Starting phenix.real_space_refine
on Sat Aug 23 14:09:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8txv_41706/08_2025/8txv_41706.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8txv_41706/08_2025/8txv_41706.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8txv_41706/08_2025/8txv_41706.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8txv_41706/08_2025/8txv_41706.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8txv_41706/08_2025/8txv_41706.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8txv_41706/08_2025/8txv_41706.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     294      5.49       5
     S      15      5.16       5
     C    7144      2.51       5
     N    2407      2.21       5
     O    2976      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-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12836
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 740
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "H"
      Number of atoms: 743
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 728
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 117
          Classifications: {'peptide': 14}
          Link IDs: {'PTRANS': 1, 'TRANS': 12}
    Chain: "M"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 602
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "C"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 827
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "G"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 836
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   LEU M  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU M  73 " occ=0.45
    residue:
      pdb=" N   ARG M  74 " occ=0.45
      ... (9 atoms not shown)
      pdb=" NH2 ARG M  74 " occ=0.45
    residue:
      pdb=" N   GLY M  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY M  75 " occ=0.25
    residue:
      pdb=" N   GLY M  76 " occ=0.25
      ... (3 atoms not shown)
      pdb=" OXT GLY M  76 " occ=0.25
  Time building chain proxies: 2.77, per 1000 atoms: 0.22
  Number of scatterers: 12836
  At special positions: 0
  Unit cell: (94.288, 124.832, 120.848, 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      15     16.00
     P     294     15.00
     O    2976      8.00
     N    2407      7.00
     C    7144      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    TRANS
      " SER C  11 " - " SER D 123 "
      " SER G  11 " - " SER H 123 "
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 439.6 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1600

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 10 sheets defined
      66.7% alpha, 4.4% beta
      135 base pairs and 243 stacking pairs defined.
    Time for finding SS restraints: 1.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.527A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.576A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.010A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.596A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   VAL D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.567A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 123
      removed outlier: 3.881A  pdb=" N   SER D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
      removed outlier: 3.793A  pdb=" N   LEU E  48 " --> pdb=" O   GLY E  44 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ARG E  49 " --> pdb=" O   THR E  45 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.523A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.601A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
    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: 4.014A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.504A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.629A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.615A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.712A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 22 through 35
    Processing helix  chain 'M' and resid 37 through 39
      No H-bonds generated for 'chain 'M' and resid 37 through 39'
    Processing helix  chain 'M' and resid 56 through 60
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.640A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.825A  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
      removed outlier: 3.603A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54
      removed outlier: 7.528A  pdb=" N   GLY D  53 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.709A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'F' and resid 97 through 98
    Processing sheet with id=AA9, first strand: chain 'H' and resid 88 through 89
    Processing sheet with id=AB1, first strand: chain 'M' and resid 12 through 16
      removed outlier: 8.825A  pdb=" N   LEU M  67 " --> pdb=" O   GLN M   2 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   PHE M   4 " --> pdb=" O   LEU M  67 " (cutoff:3.500A)
      removed outlier: 7.318A  pdb=" N   LEU M  69 " --> pdb=" O   PHE M   4 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   LYS M   6 " --> pdb=" O   LEU M  69 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   LEU M  71 " --> pdb=" O   LYS M   6 " (cutoff:3.500A)

    420 hydrogen bonds defined for protein.
    1228 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      348 hydrogen bonds
      692 hydrogen bond angles
      0 basepair planarities
      135 basepair parallelities
      243 stacking parallelities
  Total time for adding SS restraints: 1.89

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2529
        1.33 -     1.45: 4339
        1.45 -     1.57: 6179
        1.57 -     1.69: 586
        1.69 -     1.81: 26
  Bond restraints: 13659
  Sorted by residual:
  bond pdb=" CG1 ILE A 112 "
       pdb=" CD1 ILE A 112 "
    ideal  model  delta    sigma   weight residual
    1.513  1.464  0.049 3.90e-02 6.57e+02 1.59e+00
  bond pdb=" CG  LEU A 126 "
       pdb=" CD1 LEU A 126 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.035 3.30e-02 9.18e+02 1.13e+00
  bond pdb=" CB  CYS E  96 "
       pdb=" SG  CYS E  96 "
    ideal  model  delta    sigma   weight residual
    1.808  1.774  0.034 3.30e-02 9.18e+02 1.06e+00
  bond pdb=" CB  ASP C  72 "
       pdb=" CG  ASP C  72 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 2.50e-02 1.60e+03 1.01e+00
  bond pdb=" CB  ASP E  81 "
       pdb=" CG  ASP E  81 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 2.50e-02 1.60e+03 9.98e-01
