 (p)
REVERT: h  105 GLU cc_start: 0.7405 (tp30) cc_final: 0.7116 (tp30)
REVERT: h  121 TYR cc_start: 0.8763 (t80) cc_final: 0.8556 (t80)
  outliers start: 6
  outliers final: 3
  residues processed: 470
  average time/residue: 0.3451
  time to fit residues: 214.5599
Evaluate side-chains
  299 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 296
  time to evaluate  : 0.538 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 117 optimal weight:    1.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
a  86 GLN
f  93 GLN
g  25 GLN
j 949 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.088270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.061117 restraints weight = 80434.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.063908 restraints weight = 35858.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.065725 restraints weight = 22416.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.066725 restraints weight = 17205.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2833 r_free = 0.2833 target = 0.067451 restraints weight = 14961.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.2819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.3271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.100  13856  Z= 0.234
  Angle     :  0.799  10.501  19760  Z= 0.488
  Chirality :  0.050   0.296   2213
  Planarity :  0.007   0.083   1657
  Dihedral  : 28.237 176.135   3850
  Min Nonbonded Distance : 2.044

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  2.36 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.25), residues: 983
  helix:  1.13 (0.20), residues: 587
  sheet: -1.01 (1.15), residues: 18
  loop : -1.12 (0.29), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG g  18 
 TYR   0.024   0.002   TYR f  88 
 PHE   0.028   0.002   PHE O1668 
 TRP   0.007   0.001   TRP O1562 
 HIS   0.006   0.001   HIS f  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00432 /  0.23 (13856)
  covalent geometry    : angle       0.79906 /  0.49 (19760)
  hydrogen bonds       : bond        0.06404 /  7.07 (  776)
  hydrogen bonds       : angle       4.20958 /  5.49 ( 1961)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 327
  time to evaluate  : 0.536 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1482 LEU cc_start: 0.8456 (mp) cc_final: 0.7308 (tt)
REVERT: O 1587 LYS cc_start: 0.7603 (tttt) cc_final: 0.7211 (mttt)
REVERT: O 1595 GLU cc_start: 0.8474 (tt0) cc_final: 0.8168 (tt0)
REVERT: O 1614 ILE cc_start: 0.6790 (mp) cc_final: 0.5849 (mp)
REVERT: a   60 GLU cc_start: 0.8289 (pt0) cc_final: 0.8005 (pt0)
REVERT: a   74 GLU cc_start: 0.7722 (tt0) cc_final: 0.7512 (tt0)
REVERT: a   94 GLN cc_start: 0.8307 (tt0) cc_final: 0.7143 (tp40)
REVERT: a  100 TYR cc_start: 0.7970 (t80) cc_final: 0.7699 (t80)
REVERT: a  108 THR cc_start: 0.8638 (m) cc_final: 0.8349 (m)
REVERT: a  130 ARG cc_start: 0.8727 (tpt90) cc_final: 0.8506 (tpt90)
REVERT: b   43 VAL cc_start: 0.8512 (t) cc_final: 0.8248 (p)
REVERT: b   53 GLU cc_start: 0.8340 (tp30) cc_final: 0.8136 (tp30)
REVERT: b   80 THR cc_start: 0.9057 (m) cc_final: 0.8852 (m)
REVERT: c   44 VAL cc_start: 0.8758 (t) cc_final: 0.8377 (p)
REVERT: c   62 GLU cc_start: 0.8311 (tp30) cc_final: 0.7819 (tp30)
REVERT: c   79 ILE cc_start: 0.8230 (mt) cc_final: 0.7987 (mm)
REVERT: d   41 VAL cc_start: 0.7886 (t) cc_final: 0.7659 (t)
REVERT: d   71 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7641 (tm-30)
REVERT: d   85 LYS cc_start: 0.8319 (mttp) cc_final: 0.7814 (mtpt)
REVERT: d  113 GLU cc_start: 0.8580 (tp30) cc_final: 0.8160 (tm-30)
REVERT: d  120 LYS cc_start: 0.8589 (mttt) cc_final: 0.7884 (tptp)
REVERT: e   57 LYS cc_start: 0.8420 (ttpp) cc_final: 0.8158 (ttmm)
REVERT: e   74 GLU cc_start: 0.7408 (tt0) cc_final: 0.7115 (tt0)
REVERT: e   94 GLN cc_start: 0.8291 (tt0) cc_final: 0.7390 (tt0)
REVERT: e   98 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8000 (mt-10)
REVERT: f   25 ASN cc_start: 0.8369 (m-40) cc_final: 0.7955 (m-40)
REVERT: f   43 VAL cc_start: 0.9086 (t) cc_final: 0.8879 (p)
REVERT: f   74 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8753 (tt0)
REVERT: g   85 GLN cc_start: 0.7322 (tp40) cc_final: 0.6986 (tp40)
REVERT: g   96 LYS cc_start: 0.8833 (ttmt) cc_final: 0.8258 (tptt)
REVERT: g  105 GLN cc_start: 0.7789 (mm-40) cc_final: 0.6684 (mm-40)
REVERT: h   54 ILE cc_start: 0.8367 (tt) cc_final: 0.8096 (tt)
REVERT: h   85 LYS cc_start: 0.8519 (mtmm) cc_final: 0.8206 (mptt)
REVERT: h  105 GLU cc_start: 0.7502 (tp30) cc_final: 0.7293 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 327
  average time/residue: 0.2857
  time to fit residues: 130.6298
Evaluate side-chains
  265 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 265
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 11 optimal weight:    9.9990
   chunk 52 optimal weight:    1.9990
   chunk 117 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 37 optimal weight:    7.9990
   chunk 104 optimal weight:    1.9990
   chunk 44 optimal weight:    9.9990
   chunk 15 optimal weight:   10.0000
