Starting phenix.real_space_refine
on Wed Jul 30 17:29:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6s3r_10095/07_2025/6s3r_10095.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6s3r_10095/07_2025/6s3r_10095.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6s3r_10095/07_2025/6s3r_10095.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6s3r_10095/07_2025/6s3r_10095.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6s3r_10095/07_2025/6s3r_10095.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6s3r_10095/07_2025/6s3r_10095.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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: 4
    Type Number    sf(0)   Gaussians
     S     117      5.16       5
     C    8592      2.51       5
     N    1970      2.21       5
     O    2176      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 81 residue(s): 0.10s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12855
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 1510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1510
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 12, 'TRANS': 183}
    Chain: "B"
      Number of atoms: 1522
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1522
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 12, 'TRANS': 185}
    Chain: "C"
      Number of atoms: 1522
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1522
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 12, 'TRANS': 185}
    Chain: "D"
      Number of atoms: 1522
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1522
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 12, 'TRANS': 185}
    Chain: "E"
      Number of atoms: 1522
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1522
          Classifications: {'peptide': 198}
          Link IDs: {'PTRANS': 12, 'TRANS': 185}
    Chain: "F"
      Number of atoms: 1907
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 252, 1907
          Classifications: {'peptide': 252}
          Link IDs: {'PTRANS': 13, 'TRANS': 238}
    Chain: "G"
      Number of atoms: 695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 695
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 5, 'TRANS': 83}
    Chain: "H"
      Number of atoms: 695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 695
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 5, 'TRANS': 83}
    Chain: "I"
      Number of atoms: 695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 695
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 5, 'TRANS': 83}
    Chain: "J"
      Number of atoms: 695
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 89, 695
          Classifications: {'peptide': 89}
          Link IDs: {'PTRANS': 5, 'TRANS': 83}
    Chain: "K"
      Number of atoms: 570
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 570
          Classifications: {'peptide': 73}
          Link IDs: {'PTRANS': 5, 'TRANS': 67}
          Chain breaks: 1
  Time building chain proxies: 8.80, per 1000 atoms: 0.68
  Number of scatterers: 12855
  At special positions: 0
  Unit cell: (107.682, 98.64, 120.834, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S     117     16.00
     O    2176      8.00
     N    1970      7.00
     C    8592      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.61
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3174

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 0 sheets defined
      81.8% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 56 through 66
      removed outlier: 3.556A  pdb=" N   PHE A  61 " --> pdb=" O   PHE A  57 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   VAL A  62 " --> pdb=" O   ILE A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 82
    Processing helix  chain 'A' and resid 91 through 116
      removed outlier: 3.610A  pdb=" N   GLY A  95 " --> pdb=" O   GLN A  91 " (cutoff:3.500A)
      Proline residue:  A 107  - end of helix
    Processing helix  chain 'A' and resid 118 through 122
      removed outlier: 4.156A  pdb=" N   LEU A 121 " --> pdb=" O   GLN A 118 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ALA A 122 " --> pdb=" O   PRO A 119 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 118 through 122'
    Processing helix  chain 'A' and resid 129 through 144
      Proline residue:  A 137  - end of helix
    Processing helix  chain 'A' and resid 147 through 159
      removed outlier: 3.556A  pdb=" N   LEU A 151 " --> pdb=" O   ARG A 147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 211
      Proline residue:  A 196  - end of helix
    Processing helix  chain 'A' and resid 217 through 233
      removed outlier: 3.943A  pdb=" N   ILE A 221 " --> pdb=" O   SER A 217 " (cutoff:3.500A)
      Proline residue:  A 224  - end of helix