  ... (remaining 13654 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 19072
        1.44 -     2.87: 566
        2.87 -     4.31: 41
        4.31 -     5.74: 14
        5.74 -     7.18: 5
  Bond angle restraints: 19698
  Sorted by residual:
  angle pdb=" C   ARG B  23 "
        pdb=" N   ASP B  24 "
        pdb=" CA  ASP B  24 "
      ideal   model   delta    sigma   weight residual
     121.54  128.48   -6.94 1.91e+00 2.74e-01 1.32e+01
  angle pdb=" C   ARG F  23 "
        pdb=" N   ASP F  24 "
        pdb=" CA  ASP F  24 "
      ideal   model   delta    sigma   weight residual
     121.54  127.71   -6.17 1.91e+00 2.74e-01 1.04e+01
  angle pdb=" CB  ARG B  67 "
        pdb=" CG  ARG B  67 "
        pdb=" CD  ARG B  67 "
      ideal   model   delta    sigma   weight residual
     111.30  118.48   -7.18 2.30e+00 1.89e-01 9.74e+00
  angle pdb=" CA  ARG B  67 "
        pdb=" CB  ARG B  67 "
        pdb=" CG  ARG B  67 "
      ideal   model   delta    sigma   weight residual
     114.10  119.28   -5.18 2.00e+00 2.50e-01 6.72e+00
  angle pdb=" N   GLN A 125 "
        pdb=" CA  GLN A 125 "
        pdb=" CB  GLN A 125 "
      ideal   model   delta    sigma   weight residual
     110.28  113.84   -3.56 1.55e+00 4.16e-01 5.28e+00
  ... (remaining 19693 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.37: 5861
       29.37 -    58.74: 1527
       58.74 -    88.12: 105
       88.12 -   117.49: 2
      117.49 -   146.86: 2
  Dihedral angle restraints: 7497
    sinusoidal: 5012
      harmonic: 2485
  Sorted by residual:
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   73.14  146.86     1      3.50e+01 8.16e-04 1.44e+01
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   75.89  144.11     1      3.50e+01 8.16e-04 1.42e+01
  dihedral pdb=" CB  GLU C  56 "
           pdb=" CG  GLU C  56 "
           pdb=" CD  GLU C  56 "
           pdb=" OE1 GLU C  56 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.75  -89.75     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 7494 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1558
       0.028 -    0.055: 471
       0.055 -    0.083: 135
       0.083 -    0.110: 62
       0.110 -    0.138: 14
  Chirality restraints: 2240
  Sorted by residual:
  chirality pdb=" CA  ASP B  24 "
            pdb=" N   ASP B  24 "
            pdb=" C   ASP B  24 "
            pdb=" CB  ASP B  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.76e-01
  chirality pdb=" CA  ASP F  24 "
            pdb=" N   ASP F  24 "
            pdb=" C   ASP F  24 "
            pdb=" CB  ASP F  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.14 2.00e-01 2.50e+01 4.58e-01
  chirality pdb=" CA  ILE C 111 "
            pdb=" N   ILE C 111 "
            pdb=" C   ILE C 111 "
            pdb=" CB  ILE C 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.98e-01
  ... (remaining 2237 not shown)

  Planarity restraints: 1480
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "    0.021 2.00e-02 2.50e+03   8.92e-03 2.19e+00
        pdb=" N9   DA I -35 "   -0.018 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "   -0.005 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "    0.003 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "    0.008 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  47 "    0.021 2.00e-02 2.50e+03   8.33e-03 2.08e+00
        pdb=" N9   DG I  47 "   -0.017 2.00e-02 2.50e+03
        pdb=" C8   DG I  47 "   -0.006 2.00e-02 2.50e+03
        pdb=" N7   DG I  47 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5   DG I  47 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  47 "    0.003 2.00e-02 2.50e+03
        pdb=" O6   DG I  47 "    0.007 2.00e-02 2.50e+03
        pdb=" N1   DG I  47 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DG I  47 "   -0.000 2.00e-02 2.50e+03
        pdb=" N2   DG I  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3   DG I  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DG I  47 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  26 "    0.018 2.00e-02 2.50e+03   7.34e-03 1.61e+00
        pdb=" N9   DG I  26 "   -0.015 2.00e-02 2.50e+03
        pdb=" C8   DG I  26 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7   DG I  26 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5   DG I  26 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  26 "    0.003 2.00e-02 2.50e+03
        pdb=" O6   DG I  26 "    0.005 2.00e-02 2.50e+03
        pdb=" N1   DG I  26 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I  26 "    0.002 2.00e-02 2.50e+03
        pdb=" N2   DG I  26 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3   DG I  26 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I  26 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1477 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 493
        2.70 -     3.25: 11464
        3.25 -     3.80: 23895
        3.80 -     4.35: 28492
        4.35 -     4.90: 41650
  Nonbonded interactions: 105994
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.151 2.496
  nonbonded pdb=" OG1 THR H  90 "
            pdb=" OE1 GLU H  93 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" NH2 ARG F  35 "
            pdb=" OP2  DC I   8 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" OH  TYR A  99 "
            pdb=" OE1 GLU A 133 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" NH2 ARG D  31 "
            pdb=" OP1  DG J  51 "
     model   vdw
     2.297 3.120
  ... (remaining 105989 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 21 through 102)
  selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ 
e C or name O ))))
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 11 through 118)
}
ncs_group {
  reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
  selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.25 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.520
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.990
  Find NCS groups from input model:        0.080
  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:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
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      :  0.003   0.049  13661  Z= 0.151
  Angle     :  0.557   7.178  19704  Z= 0.330
  Chirality :  0.033   0.138   2240
  Planarity :  0.003   0.038   1478
  Dihedral  : 26.649 146.860   5891
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.00 %
    Favored  : 99.86 %
  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 aren not related in a simple way.
