Starting phenix.real_space_refine
on Wed Feb  4 16:49:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9y47_72473/02_2026/9y47_72473.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9y47_72473/02_2026/9y47_72473.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9y47_72473/02_2026/9y47_72473.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9y47_72473/02_2026/9y47_72473.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9y47_72473/02_2026/9y47_72473.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9y47_72473/02_2026/9y47_72473.cif"
  }
  resolution = 2.74
  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=   0.002 sd=   0.031
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      12      5.16       5
     C    6598      2.51       5
     N    2245      2.21       5
     O    2798      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11943
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 810
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "C"
      Number of atoms: 837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 837
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 619
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 837
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 2990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2990
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2955
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 2.97, per 1000 atoms: 0.25
  Number of scatterers: 11943
  At special positions: 0
  Unit cell: (119.21, 102.83, 120.12, 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      12     16.00
     P     290     15.00
     O    2798      8.00
     N    2245      7.00
     C    6598      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: 0.97
  Conformation dependent library (CDL) restraints added in 434.9 milliseconds
  

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1412

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 9 sheets defined
      72.7% alpha, 2.9% beta
      144 base pairs and 267 stacking pairs defined.
    Time for finding SS restraints: 1.84
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 76
      removed outlier: 3.610A  pdb=" N   GLN A  76 " --> pdb=" O   ARG A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.928A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   MET A  90 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LEU A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.750A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 77
      removed outlier: 4.073A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.537A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 36
      removed outlier: 3.814A  pdb=" N   VAL C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.690A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.582A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 97
      removed outlier: 3.526A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.684A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 124
      removed outlier: 3.599A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.956A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   MET E  90 " --> pdb=" O   SER E  86 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   LEU E 109 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.547A  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 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.101A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.770A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 27 through 36
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.772A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.624A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.525A  pdb=" N   GLN H  47 " --> pdb=" O   LYS H  43 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 124
      removed outlier: 3.857A  pdb=" N   ALA H 107 " --> pdb=" O   PRO H 103 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   SER H 124 " --> pdb=" O   LYS H 120 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.857A  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 'C' and resid 42 through 43
      removed outlier: 7.306A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102
      removed outlier: 6.694A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.970A  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 'G' and resid 42 through 43
      removed outlier: 7.195A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78

    386 hydrogen bonds defined for protein.
    1134 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      370 hydrogen bonds
      740 hydrogen bond angles
      0 basepair planarities
      144 basepair parallelities
      267 stacking parallelities
  Total time for adding SS restraints: 2.40

  Time building geometry restraints manager: 1.34 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: 2014
        1.33 -     1.45: 4312
        1.45 -     1.57: 5820
        1.57 -     1.69: 578
        1.69 -     1.80: 22
  Bond restraints: 12746
  Sorted by residual:
  bond pdb=" C3'  DT I -59 "
