Starting phenix.real_space_refine
on Thu Jul 31 04:27:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ohb_12899/07_2025/7ohb_12899.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ohb_12899/07_2025/7ohb_12899.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ohb_12899/07_2025/7ohb_12899.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ohb_12899/07_2025/7ohb_12899.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ohb_12899/07_2025/7ohb_12899.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ohb_12899/07_2025/7ohb_12899.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     290      5.49       5
     S      18      5.16       5
     C    7560      2.51       5
     N    2501      2.21       5
     O    3055      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13424
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 756
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 756
          Classifications: {'peptide': 96}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
    Chain: "E"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "G"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 746
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 746
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 2955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2955
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2990
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "K"
      Number of atoms: 1416
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 1416
          Classifications: {'peptide': 180}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 171}
  Time building chain proxies: 7.57, per 1000 atoms: 0.56
  Number of scatterers: 13424
  At special positions: 0
  Unit cell: (92.4, 116.55, 133.35, 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      18     16.00
     P     290     15.00
     O    3055      8.00
     N    2501      7.00
     C    7560      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
  Time building additional restraints: 3.42
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1768

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 10 sheets defined
      64.8% alpha, 7.2% beta
      144 base pairs and 266 stacking pairs defined.
    Time for finding SS restraints: 6.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.991A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    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: 3.807A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.318A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 100 through 121
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 4.144A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.853A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.563A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
      removed outlier: 3.590A  pdb=" N   ARG G  20 " --> pdb=" O   THR G  16 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.377A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
    Processing helix  chain 'K' and resid 81 through 88
      removed outlier: 3.649A  pdb=" N   VAL K  85 " --> pdb=" O   ASP K  81 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 128 through 147
    Processing helix  chain 'K' and resid 171 through 179
      removed outlier: 3.599A  pdb=" N   LEU K 175 " --> pdb=" O   ARG K 171 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 219 through 236
      removed outlier: 4.087A  pdb=" N   ILE K 223 " --> pdb=" O   GLN K 219 " (cutoff:3.500A)
      Proline residue:  K 232  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.004A  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
      removed outlier: 6.471A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.132A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.998A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.512A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'K' and resid 92 through 93
      removed outlier: 3.602A  pdb=" N   VAL K 102 " --> pdb=" O   ILE K 115 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   THR K 124 " --> pdb=" O   THR K 112 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   LYS K 120 " --> pdb=" O   PHE K 116 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   GLY K 125 " --> pdb=" O   ILE K  70 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   ILE K  70 " --> pdb=" O   GLY K 125 " (cutoff:3.500A)
      removed outlier: 6.727A  pdb=" N   VAL K 161 " --> pdb=" O   GLN K  68 " (cutoff:3.500A)
      removed outlier: 4.700A  pdb=" N   ILE K  70 " --> pdb=" O   ASN K 159 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   ASN K 159 " --> pdb=" O   ILE K  70 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   ALA K  72 " --> pdb=" O   ILE K 157 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   ILE K 157 " --> pdb=" O   ALA K  72 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   VAL K  74 " --> pdb=" O   PHE K 155 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   PHE K 155 " --> pdb=" O   VAL K  74 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ILE K 212 " --> pdb=" O   CYS K 164 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   VAL K 213 " --> pdb=" O   LEU K 205 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LEU K 205 " --> pdb=" O   VAL K 213 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   THR K 215 " --> pdb=" O   VAL K 203 " (cutoff:3.500A)
      removed outlier: 4.461A  pdb=" N   VAL K 203 " --> pdb=" O   THR K 215 " (cutoff:3.500A)

    472 hydrogen bonds defined for protein.
