Starting phenix.real_space_refine
on Wed Mar  4 21:12:30 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lya_23590/03_2026/7lya_23590.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lya_23590/03_2026/7lya_23590.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.91
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lya_23590/03_2026/7lya_23590.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lya_23590/03_2026/7lya_23590.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lya_23590/03_2026/7lya_23590.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lya_23590/03_2026/7lya_23590.map"
  }
  resolution = 2.91
  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=   0.068
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     P     293      5.49       5
     S      14      5.16       5
     C    6687      2.51       5
     N    2275      2.21       5
     O    2829      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12098
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 652
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 652
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "D"
      Number of atoms: 751
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 751
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "H"
      Number of atoms: 737
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 735
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3010
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3010
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "C"
      Number of atoms: 839
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 839
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "G"
      Number of atoms: 830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 830
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
  Time building chain proxies: 2.55, per 1000 atoms: 0.21
  Number of scatterers: 12098
  At special positions: 0
  Unit cell: (86.604, 126.813, 117.534, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     293     15.00
     O    2829      8.00
     N    2275      7.00
     C    6687      6.00
    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
  Links applied
    TRANS
      " SER C  11 " - " SER D 123 "
      " SER G  11 " - " SER H 123 "
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 356.5 milliseconds
  

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1432

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      71.4% alpha, 3.1% beta
      139 base pairs and 259 stacking pairs defined.
    Time for finding SS restraints: 1.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 56
      removed outlier: 3.539A  pdb=" N   LEU A  48 " --> pdb=" O   GLY A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.606A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.548A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.719A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
      removed outlier: 3.550A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.595A  pdb=" N   MET D  59 " --> pdb=" O   SER D  55 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
    Processing helix  chain 'E' and resid 44 through 56
      removed outlier: 3.538A  pdb=" N   LEU E  48 " --> pdb=" O   GLY E  44 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.605A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.548A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    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: 3.694A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   GLY F  56 " --> pdb=" O   GLU F  52 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LYS F  59 " --> pdb=" O   ARG F  55 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.555A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.600A  pdb=" N   MET H  59 " --> pdb=" O   SER H  55 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.607A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
      removed outlier: 3.520A  pdb=" N   VAL C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 72
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.507A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 97
    Processing helix  chain 'C' and resid 112 through 116
      removed outlier: 3.732A  pdb=" N   LEU C 116 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
      removed outlier: 3.697A  pdb=" N   VAL G  30 " --> pdb=" O   PRO G  26 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 72
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 92 through 97
    Processing helix  chain 'G' and resid 112 through 116
      removed outlier: 3.695A  pdb=" N   LEU G 116 " --> pdb=" O   ALA G 113 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.127A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54
      removed outlier: 7.391A  pdb=" N   GLY D  53 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.165A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'F' and resid 96 through 98
    Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54
      removed outlier: 7.378A  pdb=" N   GLY H  53 " --> pdb=" O   ILE G  78 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89

    393 hydrogen bonds defined for protein.
    1160 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      356 hydrogen bonds
      708 hydrogen bond angles
      0 basepair planarities
      139 basepair parallelities
      259 stacking parallelities
  Total time for adding SS restraints: 2.21