       pdb=" O3'  DT I -59 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.67e+00
  bond pdb=" C   GLU G  61 "
       pdb=" O   GLU G  61 "
    ideal  model  delta    sigma   weight residual
    1.236  1.249 -0.012 1.15e-02 7.56e+03 1.11e+00
  bond pdb=" C   GLU C  61 "
       pdb=" O   GLU C  61 "
    ideal  model  delta    sigma   weight residual
    1.236  1.248 -0.011 1.15e-02 7.56e+03 9.87e-01
  bond pdb=" C3'  DG I  20 "
       pdb=" C2'  DG I  20 "
    ideal  model  delta    sigma   weight residual
    1.525  1.545 -0.020 2.00e-02 2.50e+03 9.79e-01
  bond pdb=" C3'  DA J  65 "
       pdb=" C2'  DA J  65 "
    ideal  model  delta    sigma   weight residual
    1.525  1.544 -0.019 2.00e-02 2.50e+03 9.47e-01
  ... (remaining 12741 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.15: 17222
        1.15 -     2.30: 1095
        2.30 -     3.45: 123
        3.45 -     4.60: 9
        4.60 -     5.75: 4
  Bond angle restraints: 18453
  Sorted by residual:
  angle pdb=" C   THR B  30 "
        pdb=" N   LYS B  31 "
        pdb=" CA  LYS B  31 "
      ideal   model   delta    sigma   weight residual
     120.26  126.01   -5.75 1.34e+00 5.57e-01 1.84e+01
  angle pdb=" N   MET A 120 "
        pdb=" CA  MET A 120 "
        pdb=" C   MET A 120 "
      ideal   model   delta    sigma   weight residual
     108.25  112.39   -4.14 1.16e+00 7.43e-01 1.27e+01
  angle pdb=" CA  ASN C  73 "
        pdb=" CB  ASN C  73 "
        pdb=" CG  ASN C  73 "
      ideal   model   delta    sigma   weight residual
     112.60  115.00   -2.40 1.00e+00 1.00e+00 5.75e+00
  angle pdb=" CA  ASN G  73 "
        pdb=" CB  ASN G  73 "
        pdb=" CG  ASN G  73 "
      ideal   model   delta    sigma   weight residual
     112.60  114.71   -2.11 1.00e+00 1.00e+00 4.46e+00
  angle pdb=" O4'  DC I -25 "
        pdb=" C1'  DC I -25 "
        pdb=" C2'  DC I -25 "
      ideal   model   delta    sigma   weight residual
     106.40  103.33    3.07 1.50e+00 4.44e-01 4.20e+00
  ... (remaining 18448 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.78: 5496
       34.78 -    69.55: 1418
       69.55 -   104.33: 5
      104.33 -   139.11: 0
      139.11 -   173.88: 1
  Dihedral angle restraints: 6920
    sinusoidal: 4729
      harmonic: 2191
  Sorted by residual:
  dihedral pdb=" C4'  DT I -59 "
           pdb=" C3'  DT I -59 "
           pdb=" O3'  DT I -59 "
           pdb=" P    DC I -58 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   46.12  173.88     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" CA  ASP A  77 "
           pdb=" CB  ASP A  77 "
           pdb=" CG  ASP A  77 "
           pdb=" OD1 ASP A  77 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.73   59.73     1      2.00e+01 2.50e-03 1.19e+01
  dihedral pdb=" CG  ARG E  52 "
           pdb=" CD  ARG E  52 "
           pdb=" NE  ARG E  52 "
           pdb=" CZ  ARG E  52 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  135.67   44.33     2      1.50e+01 4.44e-03 1.04e+01
  ... (remaining 6917 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 1433
       0.035 -    0.070: 538
       0.070 -    0.105: 104
       0.105 -    0.140: 20
       0.140 -    0.175: 3
  Chirality restraints: 2098
  Sorted by residual:
  chirality pdb=" CA  ASN G  73 "
            pdb=" N   ASN G  73 "
            pdb=" C   ASN G  73 "
            pdb=" CB  ASN G  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.18 2.00e-01 2.50e+01 7.68e-01
  chirality pdb=" CA  ASN C  73 "
            pdb=" N   ASN C  73 "
            pdb=" C   ASN C  73 "
            pdb=" CB  ASN C  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.73e-01
  chirality pdb=" C4'  DG I -35 "
            pdb=" C5'  DG I -35 "
            pdb=" O4'  DG I -35 "
            pdb=" C3'  DG I -35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.38   -0.14 2.00e-01 2.50e+01 5.11e-01
  ... (remaining 2095 not shown)

  Planarity restraints: 1330
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  17 "   -0.026 2.00e-02 2.50e+03   1.15e-02 3.61e+00
        pdb=" N9   DA I  17 "    0.026 2.00e-02 2.50e+03
        pdb=" C8   DA I  17 "    0.003 2.00e-02 2.50e+03
        pdb=" N7   DA I  17 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I  17 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6   DA I  17 "   -0.002 2.00e-02 2.50e+03
        pdb=" N6   DA I  17 "   -0.007 2.00e-02 2.50e+03
        pdb=" N1   DA I  17 "   -0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I  17 "    0.002 2.00e-02 2.50e+03
        pdb=" N3   DA I  17 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DA I  17 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU C 108 "   -0.031 5.00e-02 4.00e+02   4.63e-02 3.42e+00
        pdb=" N   PRO C 109 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO C 109 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C 109 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I -35 "   -0.025 2.00e-02 2.50e+03   1.03e-02 3.20e+00
        pdb=" N9   DG I -35 "    0.024 2.00e-02 2.50e+03
        pdb=" C8   DG I -35 "    0.003 2.00e-02 2.50e+03
        pdb=" N7   DG I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" C5   DG I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" O6   DG I -35 "   -0.008 2.00e-02 2.50e+03