   chunk 105 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   overall best weight:    1.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
b  25 ASN
c  85 GLN
g  25 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.087197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2666 r_free = 0.2666 target = 0.059683 restraints weight = 81321.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.062429 restraints weight = 36713.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.064218 restraints weight = 23064.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.065300 restraints weight = 17830.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.065995 restraints weight = 15394.732|
|-----------------------------------------------------------------------------|
r_work (final): 0.2798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7333
moved from start:          0.3996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.102  13856  Z= 0.250
  Angle     :  0.737   7.145  19760  Z= 0.458
  Chirality :  0.045   0.302   2213
  Planarity :  0.006   0.110   1657
  Dihedral  : 28.444 172.598   3850
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.25), residues: 983
  helix:  1.04 (0.20), residues: 597
  sheet: -0.67 (1.28), residues: 18
  loop : -1.18 (0.29), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG d  72 
 TYR   0.018   0.002   TYR d  83 
 PHE   0.023   0.002   PHE O1544 
 TRP   0.002   0.001   TRP O1640 
 HIS   0.007   0.001   HIS f  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00477 /  0.25 (13856)
  covalent geometry    : angle       0.73672 /  0.46 (19760)
  hydrogen bonds       : bond        0.05843 /  6.46 (  776)
  hydrogen bonds       : angle       4.14854 /  5.39 ( 1961)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  309 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 309
  time to evaluate  : 0.724 
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: O 1462 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7499 (tt0)
REVERT: O 1482 LEU cc_start: 0.8457 (mp) cc_final: 0.7279 (tt)
REVERT: O 1587 LYS cc_start: 0.7637 (tttt) cc_final: 0.7227 (mttt)
REVERT: O 1595 GLU cc_start: 0.8464 (tt0) cc_final: 0.8124 (tm-30)
REVERT: a   94 GLN cc_start: 0.8149 (tt0) cc_final: 0.7914 (tt0)
REVERT: a  108 THR cc_start: 0.8739 (m) cc_final: 0.8515 (m)
REVERT: a  130 ARG cc_start: 0.8793 (tpt90) cc_final: 0.8554 (tpt90)
REVERT: b   84 MET cc_start: 0.6528 (mmt) cc_final: 0.6073 (mmt)
REVERT: c   44 VAL cc_start: 0.8811 (t) cc_final: 0.8416 (p)
REVERT: c   62 GLU cc_start: 0.8161 (tp30) cc_final: 0.7755 (tp30)
REVERT: d   41 VAL cc_start: 0.7914 (t) cc_final: 0.7695 (t)
REVERT: d   71 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7723 (tm-30)
REVERT: d   85 LYS cc_start: 0.8339 (mttp) cc_final: 0.7761 (mtpt)
REVERT: d  113 GLU cc_start: 0.8705 (tp30) cc_final: 0.8192 (tm-30)
REVERT: d  120 LYS cc_start: 0.8529 (mttt) cc_final: 0.7836 (tptp)
REVERT: e   57 LYS cc_start: 0.8498 (ttpp) cc_final: 0.8198 (ttmm)
REVERT: e   74 GLU cc_start: 0.7393 (tt0) cc_final: 0.6677 (tt0)
REVERT: e   94 GLN cc_start: 0.8469 (tt0) cc_final: 0.7511 (tt0)
REVERT: e   98 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8046 (mt-10)
REVERT: f   25 ASN cc_start: 0.8348 (m-40) cc_final: 0.7766 (m-40)
REVERT: f   51 TYR cc_start: 0.8757 (m-80) cc_final: 0.8210 (m-80)
REVERT: f   74 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8798 (tt0)
REVERT: g   85 GLN cc_start: 0.7344 (tp40) cc_final: 0.7087 (tp40)
REVERT: g   96 LYS cc_start: 0.8824 (ttmt) cc_final: 0.8284 (tptt)
REVERT: h   85 LYS cc_start: 0.8471 (mtmm) cc_final: 0.8256 (mptt)
REVERT: h   86 ARG cc_start: 0.7803 (mmt-90) cc_final: 0.7388 (mmt-90)
REVERT: h  105 GLU cc_start: 0.7382 (tp30) cc_final: 0.7008 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 309
  average time/residue: 0.2969
  time to fit residues: 126.7735
Evaluate side-chains
  256 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 256
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 108 optimal weight:    0.9980
   chunk 42 optimal weight:    7.9990
   chunk 80 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9980
   chunk 98 optimal weight:    1.9990
   chunk 92 optimal weight:    0.5980
   chunk 72 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 82 optimal weight:    0.7980
   chunk 84 optimal weight:    3.9990
   overall best weight:    1.0782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
g  25 GLN
g 105 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.088504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.060832 restraints weight = 79945.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.063587 restraints weight = 35863.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.065408 restraints weight = 22541.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.066585 restraints weight = 17362.761|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.067169 restraints weight = 15006.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7316
moved from start:          0.4361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  13856  Z= 0.178
  Angle     :  0.654   6.304  19760  Z= 0.414