  Time building geometry restraints manager: 1.30 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2063
        1.33 -     1.45: 4276
        1.45 -     1.57: 5962
        1.57 -     1.68: 584
        1.68 -     1.80: 24
  Bond restraints: 12909
  Sorted by residual:
  bond pdb=" C3'  DT J -17 "
       pdb=" O3'  DT J -17 "
    ideal  model  delta    sigma   weight residual
    1.422  1.465 -0.043 3.00e-02 1.11e+03 2.08e+00
  bond pdb=" CB  ARG E 131 "
       pdb=" CG  ARG E 131 "
    ideal  model  delta    sigma   weight residual
    1.520  1.479  0.041 3.00e-02 1.11e+03 1.89e+00
  bond pdb=" CB  ARG A 131 "
       pdb=" CG  ARG A 131 "
    ideal  model  delta    sigma   weight residual
    1.520  1.480  0.040 3.00e-02 1.11e+03 1.81e+00
  bond pdb=" CB  ARG C  35 "
       pdb=" CG  ARG C  35 "
    ideal  model  delta    sigma   weight residual
    1.520  1.480  0.040 3.00e-02 1.11e+03 1.74e+00
  bond pdb=" CB  LEU D  80 "
       pdb=" CG  LEU D  80 "
    ideal  model  delta    sigma   weight residual
    1.530  1.508  0.022 2.00e-02 2.50e+03 1.26e+00
  ... (remaining 12904 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 17958
        1.59 -     3.17: 675
        3.17 -     4.76: 40
        4.76 -     6.34: 8
        6.34 -     7.93: 3
  Bond angle restraints: 18684
  Sorted by residual:
  angle pdb=" C   GLN A  76 "
        pdb=" N   ASP A  77 "
        pdb=" CA  ASP A  77 "
      ideal   model   delta    sigma   weight residual
     122.06  114.13    7.93 1.86e+00 2.89e-01 1.82e+01
  angle pdb=" C   GLN E  76 "
        pdb=" N   ASP E  77 "
        pdb=" CA  ASP E  77 "
      ideal   model   delta    sigma   weight residual
     122.06  114.20    7.86 1.86e+00 2.89e-01 1.79e+01
  angle pdb=" C   LEU B  22 "
        pdb=" CA  LEU B  22 "
        pdb=" CB  LEU B  22 "
      ideal   model   delta    sigma   weight residual
     110.96  115.76   -4.80 1.54e+00 4.22e-01 9.71e+00
  angle pdb=" CA  LEU B  22 "
        pdb=" C   LEU B  22 "
        pdb=" N   ARG B  23 "
      ideal   model   delta    sigma   weight residual
     116.92  120.09   -3.17 1.16e+00 7.43e-01 7.48e+00
  angle pdb=" N   GLY H 104 "
        pdb=" CA  GLY H 104 "
        pdb=" C   GLY H 104 "
      ideal   model   delta    sigma   weight residual
     113.18  119.59   -6.41 2.37e+00 1.78e-01 7.33e+00
  ... (remaining 18679 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.23: 5579
       34.23 -    68.45: 1430
       68.45 -   102.68: 16
      102.68 -   136.91: 0
      136.91 -   171.14: 2
  Dihedral angle restraints: 7027
    sinusoidal: 4802
      harmonic: 2225
  Sorted by residual:
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   48.86  171.14     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   71.26  148.74     1      3.50e+01 8.16e-04 1.45e+01
  dihedral pdb=" CA  LEU F  22 "
           pdb=" C   LEU F  22 "
           pdb=" N   ARG F  23 "
           pdb=" CA  ARG F  23 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.07  -18.93     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 7024 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 1134
       0.029 -    0.058: 688
       0.058 -    0.087: 220
       0.087 -    0.116: 61
       0.116 -    0.144: 21
  Chirality restraints: 2124
  Sorted by residual:
  chirality pdb=" CA  ILE B  29 "
            pdb=" N   ILE B  29 "
            pdb=" C   ILE B  29 "
            pdb=" CB  ILE B  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.22e-01
  chirality pdb=" CA  ASP E  77 "
            pdb=" N   ASP E  77 "
            pdb=" C   ASP E  77 "
            pdb=" CB  ASP E  77 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.12e-01
  chirality pdb=" CA  ILE F  29 "
            pdb=" N   ILE F  29 "
            pdb=" C   ILE F  29 "
            pdb=" CB  ILE F  29 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.90e-01
  ... (remaining 2121 not shown)