  whole:  2.47 (0.30), residues: 839
  helix:  2.61 (0.22), residues: 544
  sheet:  1.56 (1.19), residues: 26
  loop : -0.45 (0.37), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG B  67 
 TYR   0.020   0.001   TYR H  40 
 PHE   0.009   0.001   PHE E  78 
 HIS   0.005   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (13659)
  covalent geometry    : angle       0.55738 (19698)
  hydrogen bonds       : bond        0.10334 (  768)
  hydrogen bonds       : angle       3.99937 ( 1920)
  link_TRANS           : bond        0.00080 (    2)
  link_TRANS           : angle       0.53035 (    6)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.8392 (m-30) cc_final: 0.7864 (t70)
REVERT: B   31 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8770 (ttpp)
REVERT: B   91 LYS cc_start: 0.9420 (ttmm) cc_final: 0.9160 (ttmt)
REVERT: D   51 ASP cc_start: 0.9279 (p0) cc_final: 0.8710 (p0)
REVERT: D  116 LYS cc_start: 0.9197 (mtmt) cc_final: 0.8989 (ttmt)
REVERT: D  120 LYS cc_start: 0.8988 (ttpt) cc_final: 0.8735 (tttt)
REVERT: E   57 SER cc_start: 0.9388 (p) cc_final: 0.8894 (p)
REVERT: E   59 GLU cc_start: 0.8782 (pm20) cc_final: 0.7941 (pm20)
REVERT: E   82 LEU cc_start: 0.9341 (mt) cc_final: 0.9119 (mm)
REVERT: E   94 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8359 (mm-30)
REVERT: E  110 CYS cc_start: 0.7931 (m) cc_final: 0.7656 (m)
REVERT: E  129 ARG cc_start: 0.8949 (tpt90) cc_final: 0.8743 (tpt-90)
REVERT: F   91 LYS cc_start: 0.9101 (tttp) cc_final: 0.8743 (ttmt)
REVERT: H   59 MET cc_start: 0.8960 (tpt) cc_final: 0.8643 (tpp)
REVERT: H   85 LYS cc_start: 0.9341 (mttm) cc_final: 0.8926 (mttp)
REVERT: C   64 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8415 (tm-30)
REVERT: G   41 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8418 (tm-30)
REVERT: G   64 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8684 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.1139
  time to fit residues: 34.9707
Evaluate side-chains
  179 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.319 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.088689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.057030 restraints weight = 52896.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.059382 restraints weight = 22288.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.060902 restraints weight = 13736.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.061854 restraints weight = 10490.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.062342 restraints weight = 9061.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2778
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2778 r_free = 0.2778    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2776 r_free = 0.2776    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2776
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8624
moved from start:          0.1143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13661  Z= 0.163
  Angle     :  0.569   6.575  19704  Z= 0.335
  Chirality :  0.034   0.166   2240
  Planarity :  0.004   0.036   1478
  Dihedral  : 29.558 147.684   4171
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 7.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 11.65 %
    Favored  : 86.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.56 (0.29), residues: 839
  helix:  2.68 (0.22), residues: 554
  sheet:  1.15 (1.15), residues: 26
  loop : -0.50 (0.36), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  33 
 TYR   0.014   0.001   TYR F  88 
 PHE   0.012   0.001   PHE A  78 
 HIS   0.004   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (13659)
  covalent geometry    : angle       0.56857 (19698)
  hydrogen bonds       : bond        0.04450 (  768)
  hydrogen bonds       : angle       3.15521 ( 1920)
  link_TRANS           : bond        0.00102 (    2)
  link_TRANS           : angle       0.49678 (    6)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 192
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8165 (tt0) cc_final: 0.7528 (tt0)
REVERT: A   81 ASP cc_start: 0.8189 (m-30) cc_final: 0.7951 (t70)
REVERT: A  129 ARG cc_start: 0.8835 (tpt90) cc_final: 0.8376 (tpt90)
REVERT: B   25 ASN cc_start: 0.8603 (m-40) cc_final: 0.7949 (m110)
REVERT: B   31 LYS cc_start: 0.9183 (ttmt) cc_final: 0.8977 (ttpp)
REVERT: B   91 LYS cc_start: 0.9465 (ttmm) cc_final: 0.9173 (ttmt)
REVERT: D   51 ASP cc_start: 0.9006 (p0) cc_final: 0.8409 (p0)
REVERT: D   85 LYS cc_start: 0.9345 (mttm) cc_final: 0.9079 (mmtt)
REVERT: D   92 ARG cc_start: 0.8755 (ttt-90) cc_final: 0.8523 (ttm170)
REVERT: D  120 LYS cc_start: 0.9017 (ttpt) cc_final: 0.8811 (tttt)
REVERT: E   57 SER cc_start: 0.9365 (p) cc_final: 0.8854 (p)
REVERT: E   59 GLU cc_start: 0.8814 (pm20) cc_final: 0.7998 (pm20)
REVERT: E   82 LEU cc_start: 0.9445 (mt) cc_final: 0.9213 (mm)
REVERT: E  105 GLU cc_start: 0.8530 (tp30) cc_final: 0.8183 (tp30)
REVERT: F   85 ASP cc_start: 0.8753 (m-30) cc_final: 0.8200 (m-30)
REVERT: F   88 TYR cc_start: 0.8299 (m-10) cc_final: 0.7992 (m-10)
REVERT: F   91 LYS cc_start: 0.9312 (tttp) cc_final: 0.8959 (ttmt)
REVERT: H   83 TYR cc_start: 0.8690 (m-10) cc_final: 0.8442 (m-80)
REVERT: H   85 LYS cc_start: 0.9296 (mttm) cc_final: 0.8845 (mtmm)
REVERT: M   44 ILE cc_start: 0.5070 (mm) cc_final: 0.4320 (mp)
REVERT: C   64 GLU cc_start: 0.9101 (tm-30) cc_final: 0.8450 (tm-30)
REVERT: G   41 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8066 (tm-30)
REVERT: G   64 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8749 (tm-30)
  outliers start: 10
  outliers final: 9
  residues processed: 197
  average time/residue: 0.1129
  time to fit residues: 30.2684
Evaluate side-chains
  183 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 174
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 78 optimal weight:    4.9990
   chunk 105 optimal weight:    0.5980
   chunk 53 optimal weight:    5.9990
   chunk 67 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9990
   chunk 104 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0970
   chunk 100 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 83 optimal weight:   20.0000
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.088406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.056266 restraints weight = 61392.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.058682 restraints weight = 24307.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.060247 restraints weight = 14588.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.061256 restraints weight = 10994.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.061767 restraints weight = 9403.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.2767
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2768
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2768 r_free = 0.2768    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2767 r_free = 0.2767    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2767
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8630
moved from start:          0.1459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  13661  Z= 0.162
  Angle     :  0.564   7.961  19704  Z= 0.330
  Chirality :  0.034   0.156   2240
  Planarity :  0.004   0.038   1478
  Dihedral  : 29.530 147.916   4171
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 13.73 %
    Favored  : 83.91 %
  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 aren not related in a simple way.
