Starting phenix.real_space_refine
on Thu Sep 18 18:22:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9h9k_51967/09_2025/9h9k_51967_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9h9k_51967/09_2025/9h9k_51967.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9h9k_51967/09_2025/9h9k_51967.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9h9k_51967/09_2025/9h9k_51967.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9h9k_51967/09_2025/9h9k_51967_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9h9k_51967/09_2025/9h9k_51967_neut.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
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: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     478      5.49       5
     Mg     30      5.21       5
     S      27      5.16       5
     C    9970      2.51       5
     N    3505      2.21       5
     O    4858      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 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: 18869
  Number of models: 1
  Model: ""
    Number of chains: 15
    Chain: "1"
      Number of atoms: 9758
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 456, 9758
          Classifications: {'RNA': 456}
          Modifications used: {'rna2p_pur': 36, 'rna2p_pyr': 35, 'rna3p': 3, 'rna3p_pur': 212, 'rna3p_pyr': 170}
          Link IDs: {'rna2p': 71, 'rna3p': 384}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 3
    Chain: "2"
      Number of atoms: 107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 107
          Classifications: {'RNA': 5}
          Modifications used: {'rna2p_pyr': 1, 'rna3p_pur': 3, 'rna3p_pyr': 1}
          Link IDs: {'rna3p': 4}
    Chain: "3"
      Number of atoms: 361
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 361
          Classifications: {'RNA': 17}
          Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 9}
          Link IDs: {'rna3p': 16}
    Chain: "B"
      Number of atoms: 1753
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 224, 1753
          Classifications: {'peptide': 224}
          Link IDs: {'PTRANS': 7, 'TRANS': 216}
    Chain: "C"
      Number of atoms: 1653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1653
          Classifications: {'peptide': 211}
          Link IDs: {'PTRANS': 7, 'TRANS': 203}
    Chain: "G"
      Number of atoms: 1023
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 131, 1023
          Classifications: {'peptide': 131}
          Link IDs: {'PTRANS': 5, 'TRANS': 125}
    Chain: "I"
      Number of atoms: 1021
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 1021
          Classifications: {'peptide': 127}
          Link IDs: {'PTRANS': 3, 'TRANS': 123}
    Chain: "J"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 803
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 5, 'TRANS': 94}
    Chain: "M"
      Number of atoms: 891
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 115, 891
          Classifications: {'peptide': 115}
          Link IDs: {'PTRANS': 4, 'TRANS': 110}
    Chain: "N"
      Number of atoms: 805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 805
          Classifications: {'peptide': 100}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
    Chain: "S"
      Number of atoms: 663
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 663
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 5, 'TRANS': 77}
    Chain: "1"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 28
          Unusual residues: {' MG': 28}
          Classifications: {'undetermined': 28}
          Link IDs: {None: 27}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "I"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "N"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 4.13, per 1000 atoms: 0.22
  Number of scatterers: 18869
  At special positions: 0
  Unit cell: (140.238, 115.752, 168.063, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      27     16.00
     P     478     15.00
     Mg     30     11.99
     O    4858      8.00
     N    3505      7.00
     C    9970      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.50
  Conformation dependent library (CDL) restraints added in 423.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN B 301 "
        pdb="ZN    ZN B 301 " - pdb=" NE2 HIS B  18 "