    Processing helix  chain 'A' and resid 235 through 248
      removed outlier: 4.354A  pdb=" N   GLY A 248 " --> pdb=" O   ALA A 244 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 62
    Processing helix  chain 'B' and resid 67 through 82
    Processing helix  chain 'B' and resid 90 through 105
    Processing helix  chain 'B' and resid 105 through 116
    Processing helix  chain 'B' and resid 129 through 144
      Proline residue:  B 137  - end of helix
    Processing helix  chain 'B' and resid 147 through 159
    Processing helix  chain 'B' and resid 173 through 211
      removed outlier: 3.881A  pdb=" N   ALA B 177 " --> pdb=" O   ILE B 173 " (cutoff:3.500A)
      Proline residue:  B 196  - end of helix
    Processing helix  chain 'B' and resid 217 through 233
      removed outlier: 3.777A  pdb=" N   ILE B 221 " --> pdb=" O   SER B 217 " (cutoff:3.500A)
      Proline residue:  B 224  - end of helix
    Processing helix  chain 'B' and resid 235 through 248
      removed outlier: 4.006A  pdb=" N   GLY B 248 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 54 through 65
      Proline residue:  C  59  - end of helix
    Processing helix  chain 'C' and resid 67 through 82
      removed outlier: 3.520A  pdb=" N   ILE C  73 " --> pdb=" O   THR C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 116
      Proline residue:  C 107  - end of helix
    Processing helix  chain 'C' and resid 118 through 122
      removed outlier: 4.250A  pdb=" N   LEU C 121 " --> pdb=" O   GLN C 118 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ALA C 122 " --> pdb=" O   PRO C 119 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 118 through 122'
    Processing helix  chain 'C' and resid 129 through 146
      Proline residue:  C 137  - end of helix
      removed outlier: 3.725A  pdb=" N   GLN C 145 " --> pdb=" O   PHE C 141 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 147 through 159
    Processing helix  chain 'C' and resid 170 through 211
      removed outlier: 3.704A  pdb=" N   LEU C 174 " --> pdb=" O   PRO C 170 " (cutoff:3.500A)
      Proline residue:  C 176  - end of helix
      Proline residue:  C 196  - end of helix
    Processing helix  chain 'C' and resid 217 through 233
      removed outlier: 3.730A  pdb=" N   ILE C 221 " --> pdb=" O   SER C 217 " (cutoff:3.500A)
      Proline residue:  C 224  - end of helix
    Processing helix  chain 'C' and resid 235 through 248
      removed outlier: 4.133A  pdb=" N   GLY C 248 " --> pdb=" O   ALA C 244 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 54 through 65
      Proline residue:  D  59  - end of helix
      removed outlier: 3.824A  pdb=" N   MET D  65 " --> pdb=" O   PHE D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 67 through 82
      removed outlier: 3.727A  pdb=" N   ILE D  73 " --> pdb=" O   THR D  69 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 91 through 105
      removed outlier: 3.718A  pdb=" N   GLY D  95 " --> pdb=" O   GLN D  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 105 through 116
    Processing helix  chain 'D' and resid 118 through 122
      removed outlier: 4.143A  pdb=" N   LEU D 121 " --> pdb=" O   GLN D 118 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ALA D 122 " --> pdb=" O   PRO D 119 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 118 through 122'
    Processing helix  chain 'D' and resid 129 through 146
      Proline residue:  D 137  - end of helix
      removed outlier: 3.710A  pdb=" N   GLN D 145 " --> pdb=" O   PHE D 141 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 147 through 159
    Processing helix  chain 'D' and resid 170 through 211
      removed outlier: 3.749A  pdb=" N   LEU D 174 " --> pdb=" O   PRO D 170 " (cutoff:3.500A)
      Proline residue:  D 176  - end of helix
      Proline residue:  D 196  - end of helix
    Processing helix  chain 'D' and resid 217 through 233
      removed outlier: 3.742A  pdb=" N   ILE D 221 " --> pdb=" O   SER D 217 " (cutoff:3.500A)
      Proline residue:  D 224  - end of helix
    Processing helix  chain 'D' and resid 235 through 248
      removed outlier: 4.007A  pdb=" N   GLY D 248 " --> pdb=" O   ALA D 244 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 54 through 62
      removed outlier: 3.576A  pdb=" N   ILE E  58 " --> pdb=" O   ALA E  54 " (cutoff:3.500A)
      Proline residue:  E  59  - end of helix
    Processing helix  chain 'E' and resid 67 through 82
    Processing helix  chain 'E' and resid 91 through 116
      removed outlier: 3.592A  pdb=" N   GLY E  95 " --> pdb=" O   GLN E  91 " (cutoff:3.500A)
      Proline residue:  E 107  - end of helix
    Processing helix  chain 'E' and resid 118 through 122
      removed outlier: 4.059A  pdb=" N   LEU E 121 " --> pdb=" O   GLN E 118 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ALA E 122 " --> pdb=" O   PRO E 119 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 118 through 122'