  whole:  2.64 (0.29), residues: 839
  helix:  2.78 (0.22), residues: 554
  sheet:  1.14 (1.13), residues: 26
  loop : -0.56 (0.36), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  33 
 TYR   0.019   0.001   TYR B  88 
 PHE   0.016   0.001   PHE A  78 
 HIS   0.004   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (13659)
  covalent geometry    : angle       0.56380 (19698)
  hydrogen bonds       : bond        0.04252 (  768)
  hydrogen bonds       : angle       3.01947 ( 1920)
  link_TRANS           : bond        0.00026 (    2)
  link_TRANS           : angle       0.48582 (    6)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 192
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.8200 (m-30) cc_final: 0.7981 (t70)
REVERT: A  125 GLN cc_start: 0.8133 (mt0) cc_final: 0.7251 (mt0)
REVERT: B   25 ASN cc_start: 0.8620 (m-40) cc_final: 0.7951 (m110)
REVERT: B   31 LYS cc_start: 0.9180 (ttmt) cc_final: 0.8978 (ttpp)
REVERT: B   91 LYS cc_start: 0.9456 (ttmm) cc_final: 0.9168 (ttmt)
REVERT: D   46 LYS cc_start: 0.9468 (tppt) cc_final: 0.9109 (tppt)
REVERT: D   51 ASP cc_start: 0.8983 (p0) cc_final: 0.8333 (p0)
REVERT: D   59 MET cc_start: 0.9268 (tpp) cc_final: 0.9046 (tpp)
REVERT: D   85 LYS cc_start: 0.9383 (mttm) cc_final: 0.9152 (mmtt)
REVERT: D  120 LYS cc_start: 0.9034 (ttpt) cc_final: 0.8782 (tttt)
REVERT: E   57 SER cc_start: 0.9374 (p) cc_final: 0.8871 (p)
REVERT: E   59 GLU cc_start: 0.8802 (pm20) cc_final: 0.8106 (pm20)
REVERT: E  105 GLU cc_start: 0.8586 (tp30) cc_final: 0.8350 (tp30)
REVERT: F   85 ASP cc_start: 0.8777 (m-30) cc_final: 0.8336 (m-30)
REVERT: F   88 TYR cc_start: 0.8493 (m-10) cc_final: 0.8163 (m-10)
REVERT: F   91 LYS cc_start: 0.9341 (tttp) cc_final: 0.8999 (ttmt)
REVERT: H   83 TYR cc_start: 0.8786 (m-10) cc_final: 0.8536 (m-80)
REVERT: H   85 LYS cc_start: 0.9316 (mttm) cc_final: 0.8866 (mtmm)
REVERT: C   64 GLU cc_start: 0.9108 (tm-30) cc_final: 0.8595 (tm-30)
REVERT: G   41 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7936 (tm-30)
REVERT: G   64 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8781 (tm-30)
  outliers start: 16
  outliers final: 13
  residues processed: 197
  average time/residue: 0.1059
  time to fit residues: 29.0069
Evaluate side-chains
  190 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 177
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain M residue   25 ASN
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 21 optimal weight:    0.6980
   chunk 74 optimal weight:    3.9990
   chunk 80 optimal weight:    7.9990
   chunk 76 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    4.9990
   chunk 107 optimal weight:    3.9990
   chunk 73 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
F  25 ASN
M  49 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.083728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2566 r_free = 0.2566 target = 0.052107 restraints weight = 52344.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.054270 restraints weight = 22937.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2648 r_free = 0.2648 target = 0.055642 restraints weight = 14475.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.056524 restraints weight = 11251.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.056979 restraints weight = 9777.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.2659
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2659
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2659 r_free = 0.2659    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2659 r_free = 0.2659    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2659
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8732
moved from start:          0.1984

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.044  13661  Z= 0.318
  Angle     :  0.676  12.453  19704  Z= 0.387
  Chirality :  0.040   0.157   2240
  Planarity :  0.005   0.038   1478
  Dihedral  : 29.933 150.145   4171
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 15.67 %
    Favored  : 80.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.19 (0.29), residues: 839
  helix:  2.43 (0.22), residues: 553
  sheet:  1.18 (1.13), residues: 26
  loop : -0.72 (0.36), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B  67 
 TYR   0.019   0.002   TYR A  99 
 PHE   0.019   0.002   PHE A  78 
 HIS   0.006   0.002   HIS H 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00738 (13659)
  covalent geometry    : angle       0.67572 (19698)
  hydrogen bonds       : bond        0.05820 (  768)
  hydrogen bonds       : angle       3.54665 ( 1920)
  link_TRANS           : bond        0.00225 (    2)
  link_TRANS           : angle       0.34742 (    6)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 179
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 ASP cc_start: 0.9319 (m-30) cc_final: 0.8862 (m-30)
REVERT: A  125 GLN cc_start: 0.8272 (mt0) cc_final: 0.7493 (mp10)
REVERT: B   25 ASN cc_start: 0.8716 (m-40) cc_final: 0.8049 (m110)
REVERT: B   31 LYS cc_start: 0.9237 (ttmt) cc_final: 0.9017 (ttpp)
REVERT: B   88 TYR cc_start: 0.8576 (m-10) cc_final: 0.8364 (m-10)
REVERT: B   91 LYS cc_start: 0.9483 (ttmm) cc_final: 0.9182 (ttmt)
REVERT: D   46 LYS cc_start: 0.9482 (tppt) cc_final: 0.9141 (tppt)
REVERT: D   51 ASP cc_start: 0.9103 (p0) cc_final: 0.8672 (p0)
REVERT: D   85 LYS cc_start: 0.9387 (mttm) cc_final: 0.9179 (mmtt)
REVERT: D  120 LYS cc_start: 0.9184 (ttpt) cc_final: 0.8952 (ttmm)
REVERT: E   57 SER cc_start: 0.9405 (p) cc_final: 0.9020 (p)
REVERT: E   59 GLU cc_start: 0.8794 (pm20) cc_final: 0.8089 (pm20)
REVERT: F   88 TYR cc_start: 0.8837 (m-10) cc_final: 0.8301 (m-10)
REVERT: F   91 LYS cc_start: 0.9453 (tttp) cc_final: 0.9199 (ttmt)
REVERT: H   85 LYS cc_start: 0.9345 (mttm) cc_final: 0.8854 (mtmm)
REVERT: C   64 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8465 (tm-30)
REVERT: G   41 GLU cc_start: 0.8518 (tm-30) cc_final: 0.8078 (tm-30)
  outliers start: 29