  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2018

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 9 sheets defined
      50.2% alpha, 10.4% beta
      123 base pairs and 221 stacking pairs defined.
    Time for finding SS restraints: 3.09
  Creating SS restraints...
    Processing helix  chain 'B' and resid 5 through 12
    Processing helix  chain 'B' and resid 42 through 63
      Proline residue:  B  48  - end of helix
      removed outlier: 3.667A  pdb=" N   LYS B  59 " --> pdb=" O   ALA B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 75
      No H-bonds generated for 'chain 'B' and resid 73 through 75'
    Processing helix  chain 'B' and resid 76 through 87
      removed outlier: 3.606A  pdb=" N   LYS B  81 " --> pdb=" O   SER B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 103 through 124
      removed outlier: 4.468A  pdb=" N   GLN B 109 " --> pdb=" O   LYS B 105 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   SER B 110 " --> pdb=" O   THR B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 129
    Processing helix  chain 'B' and resid 130 through 149
      removed outlier: 4.068A  pdb=" N   SER B 147 " --> pdb=" O   LYS B 143 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 155
      removed outlier: 5.841A  pdb=" N   ASP B 153 " --> pdb=" O   GLY B 150 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   GLY B 155 " --> pdb=" O   LYS B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 179
      removed outlier: 3.741A  pdb=" N   ASN B 178 " --> pdb=" O   LYS B 174 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   LEU B 179 " --> pdb=" O   GLU B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 196
      removed outlier: 4.223A  pdb=" N   GLY B 195 " --> pdb=" O   ASP B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 206 through 226
    Processing helix  chain 'C' and resid 6 through 13
      removed outlier: 4.349A  pdb=" N   GLY C  13 " --> pdb=" O   GLY C   9 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 25 through 48
      removed outlier: 4.440A  pdb=" N   ALA C  30 " --> pdb=" O   THR C  26 " (cutoff:3.500A)
      removed outlier: 5.430A  pdb=" N   ASP C  31 " --> pdb=" O   LYS C  27 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 78
      removed outlier: 3.633A  pdb=" N   VAL C  76 " --> pdb=" O   ARG C  72 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 81 through 95
      removed outlier: 4.130A  pdb=" N   GLU C  85 " --> pdb=" O   GLY C  81 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   LYS C  86 " --> pdb=" O   GLU C  82 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   VAL C  90 " --> pdb=" O   LYS C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 108 through 111
    Processing helix  chain 'C' and resid 112 through 126
    Processing helix  chain 'C' and resid 129 through 146
    Processing helix  chain 'C' and resid 157 through 160
    Processing helix  chain 'G' and resid 20 through 31
    Processing helix  chain 'G' and resid 35 through 52
    Processing helix  chain 'G' and resid 57 through 70
      removed outlier: 3.648A  pdb=" N   VAL G  69 " --> pdb=" O   ALA G  65 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 92 through 112
      removed outlier: 4.298A  pdb=" N   GLY G 112 " --> pdb=" O   ALA G 108 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 115 through 130
    Processing helix  chain 'I' and resid 35 through 39
    Processing helix  chain 'I' and resid 41 through 56
      removed outlier: 4.112A  pdb=" N   ARG I  45 " --> pdb=" O   ARG I  41 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLN I  50 " --> pdb=" O   MET I  46 " (cutoff:3.500A)
      Proline residue:  I  51  - end of helix
      removed outlier: 3.558A  pdb=" N   VAL I  55 " --> pdb=" O   PRO I  51 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 71 through 91
    Processing helix  chain 'I' and resid 94 through 101
    Processing helix  chain 'J' and resid 14 through 32
      removed outlier: 3.714A  pdb=" N   THR J  32 " --> pdb=" O   THR J  28 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 80 through 90
    Processing helix  chain 'M' and resid 14 through 21
    Processing helix  chain 'M' and resid 26 through 37
    Processing helix  chain 'M' and resid 49 through 62
      removed outlier: 3.611A  pdb=" N   LYS M  62 " --> pdb=" O   ASP M  58 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 65 through 82
    Processing helix  chain 'M' and resid 85 through 93
    Processing helix  chain 'M' and resid 106 through 111
    Processing helix  chain 'N' and resid 3 through 33
      removed outlier: 3.506A  pdb=" N   PHE N  21 " --> pdb=" O   ALA N  17 " (cutoff:3.500A)
      removed outlier: 5.419A  pdb=" N   ALA N  22 " --> pdb=" O   ASP N  18 " (cutoff:3.500A)
      removed outlier: 5.848A  pdb=" N   LYS N  23 " --> pdb=" O   LYS N  19 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 37 through 49
      removed outlier: 3.634A  pdb=" N   GLN N  49 " --> pdb=" O   VAL N  45 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 50 through 51
      No H-bonds generated for 'chain 'N' and resid 50 through 51'
    Processing helix  chain 'N' and resid 52 through 60
      Proline residue:  N  57  - end of helix
    Processing helix  chain 'N' and resid 81 through 90
      removed outlier: 3.794A  pdb=" N   ARG N  85 " --> pdb=" O   ARG N  81 " (cutoff:3.500A)
      removed outlier: 4.644A  pdb=" N   GLU N  86 " --> pdb=" O   ILE N  82 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 12 through 26
    Processing helix  chain 'S' and resid 63 through 67
    Processing helix  chain 'S' and resid 71 through 75
    Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 35
    Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 92
      removed outlier: 6.693A  pdb=" N   ILE B  67 " --> pdb=" O   PHE B  90 " (cutoff:3.500A)
      removed outlier: 8.582A  pdb=" N   VAL B  92 " --> pdb=" O   ILE B  67 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   PHE B  69 " --> pdb=" O   VAL B  92 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   LEU B  68 " --> pdb=" O   PHE B 162 " (cutoff:3.500A)
      removed outlier: 6.026A  pdb=" N   VAL B 183 " --> pdb=" O   PHE B 198 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   ILE B 200 " --> pdb=" O   VAL B 183 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   ALA B 185 " --> pdb=" O   ILE B 200 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 54 through 58
      removed outlier: 6.822A  pdb=" N   VAL C  66 " --> pdb=" O   ASN C 102 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   ALA C 104 " --> pdb=" O   VAL C  66 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   ILE C  68 " --> pdb=" O   ALA C 104 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 164 through 170
    Processing sheet with id=AA5, first strand: chain 'G' and resid 73 through 74
    Processing sheet with id=AA6, first strand: chain 'I' and resid 6 through 12
      removed outlier: 3.501A  pdb=" N   ARG I  12 " --> pdb=" O   SER I  15 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'I' and resid 15 through 23
    current: chain 'I' and resid 33 through 34
    Processing sheet with id=AA7, first strand: chain 'J' and resid 5 through 12
  WARNING: can't find start of bonding for strands!
    previous: chain 'J' and resid 5 through 12
    current: chain 'J' and resid 63 through 77
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'N' and resid 73 through 74
    Processing sheet with id=AA9, first strand: chain 'S' and resid 31 through 33
      removed outlier: 6.071A  pdb=" N   LEU S  31 " --> pdb=" O   ALA S  50 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   HIS S  52 " --> pdb=" O   LEU S  31 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   THR S  33 " --> pdb=" O   HIS S  52 " (cutoff:3.500A)

    394 hydrogen bonds defined for protein.
    1116 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      306 hydrogen bonds
      482 hydrogen bond angles
      0 basepair planarities
      123 basepair parallelities
      221 stacking parallelities
  Total time for adding SS restraints: 4.26

  Time building geometry restraints manager: 1.86 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2236
        1.32 -     1.44: 7994
        1.44 -     1.57: 8948
        1.57 -     1.69: 953
        1.69 -     1.81: 51
  Bond restraints: 20182
  Sorted by residual:
  bond pdb=" C5  2MG 1 966 "
       pdb=" C4  2MG 1 966 "
    ideal  model  delta    sigma   weight residual
    1.382  1.469 -0.087 2.00e-02 2.50e+03 1.87e+01
  bond pdb=" C5  2MG 11207 "
       pdb=" C4  2MG 11207 "
    ideal  model  delta    sigma   weight residual
    1.382  1.465 -0.083 2.00e-02 2.50e+03 1.73e+01
  bond pdb=" N   PRO B  25 "
       pdb=" CA  PRO B  25 "
    ideal  model  delta    sigma   weight residual
    1.469  1.425  0.044 1.28e-02 6.10e+03 1.18e+01
  bond pdb=" CA  PRO B  25 "
       pdb=" C   PRO B  25 "
    ideal  model  delta    sigma   weight residual
    1.520  1.471  0.048 1.42e-02 4.96e+03 1.14e+01
  bond pdb=" C   HIS J  56 "
       pdb=" O   HIS J  56 "
    ideal  model  delta    sigma   weight residual
    1.241  1.205  0.036 1.08e-02 8.57e+03 1.11e+01
  ... (remaining 20177 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 28978
        2.56 -     5.11: 520
        5.11 -     7.67: 47
        7.67 -    10.22: 18
       10.22 -    12.78: 7
  Bond angle restraints: 29570
  Sorted by residual:
  angle pdb=" N   LYS G 114 "
        pdb=" CA  LYS G 114 "
        pdb=" C   LYS G 114 "
      ideal   model   delta    sigma   weight residual
     111.07  123.85  -12.78 1.07e+00 8.73e-01 1.43e+02
  angle pdb=" N   VAL J  57 "
        pdb=" CA  VAL J  57 "
        pdb=" C   VAL J  57 "
      ideal   model   delta    sigma   weight residual
     110.62  121.00  -10.38 1.02e+00 9.61e-01 1.04e+02
  angle pdb=" P     A 11101 "
        pdb=" O5'   A 11101 "
        pdb=" C5'   A 11101 "
      ideal   model   delta    sigma   weight residual
     120.90  131.60  -10.70 1.50e+00 4.44e-01 5.09e+01
  angle pdb=" N   HIS J  56 "
        pdb=" CA  HIS J  56 "
        pdb=" C   HIS J  56 "
      ideal   model   delta    sigma   weight residual
     108.00  118.17  -10.17 1.48e+00 4.57e-01 4.72e+01
  angle pdb=" N   PRO B  25 "
        pdb=" CA  PRO B  25 "
        pdb=" C   PRO B  25 "
      ideal   model   delta    sigma   weight residual
     112.47  101.36   11.11 2.06e+00 2.36e-01 2.91e+01
  ... (remaining 29565 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.93: 11599
       34.93 -    69.86: 1149
       69.86 -   104.80: 141
      104.80 -   139.73: 7
      139.73 -   174.66: 3
  Dihedral angle restraints: 12899
    sinusoidal: 9780
      harmonic: 3119
  Sorted by residual:
  dihedral pdb=" C4'   A 11101 "
           pdb=" C3'   A 11101 "
           pdb=" C2'   A 11101 "
           pdb=" C1'   A 11101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   30.03  -65.03     1      8.00e+00 1.56e-02 8.67e+01
  dihedral pdb=" C5'   A 11101 "
           pdb=" C4'   A 11101 "
           pdb=" C3'   A 11101 "
           pdb=" O3'   A 11101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   83.23   63.77     1      8.00e+00 1.56e-02 8.37e+01
  dihedral pdb=" O4'   U 1 960 "
           pdb=" C1'   U 1 960 "
           pdb=" N1    U 1 960 "
           pdb=" C2    U 1 960 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   46.66 -174.66     1      1.70e+01 3.46e-03 6.63e+01
  ... (remaining 12896 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.336: 3697
       0.336 -    0.672: 2
       0.672 -    1.009: 0
       1.009 -    1.345: 0
       1.345 -    1.681: 1
  Chirality restraints: 3700
  Sorted by residual:
  chirality pdb=" CG  LEU S  15 "
            pdb=" CB  LEU S  15 "
            pdb=" CD1 LEU S  15 "
            pdb=" CD2 LEU S  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -0.91   -1.68 2.00e-01 2.50e+01 7.07e+01
  chirality pdb=" P     A 2  15 "
            pdb=" OP1   A 2  15 "
            pdb=" OP2   A 2  15 "
            pdb=" O5'   A 2  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.96   -0.55 2.00e-01 2.50e+01 7.47e+00
  chirality pdb=" P     C 1 931 "
            pdb=" OP1   C 1 931 "
            pdb=" OP2   C 1 931 "
            pdb=" O5'   C 1 931 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.89   -0.48 2.00e-01 2.50e+01 5.72e+00
  ... (remaining 3697 not shown)