        pdb=" N1   DG I -35 "   -0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I -35 "    0.000 2.00e-02 2.50e+03
        pdb=" N2   DG I -35 "    0.004 2.00e-02 2.50e+03
        pdb=" N3   DG I -35 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I -35 "    0.002 2.00e-02 2.50e+03
  ... (remaining 1327 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1927
        2.78 -     3.31: 9138
        3.31 -     3.84: 21490
        3.84 -     4.37: 26178
        4.37 -     4.90: 37615
  Nonbonded interactions: 96348
  Sorted by model distance:
  nonbonded pdb=" O   SER H 124 "
            pdb=" OG  SER H 124 "
     model   vdw
     2.254 3.040
  nonbonded pdb=" OG  SER E  57 "
            pdb=" OE1 GLU E  59 "
     model   vdw
     2.415 3.040
  nonbonded pdb=" OG  SER A  57 "
            pdb=" OE1 GLU A  59 "
     model   vdw
     2.440 3.040
  nonbonded pdb=" N   ASP H  51 "
            pdb=" OD1 ASP H  51 "
     model   vdw
     2.450 3.120
  nonbonded pdb=" N   ASP D  51 "
            pdb=" OD1 ASP D  51 "
     model   vdw
     2.461 3.120
  ... (remaining 96343 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 38 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 25 through 101)
  selection = (chain 'F' and resid 25 through 101)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.580
  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:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.970
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  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:8.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12746  Z= 0.197
  Angle     :  0.608   5.751  18453  Z= 0.382
  Chirality :  0.037   0.175   2098
  Planarity :  0.004   0.046   1330
  Dihedral  : 27.271 173.884   5508
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 20.06 %
    Favored  : 77.55 %
  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:  2.30 (0.31), residues: 741
  helix:  2.79 (0.23), residues: 518
  sheet:  None (None), residues: 0
  loop : -1.76 (0.32), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 129 
 TYR   0.011   0.002   TYR D 121 
 PHE   0.010   0.002   PHE C  25 
 HIS   0.005   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 (12746)
  covalent geometry    : angle       0.60765 (18453)
  hydrogen bonds       : bond        0.10641 (  756)
  hydrogen bonds       : angle       3.14648 ( 1874)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 163
  time to evaluate  : 0.303 
Fit side-chains
REVERT: A  120 MET cc_start: 0.7743 (mtt) cc_final: 0.7430 (mtt)
REVERT: B   78 ARG cc_start: 0.8604 (mtm110) cc_final: 0.8372 (mtm-85)
REVERT: C   42 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7966 (ptp-170)
REVERT: D   84 ASN cc_start: 0.8416 (m-40) cc_final: 0.8169 (m-40)
REVERT: D   85 LYS cc_start: 0.8444 (mmtp) cc_final: 0.8118 (mttp)
REVERT: G   13 LYS cc_start: 0.7494 (OUTLIER) cc_final: 0.7011 (tmtm)
REVERT: G   62 ILE cc_start: 0.8241 (mt) cc_final: 0.7913 (tt)
REVERT: G   64 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7857 (tt0)
REVERT: G   99 LYS cc_start: 0.8376 (mmtm) cc_final: 0.8121 (mmtm)
REVERT: H   62 MET cc_start: 0.8446 (mmp) cc_final: 0.8131 (mmm)
REVERT: H   85 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.8162 (mptt)
REVERT: H  116 LYS cc_start: 0.8689 (ttmt) cc_final: 0.8440 (ttpp)
  outliers start: 15
  outliers final: 8
  residues processed: 169
  average time/residue: 0.9098
  time to fit residues: 161.5074
Evaluate side-chains
  175 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 163
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain H residue   85 LYS
Chi-restraints excluded: chain H residue   91 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0970
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.3980
   chunk 45 optimal weight:    2.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
C  24 GLN
G  24 GLN
G 104 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.111292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.098882 restraints weight = 15008.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 0.76
r_work: 0.3052 rms_B_bonded: 1.55 restraints_weight: 0.5000
r_work: 0.2929 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.2929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.0394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12746  Z= 0.203
  Angle     :  0.586   6.349  18453  Z= 0.362
  Chirality :  0.037   0.146   2098
  Planarity :  0.004   0.045   1330
  Dihedral  : 29.040 174.568   4040
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 19.43 %
    Favored  : 78.50 %
  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:  2.46 (0.31), residues: 741
  helix:  2.86 (0.23), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.61 (0.33), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 129 
 TYR   0.011   0.002   TYR D 121 
 PHE   0.009   0.002   PHE E  67 
 HIS   0.004   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 (12746)
  covalent geometry    : angle       0.58587 (18453)
  hydrogen bonds       : bond        0.07235 (  756)