  outliers final: 27
  residues processed: 192
  average time/residue: 0.1097
  time to fit residues: 29.1930
Evaluate side-chains
  192 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 165
  time to evaluate  : 0.216 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   69 ILE
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   47 SER
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain M residue   25 ASN
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 87 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 82 optimal weight:   10.0000
   chunk 55 optimal weight:    4.9990
   chunk 23 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 84 optimal weight:    0.9990
   chunk 98 optimal weight:    5.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
M  40 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.084275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2587 r_free = 0.2587 target = 0.053009 restraints weight = 43350.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2634 r_free = 0.2634 target = 0.055041 restraints weight = 20686.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.056331 restraints weight = 13676.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.057148 restraints weight = 10891.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.057536 restraints weight = 9589.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2672
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2672 r_free = 0.2672    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2672 r_free = 0.2672    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2672
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8720
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038  13661  Z= 0.259
  Angle     :  0.634   8.570  19704  Z= 0.366
  Chirality :  0.037   0.155   2240
  Planarity :  0.004   0.036   1478
  Dihedral  : 29.878 149.570   4171
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 17.89 %
    Favored  : 77.39 %
  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 aren not related in a simple way.
  whole:  2.21 (0.29), residues: 839
  helix:  2.46 (0.22), residues: 554
  sheet:  1.06 (1.12), residues: 26
  loop : -0.76 (0.36), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  33 
 TYR   0.013   0.002   TYR A  99 
 PHE   0.015   0.002   PHE A  78 
 HIS   0.005   0.001   HIS H 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00598 (13659)
  covalent geometry    : angle       0.63399 (19698)
  hydrogen bonds       : bond        0.05230 (  768)
  hydrogen bonds       : angle       3.34417 ( 1920)
  link_TRANS           : bond        0.00157 (    2)
  link_TRANS           : angle       0.26715 (    6)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 172
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 ASP cc_start: 0.9354 (m-30) cc_final: 0.8865 (m-30)
REVERT: A  125 GLN cc_start: 0.8270 (mt0) cc_final: 0.7500 (mt0)
REVERT: B   25 ASN cc_start: 0.8666 (m-40) cc_final: 0.8037 (m110)
REVERT: B   31 LYS cc_start: 0.9225 (ttmt) cc_final: 0.9007 (ttpp)
REVERT: B   88 TYR cc_start: 0.8573 (m-10) cc_final: 0.8339 (m-10)
REVERT: B   91 LYS cc_start: 0.9478 (ttmm) cc_final: 0.9178 (ttmt)
REVERT: D   46 LYS cc_start: 0.9449 (tppt) cc_final: 0.9234 (tppt)
REVERT: D   51 ASP cc_start: 0.9079 (p0) cc_final: 0.8652 (p0)
REVERT: D  120 LYS cc_start: 0.9168 (ttpt) cc_final: 0.8927 (ttmm)
REVERT: E   57 SER cc_start: 0.9363 (p) cc_final: 0.8931 (p)
REVERT: E   59 GLU cc_start: 0.8738 (pm20) cc_final: 0.8033 (pm20)
REVERT: F   88 TYR cc_start: 0.8800 (m-10) cc_final: 0.8237 (m-10)
REVERT: F   91 LYS cc_start: 0.9428 (tttp) cc_final: 0.9181 (ttmt)
REVERT: H   85 LYS cc_start: 0.9337 (mttm) cc_final: 0.8856 (mtmm)
REVERT: C   64 GLU cc_start: 0.9161 (tm-30) cc_final: 0.8491 (tm-30)
REVERT: G   41 GLU cc_start: 0.8512 (tm-30) cc_final: 0.8069 (tm-30)
  outliers start: 33
  outliers final: 28
  residues processed: 186
  average time/residue: 0.0987
  time to fit residues: 26.0582
Evaluate side-chains
  197 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 169
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   47 SER
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain M residue   25 ASN
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 107 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 45 optimal weight:    4.9990
   chunk 86 optimal weight:    8.9990
   chunk 78 optimal weight:    4.9990
   chunk 63 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 93 optimal weight:    0.6980
   chunk 10 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
K 475 HIS
** M  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  62 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.085419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.053948 restraints weight = 45830.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.056064 restraints weight = 21049.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.057421 restraints weight = 13681.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.058253 restraints weight = 10754.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.058767 restraints weight = 9456.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.2701
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2701
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2701 r_free = 0.2701    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2701 r_free = 0.2701    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2701
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8692
moved from start:          0.2069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  13661  Z= 0.200
  Angle     :  0.601   8.752  19704  Z= 0.350
  Chirality :  0.035   0.152   2240
  Planarity :  0.004   0.036   1478
  Dihedral  : 29.789 149.432   4171
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 18.59 %
    Favored  : 77.39 %
  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 aren not related in a simple way.