  Planarity restraints: 1992
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' 2MG 1 966 "   -0.024 2.00e-02 2.50e+03   4.63e-02 6.96e+01
        pdb=" N9  2MG 1 966 "   -0.004 2.00e-02 2.50e+03
        pdb=" C8  2MG 1 966 "    0.022 2.00e-02 2.50e+03
        pdb=" N7  2MG 1 966 "    0.031 2.00e-02 2.50e+03
        pdb=" C5  2MG 1 966 "    0.009 2.00e-02 2.50e+03
        pdb=" C6  2MG 1 966 "    0.006 2.00e-02 2.50e+03
        pdb=" O6  2MG 1 966 "    0.024 2.00e-02 2.50e+03
        pdb=" N1  2MG 1 966 "   -0.022 2.00e-02 2.50e+03
        pdb=" C2  2MG 1 966 "   -0.043 2.00e-02 2.50e+03
        pdb=" N2  2MG 1 966 "   -0.069 2.00e-02 2.50e+03
        pdb=" N3  2MG 1 966 "   -0.041 2.00e-02 2.50e+03
        pdb=" C4  2MG 1 966 "   -0.016 2.00e-02 2.50e+03
        pdb=" CM2 2MG 1 966 "    0.127 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' 2MG 11207 "   -0.031 2.00e-02 2.50e+03   4.36e-02 6.17e+01
        pdb=" N9  2MG 11207 "    0.004 2.00e-02 2.50e+03
        pdb=" C8  2MG 11207 "    0.019 2.00e-02 2.50e+03
        pdb=" N7  2MG 11207 "    0.029 2.00e-02 2.50e+03
        pdb=" C5  2MG 11207 "    0.007 2.00e-02 2.50e+03
        pdb=" C6  2MG 11207 "    0.005 2.00e-02 2.50e+03
        pdb=" O6  2MG 11207 "    0.023 2.00e-02 2.50e+03
        pdb=" N1  2MG 11207 "   -0.022 2.00e-02 2.50e+03
        pdb=" C2  2MG 11207 "   -0.040 2.00e-02 2.50e+03
        pdb=" N2  2MG 11207 "   -0.065 2.00e-02 2.50e+03
        pdb=" N3  2MG 11207 "   -0.035 2.00e-02 2.50e+03
        pdb=" C4  2MG 11207 "   -0.013 2.00e-02 2.50e+03
        pdb=" CM2 2MG 11207 "    0.120 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS I 129 "    0.031 2.00e-02 2.50e+03   6.17e-02 3.81e+01
        pdb=" C   LYS I 129 "   -0.107 2.00e-02 2.50e+03
        pdb=" O   LYS I 129 "    0.040 2.00e-02 2.50e+03
        pdb=" N   ARG I 130 "    0.036 2.00e-02 2.50e+03
  ... (remaining 1989 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.48: 255
        2.48 -     3.08: 15242
        3.08 -     3.69: 36835
        3.69 -     4.29: 51201
        4.29 -     4.90: 71323
  Nonbonded interactions: 174856
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 205 "
            pdb="ZN    ZN B 301 "
     model   vdw
     1.872 2.230
  nonbonded pdb=" O2'   C 11226 "
            pdb=" O   THR M 102 "
     model   vdw
     1.885 3.040
  nonbonded pdb=" O2'   A 11067 "
            pdb=" O2'   A 11093 "
     model   vdw
     1.894 3.040
  nonbonded pdb=" OD2 ASP B 188 "
            pdb="ZN    ZN B 301 "
     model   vdw
     1.908 2.230
  nonbonded pdb=" O2'   C 11237 "
            pdb=" O4'   U 11335 "
     model   vdw
     1.919 3.040
  ... (remaining 174851 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             5.500
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     21.550
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5777
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.175  20184  Z= 0.373
  Angle     :  0.894  12.776  29570  Z= 0.521
  Chirality :  0.056   1.681   3700
  Planarity :  0.007   0.098   1992
  Dihedral  : 22.145 174.660  10881
  Min Nonbonded Distance : 1.872

Molprobity Statistics.
  All-atom Clashscore : 28.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  7.71 %
    Favored  : 91.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.55 (0.24), residues: 1075
  helix: -0.78 (0.22), residues: 475
  sheet: -0.55 (0.40), residues: 152
  loop : -1.32 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG I  41 
 TYR   0.015   0.002   TYR I  38 
 PHE   0.023   0.002   PHE B  90 
 TRP   0.013   0.002   TRP C 167 
 HIS   0.011   0.002   HIS J  56 