    1389 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      368 hydrogen bonds
      736 hydrogen bond angles
      0 basepair planarities
      144 basepair parallelities
      266 stacking parallelities
  Total time for adding SS restraints: 5.33

  Time building geometry restraints manager: 4.07 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: 2665
        1.33 -     1.45: 4528
        1.45 -     1.57: 6451
        1.57 -     1.69: 578
        1.69 -     1.82: 32
  Bond restraints: 14254
  Sorted by residual:
  bond pdb=" C3'  DT I  60 "
       pdb=" O3'  DT I  60 "
    ideal  model  delta    sigma   weight residual
    1.422  1.519 -0.097 3.00e-02 1.11e+03 1.05e+01
  bond pdb=" O5'  DA I  61 "
       pdb=" C5'  DA I  61 "
    ideal  model  delta    sigma   weight residual
    1.423  1.468 -0.045 3.00e-02 1.11e+03 2.30e+00
  bond pdb=" C5'  DA I  61 "
       pdb=" C4'  DA I  61 "
    ideal  model  delta    sigma   weight residual
    1.518  1.548 -0.030 2.00e-02 2.50e+03 2.23e+00
  bond pdb=" CB  VAL A  46 "
       pdb=" CG1 VAL A  46 "
    ideal  model  delta    sigma   weight residual
    1.521  1.473  0.048 3.30e-02 9.18e+02 2.13e+00
  bond pdb=" CB  VAL E  46 "
       pdb=" CG1 VAL E  46 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 2.02e+00
  ... (remaining 14249 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.06: 19692
        2.06 -     4.11: 711
        4.11 -     6.17: 64
        6.17 -     8.22: 16
        8.22 -    10.28: 3
  Bond angle restraints: 20486
  Sorted by residual:
  angle pdb=" CB  ARG B  40 "
        pdb=" CG  ARG B  40 "
        pdb=" CD  ARG B  40 "
      ideal   model   delta    sigma   weight residual
     111.30  121.58  -10.28 2.30e+00 1.89e-01 2.00e+01
  angle pdb=" C   ASN G  73 "
        pdb=" N   LYS G  74 "
        pdb=" CA  LYS G  74 "
      ideal   model   delta    sigma   weight residual
     122.40  127.54   -5.14 1.45e+00 4.76e-01 1.26e+01
  angle pdb=" O3'  DT I  60 "
        pdb=" C3'  DT I  60 "
        pdb=" C2'  DT I  60 "
      ideal   model   delta    sigma   weight residual
     111.50  116.71   -5.21 1.50e+00 4.44e-01 1.21e+01
  angle pdb=" N   GLY H 101 "
        pdb=" CA  GLY H 101 "
        pdb=" C   GLY H 101 "
      ideal   model   delta    sigma   weight residual
     113.18  121.37   -8.19 2.37e+00 1.78e-01 1.19e+01
  angle pdb=" CB  LYS G  15 "
        pdb=" CG  LYS G  15 "
        pdb=" CD  LYS G  15 "
      ideal   model   delta    sigma   weight residual
     111.30  119.22   -7.92 2.30e+00 1.89e-01 1.19e+01
  ... (remaining 20481 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.96: 5269
       20.96 -    41.91: 1340
       41.91 -    62.87: 1178
       62.87 -    83.83: 66
       83.83 -   104.78: 6
  Dihedral angle restraints: 7859
    sinusoidal: 5121
      harmonic: 2738
  Sorted by residual:
  dihedral pdb=" CA  GLU K 108 "
           pdb=" C   GLU K 108 "
           pdb=" N   PRO K 109 "
           pdb=" CA  PRO K 109 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -39.57   39.57     0      5.00e+00 4.00e-02 6.26e+01
  dihedral pdb=" CA  PRO D 100 "
           pdb=" C   PRO D 100 "
           pdb=" N   GLY D 101 "
           pdb=" CA  GLY D 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.58  -21.42     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  LYS K 199 "
           pdb=" C   LYS K 199 "
           pdb=" N   PRO K 200 "
           pdb=" CA  PRO K 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.94   20.06     0      5.00e+00 4.00e-02 1.61e+01
  ... (remaining 7856 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 2073
       0.080 -    0.161: 242
       0.161 -    0.241: 17
       0.241 -    0.321: 3
       0.321 -    0.402: 1
  Chirality restraints: 2336
  Sorted by residual:
  chirality pdb=" C1'  DT I  60 "
            pdb=" O4'  DT I  60 "
            pdb=" C2'  DT I  60 "
            pdb=" N1   DT I  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.07    0.40 2.00e-01 2.50e+01 4.03e+00
  chirality pdb=" CB  ILE K 212 "
            pdb=" CA  ILE K 212 "
            pdb=" CG1 ILE K 212 "
            pdb=" CG2 ILE K 212 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.29 2.00e-01 2.50e+01 2.14e+00
  chirality pdb=" CB  THR K 111 "
            pdb=" CA  THR K 111 "
            pdb=" OG1 THR K 111 "
            pdb=" CG2 THR K 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.29    0.27 2.00e-01 2.50e+01 1.77e+00
  ... (remaining 2333 not shown)

  Planarity restraints: 1584
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL G  27 "   -0.017 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" C   VAL G  27 "    0.058 2.00e-02 2.50e+03
        pdb=" O   VAL G  27 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   GLY G  28 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I  60 "    0.006 2.00e-02 2.50e+03   1.84e-02 8.44e+00
        pdb=" N1   DT I  60 "   -0.037 2.00e-02 2.50e+03
        pdb=" C2   DT I  60 "    0.041 2.00e-02 2.50e+03
        pdb=" O2   DT I  60 "   -0.008 2.00e-02 2.50e+03
        pdb=" N3   DT I  60 "   -0.009 2.00e-02 2.50e+03
        pdb=" C4   DT I  60 "    0.004 2.00e-02 2.50e+03
        pdb=" O4   DT I  60 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5   DT I  60 "    0.004 2.00e-02 2.50e+03
        pdb=" C7   DT I  60 "    0.005 2.00e-02 2.50e+03
        pdb=" C6   DT I  60 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "    0.046 5.00e-02 4.00e+02   7.00e-02 7.84e+00
        pdb=" N   PRO G  80 "   -0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "    0.039 5.00e-02 4.00e+02