  Chirality :  0.043   0.297   2213
  Planarity :  0.005   0.054   1657
  Dihedral  : 28.501 172.411   3850
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.26), residues: 983
  helix:  1.33 (0.21), residues: 598
  sheet: -0.62 (1.28), residues: 18
  loop : -1.05 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG g  89 
 TYR   0.016   0.002   TYR d  42 
 PHE   0.019   0.001   PHE O1668 
 TRP   0.001   0.000   TRP O1562 
 HIS   0.004   0.001   HIS f  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.18 (13856)
  covalent geometry    : angle       0.65404 /  0.41 (19760)
  hydrogen bonds       : bond        0.05145 /  5.61 (  776)
  hydrogen bonds       : angle       3.81995 /  4.94 ( 1961)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 306
  time to evaluate  : 0.488 
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: O 1462 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7349 (tt0)
REVERT: O 1482 LEU cc_start: 0.8421 (mp) cc_final: 0.7238 (tt)
REVERT: O 1587 LYS cc_start: 0.7626 (tttt) cc_final: 0.7229 (mttt)
REVERT: O 1595 GLU cc_start: 0.8487 (tt0) cc_final: 0.8236 (tm-30)
REVERT: O 1607 MET cc_start: 0.6236 (tpp) cc_final: 0.5670 (mmt)
REVERT: a   61 LEU cc_start: 0.8776 (mm) cc_final: 0.8394 (mm)
REVERT: a   94 GLN cc_start: 0.8289 (tt0) cc_final: 0.7933 (tt0)
REVERT: a  100 TYR cc_start: 0.7929 (t80) cc_final: 0.7675 (t80)
REVERT: a  108 THR cc_start: 0.8773 (m) cc_final: 0.8560 (m)
REVERT: a  130 ARG cc_start: 0.8792 (tpt90) cc_final: 0.8393 (tpt90)
REVERT: b   26 ILE cc_start: 0.8526 (tp) cc_final: 0.8226 (mp)
REVERT: b   84 MET cc_start: 0.6650 (mmt) cc_final: 0.6306 (mmt)
REVERT: c   44 VAL cc_start: 0.8754 (t) cc_final: 0.8304 (p)
REVERT: c   62 GLU cc_start: 0.8148 (tp30) cc_final: 0.7702 (tp30)
REVERT: c   73 ASP cc_start: 0.7706 (m-30) cc_final: 0.7485 (m-30)
REVERT: d   41 VAL cc_start: 0.7941 (t) cc_final: 0.7703 (t)
REVERT: d   46 LYS cc_start: 0.8931 (mmtp) cc_final: 0.8723 (mmtt)
REVERT: d   71 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7706 (tm-30)
REVERT: d   85 LYS cc_start: 0.8254 (mttp) cc_final: 0.7715 (mtpt)
REVERT: d  113 GLU cc_start: 0.8703 (tp30) cc_final: 0.8178 (tm-30)
REVERT: d  120 LYS cc_start: 0.8479 (mttt) cc_final: 0.7791 (tptp)
REVERT: e   94 GLN cc_start: 0.8510 (tt0) cc_final: 0.7583 (tt0)
REVERT: e   98 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8087 (mt-10)
REVERT: f   25 ASN cc_start: 0.8250 (m-40) cc_final: 0.7514 (m-40)
REVERT: f   51 TYR cc_start: 0.8717 (m-80) cc_final: 0.8138 (m-80)
REVERT: f   74 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8768 (tt0)
REVERT: g   85 GLN cc_start: 0.7259 (tp40) cc_final: 0.7046 (tp40)
REVERT: g   96 LYS cc_start: 0.8737 (ttmt) cc_final: 0.8239 (tptp)
REVERT: h   93 GLU cc_start: 0.7949 (mm-30) cc_final: 0.7701 (mm-30)
REVERT: h  105 GLU cc_start: 0.7324 (tp30) cc_final: 0.6893 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 306
  average time/residue: 0.2682
  time to fit residues: 116.8861
Evaluate side-chains
  261 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 11 optimal weight:    9.9990
   chunk 85 optimal weight:    3.9990
   chunk 35 optimal weight:    9.9990
   chunk 108 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 40 optimal weight:   10.0000
   chunk 18 optimal weight:    3.9990
   chunk 58 optimal weight:    0.2980
   chunk 7 optimal weight:    8.9990
   chunk 25 optimal weight:    8.9990
   overall best weight:    2.6588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
a  69 GLN
b  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.085615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.058458 restraints weight = 82609.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.061118 restraints weight = 37387.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.062851 restraints weight = 23661.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.063815 restraints weight = 18341.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.064497 restraints weight = 16049.270|
|-----------------------------------------------------------------------------|
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7375
moved from start:          0.4690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.149  13856  Z= 0.314
  Angle     :  0.736   7.121  19760  Z= 0.453
  Chirality :  0.044   0.308   2213
  Planarity :  0.005   0.044   1657
  Dihedral  : 28.516 171.810   3850
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.15 %
    Favored  : 96.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.26), residues: 983
  helix:  0.95 (0.21), residues: 601
  sheet: -0.60 (1.29), residues: 18
  loop : -1.07 (0.31), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG b  35 
 TYR   0.031   0.003   TYR d  83 
 PHE   0.016   0.002   PHE O1668 
 TRP   0.006   0.001   TRP O1640 
 HIS   0.011   0.002   HIS f  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00622 /  0.31 (13856)
  covalent geometry    : angle       0.73623 /  0.45 (19760)
  hydrogen bonds       : bond        0.05673 /  6.21 (  776)
