Starting phenix.real_space_refine
on Wed Sep 17 23:43:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vmn_43360/09_2025/8vmn_43360.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vmn_43360/09_2025/8vmn_43360.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vmn_43360/09_2025/8vmn_43360.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vmn_43360/09_2025/8vmn_43360.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vmn_43360/09_2025/8vmn_43360.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vmn_43360/09_2025/8vmn_43360.cif"
  }
  resolution = 3.5
  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=   0.034
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     314      5.49       5
     S      14      5.16       5
     C    6889      2.51       5
     N    2355      2.21       5
     O    2968      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12540
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "H"
      Number of atoms: 3237
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 3237
          Classifications: {'DNA': 157}
          Link IDs: {'rna3p': 156}
    Chain: "I"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 825
          Classifications: {'peptide': 100}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
    Chain: "J"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "K"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 825
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "M"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 736
          Classifications: {'peptide': 95}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 8
    Chain: "O"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 816
          Classifications: {'peptide': 99}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "Q"
      Number of atoms: 667
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 667
          Classifications: {'peptide': 87}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 1, 'TRANS': 85}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "R"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 829
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "S"
      Number of atoms: 741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 741
          Classifications: {'peptide': 96}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 2, 'TRANS': 93}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "D"
      Number of atoms: 3202
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 157, 3202
          Classifications: {'DNA': 157}
          Link IDs: {'rna3p': 156}
  Time building chain proxies: 2.77, per 1000 atoms: 0.22
  Number of scatterers: 12540
  At special positions: 0
  Unit cell: (106.64, 141.04, 122.12, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      14     16.00
     P     314     15.00
     O    2968      8.00
     N    2355      7.00
     C    6889      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: 1.03
  Conformation dependent library (CDL) restraints added in 360.2 milliseconds
  
  Enol-peptide restraints added in 1.7 microseconds
  

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1452

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 7 sheets defined
      69.2% alpha, 1.8% beta
      156 base pairs and 255 stacking pairs defined.
    Time for finding SS restraints: 1.84
  Creating SS restraints...
    Processing helix  chain 'I' and resid 45 through 55
    Processing helix  chain 'I' and resid 63 through 75
      removed outlier: 3.547A  pdb=" N   PHE I  67 " --> pdb=" O   ARG I  63 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 85 through 114
      removed outlier: 3.676A  pdb=" N   VAL I  89 " --> pdb=" O   GLN I  85 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   MET I  90 " --> pdb=" O   SER I  86 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 120 through 131
      removed outlier: 3.535A  pdb=" N   ILE I 124 " --> pdb=" O   MET I 120 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 24 through 29
      removed outlier: 3.526A  pdb=" N   ILE J  29 " --> pdb=" O   ILE J  26 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 30 through 42
    Processing helix  chain 'J' and resid 49 through 76
      removed outlier: 3.915A  pdb=" N   GLU J  53 " --> pdb=" O   LEU J  49 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   ARG J  55 " --> pdb=" O   TYR J  51 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   VAL J  65 " --> pdb=" O   PHE J  61 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   ASP J  68 " --> pdb=" O   ASN J  64 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ALA J  76 " --> pdb=" O   TYR J  72 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 82 through 94
    Processing helix  chain 'K' and resid 16 through 22
    Processing helix  chain 'K' and resid 26 through 37
    Processing helix  chain 'K' and resid 45 through 73
      removed outlier: 4.577A  pdb=" N   VAL K  49 " --> pdb=" O   ALA K  45 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 79 through 88
    Processing helix  chain 'K' and resid 90 through 97
      removed outlier: 3.587A  pdb=" N   LEU K  96 " --> pdb=" O   GLU K  92 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 34 through 46
    Processing helix  chain 'M' and resid 53 through 81
      removed outlier: 3.869A  pdb=" N   MET M  59 " --> pdb=" O   ALA M  55 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU M  68 " --> pdb=" O   ASN M  64 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   GLU M  73 " --> pdb=" O   ARG M  69 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ASN M  81 " --> pdb=" O   LEU M  77 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 87 through 99
      removed outlier: 3.624A  pdb=" N   ILE M  91 " --> pdb=" O   THR M  87 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 101 through 121
      removed outlier: 4.461A  pdb=" N   SER M 109 " --> pdb=" O   LYS M 105 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLU M 110 " --> pdb=" O   HIS M 106 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   TYR M 118 " --> pdb=" O   ALA M 114 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   SER M 120 " --> pdb=" O   THR M 116 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 44 through 55
      removed outlier: 3.565A  pdb=" N   LEU O  48 " --> pdb=" O   GLY O  44 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 63 through 76
      removed outlier: 3.622A  pdb=" N   PHE O  67 " --> pdb=" O   ARG O  63 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   GLN O  76 " --> pdb=" O   ARG O  72 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 85 through 114
    Processing helix  chain 'O' and resid 120 through 131
      removed outlier: 3.633A  pdb=" N   ILE O 124 " --> pdb=" O   MET O 120 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 25 through 29
    Processing helix  chain 'Q' and resid 30 through 42
    Processing helix  chain 'Q' and resid 49 through 77
      removed outlier: 4.254A  pdb=" N   GLU Q  53 " --> pdb=" O   LEU Q  49 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   ARG Q  55 " --> pdb=" O   TYR Q  51 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ASP Q  68 " --> pdb=" O   ASN Q  64 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   THR Q  73 " --> pdb=" O   ALA Q  69 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 82 through 93
      removed outlier: 3.830A  pdb=" N   VAL Q  86 " --> pdb=" O   THR Q  82 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 16 through 22
    Processing helix  chain 'R' and resid 26 through 37
    Processing helix  chain 'R' and resid 45 through 73
      removed outlier: 4.413A  pdb=" N   VAL R  49 " --> pdb=" O   ALA R  45 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA R  69 " --> pdb=" O   LEU R  65 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 79 through 89
    Processing helix  chain 'R' and resid 90 through 97
    Processing helix  chain 'S' and resid 34 through 44
    Processing helix  chain 'S' and resid 52 through 81
    Processing helix  chain 'S' and resid 87 through 99
    Processing helix  chain 'S' and resid 101 through 121
    Processing sheet with id=AA1, first strand: chain 'I' and resid 83 through 84
      removed outlier: 7.836A  pdb=" N   ARG I  83 " --> pdb=" O   VAL J  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'I' and resid 118 through 119
      removed outlier: 3.810A  pdb=" N   ILE I 119 " --> pdb=" O   ARG J  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'J' and resid 97 through 98
      removed outlier: 3.618A  pdb=" N   TYR J  98 " --> pdb=" O   THR R 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'K' and resid 42 through 43
      removed outlier: 7.732A  pdb=" N   ARG K  42 " --> pdb=" O   ILE M  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'K' and resid 101 through 102
      removed outlier: 6.804A  pdb=" N   THR K 101 " --> pdb=" O   TYR Q  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'R' and resid 42 through 43
      removed outlier: 7.328A  pdb=" N   ARG R  42 " --> pdb=" O   ILE S  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'R' and resid 77 through 78