  ... (remaining 1581 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2703
        2.78 -     3.31: 11633
        3.31 -     3.84: 27034
        3.84 -     4.37: 31845
        4.37 -     4.90: 45229
  Nonbonded interactions: 118444
  Sorted by model distance:
  nonbonded pdb=" OG1 THR D  29 "
            pdb=" OP1  DT I  30 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OG1 THR H  87 "
            pdb=" OE1 GLU H  90 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" O   GLY K 174 "
            pdb=" OG  SER K 178 "
     model   vdw
     2.278 3.040
  nonbonded pdb=" NE2 GLN G  24 "
            pdb=" OE1 GLN H  44 "
     model   vdw
     2.302 3.120
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NH1 ARG E 131 "
     model   vdw
     2.322 3.120
  ... (remaining 118439 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' and resid 24 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 27 through 121)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.99
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:             1.200
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     36.230
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
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      :  0.005   0.097  14254  Z= 0.222
  Angle     :  0.856  10.276  20486  Z= 0.496
  Chirality :  0.053   0.402   2336
  Planarity :  0.007   0.070   1584
  Dihedral  : 28.695 104.782   6091
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  4.32 %
    Favored  : 94.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.33 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.23), residues: 925
  helix: -1.01 (0.18), residues: 588
  sheet: -0.37 (0.82), residues: 41
  loop : -1.97 (0.29), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS F  75 
 PHE   0.025   0.002   PHE K  99 
 TYR   0.039   0.002   TYR G  50 
 ARG   0.012   0.001   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12750 (  840)
  hydrogen bonds       : angle       5.17632 ( 2125)
  covalent geometry    : bond        0.00501 (14254)
  covalent geometry    : angle       0.85562 (20486)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 192
  time to evaluate  : 1.034 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.7946 (t0) cc_final: 0.7504 (t70)
REVERT: B   25 ASN cc_start: 0.8125 (m-40) cc_final: 0.7909 (m110)
REVERT: C   74 LYS cc_start: 0.8764 (mppt) cc_final: 0.8530 (mptt)
REVERT: E  106 ASP cc_start: 0.7443 (m-30) cc_final: 0.7181 (m-30)
REVERT: F   74 GLU cc_start: 0.8008 (mt-10) cc_final: 0.7766 (mt-10)
REVERT: G   91 GLU cc_start: 0.8048 (tt0) cc_final: 0.7820 (tt0)
REVERT: H   33 SER cc_start: 0.8880 (t) cc_final: 0.8491 (p)
REVERT: H   34 TYR cc_start: 0.8858 (m-80) cc_final: 0.8614 (m-80)
REVERT: K   69 ASN cc_start: 0.7863 (t0) cc_final: 0.6761 (m110)
REVERT: K  121 MET cc_start: 0.7527 (tpt) cc_final: 0.7034 (mtm)
  outliers start: 7
  outliers final: 1
  residues processed: 196
  average time/residue: 0.3255
  time to fit residues: 85.6044
Evaluate side-chains
  144 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 143
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 98 optimal weight:    8.9990
   chunk 88 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 59 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 91 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 68 optimal weight:    0.7980
   chunk 106 optimal weight:    6.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
C 110 ASN
D  92 GLN
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  76 GLN
** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  93 GLN
** G  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 112 GLN
** H  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K  95 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.091275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.055324 restraints weight = 38179.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.2875 rms_B_bonded: 2.03
r_work: 0.2669 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.1758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14254  Z= 0.165
  Angle     :  0.597   6.829  20486  Z= 0.355
  Chirality :  0.037   0.169   2336
  Planarity :  0.005   0.048   1584
  Dihedral  : 30.914  90.219   4227
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 10.93 %
    Favored  : 88.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.26), residues: 925
  helix:  1.08 (0.20), residues: 599
  sheet: -0.09 (0.71), residues: 47
  loop : -1.69 (0.31), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS F  75 
 PHE   0.014   0.001   PHE K  99 
 TYR   0.017   0.002   TYR K 231 
 ARG   0.008   0.001   ARG B  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03858 (  840)
  hydrogen bonds       : angle       3.31314 ( 2125)
  covalent geometry    : bond        0.00360 (14254)
  covalent geometry    : angle       0.59703 (20486)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 163
  time to evaluate  : 1.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9069 (pm20) cc_final: 0.8684 (pm20)
REVERT: A   81 ASP cc_start: 0.8680 (t0) cc_final: 0.8316 (t70)
REVERT: B   25 ASN cc_start: 0.8312 (m-40) cc_final: 0.8014 (m110)
REVERT: E   76 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8298 (tp-100)
REVERT: F   74 GLU cc_start: 0.8674 (mt-10) cc_final: 0.8412 (mt-10)
REVERT: H   30 ARG cc_start: 0.8228 (mtp85) cc_final: 0.7888 (mtp85)
REVERT: H   33 SER cc_start: 0.8876 (t) cc_final: 0.8584 (p)
REVERT: H   42 LEU cc_start: 0.9431 (tp) cc_final: 0.9211 (tp)
REVERT: K   69 ASN cc_start: 0.7911 (t0) cc_final: 0.6414 (m110)
  outliers start: 8
  outliers final: 5