    Processing helix  chain 'E' and resid 129 through 146
      Proline residue:  E 137  - end of helix
      removed outlier: 3.812A  pdb=" N   GLN E 145 " --> pdb=" O   PHE E 141 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 147 through 159
    Processing helix  chain 'E' and resid 173 through 211
      removed outlier: 3.843A  pdb=" N   ALA E 177 " --> pdb=" O   ILE E 173 " (cutoff:3.500A)
      Proline residue:  E 196  - end of helix
    Processing helix  chain 'E' and resid 217 through 233
      removed outlier: 3.661A  pdb=" N   ILE E 221 " --> pdb=" O   SER E 217 " (cutoff:3.500A)
      Proline residue:  E 224  - end of helix
      removed outlier: 3.592A  pdb=" N   VAL E 233 " --> pdb=" O   LEU E 229 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 235 through 248
      removed outlier: 3.858A  pdb=" N   GLY E 248 " --> pdb=" O   ALA E 244 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 20 through 32
      removed outlier: 3.805A  pdb=" N   PHE F  24 " --> pdb=" O   MET F  20 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 42 through 58
    Processing helix  chain 'F' and resid 73 through 111
      removed outlier: 4.115A  pdb=" N   PHE F  95 " --> pdb=" O   SER F  91 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   PHE F  96 " --> pdb=" O   LEU F  92 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   PHE F  99 " --> pdb=" O   PHE F  95 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 129 through 144
    Processing helix  chain 'F' and resid 145 through 161
      removed outlier: 4.321A  pdb=" N   LEU F 151 " --> pdb=" O   HIS F 147 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   THR F 159 " --> pdb=" O   VAL F 155 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 172 through 177
    Processing helix  chain 'F' and resid 177 through 211
      removed outlier: 4.289A  pdb=" N   TRP F 181 " --> pdb=" O   ASN F 177 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ALA F 182 " --> pdb=" O   GLY F 178 " (cutoff:3.500A)
      Proline residue:  F 192  - end of helix
      removed outlier: 3.844A  pdb=" N   ALA F 196 " --> pdb=" O   PRO F 192 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 219 through 260
      removed outlier: 3.553A  pdb=" N   VAL F 230 " --> pdb=" O   VAL F 226 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLY F 237 " --> pdb=" O   TRP F 233 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   ASP F 238 " --> pdb=" O   MET F 234 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   LEU F 240 " --> pdb=" O   MET F 236 " (cutoff:3.500A)
      removed outlier: 5.251A  pdb=" N   ASN F 241 " --> pdb=" O   GLY F 237 " (cutoff:3.500A)
      Proline residue:  F 245  - end of helix
      removed outlier: 3.515A  pdb=" N   SER F 248 " --> pdb=" O   GLN F 244 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 2 through 42
      Proline residue:  G  27  - end of helix
      removed outlier: 3.654A  pdb=" N   THR G  42 " --> pdb=" O   PHE G  38 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 51 through 66
    Processing helix  chain 'G' and resid 66 through 88
      Proline residue:  G  85  - end of helix
    Processing helix  chain 'H' and resid 2 through 42
      Proline residue:  H  27  - end of helix
      removed outlier: 3.655A  pdb=" N   THR H  42 " --> pdb=" O   PHE H  38 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 51 through 66
    Processing helix  chain 'H' and resid 66 through 88
      Proline residue:  H  85  - end of helix
    Processing helix  chain 'I' and resid 2 through 42
      Proline residue:  I  27  - end of helix
      removed outlier: 3.654A  pdb=" N   THR I  42 " --> pdb=" O   PHE I  38 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 51 through 66
    Processing helix  chain 'I' and resid 66 through 88
      Proline residue:  I  85  - end of helix
    Processing helix  chain 'J' and resid 2 through 42
      Proline residue:  J  27  - end of helix
      removed outlier: 3.656A  pdb=" N   THR J  42 " --> pdb=" O   PHE J  38 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 51 through 66
    Processing helix  chain 'J' and resid 66 through 88
      Proline residue:  J  85  - end of helix
    Processing helix  chain 'K' and resid 3 through 35
      Proline residue:  K  27  - end of helix
    Processing helix  chain 'K' and resid 53 through 66
    Processing helix  chain 'K' and resid 66 through 89
      removed outlier: 3.601A  pdb=" N   LEU K  70 " --> pdb=" O   GLY K  66 " (cutoff:3.500A)
      Proline residue:  K  85  - end of helix
      removed outlier: 3.907A  pdb=" N   GLY K  89 " --> pdb=" O   PRO K  85 " (cutoff:3.500A)

    931 hydrogen bonds defined for protein.