    372 hydrogen bonds defined for protein.
    1104 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      396 hydrogen bonds
      756 hydrogen bond angles
      0 basepair planarities
      156 basepair parallelities
      255 stacking parallelities
  Total time for adding SS restraints: 2.46

  Time building geometry restraints manager: 1.41 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: 2483
        1.33 -     1.45: 4422
        1.45 -     1.57: 5848
        1.57 -     1.69: 626
        1.69 -     1.81: 24
  Bond restraints: 13403
  Sorted by residual:
  bond pdb=" C3'  DA H  20 "
       pdb=" O3'  DA H  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.477 -0.055 3.00e-02 1.11e+03 3.35e+00
  bond pdb=" C3'  DC D 185 "
       pdb=" O3'  DC D 185 "
    ideal  model  delta    sigma   weight residual
    1.422  1.473 -0.051 3.00e-02 1.11e+03 2.86e+00
  bond pdb=" CG  PRO R  26 "
       pdb=" CD  PRO R  26 "
    ideal  model  delta    sigma   weight residual
    1.503  1.561 -0.058 3.40e-02 8.65e+02 2.86e+00
  bond pdb=" CB  LYS O  37 "
       pdb=" CG  LYS O  37 "
    ideal  model  delta    sigma   weight residual
    1.520  1.570 -0.050 3.00e-02 1.11e+03 2.82e+00
  bond pdb=" C3'  DG D 161 "
       pdb=" O3'  DG D 161 "
    ideal  model  delta    sigma   weight residual
    1.422  1.470 -0.048 3.00e-02 1.11e+03 2.60e+00
  ... (remaining 13398 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 18993
        2.08 -     4.16: 437
        4.16 -     6.24: 24
        6.24 -     8.33: 3
        8.33 -    10.41: 2
  Bond angle restraints: 19459
  Sorted by residual:
  angle pdb=" CB  LYS O  37 "
        pdb=" CG  LYS O  37 "
        pdb=" CD  LYS O  37 "
      ideal   model   delta    sigma   weight residual
     111.30  121.71  -10.41 2.30e+00 1.89e-01 2.05e+01
  angle pdb=" N   VAL I 117 "
        pdb=" CA  VAL I 117 "
        pdb=" C   VAL I 117 "
      ideal   model   delta    sigma   weight residual
     113.47  109.04    4.43 1.01e+00 9.80e-01 1.93e+01
  angle pdb=" CA  PRO R  26 "
        pdb=" N   PRO R  26 "
        pdb=" CD  PRO R  26 "
      ideal   model   delta    sigma   weight residual
     112.00  106.84    5.16 1.40e+00 5.10e-01 1.36e+01
  angle pdb=" N   GLY R  98 "
        pdb=" CA  GLY R  98 "
        pdb=" C   GLY R  98 "
      ideal   model   delta    sigma   weight residual
     112.73  116.87   -4.14 1.20e+00 6.94e-01 1.19e+01
  angle pdb=" C   THR M  87 "
        pdb=" CA  THR M  87 "
        pdb=" CB  THR M  87 "
      ideal   model   delta    sigma   weight residual
     110.24  116.41   -6.17 1.88e+00 2.83e-01 1.08e+01
  ... (remaining 19454 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.96: 5750
       35.96 -    71.92: 1411
       71.92 -   107.87: 28
      107.87 -   143.83: 8
      143.83 -   179.79: 25
  Dihedral angle restraints: 7222
    sinusoidal: 4972
      harmonic: 2250
  Sorted by residual:
  dihedral pdb=" C4'  DT D 236 "
           pdb=" C3'  DT D 236 "
           pdb=" O3'  DT D 236 "
           pdb=" P    DA D 237 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   40.21  179.79     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG D 167 "
           pdb=" C3'  DG D 167 "
           pdb=" O3'  DG D 167 "
           pdb=" P    DG D 168 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   41.08  178.92     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DT D 195 "
           pdb=" C3'  DT D 195 "
           pdb=" O3'  DT D 195 "
           pdb=" P    DC D 196 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   38.06 -178.06     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 7219 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1672
       0.037 -    0.074: 409
       0.074 -    0.110: 105
       0.110 -    0.147: 30
       0.147 -    0.184: 2
  Chirality restraints: 2218
  Sorted by residual:
  chirality pdb=" CA  MET O  90 "
            pdb=" N   MET O  90 "
            pdb=" C   MET O  90 "
            pdb=" CB  MET O  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.45e-01
  chirality pdb=" CA  PRO R  26 "
            pdb=" N   PRO R  26 "
            pdb=" C   PRO R  26 "
            pdb=" CB  PRO R  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.57    0.15 2.00e-01 2.50e+01 5.80e-01
  chirality pdb=" P    DC D 250 "
            pdb=" OP1  DC D 250 "
            pdb=" OP2  DC D 250 "
            pdb=" O5'  DC D 250 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.49   -0.15 2.00e-01 2.50e+01 5.29e-01
  ... (remaining 2215 not shown)