  residues processed: 165
  average time/residue: 0.3472
  time to fit residues: 79.9013
Evaluate side-chains
  146 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 140
  time to evaluate  : 1.021 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain K residue  164 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 13 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 71 optimal weight:    8.9990
   chunk 76 optimal weight:    6.9990
   chunk 116 optimal weight:    9.9990
   chunk 81 optimal weight:    6.9990
   chunk 105 optimal weight:   30.0000
   chunk 83 optimal weight:    6.9990
   chunk 99 optimal weight:   50.0000
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  76 GLN
F  93 GLN
** G  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 112 GLN
H  81 ASN
K 159 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.088581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.051888 restraints weight = 38345.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.2775 rms_B_bonded: 1.97
r_work: 0.2565 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.2565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8732
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.069  14254  Z= 0.295
  Angle     :  0.640   7.053  20486  Z= 0.375
  Chirality :  0.040   0.183   2336
  Planarity :  0.005   0.043   1584
  Dihedral  : 30.902  88.074   4226
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 14.61 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.26), residues: 925
  helix:  1.51 (0.20), residues: 599
  sheet:  0.02 (0.72), residues: 47
  loop : -1.53 (0.33), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS C  82 
 PHE   0.012   0.002   PHE K  99 
 TYR   0.014   0.002   TYR G  39 
 ARG   0.004   0.001   ARG B  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04190 (  840)
  hydrogen bonds       : angle       3.38106 ( 2125)
  covalent geometry    : bond        0.00673 (14254)
  covalent geometry    : angle       0.64002 (20486)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 140
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9046 (pm20) cc_final: 0.8612 (pm20)
REVERT: A   81 ASP cc_start: 0.8717 (t0) cc_final: 0.8396 (t70)
REVERT: B   25 ASN cc_start: 0.8477 (m-40) cc_final: 0.8191 (m110)
REVERT: C   64 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8392 (tm-30)
REVERT: F   74 GLU cc_start: 0.8759 (mt-10) cc_final: 0.8545 (mt-10)
REVERT: H   28 LYS cc_start: 0.7508 (ptmt) cc_final: 0.7118 (pttt)
REVERT: H   30 ARG cc_start: 0.8358 (mtp85) cc_final: 0.8055 (mtp85)
REVERT: K   69 ASN cc_start: 0.8071 (t0) cc_final: 0.6358 (m110)
  outliers start: 16
  outliers final: 10
  residues processed: 148
  average time/residue: 0.3095
  time to fit residues: 63.5172
Evaluate side-chains
  140 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue   65 ASP
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   72 ASP
Chi-restraints excluded: chain H residue   57 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 1 optimal weight:    1.9990
   chunk 83 optimal weight:    6.9990
   chunk 111 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 5 optimal weight:    0.6980
   chunk 6 optimal weight:    0.6980
   chunk 14 optimal weight:    0.8980
   chunk 99 optimal weight:   50.0000
   chunk 37 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
E  85 GLN
** G  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 159 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.090906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.054765 restraints weight = 38006.872|
|-----------------------------------------------------------------------------|
r_work (start): 0.2855 rms_B_bonded: 1.98
r_work: 0.2650 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8660
moved from start:          0.2590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14254  Z= 0.157
  Angle     :  0.572   7.579  20486  Z= 0.339
  Chirality :  0.035   0.176   2336
  Planarity :  0.004   0.044   1584
  Dihedral  : 30.298  88.881   4226
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 16.52 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.27), residues: 925
  helix:  2.06 (0.21), residues: 605
  sheet:  0.19 (0.72), residues: 47
  loop : -1.39 (0.34), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  75 
 PHE   0.010   0.001   PHE E  67 
 TYR   0.013   0.001   TYR G  57 
 ARG   0.008   0.000   ARG G  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03452 (  840)
  hydrogen bonds       : angle       2.99480 ( 2125)
  covalent geometry    : bond        0.00344 (14254)
  covalent geometry    : angle       0.57237 (20486)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 156
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8996 (pm20) cc_final: 0.8617 (pm20)
REVERT: A   81 ASP cc_start: 0.8596 (t0) cc_final: 0.8302 (t70)
REVERT: B   25 ASN cc_start: 0.8412 (m-40) cc_final: 0.8147 (m110)
REVERT: D   73 GLU cc_start: 0.8984 (tp30) cc_final: 0.8727 (tp30)
REVERT: D   86 ILE cc_start: 0.9568 (mt) cc_final: 0.9348 (mt)
REVERT: F   74 GLU cc_start: 0.8722 (mt-10) cc_final: 0.8490 (mt-10)
REVERT: H   28 LYS cc_start: 0.7559 (ptmt) cc_final: 0.7154 (pttt)
REVERT: H   30 ARG cc_start: 0.8304 (mtp85) cc_final: 0.7992 (mtp85)
REVERT: H   42 LEU cc_start: 0.9364 (tp) cc_final: 0.9161 (tp)
REVERT: K   69 ASN cc_start: 0.7936 (t0) cc_final: 0.6146 (m-40)
REVERT: K  159 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.7892 (t0)
  outliers start: 11
  outliers final: 6
  residues processed: 162
  average time/residue: 0.3001
  time to fit residues: 67.0056
Evaluate side-chains