  hydrogen bonds       : angle       4.27349 /  5.64 ( 1961)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 279
  time to evaluate  : 0.644 
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: O 1462 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7341 (tt0)
REVERT: O 1482 LEU cc_start: 0.8384 (mp) cc_final: 0.7310 (tt)
REVERT: O 1579 TYR cc_start: 0.7472 (t80) cc_final: 0.6687 (t80)
REVERT: O 1587 LYS cc_start: 0.7776 (tttt) cc_final: 0.7350 (mttt)
REVERT: O 1595 GLU cc_start: 0.8506 (tt0) cc_final: 0.8202 (tm-30)
REVERT: O 1612 ASP cc_start: 0.7932 (t0) cc_final: 0.7119 (t70)
REVERT: O 1665 ASP cc_start: 0.8680 (t0) cc_final: 0.8429 (t0)
REVERT: a   59 THR cc_start: 0.8800 (p) cc_final: 0.8330 (t)
REVERT: a  104 LEU cc_start: 0.7462 (tt) cc_final: 0.7169 (tt)
REVERT: a  130 ARG cc_start: 0.8850 (tpt90) cc_final: 0.8411 (tpt90)
REVERT: b   84 MET cc_start: 0.6465 (mmt) cc_final: 0.6251 (mmt)
REVERT: c   44 VAL cc_start: 0.8755 (t) cc_final: 0.8359 (p)
REVERT: c   62 GLU cc_start: 0.8052 (tp30) cc_final: 0.7662 (tp30)
REVERT: c   86 LEU cc_start: 0.8470 (mt) cc_final: 0.8201 (mt)
REVERT: d   71 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7797 (tm-30)
REVERT: d   85 LYS cc_start: 0.8375 (mttp) cc_final: 0.7848 (mtpt)
REVERT: d  113 GLU cc_start: 0.8835 (tp30) cc_final: 0.8370 (tm-30)
REVERT: d  120 LYS cc_start: 0.8489 (mttt) cc_final: 0.7895 (tptp)
REVERT: e   94 GLN cc_start: 0.8496 (tt0) cc_final: 0.7540 (tt0)
REVERT: e   98 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7973 (mt-10)
REVERT: f   25 ASN cc_start: 0.8246 (m-40) cc_final: 0.7521 (m110)
REVERT: f   74 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8757 (tt0)
REVERT: g   65 GLU cc_start: 0.8675 (tp30) cc_final: 0.8271 (tm-30)
REVERT: g   85 GLN cc_start: 0.7363 (tp40) cc_final: 0.7105 (tp40)
REVERT: g   91 ASP cc_start: 0.7641 (t70) cc_final: 0.7436 (t0)
REVERT: g   96 LYS cc_start: 0.8868 (ttmt) cc_final: 0.8349 (tptt)
REVERT: h   80 LEU cc_start: 0.8043 (mm) cc_final: 0.7834 (mm)
REVERT: h  100 LEU cc_start: 0.8282 (tt) cc_final: 0.7802 (tp)
REVERT: h  105 GLU cc_start: 0.7385 (tp30) cc_final: 0.7024 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 279
  average time/residue: 0.2688
  time to fit residues: 105.1773
Evaluate side-chains
  241 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9980
   chunk 11 optimal weight:   10.0000
   chunk 69 optimal weight:    0.6980
   chunk 74 optimal weight:    0.6980
   chunk 87 optimal weight:    0.5980
   chunk 62 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 47 optimal weight:   20.0000
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
O1498 GLN
a  69 GLN
a 109 ASN
g  25 GLN
j 949 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.088102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.060589 restraints weight = 80759.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2750 r_free = 0.2750 target = 0.063338 restraints weight = 36527.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.065148 restraints weight = 23062.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2815 r_free = 0.2815 target = 0.066260 restraints weight = 17850.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.066928 restraints weight = 15463.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.4881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  13856  Z= 0.165
  Angle     :  0.631   6.284  19760  Z= 0.402
  Chirality :  0.041   0.285   2213
  Planarity :  0.005   0.059   1657
  Dihedral  : 28.500 171.590   3850
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.77 %
    Favored  : 98.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.26), residues: 983
  helix:  1.24 (0.21), residues: 597
  sheet: -0.39 (1.27), residues: 18
  loop : -0.90 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.028   0.001   ARG f  92 
 TYR   0.039   0.002   TYR d  83 
 PHE   0.015   0.001   PHE O1668 
 TRP   0.001   0.000   TRP O1460 
 HIS   0.007   0.001   HIS b  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.16 (13856)
  covalent geometry    : angle       0.63141 /  0.40 (19760)
  hydrogen bonds       : bond        0.04951 /  5.38 (  776)
  hydrogen bonds       : angle       3.76125 /  4.88 ( 1961)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 285
  time to evaluate  : 0.484 
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: O 1482 LEU cc_start: 0.8382 (mp) cc_final: 0.7230 (tt)
REVERT: O 1579 TYR cc_start: 0.7524 (t80) cc_final: 0.6582 (t80)
REVERT: O 1587 LYS cc_start: 0.7775 (tttt) cc_final: 0.7324 (mttt)
REVERT: O 1595 GLU cc_start: 0.8489 (tt0) cc_final: 0.8287 (tp30)
REVERT: O 1612 ASP cc_start: 0.7437 (t0) cc_final: 0.7132 (t0)
REVERT: O 1615 ILE cc_start: 0.8146 (mt) cc_final: 0.7635 (mt)
REVERT: a   59 THR cc_start: 0.8712 (p) cc_final: 0.8323 (t)
REVERT: a  104 LEU cc_start: 0.7551 (tt) cc_final: 0.7305 (tt)
REVERT: a  108 THR cc_start: 0.8707 (m) cc_final: 0.8438 (m)
REVERT: a  130 ARG cc_start: 0.8880 (tpt90) cc_final: 0.8486 (tpt90)
REVERT: b   26 ILE cc_start: 0.8531 (tp) cc_final: 0.8235 (mp)
REVERT: b   84 MET cc_start: 0.6331 (mmt) cc_final: 0.6112 (mmt)
