Starting phenix.real_space_refine
on Wed Mar  4 09:28:50 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9e09_47353/03_2026/9e09_47353.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9e09_47353/03_2026/9e09_47353.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9e09_47353/03_2026/9e09_47353.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9e09_47353/03_2026/9e09_47353.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9e09_47353/03_2026/9e09_47353.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9e09_47353/03_2026/9e09_47353.map"
  }
  resolution = 3.72
  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=   0.015
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     312      5.49       5
     S      14      5.16       5
     C    6779      2.51       5
     N    2325      2.21       5
     O    2925      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12355
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "M"
      Number of atoms: 820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 820
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "N"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "O"
      Number of atoms: 755
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 755
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "P"
      Number of atoms: 708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 708
          Classifications: {'peptide': 91}
          Link IDs: {'PTRANS': 2, 'TRANS': 88}
    Chain: "Q"
      Number of atoms: 785
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 785
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "R"
      Number of atoms: 622
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 622
          Classifications: {'peptide': 78}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "S"
      Number of atoms: 752
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 752
          Classifications: {'peptide': 98}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "T"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 3218
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 3218
          Classifications: {'DNA': 156}
          Link IDs: {'rna3p': 155}
    Chain: "J"
      Number of atoms: 3178
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 3178
          Classifications: {'DNA': 156}
          Link IDs: {'rna3p': 155}
    Chain: "X"
      Number of atoms: 92
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 92
          Classifications: {'peptide': 12}
          Link IDs: {'TRANS': 11}
    Chain: "V"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 84
          Classifications: {'peptide': 11}
          Link IDs: {'TRANS': 10}
  Time building chain proxies: 2.72, per 1000 atoms: 0.22
  Number of scatterers: 12355
  At special positions: 0
  Unit cell: (117.576, 116.748, 125.856, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     312     15.00
     O    2925      8.00
     N    2325      7.00
     C    6779      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 328.6 milliseconds
  

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1408

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 7 sheets defined
      73.0% alpha, 2.1% beta
      155 base pairs and 285 stacking pairs defined.
    Time for finding SS restraints: 2.14
  Creating SS restraints...
    Processing helix  chain 'M' and resid 44 through 57
      removed outlier: 3.645A  pdb=" N   GLN M  55 " --> pdb=" O   ILE M  51 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   LYS M  56 " --> pdb=" O   ARG M  52 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 63 through 77
      removed outlier: 3.701A  pdb=" N   ASP M  77 " --> pdb=" O   GLU M  73 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 85 through 114
      removed outlier: 3.514A  pdb=" N   VAL M  89 " --> pdb=" O   GLN M  85 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 120 through 131
    Processing helix  chain 'N' and resid 30 through 42
    Processing helix  chain 'N' and resid 49 through 76
      removed outlier: 3.905A  pdb=" N   GLU N  53 " --> pdb=" O   LEU N  49 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ARG N  67 " --> pdb=" O   GLU N  63 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   ASP N  68 " --> pdb=" O   ASN N  64 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   THR N  71 " --> pdb=" O   ARG N  67 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 82 through 92
      removed outlier: 3.617A  pdb=" N   VAL N  86 " --> pdb=" O   THR N  82 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 16 through 21
    Processing helix  chain 'O' and resid 26 through 38
      removed outlier: 3.687A  pdb=" N   ASN O  38 " --> pdb=" O   LEU O  34 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 46 through 73
      removed outlier: 3.594A  pdb=" N   ALA O  53 " --> pdb=" O   VAL O  49 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 79 through 89
      removed outlier: 3.556A  pdb=" N   LEU O  83 " --> pdb=" O   ILE O  79 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 90 through 97
    Processing helix  chain 'P' and resid 34 through 46
    Processing helix  chain 'P' and resid 52 through 81
    Processing helix  chain 'P' and resid 87 through 99
    Processing helix  chain 'P' and resid 100 through 120
      removed outlier: 3.598A  pdb=" N   LYS P 113 " --> pdb=" O   SER P 109 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 44 through 55
    Processing helix  chain 'Q' and resid 63 through 79
      removed outlier: 4.034A  pdb=" N   ASP Q  77 " --> pdb=" O   GLU Q  73 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   PHE Q  78 " --> pdb=" O   ILE Q  74 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 85 through 114