  hydrogen bonds       : angle       2.76322 ( 1874)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 161
  time to evaluate  : 0.311 
Fit side-chains
REVERT: D   59 MET cc_start: 0.8017 (tpp) cc_final: 0.7635 (tpt)
REVERT: D   84 ASN cc_start: 0.8322 (m-40) cc_final: 0.8111 (m-40)
REVERT: D   85 LYS cc_start: 0.8502 (mmtp) cc_final: 0.8227 (mttp)
REVERT: F   79 LYS cc_start: 0.8583 (OUTLIER) cc_final: 0.8285 (mmtp)
REVERT: G   62 ILE cc_start: 0.8201 (mt) cc_final: 0.7990 (tt)
REVERT: G   99 LYS cc_start: 0.8139 (mmtm) cc_final: 0.7928 (mmtm)
REVERT: H   47 GLN cc_start: 0.8081 (mt0) cc_final: 0.7857 (mt0)
REVERT: H   62 MET cc_start: 0.8446 (mmp) cc_final: 0.7984 (mmm)
  outliers start: 13
  outliers final: 5
  residues processed: 167
  average time/residue: 0.8526
  time to fit residues: 150.2003
Evaluate side-chains
  166 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 160
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain G residue  108 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0270
   chunk 95 optimal weight:    3.9990
   chunk 75 optimal weight:    3.9990
   chunk 12 optimal weight:    0.9990
   chunk 60 optimal weight:    0.0670
   chunk 8 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
G  24 GLN
G 104 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.111735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.099394 restraints weight = 15074.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3185 rms_B_bonded: 0.76
r_work: 0.3061 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.2939 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.2939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.0432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12746  Z= 0.184
  Angle     :  0.574   6.500  18453  Z= 0.357
  Chirality :  0.036   0.153   2098
  Planarity :  0.004   0.055   1330
  Dihedral  : 29.064 174.739   4017
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 19.11 %
    Favored  : 77.71 %
  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:  2.51 (0.31), residues: 741
  helix:  2.89 (0.23), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.57 (0.33), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  79 
 TYR   0.009   0.001   TYR D 121 
 PHE   0.009   0.002   PHE E  67 
 HIS   0.004   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (12746)
  covalent geometry    : angle       0.57398 (18453)
  hydrogen bonds       : bond        0.06953 (  756)
  hydrogen bonds       : angle       2.74055 ( 1874)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 161
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A  131 ARG cc_start: 0.8326 (OUTLIER) cc_final: 0.7062 (mtp180)
REVERT: D   59 MET cc_start: 0.7995 (tpp) cc_final: 0.7642 (tpt)
REVERT: D   79 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7457 (mtp180)
REVERT: D   84 ASN cc_start: 0.8289 (m-40) cc_final: 0.8081 (m-40)
REVERT: D   85 LYS cc_start: 0.8486 (mmtp) cc_final: 0.8218 (mttp)
REVERT: F   77 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8170 (mttp)
REVERT: F   79 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.8275 (mmtp)
REVERT: G   13 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7026 (tmtm)
REVERT: G   62 ILE cc_start: 0.8190 (mt) cc_final: 0.7977 (tt)
REVERT: G   99 LYS cc_start: 0.8133 (mmtm) cc_final: 0.7921 (mmtm)
REVERT: H   47 GLN cc_start: 0.8094 (mt0) cc_final: 0.7880 (mt0)
REVERT: H   62 MET cc_start: 0.8437 (mmp) cc_final: 0.8016 (mmm)
  outliers start: 20
  outliers final: 12
  residues processed: 170
  average time/residue: 0.8703
  time to fit residues: 156.1188
Evaluate side-chains
  177 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 160
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   13 LYS
Chi-restraints excluded: chain C residue   42 ARG
Chi-restraints excluded: chain D residue   79 ARG
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   91 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 73 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
G 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.109425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.096955 restraints weight = 14967.175|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 0.76
r_work: 0.3017 rms_B_bonded: 1.54 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 2.70 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8076
moved from start:          0.0510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040  12746  Z= 0.240
  Angle     :  0.621   6.994  18453  Z= 0.381
  Chirality :  0.040   0.164   2098
  Planarity :  0.005   0.047   1330
  Dihedral  : 29.090 175.700   4017
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 2.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  4.62 %
    Allowed  : 17.52 %
    Favored  : 77.87 %
  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:  2.32 (0.31), residues: 741
  helix:  2.73 (0.23), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.60 (0.33), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 129 
 TYR   0.012   0.002   TYR D 121 
 PHE   0.010   0.002   PHE D  65 
 HIS   0.006   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00533 (12746)