Details of bonding type rmsd
  covalent geometry    : bond        0.00634 (20182)
  covalent geometry    : angle       0.89450 (29570)
  hydrogen bonds       : bond        0.24963 (  700)
  hydrogen bonds       : angle       9.12110 ( 1598)
  metal coordination   : bond        0.17457 (    1)
  Misc. bond           : bond        0.14563 (    1)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 121
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   69 PHE cc_start: 0.6918 (m-80) cc_final: 0.6412 (m-80)
REVERT: C  195 VAL cc_start: 0.5393 (t) cc_final: 0.5157 (t)
  outliers start: 3
  outliers final: 1
  residues processed: 124
  average time/residue: 0.1998
  time to fit residues: 33.4013
Evaluate side-chains
  73 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 72
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue   90 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    4.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    5.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    0.8980
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    6.9990
   chunk 149 optimal weight:    6.9990
   overall best weight:    2.9386

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

Flipped N/Q/H residues before XYZ refinement:
B  24 ASN
B  89 GLN
B 103 ASN
B 109 GLN
C  25 ASN
G   9 GLN
J  58 ASN
M   8 ASN
M  14 HIS
S  14 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.057012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.050206 restraints weight = 231617.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.050852 restraints weight = 163862.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.051290 restraints weight = 128436.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.051545 restraints weight = 108081.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.051790 restraints weight = 96799.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6901
moved from start:          0.2245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  20184  Z= 0.199
  Angle     :  0.708   8.141  29570  Z= 0.365
  Chirality :  0.039   0.263   3700
  Planarity :  0.005   0.039   1992
  Dihedral  : 22.783 175.460   8694
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 11.89 %
    Favored  : 86.67 %
  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: -0.45 (0.24), residues: 1075
  helix:  0.41 (0.22), residues: 484
  sheet: -0.62 (0.36), residues: 177
  loop : -0.85 (0.30), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG G 111 
 TYR   0.018   0.002   TYR M  86 
 PHE   0.015   0.002   PHE B  16 
 TRP   0.017   0.002   TRP C 167 
 HIS   0.015   0.002   HIS M  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (20182)
  covalent geometry    : angle       0.70836 (29570)
  hydrogen bonds       : bond        0.08407 (  700)
  hydrogen bonds       : angle       4.59489 ( 1598)
  metal coordination   : bond        0.00657 (    1)
  Misc. bond           : bond        0.00248 (    1)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    9 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8351 (ptp)
REVERT: B   88 ASP cc_start: 0.9127 (t0) cc_final: 0.8788 (m-30)
REVERT: B  100 MET cc_start: 0.8709 (mtp) cc_final: 0.8170 (mpp)
REVERT: B  109 GLN cc_start: 0.9014 (mp-120) cc_final: 0.8764 (mp10)
REVERT: C   29 PHE cc_start: 0.5027 (OUTLIER) cc_final: 0.3437 (t80)
REVERT: C  164 ARG cc_start: 0.8567 (ptt90) cc_final: 0.8060 (ptt90)
REVERT: M   75 MET cc_start: 0.8672 (mmm) cc_final: 0.8382 (mmm)
REVERT: S   81 ARG cc_start: 0.7489 (tmm160) cc_final: 0.7220 (tmm160)
  outliers start: 13
  outliers final: 6
  residues processed: 93
  average time/residue: 0.1801
  time to fit residues: 23.2512
Evaluate side-chains
  79 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    9 MET
Chi-restraints excluded: chain B residue  170 HIS
Chi-restraints excluded: chain C residue   29 PHE
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue  118 ASP
Chi-restraints excluded: chain G residue   62 PHE
Chi-restraints excluded: chain M residue    7 ILE
Chi-restraints excluded: chain M residue   86 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 8 optimal weight:   10.0000
   chunk 84 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   chunk 117 optimal weight:    8.9990
   chunk 23 optimal weight:   10.0000
   chunk 115 optimal weight:    1.9990
   chunk 31 optimal weight:   20.0000
   chunk 141 optimal weight:    0.1980
   chunk 85 optimal weight:    0.6980
   chunk 146 optimal weight:    0.9980
   chunk 53 optimal weight:    6.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
B  24 ASN
** B  94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.058084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.051154 restraints weight = 230406.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.051842 restraints weight = 161711.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.052499 restraints weight = 125527.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.052723 restraints weight = 102015.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.053016 restraints weight = 91300.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3747
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6852
moved from start:          0.3149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  20184  Z= 0.128
  Angle     :  0.573   9.829  29570  Z= 0.296
  Chirality :  0.034   0.258   3700
  Planarity :  0.004   0.040   1992
  Dihedral  : 22.422 176.654   8692
  Min Nonbonded Distance : 1.922

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 12.89 %
    Favored  : 85.02 %
  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:  0.46 (0.25), residues: 1075
  helix:  1.19 (0.24), residues: 487
  sheet:  0.00 (0.37), residues: 162
  loop : -0.52 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  79 
 TYR   0.025   0.002   TYR C 168 
 PHE   0.017   0.001   PHE S  74 
 TRP   0.010   0.001   TRP C 167 
 HIS   0.007   0.001   HIS M  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (20182)
  covalent geometry    : angle       0.57280 (29570)
  hydrogen bonds       : bond        0.06264 (  700)
  hydrogen bonds       : angle       4.10524 ( 1598)
  metal coordination   : bond        0.00037 (    1)
  Misc. bond           : bond        0.00203 (    1)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    6 MET cc_start: 0.8854 (mpp) cc_final: 0.8523 (mmm)
REVERT: B   88 ASP cc_start: 0.9267 (t0) cc_final: 0.9014 (m-30)
REVERT: B  100 MET cc_start: 0.8776 (mtp) cc_final: 0.8121 (mpp)
REVERT: B  109 GLN cc_start: 0.9197 (mp-120) cc_final: 0.8900 (mp10)
REVERT: C   29 PHE cc_start: 0.5110 (OUTLIER) cc_final: 0.3701 (t80)
REVERT: C  152 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8618 (pp20)
REVERT: C  164 ARG cc_start: 0.8585 (ptt90) cc_final: 0.8012 (ptt90)
REVERT: M   75 MET cc_start: 0.8847 (mmm) cc_final: 0.8632 (mmm)
REVERT: S   32 ARG cc_start: 0.7979 (ttp80) cc_final: 0.7596 (ttt-90)
REVERT: S   44 MET cc_start: 0.8643 (ppp) cc_final: 0.8351 (ppp)
REVERT: S   81 ARG cc_start: 0.7675 (tmm160) cc_final: 0.7403 (tmm160)
  outliers start: 19
  outliers final: 13
  residues processed: 107
  average time/residue: 0.1678
  time to fit residues: 25.5689
Evaluate side-chains
  89 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  170 HIS
Chi-restraints excluded: chain C residue   14 ILE
Chi-restraints excluded: chain C residue   29 PHE
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  152 GLU
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain G residue   62 PHE
Chi-restraints excluded: chain G residue   66 LEU
Chi-restraints excluded: chain I residue   90 TYR
Chi-restraints excluded: chain I residue   98 LEU
Chi-restraints excluded: chain I residue  126 GLN
Chi-restraints excluded: chain M residue    7 ILE
Chi-restraints excluded: chain M residue   86 TYR
Chi-restraints excluded: chain M residue   97 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 38 optimal weight:    9.9990
   chunk 128 optimal weight:    0.0270
   chunk 31 optimal weight:   20.0000
   chunk 86 optimal weight:    8.9990
   chunk 78 optimal weight:    4.9990
   chunk 44 optimal weight:   10.0000
   chunk 22 optimal weight:   10.0000
   chunk 2 optimal weight:   10.0000
   chunk 115 optimal weight:    2.9990
   chunk 53 optimal weight:    8.9990
   chunk 105 optimal weight:    3.9990
   overall best weight:    4.2046