REVERT: c   44 VAL cc_start: 0.8721 (t) cc_final: 0.8325 (p)
REVERT: c   62 GLU cc_start: 0.8229 (tp30) cc_final: 0.7701 (tp30)
REVERT: c   79 ILE cc_start: 0.7947 (mt) cc_final: 0.7300 (tp)
REVERT: c   86 LEU cc_start: 0.8534 (mt) cc_final: 0.8295 (mt)
REVERT: d   85 LYS cc_start: 0.8471 (mttp) cc_final: 0.7806 (mtpt)
REVERT: d  113 GLU cc_start: 0.8763 (tp30) cc_final: 0.8275 (tm-30)
REVERT: d  120 LYS cc_start: 0.8437 (mttt) cc_final: 0.7839 (tptp)
REVERT: f   51 TYR cc_start: 0.8752 (m-80) cc_final: 0.8135 (m-80)
REVERT: f   74 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8827 (tt0)
REVERT: g   65 GLU cc_start: 0.8576 (tp30) cc_final: 0.8311 (tm-30)
REVERT: g   85 GLN cc_start: 0.7356 (tp40) cc_final: 0.7053 (tp40)
REVERT: g   91 ASP cc_start: 0.7584 (t70) cc_final: 0.7365 (t0)
REVERT: g   96 LYS cc_start: 0.8776 (ttmt) cc_final: 0.8255 (tptt)
  outliers start: 1
  outliers final: 0
  residues processed: 285
  average time/residue: 0.2583
  time to fit residues: 104.2515
Evaluate side-chains
  253 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 253
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 1 optimal weight:   10.0000
   chunk 27 optimal weight:    9.9990
   chunk 63 optimal weight:    0.7980
   chunk 3 optimal weight:    9.9990
   chunk 96 optimal weight:    2.9990
   chunk 43 optimal weight:   10.0000
   chunk 66 optimal weight:    3.9990
   chunk 47 optimal weight:   20.0000
   chunk 26 optimal weight:    0.7980
   overall best weight:    2.3186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
a  69 GLN
b  25 ASN
e  94 GLN
g  25 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.085838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.058686 restraints weight = 82219.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.061328 restraints weight = 37228.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.063088 restraints weight = 23566.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.064035 restraints weight = 18273.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.064726 restraints weight = 16034.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.5062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.111  13856  Z= 0.280
  Angle     :  0.695   6.555  19760  Z= 0.431
  Chirality :  0.042   0.286   2213
  Planarity :  0.006   0.112   1657
  Dihedral  : 28.466 171.629   3850
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  1.42 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.26), residues: 983
  helix:  1.02 (0.21), residues: 601
  sheet: -0.63 (1.26), residues: 18
  loop : -0.91 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG f  92 
 TYR   0.031   0.002   TYR d  42 
 PHE   0.014   0.002   PHE O1668 
 TRP   0.006   0.001   TRP O1640 
 HIS   0.011   0.001   HIS b  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00547 /  0.28 (13856)
  covalent geometry    : angle       0.69456 /  0.43 (19760)
  hydrogen bonds       : bond        0.05219 /  5.69 (  776)
  hydrogen bonds       : angle       4.10490 /  5.39 ( 1961)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 275
  time to evaluate  : 0.476 
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: O 1482 LEU cc_start: 0.8303 (mp) cc_final: 0.7181 (tt)
REVERT: O 1587 LYS cc_start: 0.7796 (tttt) cc_final: 0.7335 (mttt)
REVERT: O 1595 GLU cc_start: 0.8502 (tt0) cc_final: 0.8200 (tm-30)
REVERT: a   59 THR cc_start: 0.8834 (p) cc_final: 0.8419 (t)
REVERT: a   65 LYS cc_start: 0.8177 (mttt) cc_final: 0.7968 (ttmt)
REVERT: a   94 GLN cc_start: 0.8451 (tt0) cc_final: 0.8013 (tt0)
REVERT: a  104 LEU cc_start: 0.7426 (tt) cc_final: 0.7142 (tt)
REVERT: a  119 THR cc_start: 0.8813 (m) cc_final: 0.8606 (m)
REVERT: a  130 ARG cc_start: 0.8905 (tpt90) cc_final: 0.8633 (tpt90)
REVERT: b   26 ILE cc_start: 0.8552 (tp) cc_final: 0.8240 (mp)
REVERT: c   44 VAL cc_start: 0.8717 (t) cc_final: 0.8302 (p)
REVERT: c   62 GLU cc_start: 0.8212 (tp30) cc_final: 0.7697 (tp30)
REVERT: c   79 ILE cc_start: 0.7983 (mt) cc_final: 0.7398 (tp)
REVERT: c   86 LEU cc_start: 0.8457 (mt) cc_final: 0.8199 (mt)
REVERT: d   85 LYS cc_start: 0.8376 (mttp) cc_final: 0.7883 (mtpt)
REVERT: d  113 GLU cc_start: 0.8809 (tp30) cc_final: 0.8362 (tm-30)
REVERT: d  120 LYS cc_start: 0.8509 (mttt) cc_final: 0.7937 (tptp)
REVERT: f   25 ASN cc_start: 0.8352 (m-40) cc_final: 0.7837 (m110)
REVERT: f   51 TYR cc_start: 0.8813 (m-80) cc_final: 0.8143 (m-80)
REVERT: f   74 GLU cc_start: 0.9169 (mt-10) cc_final: 0.8866 (tt0)
REVERT: g   65 GLU cc_start: 0.8676 (tp30) cc_final: 0.8384 (tm-30)
REVERT: g   85 GLN cc_start: 0.7344 (tp40) cc_final: 0.7053 (tp40)
REVERT: g   91 ASP cc_start: 0.7740 (t70) cc_final: 0.7413 (t0)
REVERT: g   96 LYS cc_start: 0.8826 (ttmt) cc_final: 0.8325 (tptt)
  outliers start: 2
  outliers final: 0
  residues processed: 275
  average time/residue: 0.2485
  time to fit residues: 98.3236
Evaluate side-chains
  237 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 101 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9990
   chunk 44 optimal weight:   10.0000
   chunk 46 optimal weight:    9.9990
   chunk 57 optimal weight:    0.5980