  Planarity restraints: 1377
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC D 250 "    0.001 2.00e-02 2.50e+03   2.16e-02 1.05e+01
        pdb=" N1   DC D 250 "   -0.009 2.00e-02 2.50e+03
        pdb=" C2   DC D 250 "    0.056 2.00e-02 2.50e+03
        pdb=" O2   DC D 250 "   -0.027 2.00e-02 2.50e+03
        pdb=" N3   DC D 250 "   -0.014 2.00e-02 2.50e+03
        pdb=" C4   DC D 250 "   -0.003 2.00e-02 2.50e+03
        pdb=" N4   DC D 250 "    0.004 2.00e-02 2.50e+03
        pdb=" C5   DC D 250 "   -0.009 2.00e-02 2.50e+03
        pdb=" C6   DC D 250 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE R  25 "   -0.051 5.00e-02 4.00e+02   7.51e-02 9.03e+00
        pdb=" N   PRO R  26 "    0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO R  26 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO R  26 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC H 114 "   -0.001 2.00e-02 2.50e+03   1.77e-02 7.02e+00
        pdb=" N1   DC H 114 "   -0.009 2.00e-02 2.50e+03
        pdb=" C2   DC H 114 "    0.044 2.00e-02 2.50e+03
        pdb=" O2   DC H 114 "   -0.024 2.00e-02 2.50e+03
        pdb=" N3   DC H 114 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4   DC H 114 "    0.008 2.00e-02 2.50e+03
        pdb=" N4   DC H 114 "   -0.010 2.00e-02 2.50e+03
        pdb=" C5   DC H 114 "   -0.002 2.00e-02 2.50e+03
        pdb=" C6   DC H 114 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1374 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.60: 129
        2.60 -     3.17: 9814
        3.17 -     3.75: 22719
        3.75 -     4.32: 28539
        4.32 -     4.90: 41403
  Nonbonded interactions: 102604
  Sorted by model distance:
  nonbonded pdb=" N2   DG H  93 "
            pdb=" O2   DC D 222 "
     model   vdw
     2.024 2.496
  nonbonded pdb=" OG  SER M 109 "
            pdb=" OE1 GLU M 110 "
     model   vdw
     2.038 3.040
  nonbonded pdb=" O2   DC H 154 "
            pdb=" N2   DG D 161 "
     model   vdw
     2.102 2.496
  nonbonded pdb=" O2   DC H 110 "
            pdb=" N2   DG D 205 "
     model   vdw
     2.113 2.496
  nonbonded pdb=" N2   DG H  94 "
            pdb=" O2   DC D 221 "
     model   vdw
     2.121 2.496
  ... (remaining 102599 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 'I' and resid 37 through 135)
  selection = chain 'O'
}
ncs_group {
  reference = (chain 'J' and ((resid 20 through 23 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 24 through 102))
  selection = (chain 'Q' and resid 20 through 102)
}
ncs_group {
  reference = chain 'K'
  selection = (chain 'R' and ((resid 12 through 14 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 15 through 119))
}
ncs_group {
  reference = chain 'M'
  selection = (chain 'S' and resid 28 through 122)
}