  Planarity restraints: 1351
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I -52 "   -0.007 2.00e-02 2.50e+03   1.17e-02 4.10e+00
        pdb=" N9   DG I -52 "   -0.001 2.00e-02 2.50e+03
        pdb=" C8   DG I -52 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7   DG I -52 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DG I -52 "    0.003 2.00e-02 2.50e+03
        pdb=" C6   DG I -52 "    0.012 2.00e-02 2.50e+03
        pdb=" O6   DG I -52 "   -0.014 2.00e-02 2.50e+03
        pdb=" N1   DG I -52 "   -0.008 2.00e-02 2.50e+03
        pdb=" C2   DG I -52 "    0.030 2.00e-02 2.50e+03
        pdb=" N2   DG I -52 "   -0.017 2.00e-02 2.50e+03
        pdb=" N3   DG I -52 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4   DG I -52 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  47 "    0.026 2.00e-02 2.50e+03   1.09e-02 3.53e+00
        pdb=" N9   DG I  47 "   -0.023 2.00e-02 2.50e+03
        pdb=" C8   DG I  47 "   -0.005 2.00e-02 2.50e+03
        pdb=" N7   DG I  47 "   -0.004 2.00e-02 2.50e+03
        pdb=" C5   DG I  47 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  47 "    0.004 2.00e-02 2.50e+03
        pdb=" O6   DG I  47 "    0.009 2.00e-02 2.50e+03
        pdb=" N1   DG I  47 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I  47 "    0.000 2.00e-02 2.50e+03
        pdb=" N2   DG I  47 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3   DG I  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DG I  47 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  57 "    0.024 2.00e-02 2.50e+03   1.05e-02 3.03e+00
        pdb=" N9   DA I  57 "   -0.022 2.00e-02 2.50e+03
        pdb=" C8   DA I  57 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7   DA I  57 "   -0.000 2.00e-02 2.50e+03
        pdb=" C5   DA I  57 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DA I  57 "    0.004 2.00e-02 2.50e+03
        pdb=" N6   DA I  57 "    0.007 2.00e-02 2.50e+03
        pdb=" N1   DA I  57 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DA I  57 "   -0.004 2.00e-02 2.50e+03
        pdb=" N3   DA I  57 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I  57 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1348 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 724
        2.72 -     3.26: 10122
        3.26 -     3.81: 21513
        3.81 -     4.35: 28626
        4.35 -     4.90: 40516
  Nonbonded interactions: 101501
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.173 2.496
  nonbonded pdb=" O   THR C  16 "
            pdb=" OG  SER C  19 "
     model   vdw
     2.209 3.040
  nonbonded pdb=" OD2 ASP A 106 "
            pdb=" NH2 ARG A 131 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH2 ARG E 131 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" N3   DC I  21 "
            pdb=" N1   DG J -21 "
     model   vdw
     2.301 2.560
  ... (remaining 101496 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'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ 
e C or name O ))))
}
ncs_group {
  reference = (chain 'C' and resid 11 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and (resid 31 through 107 or resid 109 through 123))
  selection = (chain 'H' and (resid 31 through 107 or resid 109 through 123))
}