  144 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 137
  time to evaluate  : 1.040 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain G residue   72 ASP
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain K residue  159 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 102 optimal weight:    8.9990
   chunk 67 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   chunk 100 optimal weight:   30.0000
   chunk 61 optimal weight:    4.9990
   chunk 79 optimal weight:    5.9990
   chunk 96 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  92 GLN
K 159 ASN
** K 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.087884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.050866 restraints weight = 38624.696|
|-----------------------------------------------------------------------------|
r_work (start): 0.2746 rms_B_bonded: 1.97
r_work: 0.2540 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.2540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8751
moved from start:          0.2911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.086  14254  Z= 0.354
  Angle     :  0.662   7.271  20486  Z= 0.383
  Chirality :  0.042   0.217   2336
  Planarity :  0.004   0.041   1584
  Dihedral  : 30.874  88.616   4226
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.68 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.27), residues: 925
  helix:  1.77 (0.21), residues: 605
  sheet:  0.24 (0.75), residues: 47
  loop : -1.52 (0.33), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D  46 
 PHE   0.011   0.002   PHE G  25 
 TYR   0.023   0.002   TYR K 231 
 ARG   0.010   0.001   ARG G  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04325 (  840)
  hydrogen bonds       : angle       3.35465 ( 2125)
  covalent geometry    : bond        0.00811 (14254)
  covalent geometry    : angle       0.66244 (20486)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 135
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9079 (pm20) cc_final: 0.8647 (pm20)
REVERT: A   81 ASP cc_start: 0.8690 (t0) cc_final: 0.8385 (t70)
REVERT: B   25 ASN cc_start: 0.8566 (m-40) cc_final: 0.8228 (m110)
REVERT: F   74 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8581 (mt-10)
REVERT: H   30 ARG cc_start: 0.8390 (mtp85) cc_final: 0.7971 (mtp85)
REVERT: K   64 VAL cc_start: 0.8229 (OUTLIER) cc_final: 0.7768 (p)
REVERT: K  121 MET cc_start: 0.8412 (tpt) cc_final: 0.7572 (mpp)
  outliers start: 20
  outliers final: 14
  residues processed: 148
  average time/residue: 0.3053
  time to fit residues: 62.0150
Evaluate side-chains
  145 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 130
  time to evaluate  : 1.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue   88 SER
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   72 ASP
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain K residue   64 VAL
Chi-restraints excluded: chain K residue  205 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 84 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 107 optimal weight:    5.9990
   chunk 59 optimal weight:    0.8980
   chunk 100 optimal weight:   20.0000
   chunk 63 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 93 optimal weight:    4.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 225 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.089393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2863 r_free = 0.2863 target = 0.052587 restraints weight = 38580.618|
|-----------------------------------------------------------------------------|
r_work (start): 0.2795 rms_B_bonded: 1.97
r_work: 0.2590 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.2590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8715
moved from start:          0.2949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052  14254  Z= 0.210
  Angle     :  0.598   7.898  20486  Z= 0.351
  Chirality :  0.037   0.216   2336
  Planarity :  0.004   0.039   1584
  Dihedral  : 30.526  89.475   4226
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 19.82 %
    Favored  : 77.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.27), residues: 925
  helix:  2.02 (0.21), residues: 605
  sheet:  0.44 (0.73), residues: 47
  loop : -1.47 (0.34), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  46 
 PHE   0.011   0.001   PHE E  67 
 TYR   0.031   0.002   TYR K 224 
 ARG   0.007   0.000   ARG G  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03631 (  840)
  hydrogen bonds       : angle       3.11766 ( 2125)
  covalent geometry    : bond        0.00474 (14254)
  covalent geometry    : angle       0.59793 (20486)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 143
  time to evaluate  : 1.050 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9064 (pm20) cc_final: 0.8653 (pm20)
REVERT: A   81 ASP cc_start: 0.8632 (t0) cc_final: 0.8334 (t70)
REVERT: B   25 ASN cc_start: 0.8491 (m-40) cc_final: 0.8199 (m110)
REVERT: E   90 MET cc_start: 0.8822 (mmm) cc_final: 0.8486 (mmp)
REVERT: F   74 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8542 (mt-10)
REVERT: H   30 ARG cc_start: 0.8356 (mtp85) cc_final: 0.7990 (mtp85)
REVERT: H   90 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.8201 (mp0)
REVERT: K   64 VAL cc_start: 0.8083 (OUTLIER) cc_final: 0.7754 (p)
REVERT: K   95 ASN cc_start: 0.7989 (p0) cc_final: 0.7761 (p0)
REVERT: K  121 MET cc_start: 0.8402 (tpt) cc_final: 0.7471 (mpp)
REVERT: K  159 ASN cc_start: 0.8274 (t0) cc_final: 0.8009 (t0)
  outliers start: 19
  outliers final: 15
  residues processed: 155
  average time/residue: 0.3317
  time to fit residues: 71.2054
Evaluate side-chains