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:             7.720
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.510
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071  13403  Z= 0.178
  Angle     :  0.666  10.407  19459  Z= 0.399
  Chirality :  0.036   0.184   2218
  Planarity :  0.005   0.075   1377
  Dihedral  : 30.827 179.789   5770
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 25.16 %
    Favored  : 74.21 %
  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:  0.74 (0.31), residues: 760
  helix:  1.49 (0.23), residues: 520
  sheet:  None (None), residues: 0
  loop : -1.82 (0.36), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG I 128 
 TYR   0.033   0.002   TYR M  80 
 PHE   0.015   0.001   PHE J 100 
 HIS   0.009   0.001   HIS R  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 (13403)
  covalent geometry    : angle       0.66623 (19459)
  hydrogen bonds       : bond        0.13450 (  768)
  hydrogen bonds       : angle       4.91494 ( 1860)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 122
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: J   82 THR cc_start: 0.8710 (m) cc_final: 0.8430 (p)
REVERT: M   39 TYR cc_start: 0.7613 (t80) cc_final: 0.7008 (t80)
REVERT: O   37 LYS cc_start: 0.8244 (tppt) cc_final: 0.7526 (mmmm)
  outliers start: 4
  outliers final: 2
  residues processed: 123
  average time/residue: 0.1644
  time to fit residues: 27.2584
Evaluate side-chains
  109 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 107
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain J residue   62 LEU
Chi-restraints excluded: chain R residue   74 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    4.9990
   chunk 100 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:   20.0000
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
I  39 HIS
R  31 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.124490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.095396 restraints weight = 32114.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.097584 restraints weight = 16663.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.099039 restraints weight = 11175.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.099954 restraints weight = 8852.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.100440 restraints weight = 7779.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
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      :  0.005   0.050  13403  Z= 0.215
  Angle     :  0.677   8.051  19459  Z= 0.395
  Chirality :  0.040   0.174   2218
  Planarity :  0.005   0.051   1377
  Dihedral  : 33.725 179.090   4277
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 20.73 %
    Favored  : 75.95 %
  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:  1.11 (0.31), residues: 760
  helix:  1.72 (0.23), residues: 529
  sheet:  None (None), residues: 0
  loop : -1.66 (0.38), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG Q  55 
 TYR   0.036   0.002   TYR Q  88 
 PHE   0.013   0.002   PHE S  62 
 HIS   0.003   0.001   HIS M  46 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 (13403)
  covalent geometry    : angle       0.67655 (19459)
  hydrogen bonds       : bond        0.08420 (  768)
  hydrogen bonds       : angle       3.36630 ( 1860)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
REVERT: J   88 TYR cc_start: 0.7730 (m-10) cc_final: 0.7424 (m-10)
REVERT: Q   35 ARG cc_start: 0.7281 (mtp85) cc_final: 0.7016 (mtp180)
REVERT: R   64 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7608 (tt0)
REVERT: S   77 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8053 (mp)
  outliers start: 21
  outliers final: 12
  residues processed: 140
  average time/residue: 0.1605
  time to fit residues: 29.9890
Evaluate side-chains
  122 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain J residue   62 LEU
Chi-restraints excluded: chain M residue   85 THR
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain O residue   39 HIS
Chi-restraints excluded: chain Q residue   27 GLN
Chi-restraints excluded: chain Q residue   50 ILE
Chi-restraints excluded: chain R residue   16 THR
Chi-restraints excluded: chain R residue   38 ASN
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain S residue   53 SER
Chi-restraints excluded: chain S residue   77 LEU
Chi-restraints excluded: chain S residue   87 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 11 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 83 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 65 optimal weight:    0.7980
   chunk 9 optimal weight:    7.9990
   chunk 79 optimal weight:    0.0030
   chunk 39 optimal weight:    0.4980
   chunk 4 optimal weight:    5.9990
   overall best weight:    1.0594