  covalent geometry    : angle       0.62149 (18453)
  hydrogen bonds       : bond        0.08185 (  756)
  hydrogen bonds       : angle       2.85448 ( 1874)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 158
  time to evaluate  : 0.300 
Fit side-chains
REVERT: A  131 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7086 (mtp180)
REVERT: D   85 LYS cc_start: 0.8549 (mmtp) cc_final: 0.8318 (mttp)
REVERT: F   77 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8258 (mttp)
REVERT: F   79 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8316 (mmtp)
REVERT: G   13 LYS cc_start: 0.7400 (OUTLIER) cc_final: 0.7058 (tmtm)
REVERT: G   62 ILE cc_start: 0.8271 (mt) cc_final: 0.8011 (tt)
REVERT: G   99 LYS cc_start: 0.8145 (mmtm) cc_final: 0.7932 (mmtm)
REVERT: H   47 GLN cc_start: 0.8156 (mt0) cc_final: 0.7929 (mt0)
REVERT: H   62 MET cc_start: 0.8484 (mmp) cc_final: 0.8069 (mmm)
  outliers start: 29
  outliers final: 14
  residues processed: 171
  average time/residue: 0.8811
  time to fit residues: 158.4772
Evaluate side-chains
  175 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 157
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   84 MET
Chi-restraints excluded: chain C residue   13 LYS
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue   90 ASP
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain H residue   91 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 4 optimal weight:    0.3980
   chunk 8 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 93 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    1.6786

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
C  24 GLN
G  24 GLN
G 104 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.109453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.095871 restraints weight = 15393.988|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 0.79
r_work: 0.2997 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2873 rms_B_bonded: 2.83 restraints_weight: 0.2500
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.0629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038  12746  Z= 0.257
  Angle     :  0.640   8.019  18453  Z= 0.390
  Chirality :  0.041   0.167   2098
  Planarity :  0.005   0.050   1330
  Dihedral  : 29.099 175.977   4013
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 18.63 %
    Favored  : 77.07 %
  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:  2.14 (0.31), residues: 741
  helix:  2.60 (0.23), residues: 525
  sheet:  None (None), residues: 0
  loop : -1.75 (0.33), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  40 
 TYR   0.014   0.002   TYR D 121 
 PHE   0.011   0.002   PHE E  67 
 HIS   0.006   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00575 (12746)
  covalent geometry    : angle       0.64021 (18453)
  hydrogen bonds       : bond        0.08556 (  756)
  hydrogen bonds       : angle       2.90666 ( 1874)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 151
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A  131 ARG cc_start: 0.8384 (OUTLIER) cc_final: 0.7143 (mtp180)
REVERT: D   85 LYS cc_start: 0.8528 (mmtp) cc_final: 0.8298 (mttp)
REVERT: E  120 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7977 (mtt)
REVERT: F   77 LYS cc_start: 0.8690 (OUTLIER) cc_final: 0.8319 (mttp)
REVERT: F   79 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8327 (mmtp)
REVERT: F   95 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7645 (mtp180)
REVERT: G   13 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7033 (tmtm)
REVERT: G   62 ILE cc_start: 0.8319 (mt) cc_final: 0.8030 (tt)
REVERT: G   64 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7684 (tt0)
REVERT: G   99 LYS cc_start: 0.8153 (mmtm) cc_final: 0.7950 (mmtm)
REVERT: H   47 GLN cc_start: 0.8195 (mt0) cc_final: 0.7967 (mt0)
REVERT: H   62 MET cc_start: 0.8518 (mmp) cc_final: 0.8203 (mmm)
  outliers start: 27
  outliers final: 15
  residues processed: 163
  average time/residue: 0.7747
  time to fit residues: 132.9143
Evaluate side-chains
  172 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 150
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain C residue   13 LYS
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue   90 ASP
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain H residue   91 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 23 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 9 optimal weight:    0.2980
   chunk 4 optimal weight:    0.7980
   chunk 11 optimal weight:    0.5980
   chunk 95 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
G 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.110443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.096787 restraints weight = 15381.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3140 rms_B_bonded: 0.80
r_work: 0.3012 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 2.85 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.0611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12746  Z= 0.196
  Angle     :  0.608   8.041  18453  Z= 0.375
  Chirality :  0.037   0.161   2098
  Planarity :  0.005   0.047   1330
  Dihedral  : 29.112 176.149   4013