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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             1.210
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.050
  Set scattering table:                    0.030
  Process input model:                     11.870
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  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:8.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
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      :  0.007   0.046  12911  Z= 0.307
  Angle     :  0.672   7.927  18690  Z= 0.414
  Chirality :  0.041   0.144   2124
  Planarity :  0.004   0.040   1349
  Dihedral  : 27.352 171.135   5589
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 3.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.88 %
    Favored  : 97.97 %
  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: -1.91 (0.26), residues: 752
  helix: -0.60 (0.20), residues: 537
  sheet:  None (None), residues: 0
  loop : -2.78 (0.30), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C  20 
 TYR   0.012   0.002   TYR B  51 
 PHE   0.010   0.002   PHE E  84 
 HIS   0.004   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00718 (12909)
  covalent geometry    : angle       0.67144 (18684)
  hydrogen bonds       : bond        0.13015 (  749)
  hydrogen bonds       : angle       4.73667 ( 1868)
  link_TRANS           : bond        0.00284 (    2)
  link_TRANS           : angle       1.06617 (    6)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.218 
Fit side-chains
REVERT: D   35 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8124 (mt-10)
REVERT: D   47 GLN cc_start: 0.7886 (mt0) cc_final: 0.7393 (mt0)
REVERT: E  133 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8159 (mt-10)
REVERT: F   52 GLU cc_start: 0.8330 (mm-30) cc_final: 0.8121 (tp30)
REVERT: F   91 LYS cc_start: 0.8465 (tttt) cc_final: 0.7992 (ttpt)
REVERT: C   92 GLU cc_start: 0.8229 (mt-10) cc_final: 0.7823 (mt-10)
REVERT: C   99 ARG cc_start: 0.7905 (mmm160) cc_final: 0.7680 (mmm160)
REVERT: G   92 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7774 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 1.0445
  time to fit residues: 117.9405
Evaluate side-chains
  85 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  27 GLN
D  47 GLN
F  27 GLN
F  75 HIS
H  49 HIS
C  24 GLN
C  73 ASN
G  73 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.161061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.120370 restraints weight = 19566.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 1.19
r_work: 0.3202 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3061 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3069
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3069
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8355
moved from start:          0.1351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12911  Z= 0.155
  Angle     :  0.548   6.084  18690  Z= 0.335
  Chirality :  0.033   0.127   2124
  Planarity :  0.004   0.034   1349
  Dihedral  : 29.734 173.341   4059
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  :  8.44 %
    Favored  : 90.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.66 (0.29), residues: 752
  helix:  1.36 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -2.07 (0.33), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  99 
 TYR   0.007   0.001   TYR D 121 
 PHE   0.008   0.001   PHE C  25 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 (12909)
  covalent geometry    : angle       0.54842 (18684)
  hydrogen bonds       : bond        0.05018 (  749)
  hydrogen bonds       : angle       2.70499 ( 1868)
  link_TRANS           : bond        0.00022 (    2)
  link_TRANS           : angle       0.23606 (    6)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 0.316 
Fit side-chains
REVERT: B   91 LYS cc_start: 0.8946 (OUTLIER) cc_final: 0.8724 (ttmt)
REVERT: D   46 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8729 (mptt)
REVERT: E  120 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.8674 (mtt)
REVERT: F   91 LYS cc_start: 0.8769 (tttt) cc_final: 0.8319 (ttpt)
REVERT: C   92 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8077 (mt-10)
REVERT: C   99 ARG cc_start: 0.8142 (mmm160) cc_final: 0.7899 (mmm160)
REVERT: G   92 GLU cc_start: 0.8408 (mt-10) cc_final: 0.8127 (mt-10)
  outliers start: 8
  outliers final: 1
  residues processed: 94
  average time/residue: 1.0374
  time to fit residues: 102.0500
Evaluate side-chains
  83 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain D residue   46 LYS
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain C residue   74 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 77 optimal weight:    6.9990
   chunk 74 optimal weight:    5.9990
   chunk 91 optimal weight:    6.9990
   chunk 15 optimal weight:    3.9990
   chunk 94 optimal weight:    1.9990
   chunk 71 optimal weight:    6.9990
   chunk 97 optimal weight:    0.9980
   chunk 54 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
H  49 HIS
H  95 GLN
C  24 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.156414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.116381 restraints weight = 14325.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 1.02
r_work: 0.3157 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3039
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3039 r_free = 0.3039    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3039 r_free = 0.3039    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3039
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.1235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  12911  Z= 0.212
  Angle     :  0.584   6.122  18690  Z= 0.351
  Chirality :  0.036   0.134   2124
  Planarity :  0.004   0.038   1349
  Dihedral  : 30.018 174.363   4059
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 10.31 %
    Favored  : 87.97 %
  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:  1.30 (0.30), residues: 752
  helix:  1.80 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.74 (0.35), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  99 
 TYR   0.009   0.002   TYR D 121 
 PHE   0.008   0.002   PHE H  70 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 (12909)
  covalent geometry    : angle       0.58458 (18684)
  hydrogen bonds       : bond        0.06106 (  749)
  hydrogen bonds       : angle       2.72725 ( 1868)
  link_TRANS           : bond        0.00050 (    2)
  link_TRANS           : angle       0.15560 (    6)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 87
  time to evaluate  : 0.220 
Fit side-chains
REVERT: F   91 LYS cc_start: 0.8736 (tttt) cc_final: 0.8281 (ttpt)
REVERT: C   99 ARG cc_start: 0.8121 (mmm160) cc_final: 0.7874 (mmm160)
REVERT: G   92 GLU cc_start: 0.8285 (mt-10) cc_final: 0.7974 (mt-10)
  outliers start: 10
  outliers final: 5
  residues processed: 89
  average time/residue: 1.0307
  time to fit residues: 96.0854
Evaluate side-chains
  89 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 84
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain C residue   74 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 63 optimal weight:    6.9990
   chunk 64 optimal weight:    7.9990
   chunk 31 optimal weight:    0.6980
   chunk 99 optimal weight:    0.9990
   chunk 19 optimal weight:    0.8980
   chunk 94 optimal weight:    0.8980
   chunk 76 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 60 optimal weight:    5.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
H  49 HIS
H  95 GLN
C  24 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.157867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.118044 restraints weight = 13896.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 1.00
r_work: 0.3176 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3051
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3051 r_free = 0.3051    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3051 r_free = 0.3051    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3051
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.1287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.073  12911  Z= 0.159
  Angle     :  0.566   6.199  18690  Z= 0.343
  Chirality :  0.034   0.128   2124
  Planarity :  0.004   0.037   1349
  Dihedral  : 30.005 174.363   4059
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 3.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 10.47 %
    Favored  : 86.88 %
  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:  1.70 (0.31), residues: 752
  helix:  2.08 (0.23), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.53 (0.35), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  99 
 TYR   0.010   0.001   TYR B  51 
 PHE   0.007   0.001   PHE F  61 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (12909)
  covalent geometry    : angle       0.56611 (18684)
  hydrogen bonds       : bond        0.05497 (  749)
  hydrogen bonds       : angle       2.70963 ( 1868)
  link_TRANS           : bond        0.00063 (    2)
  link_TRANS           : angle       0.17199 (    6)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.210 
Fit side-chains
REVERT: E  120 MET cc_start: 0.8989 (OUTLIER) cc_final: 0.8702 (mtt)
REVERT: E  131 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.7798 (mtp180)
REVERT: F   91 LYS cc_start: 0.8753 (tttt) cc_final: 0.8317 (ttpt)
REVERT: C   99 ARG cc_start: 0.8146 (mmm160) cc_final: 0.7883 (mmm160)
REVERT: G   92 GLU cc_start: 0.8252 (mt-10) cc_final: 0.7975 (mt-10)
  outliers start: 16
  outliers final: 11
  residues processed: 89
  average time/residue: 0.9955
  time to fit residues: 93.0177
Evaluate side-chains
  96 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain D residue   46 LYS
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain C residue   74 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 11 optimal weight:    0.0870
   chunk 47 optimal weight:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 56 optimal weight:    6.9990
   chunk 97 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0870
   chunk 13 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9980
   overall best weight:    0.5736