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

Flipped N/Q/H residues before XYZ refinement:
** R  82 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 = 0.4179 r_free = 0.4179 target = 0.125117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.096609 restraints weight = 32634.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.098635 restraints weight = 17959.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.099966 restraints weight = 12314.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.100743 restraints weight = 9871.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.101263 restraints weight = 8775.413|
|-----------------------------------------------------------------------------|
r_work (final): 0.3676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  13403  Z= 0.186
  Angle     :  0.630   6.880  19459  Z= 0.371
  Chirality :  0.038   0.167   2218
  Planarity :  0.004   0.047   1377
  Dihedral  : 33.474 179.336   4273
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 21.20 %
    Favored  : 75.95 %
  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:  1.32 (0.31), residues: 760
  helix:  1.94 (0.23), residues: 527
  sheet:  None (None), residues: 0
  loop : -1.71 (0.38), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K  71 
 TYR   0.029   0.002   TYR M  80 
 PHE   0.009   0.001   PHE S  62 
 HIS   0.006   0.001   HIS I  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (13403)
  covalent geometry    : angle       0.63049 (19459)
  hydrogen bonds       : bond        0.07777 (  768)
  hydrogen bonds       : angle       3.15317 ( 1860)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 114
  time to evaluate  : 0.441 
Fit side-chains
REVERT: M   73 GLU cc_start: 0.7858 (tp30) cc_final: 0.7567 (tp30)
REVERT: M   76 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7969 (ptp-110)
REVERT: M  117 LYS cc_start: 0.8391 (tptm) cc_final: 0.8116 (mtpt)
REVERT: Q   35 ARG cc_start: 0.7424 (mtp85) cc_final: 0.7181 (mtp85)
REVERT: S   77 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.7873 (mp)
  outliers start: 18
  outliers final: 11
  residues processed: 125
  average time/residue: 0.1570
  time to fit residues: 26.5746
Evaluate side-chains
  124 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 111
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain J residue   62 LEU
Chi-restraints excluded: chain K residue   63 LEU
Chi-restraints excluded: chain M residue   76 ARG
Chi-restraints excluded: chain M residue   85 THR
Chi-restraints excluded: chain Q residue   82 THR
Chi-restraints excluded: chain R residue   16 THR
Chi-restraints excluded: chain R residue   38 ASN
Chi-restraints excluded: chain R residue   62 ILE
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain S residue   53 SER
Chi-restraints excluded: chain S residue   77 LEU
Chi-restraints excluded: chain S residue   87 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 67 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 60 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 100 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
I  85 GLN
M  92 GLN
M 106 HIS
** R  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.114066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.085421 restraints weight = 32048.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.087353 restraints weight = 18045.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.088631 restraints weight = 12602.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.089389 restraints weight = 10222.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.089867 restraints weight = 9120.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.3796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.048  13403  Z= 0.249
  Angle     :  0.701   5.734  19459  Z= 0.412
  Chirality :  0.041   0.169   2218
  Planarity :  0.005   0.047   1377
  Dihedral  : 33.545 179.868   4273
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 20.09 %
    Favored  : 75.63 %
  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 aren not related in a simple way.
  whole:  0.97 (0.30), residues: 760
  helix:  1.63 (0.22), residues: 532
  sheet:  None (None), residues: 0
  loop : -1.81 (0.38), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG Q  55 
 TYR   0.051   0.003   TYR S  80 
 PHE   0.014   0.002   PHE S  62 
 HIS   0.010   0.002   HIS I  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 (13403)
  covalent geometry    : angle       0.70100 (19459)
  hydrogen bonds       : bond        0.09349 (  768)
  hydrogen bonds       : angle       3.45346 ( 1860)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 119
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   64 GLU cc_start: 0.8293 (tm-30) cc_final: 0.8083 (tm-30)
REVERT: M   68 GLU cc_start: 0.8320 (tp30) cc_final: 0.7684 (tp30)
REVERT: M   73 GLU cc_start: 0.7899 (tp30) cc_final: 0.7521 (tp30)
REVERT: M  102 GLU cc_start: 0.6335 (tm-30) cc_final: 0.5678 (tm-30)
REVERT: M  106 HIS cc_start: 0.8415 (OUTLIER) cc_final: 0.8203 (m-70)
REVERT: M  117 LYS cc_start: 0.8618 (tptm) cc_final: 0.8344 (mtpt)
REVERT: O   84 PHE cc_start: 0.8687 (OUTLIER) cc_final: 0.8398 (m-80)
REVERT: Q   35 ARG cc_start: 0.7407 (mtp85) cc_final: 0.7027 (mtp180)
REVERT: S   77 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8231 (mp)
  outliers start: 27
  outliers final: 16
  residues processed: 137
  average time/residue: 0.1630
  time to fit residues: 29.8487
Evaluate side-chains
  128 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain I residue   90 MET
Chi-restraints excluded: chain J residue   62 LEU
Chi-restraints excluded: chain K residue   63 LEU
Chi-restraints excluded: chain K residue   65 LEU
Chi-restraints excluded: chain M residue  106 HIS
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain O residue   39 HIS
Chi-restraints excluded: chain O residue   84 PHE
Chi-restraints excluded: chain Q residue   82 THR
Chi-restraints excluded: chain R residue   16 THR
Chi-restraints excluded: chain R residue   38 ASN
Chi-restraints excluded: chain R residue   62 ILE
Chi-restraints excluded: chain R residue   87 VAL
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain S residue   77 LEU
Chi-restraints excluded: chain S residue   87 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 94 optimal weight:    6.9990
   chunk 72 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 7 optimal weight:    4.9990
   chunk 39 optimal weight:    3.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
R  31 HIS
R  82 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.117385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.089226 restraints weight = 32123.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.091255 restraints weight = 17619.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.092588 restraints weight = 12094.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.093443 restraints weight = 9699.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.093790 restraints weight = 8559.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.3895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  13403  Z= 0.180
  Angle     :  0.629   5.252  19459  Z= 0.372
  Chirality :  0.038   0.146   2218
  Planarity :  0.004   0.049   1377
  Dihedral  : 33.330 179.671   4273
  Min Nonbonded Distance : 2.058