  whole:  2.34 (0.29), residues: 839
  helix:  2.58 (0.22), residues: 555
  sheet:  1.22 (1.12), residues: 26
  loop : -0.79 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG H  33 
 TYR   0.011   0.001   TYR C  50 
 PHE   0.013   0.001   PHE A  78 
 HIS   0.006   0.001   HIS H 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 (13659)
  covalent geometry    : angle       0.60154 (19698)
  hydrogen bonds       : bond        0.04793 (  768)
  hydrogen bonds       : angle       3.18879 ( 1920)
  link_TRANS           : bond        0.00082 (    2)
  link_TRANS           : angle       0.30468 (    6)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 175
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 ASP cc_start: 0.9326 (m-30) cc_final: 0.8826 (m-30)
REVERT: A  125 GLN cc_start: 0.8257 (mt0) cc_final: 0.7508 (mt0)
REVERT: B   25 ASN cc_start: 0.8643 (m-40) cc_final: 0.7946 (m110)
REVERT: B   31 LYS cc_start: 0.9203 (ttmt) cc_final: 0.8943 (ttpp)
REVERT: B   88 TYR cc_start: 0.8545 (m-10) cc_final: 0.8304 (m-10)
REVERT: B   91 LYS cc_start: 0.9461 (ttmm) cc_final: 0.9154 (ttmt)
REVERT: D   51 ASP cc_start: 0.9035 (p0) cc_final: 0.8553 (p0)
REVERT: D  120 LYS cc_start: 0.9132 (ttpt) cc_final: 0.8880 (tttt)
REVERT: E   57 SER cc_start: 0.9337 (p) cc_final: 0.8800 (p)
REVERT: E   59 GLU cc_start: 0.8710 (pm20) cc_final: 0.8072 (pm20)
REVERT: F   85 ASP cc_start: 0.8908 (m-30) cc_final: 0.8462 (m-30)
REVERT: F   88 TYR cc_start: 0.8719 (m-10) cc_final: 0.8342 (m-10)
REVERT: F   91 LYS cc_start: 0.9416 (tttp) cc_final: 0.9180 (ttmt)
REVERT: H   85 LYS cc_start: 0.9319 (mttm) cc_final: 0.8844 (mtmm)
REVERT: C   64 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8460 (tm-30)
REVERT: G   41 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8013 (tm-30)
  outliers start: 28
  outliers final: 24
  residues processed: 187
  average time/residue: 0.0960
  time to fit residues: 25.2207
Evaluate side-chains
  192 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 168
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   47 SER
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 75 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 49 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 76 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 82 optimal weight:   10.0000
   chunk 85 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
M  40 GLN
M  62 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.084759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2591 r_free = 0.2591 target = 0.053172 restraints weight = 48338.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.055314 restraints weight = 21760.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.056663 restraints weight = 13971.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.057509 restraints weight = 10962.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.058034 restraints weight = 9605.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2685
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2685 r_free = 0.2685    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2685 r_free = 0.2685    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2685
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035  13661  Z= 0.241
  Angle     :  0.626   7.832  19704  Z= 0.361
  Chirality :  0.037   0.161   2240
  Planarity :  0.004   0.036   1478
  Dihedral  : 29.842 150.007   4171
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 18.17 %
    Favored  : 77.12 %
  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 aren not related in a simple way.
  whole:  2.29 (0.29), residues: 839
  helix:  2.53 (0.22), residues: 555
  sheet:  1.23 (1.12), residues: 26
  loop : -0.79 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG H  33 
 TYR   0.014   0.002   TYR C  57 
 PHE   0.014   0.001   PHE A  78 
 HIS   0.005   0.001   HIS H 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00556 (13659)
  covalent geometry    : angle       0.62637 (19698)
  hydrogen bonds       : bond        0.05060 (  768)
  hydrogen bonds       : angle       3.28360 ( 1920)
  link_TRANS           : bond        0.00153 (    2)
  link_TRANS           : angle       0.28875 (    6)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 173
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 ASP cc_start: 0.9339 (m-30) cc_final: 0.8866 (m-30)
REVERT: A  125 GLN cc_start: 0.8278 (mt0) cc_final: 0.7554 (mt0)
REVERT: B   25 ASN cc_start: 0.8669 (m-40) cc_final: 0.8015 (m110)
REVERT: B   88 TYR cc_start: 0.8586 (m-10) cc_final: 0.8294 (m-10)
REVERT: B   91 LYS cc_start: 0.9465 (ttmm) cc_final: 0.9167 (ttmt)
REVERT: D   51 ASP cc_start: 0.9087 (p0) cc_final: 0.8682 (p0)
REVERT: D   59 MET cc_start: 0.9372 (tpp) cc_final: 0.8834 (tpt)
REVERT: E   57 SER cc_start: 0.9324 (p) cc_final: 0.8786 (p)
REVERT: E   59 GLU cc_start: 0.8738 (pm20) cc_final: 0.8019 (pm20)
REVERT: F   85 ASP cc_start: 0.8925 (m-30) cc_final: 0.8490 (m-30)
REVERT: F   88 TYR cc_start: 0.8763 (m-10) cc_final: 0.8388 (m-10)
REVERT: F   91 LYS cc_start: 0.9404 (tttp) cc_final: 0.9174 (ttmt)
REVERT: H   85 LYS cc_start: 0.9340 (mttm) cc_final: 0.8867 (mtmm)
REVERT: C   64 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8481 (tm-30)
REVERT: G   41 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8068 (tm-30)
  outliers start: 33
  outliers final: 29
  residues processed: 188
  average time/residue: 0.1031
  time to fit residues: 27.2755
Evaluate side-chains
  200 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 171
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 ILE
Chi-restraints excluded: chain A residue   57 SER
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   52 THR
Chi-restraints excluded: chain D residue   98 VAL
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   47 SER
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain M residue   25 ASN
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 57 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0570
   chunk 84 optimal weight:    7.9990
   chunk 18 optimal weight:    0.6980
   chunk 28 optimal weight:    0.8980
   chunk 79 optimal weight:    5.9990
   chunk 105 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 55 optimal weight:    4.9990
   overall best weight:    0.6900

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
M  40 GLN
M  62 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.086872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2633 r_free = 0.2633 target = 0.054964 restraints weight = 60526.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2685 r_free = 0.2685 target = 0.057322 restraints weight = 24105.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2720 r_free = 0.2720 target = 0.058864 restraints weight = 14563.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.059829 restraints weight = 10987.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.060317 restraints weight = 9478.902|
|-----------------------------------------------------------------------------|
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2736
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2736 r_free = 0.2736    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.27   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2736 r_free = 0.2736    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2736
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8664
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13661  Z= 0.161
  Angle     :  0.585   7.756  19704  Z= 0.340
  Chirality :  0.034   0.158   2240
  Planarity :  0.004   0.037   1478
  Dihedral  : 29.674 148.888   4171
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 19.83 %
    Favored  : 76.98 %
  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 aren not related in a simple way.