    2793 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.61

  Time building geometry restraints manager: 4.21 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3839
        1.34 -     1.46: 2590
        1.46 -     1.58: 6459
        1.58 -     1.70: 0
        1.70 -     1.81: 229
  Bond restraints: 13117
  Sorted by residual:
  bond pdb=" CA  ASN F 177 "
       pdb=" C   ASN F 177 "
    ideal  model  delta    sigma   weight residual
    1.523  1.488  0.034 1.41e-02 5.03e+03 5.98e+00
  bond pdb=" CA  ILE G  84 "
       pdb=" CB  ILE G  84 "
    ideal  model  delta    sigma   weight residual
    1.537  1.525  0.012 5.00e-03 4.00e+04 5.80e+00
  bond pdb=" CA  ILE I  84 "
       pdb=" CB  ILE I  84 "
    ideal  model  delta    sigma   weight residual
    1.537  1.525  0.012 5.00e-03 4.00e+04 5.49e+00
  bond pdb=" CA  ILE J  84 "
       pdb=" CB  ILE J  84 "
    ideal  model  delta    sigma   weight residual
    1.537  1.525  0.011 5.00e-03 4.00e+04 5.20e+00
  bond pdb=" CA  ILE H  84 "
       pdb=" CB  ILE H  84 "
    ideal  model  delta    sigma   weight residual
    1.537  1.526  0.011 5.00e-03 4.00e+04 5.10e+00
  ... (remaining 13112 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 16968
        1.77 -     3.53: 692
        3.53 -     5.30: 164
        5.30 -     7.06: 39
        7.06 -     8.83: 8
  Bond angle restraints: 17871
  Sorted by residual:
  angle pdb=" C   ILE K  84 "
        pdb=" CA  ILE K  84 "
        pdb=" CB  ILE K  84 "
      ideal   model   delta    sigma   weight residual
     113.70  109.64    4.06 9.50e-01 1.11e+00 1.82e+01
  angle pdb=" C   PRO A  88 "
        pdb=" N   SER A  89 "
        pdb=" CA  SER A  89 "
      ideal   model   delta    sigma   weight residual
     121.54  128.93   -7.39 1.91e+00 2.74e-01 1.50e+01
  angle pdb=" N   ASP E 234 "
        pdb=" CA  ASP E 234 "
        pdb=" CB  ASP E 234 "
      ideal   model   delta    sigma   weight residual
     114.17  109.77    4.40 1.14e+00 7.69e-01 1.49e+01
  angle pdb=" C   VAL F 118 "
        pdb=" N   ASP F 119 "
        pdb=" CA  ASP F 119 "
      ideal   model   delta    sigma   weight residual
     121.80  130.63   -8.83 2.44e+00 1.68e-01 1.31e+01
  angle pdb=" C   PRO F  34 "
        pdb=" N   VAL F  35 "
        pdb=" CA  VAL F  35 "
      ideal   model   delta    sigma   weight residual
     123.08  119.69    3.39 1.01e+00 9.80e-01 1.12e+01
  ... (remaining 17866 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.23: 6959
       17.23 -    34.45: 753
       34.45 -    51.68: 147
       51.68 -    68.91: 23
       68.91 -    86.14: 18
  Dihedral angle restraints: 7900
    sinusoidal: 3052
      harmonic: 4848
  Sorted by residual:
  dihedral pdb=" CA  THR B  87 "
           pdb=" C   THR B  87 "
           pdb=" N   PRO B  88 "
           pdb=" CA  PRO B  88 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  119.23   60.77     0      5.00e+00 4.00e-02 1.48e+02
  dihedral pdb=" CA  THR A  87 "
           pdb=" C   THR A  87 "
           pdb=" N   PRO A  88 "
           pdb=" CA  PRO A  88 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  119.46   60.54     0      5.00e+00 4.00e-02 1.47e+02
  dihedral pdb=" CA  THR C  87 "
           pdb=" C   THR C  87 "
           pdb=" N   PRO C  88 "
           pdb=" CA  PRO C  88 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  120.51   59.49     0      5.00e+00 4.00e-02 1.42e+02
  ... (remaining 7897 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1656
       0.046 -    0.093: 487
       0.093 -    0.139: 134
       0.139 -    0.185: 7
       0.185 -    0.232: 4
  Chirality restraints: 2288
  Sorted by residual:
  chirality pdb=" CA  GLU J  75 "
            pdb=" N   GLU J  75 "
            pdb=" C   GLU J  75 "
            pdb=" CB  GLU J  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.34e+00
  chirality pdb=" CA  GLU G  75 "
            pdb=" N   GLU G  75 "
            pdb=" C   GLU G  75 "