Molprobity Statistics.
  All-atom Clashscore : 10.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 22.31 %
    Favored  : 73.89 %
  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:  1.33 (0.31), residues: 760
  helix:  1.96 (0.23), residues: 527
  sheet:  None (None), residues: 0
  loop : -1.76 (0.37), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG K  35 
 TYR   0.037   0.002   TYR M  80 
 PHE   0.008   0.001   PHE S  62 
 HIS   0.012   0.001   HIS M 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (13403)
  covalent geometry    : angle       0.62940 (19459)
  hydrogen bonds       : bond        0.07831 (  768)
  hydrogen bonds       : angle       3.06618 ( 1860)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 118
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
REVERT: K   64 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8066 (tm-30)
REVERT: K  112 GLN cc_start: 0.7701 (mm110) cc_final: 0.7186 (mp10)
REVERT: M   73 GLU cc_start: 0.7867 (tp30) cc_final: 0.7623 (tp30)
REVERT: M   76 ARG cc_start: 0.8197 (ptp-110) cc_final: 0.7958 (ptp-110)
REVERT: M  102 GLU cc_start: 0.5980 (tm-30) cc_final: 0.5641 (tm-30)
REVERT: M  106 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7846 (m90)
REVERT: M  117 LYS cc_start: 0.8578 (tptm) cc_final: 0.8278 (mtpt)
REVERT: O   84 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8467 (m-80)
REVERT: Q   35 ARG cc_start: 0.7270 (mtp85) cc_final: 0.6915 (mtp180)
REVERT: S   77 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.7810 (mp)
  outliers start: 24
  outliers final: 14
  residues processed: 132
  average time/residue: 0.1548
  time to fit residues: 27.6787
Evaluate side-chains
  132 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain J residue   86 VAL
Chi-restraints excluded: chain K residue   16 THR
Chi-restraints excluded: chain M residue  106 HIS
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain O residue   39 HIS
Chi-restraints excluded: chain O residue   84 PHE
Chi-restraints excluded: chain Q residue   27 GLN
Chi-restraints excluded: chain Q residue   50 ILE
Chi-restraints excluded: chain Q residue   82 THR
Chi-restraints excluded: chain R residue   16 THR
Chi-restraints excluded: chain R residue   38 ASN
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain S residue   53 SER
Chi-restraints excluded: chain S residue   77 LEU
Chi-restraints excluded: chain S residue   87 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 2 optimal weight:    7.9990
   chunk 96 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 99 optimal weight:    5.9990
   chunk 36 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 9 optimal weight:    7.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
M 106 HIS
Q  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.112162 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.083284 restraints weight = 32291.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.085143 restraints weight = 18170.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.086391 restraints weight = 12810.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.087164 restraints weight = 10393.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.087618 restraints weight = 9250.810|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.4699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050  13403  Z= 0.289
  Angle     :  0.747   6.472  19459  Z= 0.435
  Chirality :  0.044   0.183   2218
  Planarity :  0.005   0.046   1377
  Dihedral  : 33.627 179.801   4271
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 11.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.00 %
    Favored  : 95.00 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 22.31 %
    Favored  : 72.47 %
  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 aren not related in a simple way.
  whole:  0.52 (0.30), residues: 760
  helix:  1.31 (0.22), residues: 532
  sheet:  None (None), residues: 0
  loop : -2.01 (0.37), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG R  35 
 TYR   0.060   0.003   TYR S  80 
 PHE   0.015   0.002   PHE S  62 
 HIS   0.011   0.002   HIS I  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00669 (13403)
  covalent geometry    : angle       0.74691 (19459)
  hydrogen bonds       : bond        0.10200 (  768)
  hydrogen bonds       : angle       3.65061 ( 1860)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 105
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   71 ARG cc_start: 0.8094 (tpt90) cc_final: 0.7796 (tmt-80)
REVERT: K   75 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8620 (ttmm)
REVERT: M  102 GLU cc_start: 0.6346 (tm-30) cc_final: 0.5984 (tm-30)
REVERT: M  106 HIS cc_start: 0.8493 (OUTLIER) cc_final: 0.8255 (m-70)
REVERT: M  117 LYS cc_start: 0.8628 (tptm) cc_final: 0.8348 (mtpt)
REVERT: O   37 LYS cc_start: 0.8094 (tppt) cc_final: 0.7757 (ptpp)
REVERT: O   84 PHE cc_start: 0.8812 (OUTLIER) cc_final: 0.8526 (m-80)
REVERT: Q   35 ARG cc_start: 0.7390 (mtp85) cc_final: 0.7153 (mtp85)
REVERT: S   77 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8176 (mp)
  outliers start: 33
  outliers final: 23
  residues processed: 129
  average time/residue: 0.1534
  time to fit residues: 26.7283
Evaluate side-chains
  125 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain I residue   90 MET
Chi-restraints excluded: chain J residue   62 LEU
Chi-restraints excluded: chain K residue   16 THR
Chi-restraints excluded: chain K residue   65 LEU
Chi-restraints excluded: chain M residue   36 ILE
Chi-restraints excluded: chain M residue   44 GLN
Chi-restraints excluded: chain M residue  106 HIS
Chi-restraints excluded: chain M residue  112 THR
Chi-restraints excluded: chain O residue   39 HIS
Chi-restraints excluded: chain O residue   84 PHE
Chi-restraints excluded: chain O residue   87 SER
Chi-restraints excluded: chain O residue  118 THR
Chi-restraints excluded: chain Q residue   27 GLN
Chi-restraints excluded: chain Q residue   50 ILE
Chi-restraints excluded: chain Q residue   82 THR
Chi-restraints excluded: chain R residue   16 THR
Chi-restraints excluded: chain R residue   38 ASN
Chi-restraints excluded: chain R residue   62 ILE
Chi-restraints excluded: chain R residue  101 THR
Chi-restraints excluded: chain S residue   53 SER
Chi-restraints excluded: chain S residue   77 LEU
Chi-restraints excluded: chain S residue   87 THR
Chi-restraints excluded: chain S residue  105 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 37 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 46 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.116734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.088777 restraints weight = 32128.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.090817 restraints weight = 17542.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.092161 restraints weight = 12013.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.092983 restraints weight = 9641.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.093446 restraints weight = 8533.110|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.4572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  13403  Z= 0.175
  Angle     :  0.632   6.612  19459  Z= 0.374
  Chirality :  0.038   0.165   2218
  Planarity :  0.004   0.051   1377
  Dihedral  : 33.274 179.950   4271
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 24.84 %
    Favored  : 72.47 %
  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 aren not related in a simple way.
  whole:  1.22 (0.31), residues: 760
  helix:  1.88 (0.23), residues: 525
  sheet:  None (None), residues: 0
  loop : -1.75 (0.37), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG R  35 
 TYR   0.047   0.002   TYR Q  88 
 PHE   0.007   0.001   PHE S  62 
 HIS   0.014   0.001   HIS M 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (13403)
  covalent geometry    : angle       0.63248 (19459)
  hydrogen bonds       : bond        0.07681 (  768)
  hydrogen bonds       : angle       3.02473 ( 1860)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 119
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   64 GLU cc_start: 0.8366 (tm-30) cc_final: 0.7993 (tm-30)
REVERT: K   75 LYS cc_start: 0.8529 (ttmm) cc_final: 0.8176 (ttmm)
REVERT: M   43 LYS cc_start: 0.7244 (tppt) cc_final: 0.6573 (ptpt)
REVERT: M  117 LYS cc_start: 0.8592 (tptm) cc_final: 0.8276 (mtpt)
REVERT: O   84 PHE cc_start: 0.8874 (OUTLIER) cc_final: 0.8613 (m-80)
REVERT: O  105 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6890 (mm-30)
REVERT: Q   35 ARG cc_start: 0.7164 (mtp85) cc_final: 0.6615 (mtt90)
  outliers start: 17
  outliers final: 11
  residues processed: 131
  average time/residue: 0.1565
  time to fit residues: 27.7260
Evaluate side-chains
  125 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 113
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain K residue   16 THR
Chi-restraints excluded: chain O residue   39 HIS
Chi-restraints excluded: chain O residue   84 PHE
Chi-restraints excluded: chain Q residue   82 THR
Chi-restraints excluded: chain R residue   16 THR
Chi-restraints excluded: chain R residue   38 ASN
Chi-restraints excluded: chain R residue   62 ILE
Chi-restraints excluded: chain S residue   53 SER
Chi-restraints excluded: chain S residue   87 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 72 optimal weight:    1.9990
   chunk 41 optimal weight:    0.6980
   chunk 86 optimal weight:    0.6980
   chunk 24 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.116784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.088741 restraints weight = 32145.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.090754 restraints weight = 17638.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.092094 restraints weight = 12098.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.092878 restraints weight = 9712.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.093394 restraints weight = 8614.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3583
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.4678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  13403  Z= 0.173
  Angle     :  0.629   5.969  19459  Z= 0.371
  Chirality :  0.038   0.151   2218
  Planarity :  0.004   0.049   1377
  Dihedral  : 33.209 179.296   4271
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 10.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 26.58 %
    Favored  : 71.36 %
  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 aren not related in a simple way.
  whole:  1.44 (0.31), residues: 760
  helix:  2.05 (0.23), residues: 527
  sheet:  None (None), residues: 0
  loop : -1.74 (0.37), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K  35 
 TYR   0.065   0.002   TYR Q  88 
 PHE   0.009   0.001   PHE S  62 
 HIS   0.011   0.001   HIS M 106 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (13403)
  covalent geometry    : angle       0.62946 (19459)
  hydrogen bonds       : bond        0.07653 (  768)
  hydrogen bonds       : angle       2.99980 ( 1860)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   64 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8120 (tm-30)
REVERT: K   75 LYS cc_start: 0.8566 (ttmm) cc_final: 0.8210 (ttmm)
REVERT: M   43 LYS cc_start: 0.7225 (tppt) cc_final: 0.6587 (ptpt)
REVERT: M  117 LYS cc_start: 0.8573 (tptm) cc_final: 0.8325 (mtpt)
REVERT: O   50 GLU cc_start: 0.8364 (mp0) cc_final: 0.8140 (mp0)
REVERT: Q   35 ARG cc_start: 0.7259 (mtp85) cc_final: 0.6780 (mtt90)
  outliers start: 13
  outliers final: 10
  residues processed: 122
  average time/residue: 0.1689
  time to fit residues: 27.2677
Evaluate side-chains
  121 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain I residue  112 ILE
Chi-restraints excluded: chain K residue   16 THR
Chi-restraints excluded: chain O residue   39 HIS
Chi-restraints excluded: chain R residue   16 THR
Chi-restraints excluded: chain R residue   38 ASN
Chi-restraints excluded: chain R residue   62 ILE
Chi-restraints excluded: chain S residue   87 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 63 optimal weight:    0.5980
   chunk 0 optimal weight:    5.9990
   chunk 14 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0010
   chunk 45 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 93 optimal weight:    6.9990
   chunk 23 optimal weight:    0.1980
   overall best weight:    0.9590