  149 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue   88 SER
Chi-restraints excluded: chain E residue   48 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   72 ASP
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   57 SER
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain K residue   64 VAL
Chi-restraints excluded: chain K residue  205 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 72 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9990
   chunk 22 optimal weight:    1.9990
   chunk 108 optimal weight:   10.0000
   chunk 42 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9990
   chunk 111 optimal weight:   30.0000
   chunk 65 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.090877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.054422 restraints weight = 38540.182|
|-----------------------------------------------------------------------------|
r_work (start): 0.2843 rms_B_bonded: 1.97
r_work: 0.2639 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8671
moved from start:          0.3131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  14254  Z= 0.159
  Angle     :  0.589  10.005  20486  Z= 0.345
  Chirality :  0.035   0.183   2336
  Planarity :  0.004   0.040   1584
  Dihedral  : 30.248  87.911   4226
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 20.20 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.27), residues: 925
  helix:  2.24 (0.21), residues: 605
  sheet:  0.43 (0.76), residues: 42
  loop : -1.40 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  75 
 PHE   0.012   0.001   PHE E  67 
 TYR   0.018   0.001   TYR K 224 
 ARG   0.006   0.000   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03419 (  840)
  hydrogen bonds       : angle       3.00102 ( 2125)
  covalent geometry    : bond        0.00351 (14254)
  covalent geometry    : angle       0.58890 (20486)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 152
  time to evaluate  : 1.184 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9029 (pm20) cc_final: 0.8666 (pm20)
REVERT: A   76 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8571 (mm-40)
REVERT: A   81 ASP cc_start: 0.8608 (t0) cc_final: 0.8270 (t0)
REVERT: D   73 GLU cc_start: 0.8989 (tp30) cc_final: 0.8718 (tp30)
REVERT: D   90 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.7780 (mp0)
REVERT: D  102 GLU cc_start: 0.7709 (tp30) cc_final: 0.7438 (tp30)
REVERT: F   74 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8405 (mt-10)
REVERT: H   28 LYS cc_start: 0.7679 (ptmt) cc_final: 0.7393 (pttt)
REVERT: H   30 ARG cc_start: 0.8301 (mtp85) cc_final: 0.7917 (mtp85)
REVERT: H   31 LYS cc_start: 0.8483 (mtmt) cc_final: 0.8235 (mttt)
REVERT: H   42 LEU cc_start: 0.9408 (tp) cc_final: 0.9201 (tp)
REVERT: H   90 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8197 (mp0)
REVERT: K   69 ASN cc_start: 0.7419 (t0) cc_final: 0.5568 (m110)
REVERT: K   95 ASN cc_start: 0.8017 (p0) cc_final: 0.7690 (p0)
REVERT: K  121 MET cc_start: 0.8361 (tpt) cc_final: 0.7450 (mpp)
REVERT: K  158 GLN cc_start: 0.8142 (pm20) cc_final: 0.7546 (pm20)
  outliers start: 20
  outliers final: 11
  residues processed: 163
  average time/residue: 0.3122
  time to fit residues: 70.1123
Evaluate side-chains
  154 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 141
  time to evaluate  : 1.082 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain D residue   88 SER
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain G residue   72 ASP
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain K residue  205 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 36 optimal weight:    7.9990
   chunk 107 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 89 optimal weight:    5.9990
   chunk 22 optimal weight:    1.9990
   chunk 98 optimal weight:    8.9990
   chunk 59 optimal weight:    0.9980
   chunk 9 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 58 optimal weight:    4.9990
   overall best weight:    1.9786

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
D 106 HIS
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  92 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.089659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.052912 restraints weight = 38598.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.2800 rms_B_bonded: 1.97
r_work: 0.2596 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.2596
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
moved from start:          0.3206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  14254  Z= 0.224
  Angle     :  0.613   9.960  20486  Z= 0.355
  Chirality :  0.037   0.180   2336
  Planarity :  0.004   0.038   1584
  Dihedral  : 30.451  87.987   4226
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 21.86 %
    Favored  : 76.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.27), residues: 925
  helix:  2.16 (0.21), residues: 605
  sheet:  0.39 (0.77), residues: 42
  loop : -1.46 (0.33), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS D 106 
 PHE   0.010   0.001   PHE E  67 
 TYR   0.041   0.002   TYR K 224 
 ARG   0.007   0.000   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03758 (  840)
  hydrogen bonds       : angle       3.14350 ( 2125)
  covalent geometry    : bond        0.00510 (14254)
  covalent geometry    : angle       0.61271 (20486)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 139
  time to evaluate  : 0.981 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9074 (pm20) cc_final: 0.8664 (pm20)
REVERT: A   81 ASP cc_start: 0.8636 (t0) cc_final: 0.8331 (t0)
REVERT: D   30 ARG cc_start: 0.8338 (ttp-110) cc_final: 0.8081 (ttm170)