            pdb=" CB  GLU G  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.33e+00
  chirality pdb=" CA  GLU I  75 "
            pdb=" N   GLU I  75 "
            pdb=" C   GLU I  75 "
            pdb=" CB  GLU I  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.33e+00
  ... (remaining 2285 not shown)

  Planarity restraints: 2149
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP F 119 "   -0.065 5.00e-02 4.00e+02   9.95e-02 1.58e+01
        pdb=" N   PRO F 120 "    0.172 5.00e-02 4.00e+02
        pdb=" CA  PRO F 120 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO F 120 "   -0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A  87 "    0.064 5.00e-02 4.00e+02   9.72e-02 1.51e+01
        pdb=" N   PRO A  88 "   -0.168 5.00e-02 4.00e+02
        pdb=" CA  PRO A  88 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A  88 "    0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D  87 "   -0.061 5.00e-02 4.00e+02   9.34e-02 1.39e+01
        pdb=" N   PRO D  88 "    0.162 5.00e-02 4.00e+02
        pdb=" CA  PRO D  88 "   -0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO D  88 "   -0.051 5.00e-02 4.00e+02
  ... (remaining 2146 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 99
        2.61 -     3.18: 12476
        3.18 -     3.75: 20709
        3.75 -     4.33: 27378
        4.33 -     4.90: 45488
  Nonbonded interactions: 106150
  Sorted by model distance:
  nonbonded pdb=" O   LEU J  78 "
            pdb=" OG1 THR J  82 "
     model   vdw
     2.035 3.040
  nonbonded pdb=" O   LEU G  78 "
            pdb=" OG1 THR G  82 "
     model   vdw
     2.035 3.040
  nonbonded pdb=" O   LEU I  78 "
            pdb=" OG1 THR I  82 "
     model   vdw
     2.035 3.040
  nonbonded pdb=" O   LEU H  78 "
            pdb=" OG1 THR H  82 "
     model   vdw
     2.035 3.040
  nonbonded pdb=" O   VAL C  62 "
            pdb=" OG1 THR C  66 "
     model   vdw
     2.163 3.040
  ... (remaining 106145 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'B' and resid 55 through 250)
  selection = (chain 'C' and resid 55 through 250)
  selection = (chain 'D' and resid 55 through 250)
  selection = (chain 'E' and resid 55 through 250)
}
ncs_group {
  reference = chain 'G'
  selection = chain 'H'
  selection = chain 'I'
  selection = chain 'J'
}

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:             18.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.520
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     32.550
  Find NCS groups from input model:        0.450
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
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      :  0.006   0.049  13117  Z= 0.254
  Angle     :  0.886   8.831  17871  Z= 0.467
  Chirality :  0.046   0.232   2288
  Planarity :  0.007   0.100   2149
  Dihedral  : 15.344  86.137   4726
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 18.37
  Ramachandran Plot:
    Outliers :  0.79 %
    Allowed  :  8.39 %
    Favored  : 90.82 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  :  5.42 %
    Favored  : 92.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.12 %
    Twisted General : 0.19 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.03 (0.18), residues: 1645
  helix: -1.31 (0.13), residues: 1302
  sheet:  None (None), residues: 0
  loop : -4.26 (0.29), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP J  68 
 HIS   0.005   0.002   HIS F  97 
 PHE   0.029   0.002   PHE F 132 
 TYR   0.012   0.002   TYR J  76 
 ARG   0.010   0.001   ARG A  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12794 (  931)
  hydrogen bonds       : angle       5.97394 ( 2793)
  covalent geometry    : bond        0.00581 (13117)
  covalent geometry    : angle       0.88629 (17871)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  408 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 376