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

Flipped N/Q/H residues before XYZ refinement:
M  92 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.116850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.088865 restraints weight = 32171.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.090820 restraints weight = 17573.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.092079 restraints weight = 11975.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.092895 restraints weight = 9630.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.093395 restraints weight = 8502.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.4758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  13403  Z= 0.179
  Angle     :  0.635   8.695  19459  Z= 0.373
  Chirality :  0.038   0.150   2218
  Planarity :  0.004   0.049   1377
  Dihedral  : 33.143 179.954   4271
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 10.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 26.11 %
    Favored  : 71.52 %
  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 aren not related in a simple way.
  whole:  1.47 (0.31), residues: 760
  helix:  2.05 (0.23), residues: 527
  sheet:  None (None), residues: 0
  loop : -1.65 (0.38), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K  35 
 TYR   0.045   0.002   TYR Q  88 
 PHE   0.009   0.001   PHE S  62 
 HIS   0.006   0.001   HIS I  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (13403)
  covalent geometry    : angle       0.63505 (19459)
  hydrogen bonds       : bond        0.07708 (  768)
  hydrogen bonds       : angle       3.00867 ( 1860)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
REVERT: K   64 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8013 (tm-30)
REVERT: K   71 ARG cc_start: 0.7747 (tpt90) cc_final: 0.7430 (tpt-90)
REVERT: K   75 LYS cc_start: 0.8456 (ttmm) cc_final: 0.8084 (ttmm)
REVERT: M   43 LYS cc_start: 0.7280 (tppt) cc_final: 0.6566 (ptpt)
REVERT: M  117 LYS cc_start: 0.8600 (tptm) cc_final: 0.8287 (mtpt)
REVERT: O   37 LYS cc_start: 0.7994 (tppt) cc_final: 0.7723 (ptpp)
REVERT: O   50 GLU cc_start: 0.8503 (mp0) cc_final: 0.8193 (mp0)
REVERT: O  105 GLU cc_start: 0.7509 (mm-30) cc_final: 0.7265 (mm-30)
REVERT: Q   35 ARG cc_start: 0.7133 (mtp85) cc_final: 0.6612 (mtt90)
REVERT: S   90 GLU cc_start: 0.7380 (mp0) cc_final: 0.7163 (mp0)
  outliers start: 15
  outliers final: 13
  residues processed: 121
  average time/residue: 0.1698
  time to fit residues: 27.1127
Evaluate side-chains
  122 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 109
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain K residue   15 LYS
Chi-restraints excluded: chain K residue   16 THR
Chi-restraints excluded: chain O residue   39 HIS
Chi-restraints excluded: chain O residue  118 THR
Chi-restraints excluded: chain Q residue   27 GLN
Chi-restraints excluded: chain R residue   16 THR
Chi-restraints excluded: chain R residue   38 ASN
Chi-restraints excluded: chain R residue   62 ILE
Chi-restraints excluded: chain S residue   53 SER
Chi-restraints excluded: chain S residue   87 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 7 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 100 optimal weight:    5.9990
   chunk 98 optimal weight:    6.9990
   chunk 1 optimal weight:    6.9990
   chunk 87 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.9382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.116757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.088703 restraints weight = 32005.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.090697 restraints weight = 17413.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.091985 restraints weight = 11944.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.092778 restraints weight = 9618.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.093272 restraints weight = 8527.624|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.4832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  13403  Z= 0.179
  Angle     :  0.638   7.855  19459  Z= 0.374
  Chirality :  0.037   0.144   2218
  Planarity :  0.004   0.049   1377
  Dihedral  : 33.121 179.949   4271
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 26.27 %
    Favored  : 71.52 %
  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 aren not related in a simple way.
  whole:  1.49 (0.31), residues: 760
  helix:  2.07 (0.23), residues: 527
  sheet:  None (None), residues: 0
  loop : -1.66 (0.38), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K  35 
 TYR   0.083   0.002   TYR Q  88 
 PHE   0.009   0.001   PHE S  62 
 HIS   0.006   0.001   HIS I  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (13403)
  covalent geometry    : angle       0.63766 (19459)
  hydrogen bonds       : bond        0.07687 (  768)
  hydrogen bonds       : angle       2.99948 ( 1860)