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  4.14 %
    Allowed  : 18.95 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.21 (0.31), residues: 741
  helix:  2.65 (0.23), residues: 525
  sheet:  None (None), residues: 0
  loop : -1.71 (0.33), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 129 
 TYR   0.011   0.001   TYR D 121 
 PHE   0.010   0.002   PHE E  67 
 HIS   0.005   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (12746)
  covalent geometry    : angle       0.60831 (18453)
  hydrogen bonds       : bond        0.07913 (  756)
  hydrogen bonds       : angle       2.88809 ( 1874)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 149
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A  131 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7115 (mtp180)
REVERT: D   85 LYS cc_start: 0.8518 (mmtp) cc_final: 0.8292 (mttp)
REVERT: E  120 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7957 (mtt)
REVERT: F   77 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8294 (mttp)
REVERT: F   79 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8303 (mmtp)
REVERT: F   95 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7645 (mtp180)
REVERT: G   13 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7026 (tmtm)
REVERT: G   62 ILE cc_start: 0.8275 (mt) cc_final: 0.8007 (tt)
REVERT: G   64 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.7668 (tt0)
REVERT: G   99 LYS cc_start: 0.8162 (mmtm) cc_final: 0.7956 (mmtm)
REVERT: H   47 GLN cc_start: 0.8159 (mt0) cc_final: 0.7929 (mt0)
REVERT: H   62 MET cc_start: 0.8503 (mmp) cc_final: 0.8197 (mmm)
  outliers start: 26
  outliers final: 15
  residues processed: 161
  average time/residue: 0.8492
  time to fit residues: 144.2308
Evaluate side-chains
  171 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 149
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain C residue   13 LYS
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue   90 ASP
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   53 ARG
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain H residue   91 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 91 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
G 104 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.107884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.094124 restraints weight = 15333.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3099 rms_B_bonded: 0.81
r_work: 0.2967 rms_B_bonded: 1.64 restraints_weight: 0.5000
r_work: 0.2840 rms_B_bonded: 2.85 restraints_weight: 0.2500
r_work (final): 0.2840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.0795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042  12746  Z= 0.307
  Angle     :  0.690   8.505  18453  Z= 0.416
  Chirality :  0.045   0.188   2098
  Planarity :  0.005   0.053   1330
  Dihedral  : 29.111 175.998   4013
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 19.27 %
    Favored  : 76.75 %
  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:  1.93 (0.31), residues: 741
  helix:  2.46 (0.23), residues: 523
  sheet:  None (None), residues: 0
  loop : -1.85 (0.32), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 129 
 TYR   0.016   0.002   TYR D 121 
 PHE   0.012   0.003   PHE D  65 
 HIS   0.008   0.002   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00701 (12746)
  covalent geometry    : angle       0.68955 (18453)
  hydrogen bonds       : bond        0.09524 (  756)
  hydrogen bonds       : angle       3.01656 ( 1874)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 151
  time to evaluate  : 0.293 
Fit side-chains
REVERT: A  131 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.7386 (mtp180)
REVERT: D   59 MET cc_start: 0.8297 (tpp) cc_final: 0.8058 (tpp)
REVERT: D   85 LYS cc_start: 0.8549 (mmtp) cc_final: 0.8330 (mttp)
REVERT: E  120 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8034 (mtt)
REVERT: F   77 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8360 (mttp)
REVERT: F   79 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8340 (mmtp)
REVERT: G   13 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7035 (tmtm)
REVERT: G   62 ILE cc_start: 0.8354 (mt) cc_final: 0.8055 (tt)
REVERT: H   47 GLN cc_start: 0.8261 (mt0) cc_final: 0.8027 (mt0)
REVERT: H   62 MET cc_start: 0.8525 (mmp) cc_final: 0.8239 (mmm)
  outliers start: 25
  outliers final: 14
  residues processed: 163
  average time/residue: 0.8477
  time to fit residues: 145.3620
Evaluate side-chains
  170 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 151
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue   90 ASP
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain H residue   39 VAL
Chi-restraints excluded: chain H residue   91 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 55 optimal weight:    0.8980
   chunk 19 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 88 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
C  24 GLN
G 104 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.110063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.096407 restraints weight = 15260.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3135 rms_B_bonded: 0.80