    Processing helix  chain 'Q' and resid 120 through 131
    Processing helix  chain 'R' and resid 25 through 29
      removed outlier: 3.699A  pdb=" N   ILE R  29 " --> pdb=" O   ILE R  26 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 30 through 42
    Processing helix  chain 'R' and resid 49 through 76
      removed outlier: 3.969A  pdb=" N   GLU R  53 " --> pdb=" O   LEU R  49 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ARG R  67 " --> pdb=" O   GLU R  63 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   ASP R  68 " --> pdb=" O   ASN R  64 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   THR R  71 " --> pdb=" O   ARG R  67 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 82 through 92
      removed outlier: 3.553A  pdb=" N   VAL R  86 " --> pdb=" O   THR R  82 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 16 through 22
    Processing helix  chain 'S' and resid 26 through 37
      removed outlier: 3.771A  pdb=" N   VAL S  30 " --> pdb=" O   PRO S  26 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   ARG S  35 " --> pdb=" O   HIS S  31 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 45 through 73
      removed outlier: 4.554A  pdb=" N   VAL S  49 " --> pdb=" O   ALA S  45 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 79 through 90
      removed outlier: 3.661A  pdb=" N   LEU S  83 " --> pdb=" O   ILE S  79 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ASP S  90 " --> pdb=" O   ALA S  86 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 90 through 97
      removed outlier: 3.524A  pdb=" N   LYS S  95 " --> pdb=" O   GLU S  91 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 34 through 46
      removed outlier: 3.598A  pdb=" N   LYS T  40 " --> pdb=" O   ILE T  36 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 52 through 81
    Processing helix  chain 'T' and resid 87 through 99
      removed outlier: 3.610A  pdb=" N   ALA T  94 " --> pdb=" O   GLU T  90 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 101 through 119
      removed outlier: 3.600A  pdb=" N   LYS T 105 " --> pdb=" O   GLY T 101 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   SER T 109 " --> pdb=" O   LYS T 105 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 741 through 746
    Processing helix  chain 'V' and resid 741 through 746
    Processing sheet with id=AA1, first strand: chain 'M' and resid 83 through 84
      removed outlier: 7.172A  pdb=" N   ARG M  83 " --> pdb=" O   VAL N  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'M' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'N' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'O' and resid 42 through 43
      removed outlier: 7.386A  pdb=" N   ARG O  42 " --> pdb=" O   ILE P  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'O' and resid 100 through 102
      removed outlier: 7.310A  pdb=" N   THR O 101 " --> pdb=" O   TYR R  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'Q' and resid 83 through 84
      removed outlier: 7.056A  pdb=" N   ARG Q  83 " --> pdb=" O   VAL R  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'S' and resid 42 through 43
      removed outlier: 7.578A  pdb=" N   ARG S  42 " --> pdb=" O   ILE T  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7

    381 hydrogen bonds defined for protein.
    1140 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      401 hydrogen bonds
      802 hydrogen bond angles
      0 basepair planarities
      155 basepair parallelities
      285 stacking parallelities
  Total time for adding SS restraints: 2.40

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1789
        1.33 -     1.45: 4807
        1.45 -     1.57: 5963
        1.57 -     1.69: 622
        1.69 -     1.81: 26
  Bond restraints: 13207
  Sorted by residual:
  bond pdb=" N   ILE R  46 "
       pdb=" CA  ILE R  46 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.17e-02 7.31e+03 9.81e+00
  bond pdb=" N   ARG Q  63 "
       pdb=" CA  ARG Q  63 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.22e-02 6.72e+03 7.94e+00
  bond pdb=" N   ILE N  34 "
       pdb=" CA  ILE N  34 "
    ideal  model  delta    sigma   weight residual
    1.461  1.492 -0.032 1.19e-02 7.06e+03 7.04e+00
  bond pdb=" N   LYS N  31 "
       pdb=" CA  LYS N  31 "
    ideal  model  delta    sigma   weight residual
    1.462  1.484 -0.022 8.50e-03 1.38e+04 6.96e+00
  bond pdb=" N   PHE O  25 "
       pdb=" CA  PHE O  25 "
    ideal  model  delta    sigma   weight residual
    1.454  1.488 -0.034 1.29e-02 6.01e+03 6.85e+00
  ... (remaining 13202 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.30: 15986
        1.30 -     2.59: 2789
        2.59 -     3.89: 346
        3.89 -     5.19: 42
        5.19 -     6.48: 7
  Bond angle restraints: 19170
  Sorted by residual:
  angle pdb=" C4'  DA I  80 "
        pdb=" C3'  DA I  80 "
        pdb=" O3'  DA I  80 "
      ideal   model   delta    sigma   weight residual
     110.00  104.25    5.75 1.50e+00 4.44e-01 1.47e+01
  angle pdb=" C4'  DA I 121 "
        pdb=" C3'  DA I 121 "
        pdb=" O3'  DA I 121 "
      ideal   model   delta    sigma   weight residual
     110.00  104.28    5.72 1.50e+00 4.44e-01 1.46e+01
  angle pdb=" CA  ILE O  62 "
        pdb=" C   ILE O  62 "
        pdb=" O   ILE O  62 "
      ideal   model   delta    sigma   weight residual
     121.17  117.24    3.93 1.06e+00 8.90e-01 1.38e+01
  angle pdb=" CA  ARG N  36 "
        pdb=" C   ARG N  36 "
        pdb=" O   ARG N  36 "
      ideal   model   delta    sigma   weight residual
     121.07  117.19    3.88 1.10e+00 8.26e-01 1.25e+01
  angle pdb=" CA  LEU O  58 "
        pdb=" C   LEU O  58 "