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

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

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1520 Ramachandran restraints generated.
    760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: K   64 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8028 (tm-30)
REVERT: K   71 ARG cc_start: 0.7705 (tpt90) cc_final: 0.7429 (tpt-90)
REVERT: K   75 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8211 (ttmm)
REVERT: M   43 LYS cc_start: 0.7100 (tppt) cc_final: 0.6513 (ptpt)
REVERT: M  117 LYS cc_start: 0.8575 (tptm) cc_final: 0.8348 (mtpt)
REVERT: O   37 LYS cc_start: 0.8032 (tppt) cc_final: 0.7751 (ptpp)
REVERT: O   50 GLU cc_start: 0.8316 (mp0) cc_final: 0.8066 (mp0)
REVERT: O  105 GLU cc_start: 0.7387 (mm-30) cc_final: 0.7161 (mm-30)
REVERT: Q   35 ARG cc_start: 0.7273 (mtp85) cc_final: 0.6797 (mtt90)
REVERT: S   43 LYS cc_start: 0.8226 (tptt) cc_final: 0.7847 (ttpt)
  outliers start: 14
  outliers final: 14
  residues processed: 122
  average time/residue: 0.1702
  time to fit residues: 27.4681
Evaluate side-chains
  125 residues out of total 646 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 111
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   46 VAL
Chi-restraints excluded: chain I residue   60 LEU
Chi-restraints excluded: chain I residue   65 LEU
Chi-restraints excluded: chain I residue   90 MET
Chi-restraints excluded: chain K residue   15 LYS
Chi-restraints excluded: chain K residue   16 THR
Chi-restraints excluded: chain O residue   39 HIS
Chi-restraints excluded: chain O residue  118 THR
Chi-restraints excluded: chain Q residue   27 GLN
Chi-restraints excluded: chain R residue   16 THR
Chi-restraints excluded: chain R residue   38 ASN
Chi-restraints excluded: chain R residue   62 ILE
Chi-restraints excluded: chain S residue   53 SER
Chi-restraints excluded: chain S residue   87 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 89 optimal weight:    5.9990
   chunk 85 optimal weight:    0.6980
   chunk 39 optimal weight:    2.9990
   chunk 48 optimal weight:    0.4980
   chunk 54 optimal weight:    0.0980
   chunk 46 optimal weight:    0.9990
   chunk 58 optimal weight:    0.6980
   chunk 7 optimal weight:    4.9990
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.118304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.090071 restraints weight = 32133.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.092190 restraints weight = 17055.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.093581 restraints weight = 11483.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.094469 restraints weight = 9130.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.094938 restraints weight = 8021.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.4888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  13403  Z= 0.166
  Angle     :  0.621   7.242  19459  Z= 0.365
  Chirality :  0.037   0.146   2218
  Planarity :  0.004   0.051   1377
  Dihedral  : 33.036 179.513   4271
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 26.58 %
    Favored  : 71.68 %
  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:  1.63 (0.31), residues: 760
  helix:  2.15 (0.23), residues: 528
  sheet:  None (None), residues: 0
  loop : -1.55 (0.38), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K  35 
 TYR   0.032   0.002   TYR S  80 
 PHE   0.007   0.001   PHE S  62 
 HIS   0.005   0.001   HIS I  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (13403)
  covalent geometry    : angle       0.62136 (19459)
  hydrogen bonds       : bond        0.07272 (  768)
  hydrogen bonds       : angle       2.91067 ( 1860)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2572.91 seconds
wall clock time: 45 minutes 3.30 seconds (2703.30 seconds total)