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

Flipped N/Q/H residues before XYZ refinement:
H  49 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.158681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.118931 restraints weight = 14024.326|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 1.01
r_work: 0.3186 rms_B_bonded: 2.33 restraints_weight: 0.5000
r_work: 0.3049 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3049
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3060
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3060 r_free = 0.3060    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3060
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.1356

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12911  Z= 0.154
  Angle     :  0.564   8.953  18690  Z= 0.341
  Chirality :  0.034   0.152   2124
  Planarity :  0.004   0.035   1349
  Dihedral  : 29.973 174.852   4059
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 11.41 %
    Favored  : 86.41 %
  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:  1.86 (0.31), residues: 752
  helix:  2.17 (0.23), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.40 (0.36), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG D  29 
 TYR   0.008   0.001   TYR D 121 
 PHE   0.007   0.001   PHE F  61 
 HIS   0.003   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 (12909)
  covalent geometry    : angle       0.56406 (18684)
  hydrogen bonds       : bond        0.05286 (  749)
  hydrogen bonds       : angle       2.65382 ( 1868)
  link_TRANS           : bond        0.00028 (    2)
  link_TRANS           : angle       0.14185 (    6)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.286 
Fit side-chains
REVERT: E  120 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8737 (mtt)
REVERT: E  131 ARG cc_start: 0.9089 (OUTLIER) cc_final: 0.7748 (mtp180)
REVERT: F   91 LYS cc_start: 0.8754 (tttt) cc_final: 0.8314 (ttpt)
REVERT: C   99 ARG cc_start: 0.8138 (mmm160) cc_final: 0.7870 (mmm160)
REVERT: G   92 GLU cc_start: 0.8241 (mt-10) cc_final: 0.7946 (mt-10)
  outliers start: 13
  outliers final: 9
  residues processed: 87
  average time/residue: 0.9968
  time to fit residues: 90.8862
Evaluate side-chains
  94 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain D residue   46 LYS
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain C residue   74 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 8 optimal weight:    0.0370
   chunk 83 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 98 optimal weight:    0.4980
   chunk 57 optimal weight:    6.9990
   chunk 69 optimal weight:    6.9990
   chunk 91 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 61 optimal weight:    6.9990
   overall best weight:    0.8060