        pdb=" O   LEU O  58 "
      ideal   model   delta    sigma   weight residual
     121.00  117.36    3.64 1.05e+00 9.07e-01 1.20e+01
  ... (remaining 19165 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.70: 5623
       34.70 -    69.41: 1476
       69.41 -   104.11: 18
      104.11 -   138.82: 0
      138.82 -   173.52: 3
  Dihedral angle restraints: 7120
    sinusoidal: 4940
      harmonic: 2180
  Sorted by residual:
  dihedral pdb=" C4'  DG I 152 "
           pdb=" C3'  DG I 152 "
           pdb=" O3'  DG I 152 "
           pdb=" P    DC I 153 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   33.52 -173.52     1      3.50e+01 8.16e-04 1.56e+01
  dihedral pdb=" C4'  DC I 126 "
           pdb=" C3'  DC I 126 "
           pdb=" O3'  DC I 126 "
           pdb=" P    DC I 127 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   54.72  165.28     1      3.50e+01 8.16e-04 1.54e+01
  dihedral pdb=" C4'  DC J   9 "
           pdb=" C3'  DC J   9 "
           pdb=" O3'  DC J   9 "
           pdb=" P    DC J  10 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   81.07  138.93     1      3.50e+01 8.16e-04 1.37e+01
  ... (remaining 7117 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1539
       0.047 -    0.095: 493
       0.095 -    0.142: 115
       0.142 -    0.189: 30
       0.189 -    0.236: 4
  Chirality restraints: 2181
  Sorted by residual:
  chirality pdb=" C3'  DC I 126 "
            pdb=" C4'  DC I 126 "
            pdb=" O3'  DC I 126 "
            pdb=" C2'  DC I 126 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.42   -0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" C4'  DG I  92 "
            pdb=" C5'  DG I  92 "
            pdb=" O4'  DG I  92 "
            pdb=" C3'  DG I  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.30   -0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  ILE R  46 "
            pdb=" N   ILE R  46 "
            pdb=" C   ILE R  46 "
            pdb=" CB  ILE R  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 2178 not shown)

  Planarity restraints: 1344
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I  88 "   -0.040 2.00e-02 2.50e+03   1.78e-02 7.88e+00
        pdb=" N1   DT I  88 "    0.032 2.00e-02 2.50e+03
        pdb=" C2   DT I  88 "    0.007 2.00e-02 2.50e+03
        pdb=" O2   DT I  88 "    0.008 2.00e-02 2.50e+03
        pdb=" N3   DT I  88 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DT I  88 "   -0.007 2.00e-02 2.50e+03
        pdb=" O4   DT I  88 "   -0.015 2.00e-02 2.50e+03
        pdb=" C5   DT I  88 "    0.002 2.00e-02 2.50e+03
        pdb=" C7   DT I  88 "    0.003 2.00e-02 2.50e+03
        pdb=" C6   DT I  88 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  91 "   -0.037 2.00e-02 2.50e+03   1.58e-02 6.90e+00
        pdb=" N9   DA I  91 "    0.031 2.00e-02 2.50e+03
        pdb=" C8   DA I  91 "    0.004 2.00e-02 2.50e+03
        pdb=" N7   DA I  91 "    0.005 2.00e-02 2.50e+03
        pdb=" C5   DA I  91 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DA I  91 "   -0.007 2.00e-02 2.50e+03
        pdb=" N6   DA I  91 "   -0.014 2.00e-02 2.50e+03
        pdb=" N1   DA I  91 "    0.000 2.00e-02 2.50e+03
        pdb=" C2   DA I  91 "    0.003 2.00e-02 2.50e+03
        pdb=" N3   DA I  91 "    0.007 2.00e-02 2.50e+03
        pdb=" C4   DA I  91 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I 121 "   -0.036 2.00e-02 2.50e+03   1.48e-02 6.00e+00
        pdb=" N9   DA I 121 "    0.026 2.00e-02 2.50e+03
        pdb=" C8   DA I 121 "    0.008 2.00e-02 2.50e+03
        pdb=" N7   DA I 121 "    0.005 2.00e-02 2.50e+03
        pdb=" C5   DA I 121 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DA I 121 "   -0.008 2.00e-02 2.50e+03
        pdb=" N6   DA I 121 "   -0.010 2.00e-02 2.50e+03
        pdb=" N1   DA I 121 "   -0.005 2.00e-02 2.50e+03
        pdb=" C2   DA I 121 "    0.006 2.00e-02 2.50e+03
        pdb=" N3   DA I 121 "    0.010 2.00e-02 2.50e+03
        pdb=" C4   DA I 121 "    0.005 2.00e-02 2.50e+03
  ... (remaining 1341 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 2751
        2.82 -     3.34: 10407
        3.34 -     3.86: 24871
        3.86 -     4.38: 28332
        4.38 -     4.90: 38665
  Nonbonded interactions: 105026
  Sorted by model distance:
  nonbonded pdb=" OH  TYR P  37 "
            pdb=" OP1  DG J 132 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" OH  TYR M  99 "
            pdb=" OE1 GLU M 133 "
     model   vdw
     2.358 3.040
  nonbonded pdb=" OE2 GLU O  61 "
            pdb=" NH2 ARG V 743 "
     model   vdw
     2.376 3.120
  nonbonded pdb=" OH  TYR T  37 "
            pdb=" OP1  DG I 122 "
     model   vdw
     2.392 3.040
  nonbonded pdb=" NH1 ARG O  81 "
            pdb=" O   GLY O 105 "
     model   vdw
     2.392 3.120
  ... (remaining 105021 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 'M' and resid 40 through 134)
  selection = chain 'Q'
}
ncs_group {
  reference = chain 'N'
  selection = chain 'R'
}
ncs_group {
  reference = (chain 'O' and (resid 14 through 72 or (resid 73 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 74 through 111))
  selection = chain 'S'
}
ncs_group {
  reference = chain 'P'
  selection = (chain 'T' and resid 31 through 121)
}
ncs_group {
  reference = chain 'V'
  selection = (chain 'X' and resid 736 through 746)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             8.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     13.460
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6256
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049  13207  Z= 0.434
  Angle     :  0.971   6.483  19170  Z= 0.671
  Chirality :  0.051   0.236   2181
  Planarity :  0.006   0.038   1344