REVERT: D   90 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.7801 (mp0)
REVERT: E   90 MET cc_start: 0.8864 (mmm) cc_final: 0.8563 (mmp)
REVERT: F   74 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8447 (mt-10)
REVERT: H   30 ARG cc_start: 0.8347 (mtp85) cc_final: 0.7961 (mtp85)
REVERT: K   95 ASN cc_start: 0.8073 (p0) cc_final: 0.7802 (p0)
REVERT: K  121 MET cc_start: 0.8465 (tpt) cc_final: 0.7526 (mpp)
REVERT: K  159 ASN cc_start: 0.9214 (t0) cc_final: 0.8844 (t0)
  outliers start: 14
  outliers final: 13
  residues processed: 146
  average time/residue: 0.3564
  time to fit residues: 71.9998
Evaluate side-chains
  146 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 1.139 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain D residue   65 ASP
Chi-restraints excluded: chain D residue   88 SER
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain G residue   72 ASP
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain K residue  205 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 55 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 35 optimal weight:    0.5980
   chunk 65 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 106 optimal weight:    9.9990
   chunk 105 optimal weight:    9.9990
   chunk 61 optimal weight:    3.9990
   chunk 110 optimal weight:   30.0000
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.091329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.055004 restraints weight = 38097.707|
|-----------------------------------------------------------------------------|
r_work (start): 0.2856 rms_B_bonded: 1.98
r_work: 0.2653 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.3349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14254  Z= 0.155
  Angle     :  0.595   8.704  20486  Z= 0.346
  Chirality :  0.035   0.207   2336
  Planarity :  0.004   0.041   1584
  Dihedral  : 30.165  87.370   4226
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 22.24 %
    Favored  : 76.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.73 (0.27), residues: 925
  helix:  2.30 (0.21), residues: 605
  sheet:  0.20 (0.74), residues: 42
  loop : -1.39 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS H 106 
 PHE   0.011   0.001   PHE E  67 
 TYR   0.015   0.001   TYR G  57 
 ARG   0.006   0.000   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03410 (  840)
  hydrogen bonds       : angle       2.98455 ( 2125)
  covalent geometry    : bond        0.00341 (14254)
  covalent geometry    : angle       0.59509 (20486)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 145
  time to evaluate  : 1.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.9004 (pm20) cc_final: 0.8653 (pm20)
REVERT: A   81 ASP cc_start: 0.8577 (t0) cc_final: 0.8246 (t0)
REVERT: D   30 ARG cc_start: 0.8414 (ttp-110) cc_final: 0.8181 (ttm170)
REVERT: D   73 GLU cc_start: 0.8968 (tp30) cc_final: 0.8730 (tp30)
REVERT: E   90 MET cc_start: 0.8863 (mmm) cc_final: 0.8552 (mmp)
REVERT: F   74 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8385 (mt-10)
REVERT: H   30 ARG cc_start: 0.8327 (mtp85) cc_final: 0.7940 (mtp85)
REVERT: H   43 LYS cc_start: 0.9143 (mmtm) cc_final: 0.8938 (mptt)
REVERT: H   90 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8163 (mp0)
REVERT: K   95 ASN cc_start: 0.8155 (p0) cc_final: 0.7900 (p0)
REVERT: K  121 MET cc_start: 0.8404 (tpt) cc_final: 0.7498 (mpp)
REVERT: K  159 ASN cc_start: 0.9116 (t0) cc_final: 0.8776 (t0)
  outliers start: 13
  outliers final: 10
  residues processed: 151
  average time/residue: 0.3247
  time to fit residues: 67.0399
Evaluate side-chains
  147 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 1.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain D residue   88 SER
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain K residue  205 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9980
   chunk 43 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0470
   chunk 36 optimal weight:    0.6980
   chunk 94 optimal weight:    6.9990
   chunk 59 optimal weight:    0.8980
   chunk 38 optimal weight:    4.9990
   chunk 116 optimal weight:    0.0050
   overall best weight:    0.5292

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

Flipped N/Q/H residues before XYZ refinement:
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.091830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.055623 restraints weight = 38228.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.2873 rms_B_bonded: 1.98
r_work: 0.2670 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.3398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14254  Z= 0.149
  Angle     :  0.587   8.611  20486  Z= 0.342
  Chirality :  0.035   0.188   2336
  Planarity :  0.004   0.041   1584
  Dihedral  : 30.123  87.259   4226
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 21.98 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.27), residues: 925
  helix:  2.38 (0.21), residues: 605
  sheet:  0.47 (0.75), residues: 42
  loop : -1.36 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  75 
 PHE   0.012   0.001   PHE E  67 
 TYR   0.015   0.001   TYR G  57 
 ARG   0.006   0.000   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03432 (  840)
  hydrogen bonds       : angle       2.95482 ( 2125)
  covalent geometry    : bond        0.00324 (14254)
  covalent geometry    : angle       0.58740 (20486)

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

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

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1850 Ramachandran restraints generated.