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

Flipped N/Q/H residues before XYZ refinement:
D  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.159120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.118016 restraints weight = 19270.143|
|-----------------------------------------------------------------------------|
r_work (start): 0.3345 rms_B_bonded: 1.20
r_work: 0.3167 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3035
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3035 r_free = 0.3035    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3035
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.1418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  12911  Z= 0.156
  Angle     :  0.550   6.416  18690  Z= 0.334
  Chirality :  0.034   0.141   2124
  Planarity :  0.004   0.036   1349
  Dihedral  : 29.932 175.138   4059
  Min Nonbonded Distance : 2.147

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 10.94 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.99 (0.31), residues: 752
  helix:  2.25 (0.23), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.30 (0.36), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  99 
 TYR   0.008   0.001   TYR D 121 
 PHE   0.007   0.001   PHE A  78 
 HIS   0.002   0.000   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (12909)
  covalent geometry    : angle       0.55004 (18684)
  hydrogen bonds       : bond        0.05209 (  749)
  hydrogen bonds       : angle       2.62023 ( 1868)
  link_TRANS           : bond        0.00028 (    2)
  link_TRANS           : angle       0.15010 (    6)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.222 
Fit side-chains
REVERT: E  120 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8723 (mtt)
REVERT: E  131 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.7849 (mtp180)
REVERT: F   91 LYS cc_start: 0.8779 (tttt) cc_final: 0.8341 (ttpt)
REVERT: C   25 PHE cc_start: 0.8963 (OUTLIER) cc_final: 0.8549 (m-80)
REVERT: C   99 ARG cc_start: 0.8187 (mmm160) cc_final: 0.7917 (mmm160)
REVERT: G   92 GLU cc_start: 0.8278 (mt-10) cc_final: 0.7986 (mt-10)
  outliers start: 15
  outliers final: 11
  residues processed: 89
  average time/residue: 0.9719
  time to fit residues: 90.7864
Evaluate side-chains
  95 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain D residue   46 LYS
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  107 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 82 optimal weight:    3.9990
   chunk 63 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 55 optimal weight:    7.9990
   chunk 64 optimal weight:    7.9990
   chunk 14 optimal weight:    3.9990
   chunk 59 optimal weight:    5.9990
   chunk 16 optimal weight:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0370
   chunk 98 optimal weight:    0.9980
   overall best weight:    2.4064