   chunk 94 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 6 optimal weight:    8.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
a  69 GLN
a 109 ASN
b  25 ASN
g  25 GLN
h  63 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.087461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.060138 restraints weight = 81113.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.062883 restraints weight = 36497.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.064659 restraints weight = 22929.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.065802 restraints weight = 17663.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.066486 restraints weight = 15263.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7326
moved from start:          0.5166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  13856  Z= 0.174
  Angle     :  0.627   6.559  19760  Z= 0.398
  Chirality :  0.041   0.281   2213
  Planarity :  0.006   0.083   1657
  Dihedral  : 28.448 171.431   3850
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  1.06 %
    Favored  : 98.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.27), residues: 983
  helix:  1.25 (0.21), residues: 597
  sheet: -0.50 (1.23), residues: 18
  loop : -0.81 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG d  72 
 TYR   0.025   0.002   TYR d  42 
 PHE   0.014   0.001   PHE O1668 
 TRP   0.001   0.000   TRP O1640 
 HIS   0.009   0.001   HIS h  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.17 (13856)
  covalent geometry    : angle       0.62719 /  0.40 (19760)
  hydrogen bonds       : bond        0.04792 /  5.19 (  776)
  hydrogen bonds       : angle       3.77877 /  4.95 ( 1961)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 284
  time to evaluate  : 0.505 
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: O 1482 LEU cc_start: 0.8286 (mp) cc_final: 0.7139 (tt)
REVERT: O 1549 HIS cc_start: 0.7672 (p-80) cc_final: 0.7196 (p-80)
REVERT: O 1579 TYR cc_start: 0.7339 (t80) cc_final: 0.6748 (t80)
REVERT: O 1587 LYS cc_start: 0.7784 (tttt) cc_final: 0.7322 (mttt)
REVERT: O 1595 GLU cc_start: 0.8461 (tt0) cc_final: 0.8239 (tp30)
REVERT: O 1612 ASP cc_start: 0.7241 (t0) cc_final: 0.6983 (t0)
REVERT: a   59 THR cc_start: 0.8821 (p) cc_final: 0.8377 (t)
REVERT: a   65 LYS cc_start: 0.8148 (mttt) cc_final: 0.7927 (ttmt)
REVERT: a   94 GLN cc_start: 0.8380 (tt0) cc_final: 0.7976 (tt0)
REVERT: a  108 THR cc_start: 0.8756 (m) cc_final: 0.8478 (m)
REVERT: a  130 ARG cc_start: 0.8925 (tpt90) cc_final: 0.8649 (tpt90)
REVERT: b   26 ILE cc_start: 0.8519 (tp) cc_final: 0.8209 (mp)
REVERT: c   44 VAL cc_start: 0.8666 (t) cc_final: 0.8266 (p)
REVERT: c   62 GLU cc_start: 0.8176 (tp30) cc_final: 0.7682 (tp30)
REVERT: c   79 ILE cc_start: 0.8042 (mt) cc_final: 0.7468 (tp)
REVERT: c   86 LEU cc_start: 0.8477 (mt) cc_final: 0.8196 (mt)
REVERT: d   71 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7248 (tm-30)
REVERT: d   85 LYS cc_start: 0.8389 (mttp) cc_final: 0.7858 (mtpt)
REVERT: d  113 GLU cc_start: 0.8787 (tp30) cc_final: 0.8314 (tm-30)
REVERT: d  120 LYS cc_start: 0.8475 (mttt) cc_final: 0.7886 (tptp)
REVERT: e   94 GLN cc_start: 0.8427 (tt0) cc_final: 0.7671 (tt0)
REVERT: f   51 TYR cc_start: 0.8776 (m-80) cc_final: 0.8099 (m-80)
REVERT: f   74 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8786 (tt0)
REVERT: g   65 GLU cc_start: 0.8558 (tp30) cc_final: 0.8344 (tm-30)
REVERT: g   85 GLN cc_start: 0.7358 (tp40) cc_final: 0.7006 (tp40)
REVERT: g   91 ASP cc_start: 0.7621 (t70) cc_final: 0.7389 (t0)
REVERT: g   96 LYS cc_start: 0.8787 (ttmt) cc_final: 0.8259 (tptt)
REVERT: h   86 ARG cc_start: 0.7972 (mmt-90) cc_final: 0.7457 (mmt-90)
REVERT: h  105 GLU cc_start: 0.7425 (tp30) cc_final: 0.7073 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 284
  average time/residue: 0.2451
  time to fit residues: 99.4686
Evaluate side-chains
  243 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 47 optimal weight:   20.0000
   chunk 36 optimal weight:   20.0000
   chunk 44 optimal weight:    8.9990
   chunk 88 optimal weight:    0.5980
   chunk 70 optimal weight:    1.9990
   chunk 3 optimal weight:    9.9990
   chunk 25 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.9188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
a  69 GLN
b  25 ASN
f  75 HIS
g  25 GLN
h  63 ASN
** j 949 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.086479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.059351 restraints weight = 82306.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2720 r_free = 0.2720 target = 0.062001 restraints weight = 37430.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.063744 restraints weight = 23763.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.064701 restraints weight = 18482.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.065362 restraints weight = 16208.849|
|-----------------------------------------------------------------------------|
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.5289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079  13856  Z= 0.232