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

Flipped N/Q/H residues before XYZ refinement:
** S  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
S  83 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.055083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.048387 restraints weight = 238780.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.049083 restraints weight = 167093.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.049508 restraints weight = 130382.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.049772 restraints weight = 109032.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.050201 restraints weight = 97830.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6988
moved from start:          0.3463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  20184  Z= 0.220
  Angle     :  0.665   8.308  29570  Z= 0.340
  Chirality :  0.038   0.439   3700
  Planarity :  0.005   0.046   1992
  Dihedral  : 22.525 176.214   8692
  Min Nonbonded Distance : 1.832

Molprobity Statistics.
  All-atom Clashscore : 17.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 14.21 %
    Favored  : 82.27 %
  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:  0.11 (0.25), residues: 1075
  helix:  0.94 (0.23), residues: 490
  sheet: -0.16 (0.40), residues: 157
  loop : -0.77 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG I  49 
 TYR   0.020   0.002   TYR I  38 
 PHE   0.020   0.002   PHE C  37 
 TRP   0.015   0.002   TRP B  23 
 HIS   0.006   0.001   HIS J  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00425 (20182)
  covalent geometry    : angle       0.66502 (29570)
  hydrogen bonds       : bond        0.07741 (  700)
  hydrogen bonds       : angle       4.14339 ( 1598)
  metal coordination   : bond        0.00293 (    1)
  Misc. bond           : bond        0.00097 (    1)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 76
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 ASP cc_start: 0.9304 (t0) cc_final: 0.9059 (m-30)
REVERT: B  161 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8110 (tp)
REVERT: C   29 PHE cc_start: 0.4985 (OUTLIER) cc_final: 0.4353 (m-80)
REVERT: C  152 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8399 (tt0)
REVERT: M   75 MET cc_start: 0.8900 (mmm) cc_final: 0.8667 (mmm)
REVERT: N   92 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7623 (tp30)
REVERT: S   32 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7661 (ptt-90)
REVERT: S   44 MET cc_start: 0.8754 (ppp) cc_final: 0.8527 (ppp)
REVERT: S   81 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7285 (tmm160)
  outliers start: 32
  outliers final: 16
  residues processed: 99
  average time/residue: 0.1659
  time to fit residues: 23.4069
Evaluate side-chains
  88 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  170 HIS
Chi-restraints excluded: chain C residue   18 TRP
Chi-restraints excluded: chain C residue   29 PHE
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  118 ASP
Chi-restraints excluded: chain C residue  152 GLU
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain G residue   62 PHE
Chi-restraints excluded: chain G residue   66 LEU
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue   72 ILE
Chi-restraints excluded: chain I residue  113 ARG
Chi-restraints excluded: chain I residue  126 GLN
Chi-restraints excluded: chain M residue    7 ILE
Chi-restraints excluded: chain M residue   86 TYR
Chi-restraints excluded: chain N residue   38 ASP
Chi-restraints excluded: chain S residue   47 LEU
Chi-restraints excluded: chain S residue   81 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 13 optimal weight:   10.0000
   chunk 61 optimal weight:    9.9990
   chunk 82 optimal weight:    2.9990
   chunk 130 optimal weight:    0.1980
   chunk 105 optimal weight:    4.9990
   chunk 133 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 120 optimal weight:    5.9990
   chunk 111 optimal weight:    0.9980
   chunk 115 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   overall best weight:    2.4386

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

Flipped N/Q/H residues before XYZ refinement:
** S  57 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 = 0.3822 r_free = 0.3822 target = 0.055799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.048942 restraints weight = 231297.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.049655 restraints weight = 161766.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.050046 restraints weight = 125127.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.050312 restraints weight = 106164.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.050646 restraints weight = 95766.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6959
moved from start:          0.3989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  20184  Z= 0.145
  Angle     :  0.589  14.847  29570  Z= 0.303
  Chirality :  0.035   0.244   3700
  Planarity :  0.004   0.046   1992
  Dihedral  : 22.477 176.073   8692
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 15.86 %
    Favored  : 81.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.22 (0.25), residues: 1075
  helix:  1.09 (0.23), residues: 489
  sheet: -0.11 (0.39), residues: 159
  loop : -0.78 (0.30), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG N  61 
 TYR   0.021   0.002   TYR C 193 
 PHE   0.016   0.002   PHE C  37 
 TRP   0.049   0.002   TRP B  23 
 HIS   0.005   0.001   HIS J  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (20182)
  covalent geometry    : angle       0.58896 (29570)
  hydrogen bonds       : bond        0.06343 (  700)
  hydrogen bonds       : angle       4.05483 ( 1598)
  metal coordination   : bond        0.00176 (    1)
  Misc. bond           : bond        0.00183 (    1)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 74
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 ASP cc_start: 0.9271 (t0) cc_final: 0.9059 (m-30)
REVERT: B  161 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8316 (tp)
REVERT: C   29 PHE cc_start: 0.5085 (OUTLIER) cc_final: 0.4387 (m-80)
REVERT: C  123 GLN cc_start: 0.9399 (mt0) cc_final: 0.8984 (mt0)
REVERT: M   75 MET cc_start: 0.8787 (mmm) cc_final: 0.8475 (mmm)
REVERT: N   92 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7230 (tp30)
REVERT: S   32 ARG cc_start: 0.8190 (ttp80) cc_final: 0.7869 (ptt-90)
REVERT: S   44 MET cc_start: 0.8819 (ppp) cc_final: 0.8502 (ppp)
REVERT: S   81 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7431 (tmm160)
  outliers start: 24
  outliers final: 15
  residues processed: 90
  average time/residue: 0.1673
  time to fit residues: 21.7103
Evaluate side-chains
  86 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  170 HIS
Chi-restraints excluded: chain C residue   18 TRP
Chi-restraints excluded: chain C residue   29 PHE
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  118 ASP
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain G residue   62 PHE
Chi-restraints excluded: chain G residue   66 LEU
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue  111 VAL
Chi-restraints excluded: chain I residue  126 GLN
Chi-restraints excluded: chain J residue   17 LEU
Chi-restraints excluded: chain M residue    7 ILE
Chi-restraints excluded: chain M residue   86 TYR
Chi-restraints excluded: chain N residue   18 ASP
Chi-restraints excluded: chain S residue   81 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 137 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 83 optimal weight:    0.9990
   chunk 32 optimal weight:   20.0000
   chunk 54 optimal weight:    5.9990
   chunk 50 optimal weight:    0.3980
   chunk 52 optimal weight:   10.0000
   chunk 69 optimal weight:    0.2980
   chunk 72 optimal weight:    8.9990
   chunk 74 optimal weight:    6.9990
   chunk 111 optimal weight:    6.9990
   overall best weight:    2.9386