  Dihedral  : 27.345 173.522   5712
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 3.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.64 %
    Favored  : 99.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.42 (0.25), residues: 732
  helix: -1.28 (0.18), residues: 519
  sheet:  None (None), residues: 0
  loop : -2.04 (0.35), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG S  88 
 TYR   0.023   0.003   TYR O  57 
 PHE   0.031   0.004   PHE S  25 
 HIS   0.005   0.002   HIS S  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00688 (13207)
  covalent geometry    : angle       0.97080 (19170)
  hydrogen bonds       : bond        0.13231 (  782)
  hydrogen bonds       : angle       4.87560 ( 1942)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.297 
Fit side-chains
REVERT: M   59 GLU cc_start: 0.7475 (pt0) cc_final: 0.7191 (pt0)
REVERT: M  115 LYS cc_start: 0.8085 (mttm) cc_final: 0.7812 (mttm)
REVERT: O   33 LEU cc_start: 0.6918 (mt) cc_final: 0.6466 (mp)
REVERT: R   59 LYS cc_start: 0.7299 (tttt) cc_final: 0.7023 (tttp)
REVERT: R   80 THR cc_start: 0.7871 (m) cc_final: 0.7594 (t)
REVERT: S   59 THR cc_start: 0.7232 (m) cc_final: 0.6885 (m)
REVERT: T   44 GLN cc_start: 0.7709 (tt0) cc_final: 0.7434 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 108
  average time/residue: 0.1773
  time to fit residues: 24.5378
Evaluate side-chains
  99 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.4980
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.3980
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.4980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
M  39 HIS
M  68 GLN
** N  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  31 HIS
** O  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  46 HIS
P 106 HIS
Q  68 GLN
S  31 HIS
T  46 HIS
T  81 ASN
T 106 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.153001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.121249 restraints weight = 18209.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.123835 restraints weight = 8997.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.125610 restraints weight = 5810.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.126661 restraints weight = 4463.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.127138 restraints weight = 3827.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6924
moved from start:          0.3667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  13207  Z= 0.241
  Angle     :  0.654   7.271  19170  Z= 0.386
  Chirality :  0.039   0.161   2181
  Planarity :  0.005   0.052   1344
  Dihedral  : 31.009 176.013   4231
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  4.35 %
    Favored  : 94.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.28), residues: 732
  helix:  0.73 (0.21), residues: 543
  sheet:  None (None), residues: 0
  loop : -1.86 (0.37), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG V 743 
 TYR   0.023   0.002   TYR T  80 
 PHE   0.017   0.002   PHE O  25 
 HIS   0.007   0.002   HIS S  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00536 (13207)
  covalent geometry    : angle       0.65421 (19170)
  hydrogen bonds       : bond        0.05262 (  782)
  hydrogen bonds       : angle       2.96757 ( 1942)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 68
  time to evaluate  : 0.297 
Fit side-chains
REVERT: M  120 MET cc_start: 0.6993 (mmm) cc_final: 0.6553 (mtt)
REVERT: O   39 TYR cc_start: 0.8086 (m-80) cc_final: 0.7813 (m-80)
REVERT: P   56 MET cc_start: 0.7536 (mmm) cc_final: 0.7278 (tpp)
REVERT: Q   90 MET cc_start: 0.6642 (tpp) cc_final: 0.6312 (mpp)
REVERT: S   20 ARG cc_start: 0.7690 (ttm110) cc_final: 0.7052 (ttm110)
REVERT: S   77 ARG cc_start: 0.8316 (ttm-80) cc_final: 0.8057 (ttm-80)
REVERT: S  108 LEU cc_start: 0.8575 (mt) cc_final: 0.8358 (mt)
  outliers start: 5
  outliers final: 1
  residues processed: 70
  average time/residue: 0.2179
  time to fit residues: 18.6445
Evaluate side-chains
  65 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   88 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 60 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 31 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0970
   chunk 14 optimal weight:    0.5980
   chunk 36 optimal weight:    0.2980
   chunk 41 optimal weight:    0.9990
   chunk 67 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 40 optimal weight:    0.1980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
O  38 ASN
S  84 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.147602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.116270 restraints weight = 18328.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.118703 restraints weight = 9487.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.120284 restraints weight = 6279.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.121176 restraints weight = 4949.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.121903 restraints weight = 4321.399|
|-----------------------------------------------------------------------------|
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
moved from start:          0.4799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13207  Z= 0.196
  Angle     :  0.577   8.302  19170  Z= 0.348
  Chirality :  0.035   0.145   2181
  Planarity :  0.004   0.037   1344
  Dihedral  : 31.046 177.408   4231
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  4.83 %
    Favored  : 94.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.64 (0.30), residues: 732
  helix:  1.91 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.47 (0.39), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG R  35 
 TYR   0.013   0.002   TYR P  80 