    925 Oldfield, 0 Emsley, 925 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 146
  time to evaluate  : 1.572 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8999 (pm20) cc_final: 0.8674 (pm20)
REVERT: A   81 ASP cc_start: 0.8561 (t0) cc_final: 0.8244 (t0)
REVERT: C   64 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8261 (tm-30)
REVERT: D   30 ARG cc_start: 0.8399 (ttp-110) cc_final: 0.8179 (ttm170)
REVERT: D   73 GLU cc_start: 0.8981 (tp30) cc_final: 0.8722 (tp30)
REVERT: D   86 ILE cc_start: 0.9562 (mt) cc_final: 0.9042 (mt)
REVERT: D   90 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.7803 (mp0)
REVERT: E   90 MET cc_start: 0.8856 (mmm) cc_final: 0.8543 (mmp)
REVERT: F   74 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8409 (mt-10)
REVERT: H   30 ARG cc_start: 0.8320 (mtp85) cc_final: 0.7931 (mtp85)
REVERT: H   43 LYS cc_start: 0.9191 (mmtm) cc_final: 0.8986 (mptt)
REVERT: H   90 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.8182 (mp0)
REVERT: K   95 ASN cc_start: 0.8138 (p0) cc_final: 0.7896 (p0)
REVERT: K  121 MET cc_start: 0.8463 (tpt) cc_final: 0.7632 (mpp)
REVERT: K  159 ASN cc_start: 0.9150 (t0) cc_final: 0.8831 (t0)
  outliers start: 16
  outliers final: 13
  residues processed: 152
  average time/residue: 0.3536
  time to fit residues: 75.1114
Evaluate side-chains
  156 residues out of total 787 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 141
  time to evaluate  : 1.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   73 GLU
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   74 GLU
Chi-restraints excluded: chain C residue  113 SER
Chi-restraints excluded: chain D residue   88 SER
Chi-restraints excluded: chain D residue   90 GLU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   97 LEU
Chi-restraints excluded: chain H residue   44 GLN
Chi-restraints excluded: chain H residue   68 GLU
Chi-restraints excluded: chain H residue   90 GLU
Chi-restraints excluded: chain K residue  205 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 63 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 116 optimal weight:    1.9990
   chunk 115 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9980
   chunk 31 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   chunk 74 optimal weight:    6.9990
   chunk 83 optimal weight:    6.9990
   chunk 106 optimal weight:   10.0000
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** F  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.091618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.055324 restraints weight = 38493.216|
|-----------------------------------------------------------------------------|
r_work (start): 0.2864 rms_B_bonded: 1.99
r_work: 0.2659 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.2659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8652
moved from start:          0.3481

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  14254  Z= 0.162
  Angle     :  0.597  10.641  20486  Z= 0.346
  Chirality :  0.035   0.200   2336
  Planarity :  0.004   0.041   1584
  Dihedral  : 30.122  87.048   4226
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 22.74 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.27), residues: 925
  helix:  2.38 (0.21), residues: 605
  sheet:  0.31 (0.74), residues: 42
  loop : -1.33 (0.34), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS F  75 
 PHE   0.010   0.001   PHE E  67 
 TYR   0.030   0.002   TYR K 195 
 ARG   0.007   0.000   ARG D  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03464 (  840)
  hydrogen bonds       : angle       2.98009 ( 2125)
  covalent geometry    : bond        0.00361 (14254)
  covalent geometry    : angle       0.59685 (20486)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6877.46 seconds
wall clock time: 122 minutes 33.88 seconds (7353.88 seconds total)