r_work: 0.3006 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2880 rms_B_bonded: 2.83 restraints_weight: 0.2500
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.0716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  12746  Z= 0.199
  Angle     :  0.621   8.860  18453  Z= 0.382
  Chirality :  0.038   0.153   2098
  Planarity :  0.005   0.050   1330
  Dihedral  : 29.139 176.409   4013
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 20.70 %
    Favored  : 75.80 %
  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:  2.12 (0.30), residues: 741
  helix:  2.59 (0.23), residues: 519
  sheet:  None (None), residues: 0
  loop : -1.66 (0.33), residues: 222

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 129 
 TYR   0.011   0.001   TYR D 121 
 PHE   0.011   0.002   PHE E  67 
 HIS   0.006   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 (12746)
  covalent geometry    : angle       0.62139 (18453)
  hydrogen bonds       : bond        0.07950 (  756)
  hydrogen bonds       : angle       3.01116 ( 1874)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 153
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A  131 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7098 (mtp180)
REVERT: B   95 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7828 (mtt-85)
REVERT: D   85 LYS cc_start: 0.8523 (mttp) cc_final: 0.8300 (mttp)
REVERT: F   77 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8318 (mttp)
REVERT: F   79 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8319 (mmtp)
REVERT: G   13 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7032 (tmtm)
REVERT: G   64 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7652 (tt0)
REVERT: H   47 GLN cc_start: 0.8180 (mt0) cc_final: 0.7942 (mt0)
REVERT: H   62 MET cc_start: 0.8510 (mmp) cc_final: 0.8155 (mmm)
  outliers start: 22
  outliers final: 13
  residues processed: 164
  average time/residue: 0.8346
  time to fit residues: 144.1817
Evaluate side-chains
  171 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 152
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   95 ARG
Chi-restraints excluded: chain C residue   13 LYS
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue   90 ASP
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain H residue   91 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 58 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 26 optimal weight:    8.9990
   chunk 18 optimal weight:    0.9980
   chunk 77 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
C  24 GLN
G 104 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.110008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.096476 restraints weight = 15156.330|
|-----------------------------------------------------------------------------|
r_work (start): 0.3136 rms_B_bonded: 0.79
r_work: 0.3009 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2884 rms_B_bonded: 2.81 restraints_weight: 0.2500
r_work (final): 0.2884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.0693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  12746  Z= 0.219
  Angle     :  0.621   8.514  18453  Z= 0.381
  Chirality :  0.039   0.152   2098
  Planarity :  0.005   0.049   1330
  Dihedral  : 29.106 176.501   4013
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 20.38 %
    Favored  : 76.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.25 (0.31), residues: 741
  helix:  2.68 (0.23), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.62 (0.33), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 129 
 TYR   0.013   0.002   TYR D 121 
 PHE   0.012   0.002   PHE E  67 
 HIS   0.005   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00471 (12746)
  covalent geometry    : angle       0.62100 (18453)
  hydrogen bonds       : bond        0.08146 (  756)
  hydrogen bonds       : angle       2.85354 ( 1874)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 151
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A  131 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7100 (mtp180)
REVERT: D   85 LYS cc_start: 0.8517 (mttp) cc_final: 0.8293 (mttp)
REVERT: F   77 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8304 (mttp)
REVERT: F   79 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8323 (mmtp)
REVERT: F   95 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7665 (mtp180)
REVERT: G   13 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7031 (tmtm)
REVERT: G   62 ILE cc_start: 0.8308 (mt) cc_final: 0.8030 (tt)
REVERT: G   64 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7645 (tt0)
REVERT: H   47 GLN cc_start: 0.8171 (mt0) cc_final: 0.7940 (mt0)
REVERT: H   62 MET cc_start: 0.8496 (mmp) cc_final: 0.8199 (mmm)
  outliers start: 22
  outliers final: 13
  residues processed: 163
  average time/residue: 0.8283
  time to fit residues: 142.0721
Evaluate side-chains
  171 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 152
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain C residue   13 LYS
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue   90 ASP