 PHE   0.013   0.001   PHE O  25 
 HIS   0.005   0.001   HIS N  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 (13207)
  covalent geometry    : angle       0.57705 (19170)
  hydrogen bonds       : bond        0.04610 (  782)
  hydrogen bonds       : angle       2.54546 ( 1942)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 78
  time to evaluate  : 0.261 
Fit side-chains
REVERT: M   72 ARG cc_start: 0.7855 (mtt-85) cc_final: 0.7438 (mtt-85)
REVERT: M  115 LYS cc_start: 0.8310 (mttm) cc_final: 0.7998 (mttm)
REVERT: M  120 MET cc_start: 0.7168 (mmm) cc_final: 0.6758 (mtt)
REVERT: N   40 ARG cc_start: 0.8528 (ttm170) cc_final: 0.8316 (ttm170)
REVERT: O   32 ARG cc_start: 0.8012 (ttp80) cc_final: 0.7757 (ttp-110)
REVERT: Q   90 MET cc_start: 0.6573 (tpp) cc_final: 0.6313 (mpp)
REVERT: S   20 ARG cc_start: 0.7715 (ttm110) cc_final: 0.7147 (ttm110)
REVERT: S  108 LEU cc_start: 0.8547 (mt) cc_final: 0.8337 (mt)
REVERT: T   59 MET cc_start: 0.7504 (mmm) cc_final: 0.6867 (mmm)
  outliers start: 4
  outliers final: 1
  residues processed: 78
  average time/residue: 0.2535
  time to fit residues: 23.2982
Evaluate side-chains
  76 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   88 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 99 optimal weight:    0.2980
   chunk 37 optimal weight:    0.2980
   chunk 75 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0970
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
** N  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.142110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.111968 restraints weight = 18237.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.114365 restraints weight = 9191.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.115939 restraints weight = 6030.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.116799 restraints weight = 4713.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.117104 restraints weight = 4107.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7098
moved from start:          0.5756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  13207  Z= 0.209
  Angle     :  0.583   7.059  19170  Z= 0.353
  Chirality :  0.036   0.151   2181
  Planarity :  0.004   0.034   1344
  Dihedral  : 31.016 178.628   4231
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  5.31 %
    Favored  : 94.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.15 (0.31), residues: 732
  helix:  2.31 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.36 (0.40), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG O  35 
 TYR   0.018   0.002   TYR P  80 
 PHE   0.016   0.002   PHE Q  84 
 HIS   0.004   0.001   HIS T  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 (13207)
  covalent geometry    : angle       0.58344 (19170)
  hydrogen bonds       : bond        0.04721 (  782)
  hydrogen bonds       : angle       2.54187 ( 1942)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 73
  time to evaluate  : 0.286 
Fit side-chains
REVERT: M   72 ARG cc_start: 0.7911 (mtt-85) cc_final: 0.7429 (mtt-85)
REVERT: M  120 MET cc_start: 0.7263 (mmm) cc_final: 0.6479 (mtt)
REVERT: O   32 ARG cc_start: 0.8069 (ttp80) cc_final: 0.7755 (ttp-110)
REVERT: P   56 MET cc_start: 0.7480 (mmm) cc_final: 0.7214 (tpp)
REVERT: Q   90 MET cc_start: 0.6573 (tpp) cc_final: 0.6308 (mpp)
REVERT: S   20 ARG cc_start: 0.7765 (ttm110) cc_final: 0.7283 (ttm110)
REVERT: S   85 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7628 (mt)
  outliers start: 3
  outliers final: 1
  residues processed: 74
  average time/residue: 0.2961
  time to fit residues: 25.5906
Evaluate side-chains
  72 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 70
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   85 LEU
Chi-restraints excluded: chain T residue  119 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0570
   chunk 2 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0870
   chunk 80 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 97 optimal weight:    3.9990
   chunk 60 optimal weight:    0.3980
   chunk 6 optimal weight:    0.0770
   chunk 44 optimal weight:    0.7980
   overall best weight:    0.2834

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

Flipped N/Q/H residues before XYZ refinement:
** N  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.145028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.113663 restraints weight = 18270.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.116342 restraints weight = 8591.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.118107 restraints weight = 5412.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.119366 restraints weight = 4091.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.119873 restraints weight = 3512.336|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7042
moved from start:          0.5918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13207  Z= 0.166
  Angle     :  0.539   9.527  19170  Z= 0.328
  Chirality :  0.033   0.136   2181
  Planarity :  0.004   0.031   1344
  Dihedral  : 30.888 179.257   4231
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  5.80 %
    Favored  : 93.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.61 (0.31), residues: 732
  helix:  2.66 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.24 (0.41), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG M  49 
 TYR   0.009   0.001   TYR R  72 
 PHE   0.010   0.001   PHE Q  67 
 HIS   0.003   0.001   HIS S  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (13207)
  covalent geometry    : angle       0.53852 (19170)
  hydrogen bonds       : bond        0.03997 (  782)
  hydrogen bonds       : angle       2.35058 ( 1942)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 71