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

Flipped N/Q/H residues before XYZ refinement:
G  52 GLN
** S  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.054829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.048037 restraints weight = 234115.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.048706 restraints weight = 165498.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.049171 restraints weight = 128359.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.049541 restraints weight = 107554.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.049738 restraints weight = 95619.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7008
moved from start:          0.4373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  20184  Z= 0.168
  Angle     :  0.613  10.156  29570  Z= 0.312
  Chirality :  0.035   0.241   3700
  Planarity :  0.004   0.045   1992
  Dihedral  : 22.479 176.018   8692
  Min Nonbonded Distance : 1.823

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 16.85 %
    Favored  : 80.62 %
  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:  0.17 (0.25), residues: 1075
  helix:  1.09 (0.23), residues: 486
  sheet: -0.11 (0.40), residues: 157
  loop : -0.86 (0.30), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 136 
 TYR   0.031   0.002   TYR C 193 
 PHE   0.019   0.002   PHE S  74 
 TRP   0.032   0.002   TRP B  23 
 HIS   0.004   0.001   HIS J  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 (20182)
  covalent geometry    : angle       0.61259 (29570)
  hydrogen bonds       : bond        0.06723 (  700)
  hydrogen bonds       : angle       4.02298 ( 1598)
  metal coordination   : bond        0.00158 (    1)
  Misc. bond           : bond        0.00123 (    1)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 73
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   29 PHE cc_start: 0.5167 (OUTLIER) cc_final: 0.4547 (m-80)
REVERT: C  123 GLN cc_start: 0.9410 (mt0) cc_final: 0.8965 (mt0)
REVERT: C  152 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8439 (pp20)
REVERT: G  101 MET cc_start: 0.7754 (mmp) cc_final: 0.7418 (mmp)
REVERT: I  126 GLN cc_start: 0.4751 (OUTLIER) cc_final: 0.4217 (mt0)
REVERT: M   75 MET cc_start: 0.8777 (mmm) cc_final: 0.8509 (mmm)
REVERT: N   92 GLU cc_start: 0.7853 (mm-30) cc_final: 0.7265 (tp30)
REVERT: S   81 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7484 (tmm160)
  outliers start: 23
  outliers final: 13
  residues processed: 90
  average time/residue: 0.1568
  time to fit residues: 20.4560
Evaluate side-chains
  82 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  170 HIS
Chi-restraints excluded: chain C residue   18 TRP
Chi-restraints excluded: chain C residue   21 THR
Chi-restraints excluded: chain C residue   29 PHE
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue  118 ASP
Chi-restraints excluded: chain C residue  152 GLU
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain G residue   62 PHE
Chi-restraints excluded: chain G residue   66 LEU
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue  126 GLN
Chi-restraints excluded: chain J residue   17 LEU
Chi-restraints excluded: chain M residue    7 ILE
Chi-restraints excluded: chain M residue   86 TYR
Chi-restraints excluded: chain N residue  100 SER
Chi-restraints excluded: chain S residue   81 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 5 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 117 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 126 optimal weight:    0.3980
   chunk 69 optimal weight:    9.9990
   chunk 108 optimal weight:    9.9990
   chunk 148 optimal weight:    0.7980
   chunk 9 optimal weight:   20.0000
   chunk 44 optimal weight:   10.0000
   chunk 125 optimal weight:    8.9990
   overall best weight:    4.4386

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

Flipped N/Q/H residues before XYZ refinement:
N  43 ASN
** S  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.053294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.046577 restraints weight = 245007.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.047391 restraints weight = 169703.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.047837 restraints weight = 131006.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.048231 restraints weight = 108985.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.048416 restraints weight = 95990.137|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7077
moved from start:          0.4775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  20184  Z= 0.226
  Angle     :  0.684  12.448  29570  Z= 0.350
  Chirality :  0.038   0.235   3700
  Planarity :  0.005   0.068   1992
  Dihedral  : 22.686 175.411   8692
  Min Nonbonded Distance : 1.839