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

Flipped N/Q/H residues before XYZ refinement:
D  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.155281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.114636 restraints weight = 15676.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 1.07
r_work: 0.3127 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3009
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3009 r_free = 0.3009    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3009 r_free = 0.3009    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3009
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  12911  Z= 0.236
  Angle     :  0.599   7.145  18690  Z= 0.357
  Chirality :  0.037   0.145   2124
  Planarity :  0.004   0.038   1349
  Dihedral  : 30.135 175.499   4059
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 2.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 11.25 %
    Favored  : 86.09 %
  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:  1.74 (0.30), residues: 752
  helix:  2.04 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.37 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  99 
 TYR   0.010   0.002   TYR B  51 
 PHE   0.011   0.002   PHE A  78 
 HIS   0.002   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 (12909)
  covalent geometry    : angle       0.59873 (18684)
  hydrogen bonds       : bond        0.06458 (  749)
  hydrogen bonds       : angle       2.74411 ( 1868)
  link_TRANS           : bond        0.00086 (    2)
  link_TRANS           : angle       0.20047 (    6)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 0.228 
Fit side-chains
REVERT: D   46 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8626 (mptt)
REVERT: E  120 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8756 (mtt)
REVERT: E  131 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.7986 (mtp180)
REVERT: H   71 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7699 (mt-10)
REVERT: C   25 PHE cc_start: 0.9087 (OUTLIER) cc_final: 0.8568 (m-80)
REVERT: C   92 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8115 (mt-10)
REVERT: C   99 ARG cc_start: 0.8163 (mmm160) cc_final: 0.7894 (mmm160)
REVERT: G   92 GLU cc_start: 0.8343 (mt-10) cc_final: 0.8006 (mt-10)
  outliers start: 16
  outliers final: 9
  residues processed: 86
  average time/residue: 1.0152
  time to fit residues: 91.3431
Evaluate side-chains
  91 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain D residue   46 LYS
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  107 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 87 optimal weight:    0.1980
   chunk 35 optimal weight:    1.9990
   chunk 67 optimal weight:   10.0000
   chunk 56 optimal weight:    6.9990
   chunk 55 optimal weight:    6.9990
   chunk 94 optimal weight:    1.9990
   chunk 79 optimal weight:   10.0000
   chunk 36 optimal weight:    0.7980
   chunk 76 optimal weight:    5.9990
   chunk 37 optimal weight:    0.5980
   chunk 62 optimal weight:    6.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
D  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.156517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.115301 restraints weight = 18153.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.15
r_work: 0.3132 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2991 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2991
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3002
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3002
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.1350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12911  Z= 0.168
  Angle     :  0.575   7.157  18690  Z= 0.347
  Chirality :  0.035   0.140   2124
  Planarity :  0.004   0.037   1349
  Dihedral  : 30.122 175.227   4059
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 11.25 %
    Favored  : 86.09 %
  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:  1.95 (0.30), residues: 752
  helix:  2.19 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.24 (0.36), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  92 
 TYR   0.011   0.001   TYR B  51 
 PHE   0.011   0.001   PHE A  78 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 (12909)
  covalent geometry    : angle       0.57478 (18684)
  hydrogen bonds       : bond        0.05819 (  749)
  hydrogen bonds       : angle       2.72553 ( 1868)
  link_TRANS           : bond        0.00051 (    2)
  link_TRANS           : angle       0.15506 (    6)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 78
  time to evaluate  : 0.279 
Fit side-chains
REVERT: D   46 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8643 (mptt)
REVERT: E  120 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8772 (mtt)
REVERT: E  131 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.7962 (mtp180)
REVERT: C   25 PHE cc_start: 0.9094 (OUTLIER) cc_final: 0.8587 (m-80)
REVERT: C   74 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8491 (mtpp)
REVERT: C   92 GLU cc_start: 0.8464 (mt-10) cc_final: 0.8149 (mt-10)
REVERT: C   99 ARG cc_start: 0.8181 (mmm160) cc_final: 0.7902 (mmm160)
REVERT: G   92 GLU cc_start: 0.8351 (mt-10) cc_final: 0.8027 (mt-10)
  outliers start: 16
  outliers final: 10
  residues processed: 86
  average time/residue: 1.0368
  time to fit residues: 93.5065
Evaluate side-chains
  93 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain D residue   46 LYS
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain H residue   71 GLU
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  107 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 55 optimal weight:    7.9990
   chunk 72 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 89 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 61 optimal weight:    6.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
D  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.155023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.114150 restraints weight = 14267.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 1.08
r_work: 0.3120 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2985
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2985 r_free = 0.2985    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2985 r_free = 0.2985    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2985
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.1385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  12911  Z= 0.233
  Angle     :  0.598   7.166  18690  Z= 0.357