  whole:  2.56 (0.29), residues: 839
  helix:  2.74 (0.22), residues: 554
  sheet:  1.34 (1.13), residues: 26
  loop : -0.66 (0.37), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG H  33 
 TYR   0.010   0.001   TYR C  57 
 PHE   0.011   0.001   PHE A  78 
 HIS   0.003   0.001   HIS H 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (13659)
  covalent geometry    : angle       0.58473 (19698)
  hydrogen bonds       : bond        0.04287 (  768)
  hydrogen bonds       : angle       2.95035 ( 1920)
  link_TRANS           : bond        0.00009 (    2)
  link_TRANS           : angle       0.42766 (    6)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 181
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   78 PHE cc_start: 0.7383 (t80) cc_final: 0.6880 (t80)
REVERT: A  123 ASP cc_start: 0.9252 (m-30) cc_final: 0.8756 (m-30)
REVERT: A  125 GLN cc_start: 0.8224 (mt0) cc_final: 0.7380 (mt0)
REVERT: B   25 ASN cc_start: 0.8602 (m-40) cc_final: 0.7823 (m110)
REVERT: B   88 TYR cc_start: 0.8505 (m-10) cc_final: 0.7671 (m-10)
REVERT: B   91 LYS cc_start: 0.9406 (ttmm) cc_final: 0.9140 (ttmt)
REVERT: D   51 ASP cc_start: 0.9001 (p0) cc_final: 0.8553 (p0)
REVERT: D   83 TYR cc_start: 0.8377 (m-10) cc_final: 0.7511 (m-10)
REVERT: D  120 LYS cc_start: 0.9054 (ttmt) cc_final: 0.8838 (tttt)
REVERT: E   57 SER cc_start: 0.9294 (p) cc_final: 0.8792 (p)
REVERT: E   59 GLU cc_start: 0.8672 (pm20) cc_final: 0.8075 (pm20)
REVERT: F   85 ASP cc_start: 0.8890 (m-30) cc_final: 0.8343 (m-30)
REVERT: F   88 TYR cc_start: 0.8682 (m-10) cc_final: 0.8337 (m-10)
REVERT: F   91 LYS cc_start: 0.9403 (tttp) cc_final: 0.9182 (ttmt)
REVERT: H   85 LYS cc_start: 0.9306 (mttm) cc_final: 0.8912 (mttp)
REVERT: C   64 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8446 (tm-30)
REVERT: G   41 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7988 (tm-30)
  outliers start: 22
  outliers final: 17
  residues processed: 189
  average time/residue: 0.1046
  time to fit residues: 28.0102
Evaluate side-chains
  190 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 173
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 105 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 84 optimal weight:    3.9990
   chunk 9 optimal weight:    0.0970
   chunk 81 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9980
   chunk 14 optimal weight:    0.5980
   chunk 101 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
F  75 HIS
M  62 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.087108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2652 r_free = 0.2652 target = 0.055943 restraints weight = 39508.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.058058 restraints weight = 19209.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.059398 restraints weight = 12762.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.060220 restraints weight = 10196.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.060633 restraints weight = 9052.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2740
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2740 r_free = 0.2740    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2740 r_free = 0.2740    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2740
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13661  Z= 0.162
  Angle     :  0.592   8.396  19704  Z= 0.342
  Chirality :  0.034   0.161   2240
  Planarity :  0.004   0.045   1478
  Dihedral  : 29.668 149.139   4171
  Min Nonbonded Distance : 2.126

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 20.80 %
    Favored  : 76.42 %
  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 aren not related in a simple way.