  Angle     :  0.662   6.451  19760  Z= 0.412
  Chirality :  0.041   0.278   2213
  Planarity :  0.006   0.072   1657
  Dihedral  : 28.429 171.476   3850
  Min Nonbonded Distance : 2.293

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.71 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.27), residues: 983
  helix:  1.18 (0.21), residues: 601
  sheet: -0.57 (1.24), residues: 18
  loop : -0.91 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG d  79 
 TYR   0.017   0.002   TYR d  83 
 PHE   0.018   0.001   PHE O1650 
 TRP   0.005   0.001   TRP O1640 
 HIS   0.009   0.001   HIS b  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00438 /  0.23 (13856)
  covalent geometry    : angle       0.66192 /  0.41 (19760)
  hydrogen bonds       : bond        0.04941 /  5.37 (  776)
  hydrogen bonds       : angle       3.91973 /  5.17 ( 1961)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 272
  time to evaluate  : 0.524 
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: O 1482 LEU cc_start: 0.8295 (mp) cc_final: 0.7161 (tt)
REVERT: O 1587 LYS cc_start: 0.7762 (tttt) cc_final: 0.7298 (mttt)
REVERT: O 1595 GLU cc_start: 0.8457 (tt0) cc_final: 0.8221 (tp30)
REVERT: O 1612 ASP cc_start: 0.7299 (t0) cc_final: 0.7063 (t0)
REVERT: a   37 MET cc_start: 0.4069 (ptm) cc_final: 0.2959 (ppp)
REVERT: a   59 THR cc_start: 0.8802 (p) cc_final: 0.8369 (t)
REVERT: a   69 GLN cc_start: 0.7868 (OUTLIER) cc_final: 0.7454 (tp-100)
REVERT: a  119 THR cc_start: 0.8824 (m) cc_final: 0.8624 (m)
REVERT: a  130 ARG cc_start: 0.8903 (tpt90) cc_final: 0.8618 (tpt90)
REVERT: b   26 ILE cc_start: 0.8553 (tp) cc_final: 0.8224 (mp)
REVERT: c   44 VAL cc_start: 0.8690 (t) cc_final: 0.8281 (p)
REVERT: c   62 GLU cc_start: 0.8157 (tp30) cc_final: 0.7630 (tp30)
REVERT: c   73 ASP cc_start: 0.7660 (m-30) cc_final: 0.7443 (m-30)
REVERT: c   79 ILE cc_start: 0.7938 (mt) cc_final: 0.7321 (tp)
REVERT: c   86 LEU cc_start: 0.8442 (mt) cc_final: 0.8143 (mt)
REVERT: d   71 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7283 (tm-30)
REVERT: d   76 GLU cc_start: 0.7169 (tp30) cc_final: 0.6659 (tp30)
REVERT: d   85 LYS cc_start: 0.8398 (mttp) cc_final: 0.7885 (mtpt)
REVERT: d  113 GLU cc_start: 0.8813 (tp30) cc_final: 0.8349 (tm-30)
REVERT: d  120 LYS cc_start: 0.8489 (mttt) cc_final: 0.7916 (tptp)
REVERT: e   94 GLN cc_start: 0.8507 (tt0) cc_final: 0.7531 (tt0)
REVERT: f   25 ASN cc_start: 0.8311 (m-40) cc_final: 0.7816 (m110)
REVERT: f   51 TYR cc_start: 0.8711 (m-80) cc_final: 0.8048 (m-80)
REVERT: f   74 GLU cc_start: 0.9097 (mt-10) cc_final: 0.8850 (tt0)
REVERT: g   85 GLN cc_start: 0.7367 (tp40) cc_final: 0.7000 (tp40)
REVERT: g   91 ASP cc_start: 0.7664 (t70) cc_final: 0.7372 (t0)
REVERT: g   96 LYS cc_start: 0.8826 (ttmt) cc_final: 0.8300 (tptt)
REVERT: h   86 ARG cc_start: 0.7945 (mmt-90) cc_final: 0.7432 (mmt-90)
  outliers start: 1
  outliers final: 0
  residues processed: 272
  average time/residue: 0.2345
  time to fit residues: 92.7022
Evaluate side-chains
  242 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 241
  time to evaluate  : 0.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 118 optimal weight:    9.9990
   chunk 90 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   chunk 43 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 42 optimal weight:    6.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** a 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
b  25 ASN
g  25 GLN
h  63 ASN
j 949 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.087216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.059975 restraints weight = 81498.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.062696 restraints weight = 36637.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.064488 restraints weight = 22968.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.065574 restraints weight = 17680.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.066165 restraints weight = 15337.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.5409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  13856  Z= 0.188
  Angle     :  0.642   8.353  19760  Z= 0.401
  Chirality :  0.041   0.274   2213
  Planarity :  0.006   0.121   1657
  Dihedral  : 28.431 171.192   3850
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.59 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.27), residues: 983
  helix:  1.22 (0.21), residues: 597
  sheet: -0.51 (1.22), residues: 18
  loop : -0.84 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG g  82 
 TYR   0.017   0.002   TYR d  83 
 PHE   0.013   0.001   PHE O1668 
 TRP   0.002   0.001   TRP O1640 
 HIS   0.010   0.001   HIS f  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00343 /  0.19 (13856)
  covalent geometry    : angle       0.64214 /  0.40 (19760)
  hydrogen bonds       : bond        0.04772 /  5.20 (  776)
  hydrogen bonds       : angle       3.81160 /  5.00 ( 1961)

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

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

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1966 Ramachandran restraints generated.