Molprobity Statistics.
  All-atom Clashscore : 19.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 17.62 %
    Favored  : 79.19 %
  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: -0.15 (0.25), residues: 1075
  helix:  0.82 (0.23), residues: 489
  sheet: -0.17 (0.40), residues: 149
  loop : -1.07 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 131 
 TYR   0.022   0.003   TYR I  38 
 PHE   0.019   0.002   PHE C  37 
 TRP   0.030   0.002   TRP B  23 
 HIS   0.006   0.001   HIS J  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 (20182)
  covalent geometry    : angle       0.68434 (29570)
  hydrogen bonds       : bond        0.07554 (  700)
  hydrogen bonds       : angle       4.27380 ( 1598)
  metal coordination   : bond        0.00252 (    1)
  Misc. bond           : bond        0.00148 (    1)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 65
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  161 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8472 (tp)
REVERT: C   29 PHE cc_start: 0.5113 (OUTLIER) cc_final: 0.4447 (m-80)
REVERT: C   45 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8628 (mttt)
REVERT: C  123 GLN cc_start: 0.9448 (mt0) cc_final: 0.9019 (mt0)
REVERT: C  152 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8226 (pp20)
REVERT: G  101 MET cc_start: 0.7861 (mmp) cc_final: 0.7522 (mmp)
REVERT: M   75 MET cc_start: 0.8792 (mmm) cc_final: 0.8544 (mmm)
REVERT: N   92 GLU cc_start: 0.7923 (mm-30) cc_final: 0.7599 (tp30)
REVERT: S   66 MET cc_start: 0.7667 (tpp) cc_final: 0.6820 (mmm)
REVERT: S   81 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7467 (tmm160)
  outliers start: 29
  outliers final: 17
  residues processed: 86
  average time/residue: 0.1554
  time to fit residues: 19.2872
Evaluate side-chains
  82 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 60
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  161 LEU
Chi-restraints excluded: chain B residue  170 HIS
Chi-restraints excluded: chain C residue   18 TRP
Chi-restraints excluded: chain C residue   29 PHE
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   45 LYS
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  118 ASP
Chi-restraints excluded: chain C residue  152 GLU
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain G residue   62 PHE
Chi-restraints excluded: chain G residue   66 LEU
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue  126 GLN
Chi-restraints excluded: chain J residue   17 LEU
Chi-restraints excluded: chain J residue   57 VAL
Chi-restraints excluded: chain J residue  101 SER
Chi-restraints excluded: chain M residue   86 TYR
Chi-restraints excluded: chain N residue   18 ASP
Chi-restraints excluded: chain N residue   37 SER
Chi-restraints excluded: chain N residue  100 SER
Chi-restraints excluded: chain S residue   81 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 135 optimal weight:    6.9990
   chunk 139 optimal weight:   10.0000
   chunk 55 optimal weight:    0.0170
   chunk 142 optimal weight:    0.9980
   chunk 104 optimal weight:    0.0570
   chunk 26 optimal weight:   10.0000
   chunk 133 optimal weight:    0.3980
   chunk 1 optimal weight:   10.0000
   chunk 82 optimal weight:    9.9990
   chunk 13 optimal weight:    9.9990
   chunk 21 optimal weight:   10.0000
   overall best weight:    1.6938

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

Flipped N/Q/H residues before XYZ refinement:
J  58 ASN
** S  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.054679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.047876 restraints weight = 241325.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.048777 restraints weight = 168883.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.049219 restraints weight = 129344.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.049651 restraints weight = 108673.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.049876 restraints weight = 95203.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6979
moved from start:          0.5076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  20184  Z= 0.127
  Angle     :  0.576   9.978  29570  Z= 0.296
  Chirality :  0.034   0.243   3700
  Planarity :  0.004   0.061   1992
  Dihedral  : 22.515 175.664   8692
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 13.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 18.94 %
    Favored  : 78.74 %
  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:  0.16 (0.25), residues: 1075
  helix:  1.06 (0.23), residues: 489
  sheet:  0.03 (0.40), residues: 154
  loop : -0.91 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG M  70 
 TYR   0.024   0.002   TYR C 168 
 PHE   0.019   0.001   PHE C  37 
 TRP   0.024   0.002   TRP B  23 
 HIS   0.004   0.001   HIS J  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (20182)
  covalent geometry    : angle       0.57608 (29570)
  hydrogen bonds       : bond        0.06206 (  700)
  hydrogen bonds       : angle       4.10632 ( 1598)
  metal coordination   : bond        0.00081 (    1)
  Misc. bond           : bond        0.00181 (    1)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 65
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   27 MET cc_start: 0.6005 (pmm) cc_final: 0.5547 (pmm)
REVERT: B  100 MET cc_start: 0.8753 (mtp) cc_final: 0.8172 (mpp)
REVERT: C   29 PHE cc_start: 0.5054 (OUTLIER) cc_final: 0.4393 (m-80)
REVERT: C   45 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8692 (mttt)
REVERT: C  123 GLN cc_start: 0.9452 (mt0) cc_final: 0.9104 (mt0)
REVERT: G  101 MET cc_start: 0.7717 (mmp) cc_final: 0.7295 (mmp)
REVERT: M   75 MET cc_start: 0.8748 (mmm) cc_final: 0.8507 (mmm)
REVERT: N   92 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7362 (tp30)
REVERT: S   81 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7450 (tmm160)
  outliers start: 21
  outliers final: 14
  residues processed: 81
  average time/residue: 0.1778
  time to fit residues: 20.9144
Evaluate side-chains
  79 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 62
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  170 HIS
Chi-restraints excluded: chain C residue   18 TRP
Chi-restraints excluded: chain C residue   29 PHE
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   45 LYS
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  118 ASP
Chi-restraints excluded: chain C residue  152 GLU
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue  126 GLN
Chi-restraints excluded: chain J residue   17 LEU
Chi-restraints excluded: chain J residue   57 VAL
Chi-restraints excluded: chain M residue   86 TYR
Chi-restraints excluded: chain N residue  100 SER
Chi-restraints excluded: chain S residue   81 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 85 optimal weight:    0.0670
   chunk 20 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 125 optimal weight:    4.9990
   chunk 26 optimal weight:   10.0000
   chunk 136 optimal weight:    1.9990
   chunk 129 optimal weight:    5.9990
   chunk 46 optimal weight:   20.0000
   chunk 77 optimal weight:    5.9990
   chunk 75 optimal weight:    2.9990
   overall best weight:    3.2126

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

Flipped N/Q/H residues before XYZ refinement:
B  18 HIS
M  14 HIS
** S  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.053622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.046885 restraints weight = 239051.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.047468 restraints weight = 173444.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.047907 restraints weight = 136763.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.048268 restraints weight = 114214.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.048452 restraints weight = 101005.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7055
moved from start:          0.5226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  20184  Z= 0.177
  Angle     :  0.625  10.725  29570  Z= 0.318
  Chirality :  0.035   0.240   3700
  Planarity :  0.005   0.096   1992
  Dihedral  : 22.541 175.728   8692
  Min Nonbonded Distance : 1.815