  Chirality :  0.037   0.135   2124
  Planarity :  0.004   0.038   1349
  Dihedral  : 30.185 175.512   4059
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 2.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 11.72 %
    Favored  : 85.78 %
  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:  1.75 (0.30), residues: 752
  helix:  2.04 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.36 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  99 
 TYR   0.011   0.002   TYR B  51 
 PHE   0.013   0.002   PHE A  78 
 HIS   0.002   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00545 (12909)
  covalent geometry    : angle       0.59833 (18684)
  hydrogen bonds       : bond        0.06505 (  749)
  hydrogen bonds       : angle       2.77014 ( 1868)
  link_TRANS           : bond        0.00083 (    2)
  link_TRANS           : angle       0.19131 (    6)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.283 
Fit side-chains
REVERT: D   46 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8602 (mptt)
REVERT: E  120 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8770 (mtt)
REVERT: C   74 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8442 (mtpp)
REVERT: C   92 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8142 (mt-10)
REVERT: C   99 ARG cc_start: 0.8145 (mmm160) cc_final: 0.7855 (mmm160)
REVERT: G   92 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8059 (mt-10)
  outliers start: 15
  outliers final: 8
  residues processed: 87
  average time/residue: 0.9993
  time to fit residues: 91.0984
Evaluate side-chains
  87 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain D residue   46 LYS
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain E residue  131 ARG
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  107 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 91 optimal weight:    0.1980
   chunk 97 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
D  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.156829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.116634 restraints weight = 14193.558|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 1.01
r_work: 0.3158 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3027
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3027
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.1433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12911  Z= 0.158
  Angle     :  0.579   7.501  18690  Z= 0.348
  Chirality :  0.035   0.154   2124
  Planarity :  0.004   0.036   1349
  Dihedral  : 30.160 175.219   4059
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 12.03 %
    Favored  : 85.78 %
  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:  1.97 (0.30), residues: 752
  helix:  2.21 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.30 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  92 
 TYR   0.011   0.001   TYR B  51 
 PHE   0.009   0.001   PHE A  78 
 HIS   0.002   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (12909)
  covalent geometry    : angle       0.57870 (18684)
  hydrogen bonds       : bond        0.05695 (  749)
  hydrogen bonds       : angle       2.75776 ( 1868)
  link_TRANS           : bond        0.00088 (    2)
  link_TRANS           : angle       0.15718 (    6)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.250 
Fit side-chains
REVERT: D   46 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8572 (mptt)
REVERT: E  120 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8739 (mtt)
REVERT: C   25 PHE cc_start: 0.9076 (OUTLIER) cc_final: 0.8487 (m-80)
REVERT: C   74 LYS cc_start: 0.8776 (OUTLIER) cc_final: 0.8439 (mtpp)
REVERT: C   92 GLU cc_start: 0.8438 (mt-10) cc_final: 0.8100 (mt-10)
REVERT: C   99 ARG cc_start: 0.8134 (mmm160) cc_final: 0.7836 (mmm160)
REVERT: G   92 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8001 (mt-10)
  outliers start: 13
  outliers final: 7
  residues processed: 83
  average time/residue: 1.0428
  time to fit residues: 90.6201
Evaluate side-chains
  87 residues out of total 638 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   76 GLN
Chi-restraints excluded: chain B residue   91 LYS
Chi-restraints excluded: chain D residue   46 LYS
Chi-restraints excluded: chain E residue   57 SER
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain C residue   25 PHE
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain C residue  107 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   chunk 3 optimal weight:    2.9990
   chunk 66 optimal weight:   10.0000
   chunk 43 optimal weight:    8.9990
   chunk 38 optimal weight:    2.9990
   chunk 10 optimal weight:    0.3980
   chunk 55 optimal weight:    6.9990
   chunk 95 optimal weight:    3.9990
   chunk 56 optimal weight:    6.9990
   chunk 73 optimal weight:    5.9990
   overall best weight:    2.6788

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

Flipped N/Q/H residues before XYZ refinement:
D  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.154418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.112816 restraints weight = 19305.304|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 1.20
r_work: 0.3096 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2954 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2957
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2957 r_free = 0.2957    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2957
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  12911  Z= 0.253
  Angle     :  0.615   8.056  18690  Z= 0.365
  Chirality :  0.038   0.139   2124
  Planarity :  0.004   0.038   1349
  Dihedral  : 30.241 175.137   4059
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 12.19 %
    Favored  : 85.94 %
  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:  1.74 (0.30), residues: 752
  helix:  2.04 (0.22), residues: 548
  sheet:  None (None), residues: 0
  loop : -1.37 (0.36), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG H  99 
 TYR   0.011   0.002   TYR B  51 
 PHE   0.013   0.002   PHE A  78 
 HIS   0.002   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00597 (12909)
  covalent geometry    : angle       0.61509 (18684)
  hydrogen bonds       : bond        0.06780 (  749)
  hydrogen bonds       : angle       2.80440 ( 1868)
  link_TRANS           : bond        0.00092 (    2)
  link_TRANS           : angle       0.22921 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4130.88 seconds
wall clock time: 70 minutes 35.39 seconds (4235.39 seconds total)