    983 Oldfield, 0 Emsley, 983 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 276
  time to evaluate  : 0.567 
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: O 1482 LEU cc_start: 0.8226 (mp) cc_final: 0.7102 (tt)
REVERT: O 1549 HIS cc_start: 0.7725 (p-80) cc_final: 0.7273 (p-80)
REVERT: O 1587 LYS cc_start: 0.7755 (tttt) cc_final: 0.7318 (mttt)
REVERT: O 1595 GLU cc_start: 0.8444 (tt0) cc_final: 0.8204 (tp30)
REVERT: a   37 MET cc_start: 0.3884 (ptm) cc_final: 0.3571 (ppp)
REVERT: a   59 THR cc_start: 0.8796 (p) cc_final: 0.8288 (t)
REVERT: a  119 THR cc_start: 0.8854 (m) cc_final: 0.8638 (m)
REVERT: a  130 ARG cc_start: 0.8892 (tpt90) cc_final: 0.8616 (tpt90)
REVERT: b   26 ILE cc_start: 0.8515 (tp) cc_final: 0.8201 (mp)
REVERT: c   62 GLU cc_start: 0.8177 (tp30) cc_final: 0.7720 (tp30)
REVERT: c   79 ILE cc_start: 0.7833 (mt) cc_final: 0.7310 (tp)
REVERT: c   86 LEU cc_start: 0.8408 (mt) cc_final: 0.8106 (mt)
REVERT: d   35 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7455 (tm-30)
REVERT: d   71 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7236 (tm-30)
REVERT: d   85 LYS cc_start: 0.8427 (mttp) cc_final: 0.7880 (mtpt)
REVERT: d  113 GLU cc_start: 0.8801 (tp30) cc_final: 0.8317 (tm-30)
REVERT: d  120 LYS cc_start: 0.8465 (mttt) cc_final: 0.7891 (tptp)
REVERT: e   57 LYS cc_start: 0.8887 (ttmm) cc_final: 0.8612 (ttpt)
REVERT: e   94 GLN cc_start: 0.8150 (tt0) cc_final: 0.7832 (tt0)
REVERT: f   51 TYR cc_start: 0.8694 (m-80) cc_final: 0.8012 (m-80)
REVERT: f   74 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8830 (tt0)
REVERT: g   85 GLN cc_start: 0.7434 (tp40) cc_final: 0.6998 (tp40)
REVERT: g   96 LYS cc_start: 0.8817 (ttmt) cc_final: 0.8261 (tptt)
REVERT: h   86 ARG cc_start: 0.7894 (mmt-90) cc_final: 0.7408 (mmt-90)
  outliers start: 1
  outliers final: 0
  residues processed: 276
  average time/residue: 0.2397
  time to fit residues: 95.3940
Evaluate side-chains
  242 residues out of total 848 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 101 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 98 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 88 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 46 optimal weight:    9.9990
   chunk 72 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
a 109 ASN
b  25 ASN
d 109 HIS
g  25 GLN
j 949 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.087249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.059855 restraints weight = 81434.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.062586 restraints weight = 36639.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.064381 restraints weight = 23011.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.065443 restraints weight = 17773.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.066004 restraints weight = 15412.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.5489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  13856  Z= 0.188
  Angle     :  0.639   7.942  19760  Z= 0.399
  Chirality :  0.041   0.268   2213
  Planarity :  0.005   0.058   1657
  Dihedral  : 28.411 171.167   3850
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.47 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.70 (0.27), residues: 983
  helix:  1.28 (0.21), residues: 600
  sheet: -0.48 (1.22), residues: 18
  loop : -0.82 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG O1485 
 TYR   0.015   0.002   TYR d  83 
 PHE   0.013   0.001   PHE O1668 
 TRP   0.003   0.001   TRP O1640 
 HIS   0.007   0.001   HIS b  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.19 (13856)
  covalent geometry    : angle       0.63861 /  0.40 (19760)
  hydrogen bonds       : bond        0.04684 /  5.09 (  776)
  hydrogen bonds       : angle       3.76355 /  4.93 ( 1961)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4152.84 seconds
wall clock time: 71 minutes 36.27 seconds (4296.27 seconds total)