Molprobity Statistics.
  All-atom Clashscore : 16.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 20.59 %
    Favored  : 77.31 %
  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: -0.07 (0.25), residues: 1075
  helix:  0.88 (0.23), residues: 490
  sheet: -0.19 (0.38), residues: 166
  loop : -1.03 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG G  79 
 TYR   0.027   0.002   TYR C 168 
 PHE   0.026   0.002   PHE S  74 
 TRP   0.023   0.002   TRP B  23 
 HIS   0.004   0.001   HIS J  15 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (20182)
  covalent geometry    : angle       0.62494 (29570)
  hydrogen bonds       : bond        0.06842 (  700)
  hydrogen bonds       : angle       4.13250 ( 1598)
  metal coordination   : bond        0.04035 (    1)
  Misc. bond           : bond        0.00106 (    1)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 63
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   27 MET cc_start: 0.5916 (pmm) cc_final: 0.5521 (pmm)
REVERT: C   29 PHE cc_start: 0.5279 (OUTLIER) cc_final: 0.4631 (m-80)
REVERT: C   45 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8699 (mttt)
REVERT: C  123 GLN cc_start: 0.9446 (mt0) cc_final: 0.9154 (mt0)
REVERT: C  134 MET cc_start: 0.8622 (mmm) cc_final: 0.8289 (mmm)
REVERT: G  101 MET cc_start: 0.7684 (mmp) cc_final: 0.7307 (mmp)
REVERT: M   75 MET cc_start: 0.8835 (mmm) cc_final: 0.8571 (mmm)
REVERT: N   92 GLU cc_start: 0.7858 (mm-30) cc_final: 0.7504 (tp30)
REVERT: S   81 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7461 (tmm160)
  outliers start: 19
  outliers final: 15
  residues processed: 75
  average time/residue: 0.1407
  time to fit residues: 15.6267
Evaluate side-chains
  81 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 63
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  170 HIS
Chi-restraints excluded: chain C residue   18 TRP
Chi-restraints excluded: chain C residue   29 PHE
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   45 LYS
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue   76 VAL
Chi-restraints excluded: chain C residue  118 ASP
Chi-restraints excluded: chain C residue  152 GLU
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue  126 GLN
Chi-restraints excluded: chain J residue   17 LEU
Chi-restraints excluded: chain J residue   57 VAL
Chi-restraints excluded: chain M residue   86 TYR
Chi-restraints excluded: chain N residue   18 ASP
Chi-restraints excluded: chain N residue  100 SER
Chi-restraints excluded: chain S residue   81 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 136 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   chunk 2 optimal weight:   10.0000
   chunk 144 optimal weight:    0.9990
   chunk 129 optimal weight:    5.9990
   chunk 86 optimal weight:    5.9990
   chunk 14 optimal weight:   10.0000
   chunk 31 optimal weight:   20.0000
   chunk 125 optimal weight:   10.0000
   chunk 133 optimal weight:    0.9980
   chunk 141 optimal weight:    4.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
M  14 HIS
** S  57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.053927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.047269 restraints weight = 245128.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.048042 restraints weight = 169852.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.048488 restraints weight = 131716.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.048917 restraints weight = 110347.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.049102 restraints weight = 96421.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7018
moved from start:          0.5523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  20184  Z= 0.145
  Angle     :  0.593  10.940  29570  Z= 0.303
  Chirality :  0.034   0.236   3700
  Planarity :  0.005   0.121   1992
  Dihedral  : 22.515 175.551   8692
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 14.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 20.81 %
    Favored  : 77.31 %
  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: -0.05 (0.25), residues: 1075
  helix:  0.91 (0.23), residues: 490
  sheet: -0.20 (0.38), residues: 168
  loop : -1.04 (0.30), residues: 417

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG G  79 
 TYR   0.028   0.002   TYR C 168 
 PHE   0.023   0.002   PHE S  74 
 TRP   0.024   0.002   TRP B  23 
 HIS   0.006   0.001   HIS M  14 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (20182)
  covalent geometry    : angle       0.59303 (29570)
  hydrogen bonds       : bond        0.06308 (  700)
  hydrogen bonds       : angle       4.09133 ( 1598)
  metal coordination   : bond        0.01413 (    1)
  Misc. bond           : bond        0.00152 (    1)

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

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

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2150 Ramachandran restraints generated.
    1075 Oldfield, 0 Emsley, 1075 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 65
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   27 MET cc_start: 0.6191 (pmm) cc_final: 0.5775 (pmm)
REVERT: B  100 MET cc_start: 0.8747 (mtp) cc_final: 0.8150 (mpp)
REVERT: C   29 PHE cc_start: 0.5253 (OUTLIER) cc_final: 0.4539 (m-80)
REVERT: C   45 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8698 (mttt)
REVERT: C  123 GLN cc_start: 0.9426 (mt0) cc_final: 0.9112 (mt0)
REVERT: G  101 MET cc_start: 0.7796 (mmp) cc_final: 0.7346 (mmp)
REVERT: M   75 MET cc_start: 0.8790 (mmm) cc_final: 0.8506 (mmm)
REVERT: N   92 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7232 (tp30)
  outliers start: 17
  outliers final: 13
  residues processed: 77
  average time/residue: 0.1574
  time to fit residues: 17.9447
Evaluate side-chains
  80 residues out of total 908 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 65
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  170 HIS
Chi-restraints excluded: chain C residue   18 TRP
Chi-restraints excluded: chain C residue   29 PHE
Chi-restraints excluded: chain C residue   33 LEU
Chi-restraints excluded: chain C residue   45 LYS
Chi-restraints excluded: chain C residue   56 VAL
Chi-restraints excluded: chain C residue  118 ASP
Chi-restraints excluded: chain C residue  152 GLU
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain I residue   58 VAL
Chi-restraints excluded: chain I residue  126 GLN
Chi-restraints excluded: chain J residue   17 LEU
Chi-restraints excluded: chain J residue   57 VAL
Chi-restraints excluded: chain M residue   86 TYR
Chi-restraints excluded: chain N residue  100 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 113 optimal weight:    0.8980
   chunk 116 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 148 optimal weight:    7.9990
   chunk 99 optimal weight:    7.9990
   chunk 145 optimal weight:    0.5980
   chunk 84 optimal weight:    6.9990
   chunk 22 optimal weight:   10.0000
   chunk 61 optimal weight:    7.9990
   chunk 75 optimal weight:    3.9990
   chunk 127 optimal weight:    0.6980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
N  60 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.055192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.048301 restraints weight = 236936.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.049033 restraints weight = 165993.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.049496 restraints weight = 131476.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.049871 restraints weight = 110273.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.050076 restraints weight = 97613.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6978
moved from start:          0.5759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  20184  Z= 0.107
  Angle     :  0.563  10.874  29570  Z= 0.288
  Chirality :  0.032   0.236   3700
  Planarity :  0.004   0.080   1992
  Dihedral  : 22.356 175.895   8692
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 11.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 21.26 %
    Favored  : 77.31 %
  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:  0.19 (0.26), residues: 1075
  helix:  1.09 (0.24), residues: 493
  sheet: -0.10 (0.38), residues: 168
  loop : -0.87 (0.31), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG G  79 
 TYR   0.029   0.002   TYR C 168 
 PHE   0.025   0.001   PHE S  74 
 TRP   0.023   0.002   TRP B  23 
 HIS   0.004   0.001   HIS S  83 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 (20182)
  covalent geometry    : angle       0.56309 (29570)
  hydrogen bonds       : bond        0.05974 (  700)
  hydrogen bonds       : angle       4.03196 ( 1598)
  metal coordination   : bond        0.00125 (    1)
  Misc. bond           : bond        0.00179 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3462.60 seconds
wall clock time: 60 minutes 33.11 seconds (3633.11 seconds total)