  whole:  2.55 (0.29), residues: 839
  helix:  2.72 (0.22), residues: 557
  sheet:  1.28 (1.13), residues: 26
  loop : -0.66 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B  67 
 TYR   0.010   0.001   TYR C  57 
 PHE   0.009   0.001   PHE E  78 
 HIS   0.003   0.001   HIS H 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 (13659)
  covalent geometry    : angle       0.59167 (19698)
  hydrogen bonds       : bond        0.04269 (  768)
  hydrogen bonds       : angle       2.94270 ( 1920)
  link_TRANS           : bond        0.00023 (    2)
  link_TRANS           : angle       0.41650 (    6)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 177
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 ASP cc_start: 0.9248 (m-30) cc_final: 0.8759 (m-30)
REVERT: A  125 GLN cc_start: 0.8218 (mt0) cc_final: 0.7362 (mt0)
REVERT: B   25 ASN cc_start: 0.8595 (m-40) cc_final: 0.7805 (m110)
REVERT: B   88 TYR cc_start: 0.8516 (m-10) cc_final: 0.7722 (m-10)
REVERT: B   91 LYS cc_start: 0.9441 (ttmm) cc_final: 0.9169 (ttmt)
REVERT: D   51 ASP cc_start: 0.9002 (p0) cc_final: 0.8482 (p0)
REVERT: D   83 TYR cc_start: 0.8371 (m-10) cc_final: 0.7584 (m-10)
REVERT: E   57 SER cc_start: 0.9336 (p) cc_final: 0.8798 (p)
REVERT: E   59 GLU cc_start: 0.8695 (pm20) cc_final: 0.8088 (pm20)
REVERT: F   85 ASP cc_start: 0.8886 (m-30) cc_final: 0.8332 (m-30)
REVERT: F   88 TYR cc_start: 0.8647 (m-10) cc_final: 0.8315 (m-10)
REVERT: F   91 LYS cc_start: 0.9402 (tttp) cc_final: 0.9186 (ttmt)
REVERT: H   85 LYS cc_start: 0.9315 (mttm) cc_final: 0.8859 (mtmm)
REVERT: C   64 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8594 (tm-30)
REVERT: G   41 GLU cc_start: 0.8369 (tm-30) cc_final: 0.7985 (tm-30)
  outliers start: 19
  outliers final: 17
  residues processed: 184
  average time/residue: 0.0983
  time to fit residues: 25.9055
Evaluate side-chains
  192 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 175
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 76 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 97 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
M  62 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.085936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2625 r_free = 0.2625 target = 0.054686 restraints weight = 45246.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2673 r_free = 0.2673 target = 0.056814 restraints weight = 20799.392|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.058171 restraints weight = 13499.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.059018 restraints weight = 10650.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.059433 restraints weight = 9353.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2715
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2715 r_free = 0.2715    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.20   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2715 r_free = 0.2715    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2715
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  13661  Z= 0.205
  Angle     :  0.606   8.442  19704  Z= 0.350
  Chirality :  0.035   0.164   2240
  Planarity :  0.004   0.037   1478
  Dihedral  : 29.732 149.713   4171
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 20.80 %
    Favored  : 76.14 %
  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 aren not related in a simple way.
  whole:  2.53 (0.29), residues: 839
  helix:  2.69 (0.22), residues: 557
  sheet:  1.26 (1.13), residues: 26
  loop : -0.65 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  33 
 TYR   0.010   0.002   TYR H  83 
 PHE   0.009   0.001   PHE E  78 
 HIS   0.004   0.001   HIS H 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 (13659)
  covalent geometry    : angle       0.60563 (19698)
  hydrogen bonds       : bond        0.04600 (  768)
  hydrogen bonds       : angle       3.07545 ( 1920)
  link_TRANS           : bond        0.00112 (    2)
  link_TRANS           : angle       0.36088 (    6)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 170
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 ASP cc_start: 0.9269 (m-30) cc_final: 0.8803 (m-30)
REVERT: A  125 GLN cc_start: 0.8234 (mt0) cc_final: 0.7444 (mt0)
REVERT: B   25 ASN cc_start: 0.8637 (m-40) cc_final: 0.7864 (m110)
REVERT: B   88 TYR cc_start: 0.8577 (m-10) cc_final: 0.7731 (m-10)
REVERT: B   91 LYS cc_start: 0.9438 (ttmm) cc_final: 0.9155 (ttmt)
REVERT: D   51 ASP cc_start: 0.9037 (p0) cc_final: 0.8591 (p0)
REVERT: D   83 TYR cc_start: 0.8437 (m-10) cc_final: 0.7638 (m-10)
REVERT: E   57 SER cc_start: 0.9306 (p) cc_final: 0.8748 (p)
REVERT: E   59 GLU cc_start: 0.8727 (pm20) cc_final: 0.8118 (pm20)
REVERT: F   85 ASP cc_start: 0.8901 (m-30) cc_final: 0.8432 (m-30)
REVERT: F   88 TYR cc_start: 0.8702 (m-10) cc_final: 0.8390 (m-10)
REVERT: F   91 LYS cc_start: 0.9386 (tttp) cc_final: 0.9176 (ttmt)
REVERT: H   85 LYS cc_start: 0.9325 (mttm) cc_final: 0.8861 (mtmm)
REVERT: C   64 GLU cc_start: 0.9142 (tm-30) cc_final: 0.8463 (tm-30)
REVERT: G   41 GLU cc_start: 0.8382 (tm-30) cc_final: 0.8020 (tm-30)
  outliers start: 21
  outliers final: 20
  residues processed: 178
  average time/residue: 0.1261
  time to fit residues: 31.6634
Evaluate side-chains
  189 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 169
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 35 optimal weight:    0.2980
   chunk 75 optimal weight:    3.9990
   chunk 58 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 61 optimal weight:    4.9990
   chunk 37 optimal weight:    0.7980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.086308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.055184 restraints weight = 39714.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.057252 restraints weight = 19173.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.058574 restraints weight = 12707.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.059365 restraints weight = 10144.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.059740 restraints weight = 8982.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2723
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2723 r_free = 0.2723    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2723 r_free = 0.2723    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2723
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8669
moved from start:          0.2241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13661  Z= 0.184
  Angle     :  0.598   8.172  19704  Z= 0.345
  Chirality :  0.034   0.162   2240
  Planarity :  0.004   0.037   1478
  Dihedral  : 29.712 149.274   4171
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 20.25 %
    Favored  : 76.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.58 (0.29), residues: 839
  helix:  2.75 (0.22), residues: 555
  sheet:  1.25 (1.13), residues: 26
  loop : -0.65 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  33 
 TYR   0.010   0.001   TYR C  50 
 PHE   0.009   0.001   PHE E  78 
 HIS   0.004   0.001   HIS H 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (13659)
  covalent geometry    : angle       0.59761 (19698)
  hydrogen bonds       : bond        0.04460 (  768)
  hydrogen bonds       : angle       2.99678 ( 1920)
  link_TRANS           : bond        0.00073 (    2)
  link_TRANS           : angle       0.40917 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1887.17 seconds
wall clock time: 33 minutes 9.77 seconds (1989.77 seconds total)