  time to evaluate  : 0.302 
Fit side-chains
REVERT: M   42 ARG cc_start: 0.7772 (mtp85) cc_final: 0.7480 (mtp85)
REVERT: M   72 ARG cc_start: 0.7869 (mtt-85) cc_final: 0.7381 (mtt180)
REVERT: O   32 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7773 (ttp-110)
REVERT: Q   90 MET cc_start: 0.6563 (tpp) cc_final: 0.6352 (mpp)
REVERT: S   20 ARG cc_start: 0.7745 (ttm110) cc_final: 0.7254 (ttm110)
REVERT: T  118 TYR cc_start: 0.8435 (t80) cc_final: 0.8172 (t80)
  outliers start: 4
  outliers final: 2
  residues processed: 71
  average time/residue: 0.3040
  time to fit residues: 25.1453
Evaluate side-chains
  73 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   71 ARG
Chi-restraints excluded: chain S residue   85 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 94 optimal weight:    0.9990
   chunk 56 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0870
   chunk 66 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 17 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 23 optimal weight:    0.0980
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
** N  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P  46 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.143454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.112679 restraints weight = 17975.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.115234 restraints weight = 8973.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.116796 restraints weight = 5830.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.117864 restraints weight = 4569.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.118155 restraints weight = 3914.918|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7142
moved from start:          0.6284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  13207  Z= 0.228
  Angle     :  0.577   5.440  19170  Z= 0.351
  Chirality :  0.036   0.139   2181
  Planarity :  0.004   0.032   1344
  Dihedral  : 31.015 178.513   4231
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  6.12 %
    Favored  : 93.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.51 (0.31), residues: 732
  helix:  2.58 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.28 (0.41), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG N  45 
 TYR   0.019   0.002   TYR R  88 
 PHE   0.011   0.002   PHE Q  84 
 HIS   0.003   0.001   HIS T  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 (13207)
  covalent geometry    : angle       0.57687 (19170)
  hydrogen bonds       : bond        0.04680 (  782)
  hydrogen bonds       : angle       2.53344 ( 1942)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 60
  time to evaluate  : 0.286 
Fit side-chains
REVERT: M   42 ARG cc_start: 0.7871 (mtp85) cc_final: 0.7583 (mtp85)
REVERT: M   72 ARG cc_start: 0.7919 (mtt-85) cc_final: 0.7458 (mtt-85)
REVERT: M  116 ARG cc_start: 0.8098 (mtm-85) cc_final: 0.7855 (mtm-85)
REVERT: M  120 MET cc_start: 0.7278 (mmm) cc_final: 0.6906 (mtt)
REVERT: O   73 ASN cc_start: 0.8307 (m-40) cc_final: 0.8067 (m110)
REVERT: P   56 MET cc_start: 0.7490 (mmm) cc_final: 0.7213 (tpp)
REVERT: Q   90 MET cc_start: 0.6609 (tpp) cc_final: 0.6327 (mpp)
REVERT: S   20 ARG cc_start: 0.7786 (ttm110) cc_final: 0.7297 (ttm170)
REVERT: T  118 TYR cc_start: 0.8508 (t80) cc_final: 0.8226 (t80)
  outliers start: 5
  outliers final: 3
  residues processed: 62
  average time/residue: 0.2942
  time to fit residues: 21.5647
Evaluate side-chains
  63 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   71 ARG
Chi-restraints excluded: chain Q residue   48 LEU
Chi-restraints excluded: chain S residue   85 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 4 optimal weight:    0.1980
   chunk 35 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
M  68 GLN
** N  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P  46 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.137676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.106698 restraints weight = 17970.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.109334 restraints weight = 8703.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.111015 restraints weight = 5606.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.112147 restraints weight = 4312.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.112711 restraints weight = 3771.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.6848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.039  13207  Z= 0.301
  Angle     :  0.633   7.363  19170  Z= 0.381
  Chirality :  0.040   0.140   2181
  Planarity :  0.005   0.035   1344
  Dihedral  : 31.294 177.858   4231
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  6.60 %
    Favored  : 92.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.16 (0.31), residues: 732
  helix:  2.34 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -1.37 (0.40), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG S  77 
 TYR   0.015   0.002   TYR R  88 
 PHE   0.013   0.002   PHE M  84 
 HIS   0.005   0.001   HIS M  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00679 (13207)
  covalent geometry    : angle       0.63302 (19170)
  hydrogen bonds       : bond        0.05157 (  782)
  hydrogen bonds       : angle       2.65880 ( 1942)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.290 
Fit side-chains
REVERT: M   42 ARG cc_start: 0.7871 (mtp85) cc_final: 0.7567 (mtp85)
REVERT: M   72 ARG cc_start: 0.7932 (mtt-85) cc_final: 0.7637 (mtt180)
REVERT: M  116 ARG cc_start: 0.8176 (mtm-85) cc_final: 0.7959 (mtm-85)
REVERT: M  120 MET cc_start: 0.7325 (mmm) cc_final: 0.6738 (mtt)
REVERT: O   23 LEU cc_start: 0.8146 (OUTLIER) cc_final: 0.7843 (mp)