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue   91 GLU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain H residue   91 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 93 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0020
   chunk 56 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    1.1592

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
C  24 GLN
G 104 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.110201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.096660 restraints weight = 15289.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 0.78
r_work: 0.3012 rms_B_bonded: 1.61 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 2.80 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8067
moved from start:          0.0680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  12746  Z= 0.214
  Angle     :  0.616   8.609  18453  Z= 0.379
  Chirality :  0.039   0.161   2098
  Planarity :  0.005   0.049   1330
  Dihedral  : 29.112 176.445   4013
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 20.86 %
    Favored  : 75.96 %
  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:  2.26 (0.31), residues: 741
  helix:  2.68 (0.23), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.61 (0.33), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E 129 
 TYR   0.012   0.002   TYR D 121 
 PHE   0.012   0.002   PHE E  67 
 HIS   0.005   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 (12746)
  covalent geometry    : angle       0.61582 (18453)
  hydrogen bonds       : bond        0.07990 (  756)
  hydrogen bonds       : angle       2.85783 ( 1874)

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

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

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1482 Ramachandran restraints generated.
    741 Oldfield, 0 Emsley, 741 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 152
  time to evaluate  : 0.302 
Fit side-chains
REVERT: A  131 ARG cc_start: 0.8356 (OUTLIER) cc_final: 0.7128 (mtp180)
REVERT: D   85 LYS cc_start: 0.8521 (mttp) cc_final: 0.8301 (mttp)
REVERT: F   77 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8294 (mttp)
REVERT: F   79 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8322 (mmtp)
REVERT: F   95 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7613 (mtp180)
REVERT: G   13 LYS cc_start: 0.7437 (OUTLIER) cc_final: 0.7025 (tmtm)
REVERT: G   62 ILE cc_start: 0.8294 (mt) cc_final: 0.8016 (tt)
REVERT: G   64 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7649 (tt0)
REVERT: H   47 GLN cc_start: 0.8173 (mt0) cc_final: 0.7941 (mt0)
REVERT: H   62 MET cc_start: 0.8492 (mmp) cc_final: 0.8200 (mmm)
  outliers start: 20
  outliers final: 12
  residues processed: 162
  average time/residue: 0.7726
  time to fit residues: 131.9536
Evaluate side-chains
  170 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 152
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 SER
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain C residue   13 LYS
Chi-restraints excluded: chain C residue   19 SER
Chi-restraints excluded: chain C residue   90 ASP
Chi-restraints excluded: chain E residue   82 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain F residue   95 ARG
Chi-restraints excluded: chain G residue   13 LYS
Chi-restraints excluded: chain G residue   16 THR
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain H residue   91 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 65 optimal weight:    0.9980
   chunk 18 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 96 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0170
   chunk 89 optimal weight:    3.9990
   chunk 67 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   overall best weight:    0.7622

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
C  24 GLN
G 104 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.110579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.096987 restraints weight = 15257.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 0.80
r_work: 0.3016 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 2.84 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8063
moved from start:          0.0674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  12746  Z= 0.187
  Angle     :  0.603   8.655  18453  Z= 0.373
  Chirality :  0.037   0.145   2098
  Planarity :  0.004   0.048   1330
  Dihedral  : 29.114 176.483   4013
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 21.18 %
    Favored  : 75.96 %
  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:  2.29 (0.31), residues: 741
  helix:  2.70 (0.23), residues: 521
  sheet:  None (None), residues: 0
  loop : -1.58 (0.33), residues: 220

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 129 
 TYR   0.011   0.001   TYR D 121 
 PHE   0.011   0.002   PHE E  67 
 HIS   0.005   0.001   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 (12746)
  covalent geometry    : angle       0.60341 (18453)
  hydrogen bonds       : bond        0.07806 (  756)
  hydrogen bonds       : angle       2.84452 ( 1874)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3959.04 seconds
wall clock time: 67 minutes 56.46 seconds (4076.46 seconds total)