REVERT: O   73 ASN cc_start: 0.8256 (m-40) cc_final: 0.8054 (m110)
REVERT: Q   90 MET cc_start: 0.6638 (tpp) cc_final: 0.6311 (mpp)
REVERT: R   84 MET cc_start: 0.7610 (mmm) cc_final: 0.7389 (tpp)
REVERT: S   20 ARG cc_start: 0.7899 (ttm110) cc_final: 0.7418 (ttm170)
REVERT: T   59 MET cc_start: 0.7422 (mmm) cc_final: 0.6982 (mmm)
REVERT: T  118 TYR cc_start: 0.8495 (t80) cc_final: 0.8226 (t80)
  outliers start: 5
  outliers final: 3
  residues processed: 63
  average time/residue: 0.3032
  time to fit residues: 22.3598
Evaluate side-chains
  67 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   23 LEU
Chi-restraints excluded: chain Q residue   48 LEU
Chi-restraints excluded: chain S residue   85 LEU
Chi-restraints excluded: chain T residue   56 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 19 optimal weight:    0.0970
   chunk 44 optimal weight:    0.4980
   chunk 22 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 0 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0980
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.3778

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

Flipped N/Q/H residues before XYZ refinement:
M  68 GLN
** N  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P  46 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.138885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.108173 restraints weight = 18111.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.110716 restraints weight = 8952.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.112353 restraints weight = 5799.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.113472 restraints weight = 4502.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.113854 restraints weight = 3892.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7129
moved from start:          0.6846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13207  Z= 0.186
  Angle     :  0.554   5.403  19170  Z= 0.339
  Chirality :  0.034   0.136   2181
  Planarity :  0.004   0.034   1344
  Dihedral  : 31.043 179.141   4231
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  7.09 %
    Favored  : 92.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.64 (0.31), residues: 732
  helix:  2.68 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.25 (0.41), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG S  77 
 TYR   0.010   0.001   TYR N  72 
 PHE   0.010   0.001   PHE Q  67 
 HIS   0.003   0.001   HIS T  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (13207)
  covalent geometry    : angle       0.55380 (19170)
  hydrogen bonds       : bond        0.04141 (  782)
  hydrogen bonds       : angle       2.42351 ( 1942)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 65
  time to evaluate  : 0.293 
Fit side-chains
REVERT: M   42 ARG cc_start: 0.7804 (mtp85) cc_final: 0.7477 (mtp85)
REVERT: M   72 ARG cc_start: 0.7878 (mtt-85) cc_final: 0.7379 (mtt180)
REVERT: M  120 MET cc_start: 0.7266 (mmm) cc_final: 0.6899 (mtt)
REVERT: O   23 LEU cc_start: 0.8045 (mp) cc_final: 0.7738 (mp)
REVERT: O   73 ASN cc_start: 0.8252 (m-40) cc_final: 0.7980 (m110)
REVERT: P   48 ASP cc_start: 0.6947 (m-30) cc_final: 0.6717 (m-30)
REVERT: P  117 LYS cc_start: 0.8462 (tttt) cc_final: 0.8048 (tttt)
REVERT: Q   90 MET cc_start: 0.6593 (tpp) cc_final: 0.6327 (mpp)
REVERT: S   20 ARG cc_start: 0.7804 (ttm110) cc_final: 0.7315 (ttm170)
REVERT: T  118 TYR cc_start: 0.8501 (t80) cc_final: 0.8250 (t80)
  outliers start: 5
  outliers final: 4
  residues processed: 66
  average time/residue: 0.3007
  time to fit residues: 23.3202
Evaluate side-chains
  69 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 65
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   71 ARG
Chi-restraints excluded: chain Q residue  112 ILE
Chi-restraints excluded: chain S residue   85 LEU
Chi-restraints excluded: chain T residue   56 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 54 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** N  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P  46 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.138016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.107247 restraints weight = 17982.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.109903 restraints weight = 8634.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.111637 restraints weight = 5520.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.112605 restraints weight = 4291.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.113249 restraints weight = 3699.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7181
moved from start:          0.6973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035  13207  Z= 0.280
  Angle     :  0.603   5.798  19170  Z= 0.367
  Chirality :  0.039   0.145   2181
  Planarity :  0.005   0.057   1344
  Dihedral  : 31.143 178.623   4231
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  8.05 %
    Favored  : 91.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.43 (0.31), residues: 732
  helix:  2.55 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -1.31 (0.40), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG S  77 
 TYR   0.011   0.002   TYR Q  99 
 PHE   0.012   0.002   PHE M  84 
 HIS   0.004   0.001   HIS T  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00629 (13207)
  covalent geometry    : angle       0.60348 (19170)
  hydrogen bonds       : bond        0.04934 (  782)
  hydrogen bonds       : angle       2.56659 ( 1942)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.306 
Fit side-chains
REVERT: M   42 ARG cc_start: 0.7831 (mtp85) cc_final: 0.7517 (mtp85)
REVERT: M   72 ARG cc_start: 0.7913 (mtt-85) cc_final: 0.7488 (mtt-85)
REVERT: M  120 MET cc_start: 0.7316 (mmm) cc_final: 0.6744 (mtt)
REVERT: O   23 LEU cc_start: 0.8151 (mp) cc_final: 0.7848 (mp)
REVERT: O   73 ASN cc_start: 0.8265 (m-40) cc_final: 0.8020 (m110)
REVERT: P   46 HIS cc_start: 0.8227 (m90) cc_final: 0.7953 (m170)
REVERT: Q   90 MET cc_start: 0.6672 (tpp) cc_final: 0.6338 (mpp)
REVERT: S   20 ARG cc_start: 0.7829 (ttm110) cc_final: 0.7357 (ttm170)
REVERT: T  118 TYR cc_start: 0.8478 (t80) cc_final: 0.8228 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 60
  average time/residue: 0.2962
  time to fit residues: 20.9258
Evaluate side-chains
  62 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   85 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9990
   chunk 13 optimal weight:    0.3980
   chunk 47 optimal weight:    0.0980
   chunk 31 optimal weight:    0.5980
   chunk 8 optimal weight:    0.8980
   chunk 64 optimal weight:    0.8980
   chunk 66 optimal weight:    0.6980
   chunk 54 optimal weight:    0.1980
   overall best weight:    0.3980

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

Flipped N/Q/H residues before XYZ refinement:
** N  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.141354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.111790 restraints weight = 18019.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.114207 restraints weight = 9077.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.115746 restraints weight = 5936.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.116866 restraints weight = 4618.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.117200 restraints weight = 3998.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7142
moved from start:          0.6980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13207  Z= 0.196
  Angle     :  0.564   6.343  19170  Z= 0.344
  Chirality :  0.034   0.139   2181
  Planarity :  0.004   0.042   1344
  Dihedral  : 31.033 179.149   4231
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  0.64 %
    Allowed  :  7.73 %
    Favored  : 91.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.64 (0.31), residues: 732
  helix:  2.68 (0.22), residues: 545
  sheet:  None (None), residues: 0
  loop : -1.24 (0.42), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG S  77 
 TYR   0.011   0.001   TYR P  80 
 PHE   0.010   0.001   PHE Q  67 
 HIS   0.003   0.001   HIS T  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 (13207)
  covalent geometry    : angle       0.56369 (19170)
  hydrogen bonds       : bond        0.04319 (  782)
  hydrogen bonds       : angle       2.45243 ( 1942)

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

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

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1464 Ramachandran restraints generated.
    732 Oldfield, 0 Emsley, 732 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 0.325 
Fit side-chains
REVERT: M   42 ARG cc_start: 0.7788 (mtp85) cc_final: 0.7497 (mtp85)
REVERT: M   72 ARG cc_start: 0.7906 (mtt-85) cc_final: 0.7432 (mtt-85)
REVERT: M  116 ARG cc_start: 0.8047 (mtm-85) cc_final: 0.7824 (mtm-85)
REVERT: M  120 MET cc_start: 0.7248 (mmm) cc_final: 0.6924 (mtt)
REVERT: O   23 LEU cc_start: 0.8160 (mp) cc_final: 0.7857 (mp)
REVERT: O   73 ASN cc_start: 0.8261 (m-40) cc_final: 0.7999 (m110)
REVERT: Q   90 MET cc_start: 0.6581 (tpp) cc_final: 0.6297 (mpp)
REVERT: S   20 ARG cc_start: 0.7791 (ttm110) cc_final: 0.7333 (ttm170)
  outliers start: 4
  outliers final: 3
  residues processed: 63
  average time/residue: 0.2959
  time to fit residues: 22.0312
Evaluate side-chains
  63 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 60
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain O residue   71 ARG
Chi-restraints excluded: chain S residue   85 LEU
Chi-restraints excluded: chain T residue  119 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 51 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   chunk 48 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 83 optimal weight:    6.9990
   chunk 99 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
M  68 GLN
** N  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
P  46 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.133065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.104457 restraints weight = 18440.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.106793 restraints weight = 9208.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.108324 restraints weight = 6003.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.109055 restraints weight = 4702.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 59)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.109781 restraints weight = 4149.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.7137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.038  13207  Z= 0.329
  Angle     :  0.632   7.899  19170  Z= 0.381
  Chirality :  0.041   0.145   2181
  Planarity :  0.005   0.047   1344
  Dihedral  : 31.164 178.600   4231
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  :  8.21 %
    Favored  : 91.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.23 (0.31), residues: 732
  helix:  2.41 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -1.38 (0.41), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG R  45 
 TYR   0.013   0.002   TYR Q  99 
 PHE   0.012   0.002   PHE M  84 
 HIS   0.005   0.002   HIS T  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00743 (13207)
  covalent geometry    : angle       0.63155 (19170)
  hydrogen bonds       : bond        0.05236 (  782)
  hydrogen bonds       : angle       2.65165 ( 1942)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1981.00 seconds
wall clock time: 34 minutes 49.86 seconds (2089.86 seconds total)