  time to evaluate  : 1.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 LYS cc_start: 0.8357 (ttmt) cc_final: 0.7914 (tttt)
REVERT: A  211 MET cc_start: 0.7489 (mmm) cc_final: 0.7261 (mmm)
REVERT: A  220 ILE cc_start: 0.8731 (tt) cc_final: 0.8497 (tt)
REVERT: B  170 PRO cc_start: 0.5769 (Cg_endo) cc_final: 0.5496 (Cg_exo)
REVERT: C  182 GLU cc_start: 0.7463 (tp30) cc_final: 0.7180 (tp30)
REVERT: D   96 MET cc_start: 0.7659 (tpt) cc_final: 0.7163 (ttm)
REVERT: D   98 LEU cc_start: 0.8623 (tp) cc_final: 0.8277 (tt)
REVERT: D  182 GLU cc_start: 0.7414 (tp30) cc_final: 0.7190 (tp30)
REVERT: E  209 MET cc_start: 0.3688 (ppp) cc_final: 0.2756 (ppp)
REVERT: F  117 MET cc_start: 0.5891 (pmm) cc_final: 0.5481 (pmm)
REVERT: F  219 ILE cc_start: 0.8821 (mm) cc_final: 0.8611 (mm)
REVERT: H   29 LEU cc_start: 0.8355 (tt) cc_final: 0.8151 (tt)
REVERT: H   34 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7361 (tp)
REVERT: J   23 ILE cc_start: 0.8869 (OUTLIER) cc_final: 0.8570 (mm)
REVERT: K   58 MET cc_start: 0.8273 (tpp) cc_final: 0.8056 (tpp)
REVERT: K   71 LYS cc_start: 0.6237 (tttp) cc_final: 0.5460 (mptt)
  outliers start: 32
  outliers final: 5
  residues processed: 393
  average time/residue: 0.2365
  time to fit residues: 137.1359
Evaluate side-chains
  302 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 295
  time to evaluate  : 1.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue    2 THR
Chi-restraints excluded: chain G residue   37 MET
Chi-restraints excluded: chain H residue   34 LEU
Chi-restraints excluded: chain H residue   37 MET
Chi-restraints excluded: chain I residue   23 ILE
Chi-restraints excluded: chain J residue   23 ILE
Chi-restraints excluded: chain J residue   37 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 134 optimal weight:    0.9980
   chunk 120 optimal weight:    0.0040
   chunk 66 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 81 optimal weight:    0.8980
   chunk 64 optimal weight:   10.0000
   chunk 124 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 92 optimal weight:    0.7980
   chunk 144 optimal weight:    3.9990
   overall best weight:    0.7192

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

Flipped N/Q/H residues before XYZ refinement:
A  80 GLN
C 113 ASN
E 118 GLN
F  11 GLN
F  97 HIS
F 109 GLN
** F 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  39 GLN
J  39 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.176383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.153238 restraints weight = 15321.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.154612 restraints weight = 11206.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.156069 restraints weight = 8753.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065  13117  Z= 0.170
  Angle     :  0.812  13.471  17871  Z= 0.402
  Chirality :  0.046   0.299   2288
  Planarity :  0.006   0.084   2149
  Dihedral  :  6.780  59.007   1739
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  7.72 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 13.62 %
    Favored  : 83.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.12 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.21), residues: 1645
  helix:  0.20 (0.14), residues: 1331
  sheet:  None (None), residues: 0
  loop : -4.12 (0.30), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP G  68 
 HIS   0.002   0.001   HIS F  97 
 PHE   0.027   0.002   PHE D 109 
 TYR   0.020   0.002   TYR B 120 
 ARG   0.004   0.001   ARG E 160 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04581 (  931)
  hydrogen bonds       : angle       4.57058 ( 2793)
  covalent geometry    : bond        0.00374 (13117)
  covalent geometry    : angle       0.81169 (17871)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  348 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 311
  time to evaluate  : 1.284 
Fit side-chains
   revert: symmetry clash
REVERT: A   90 ASN cc_start: 0.7938 (p0) cc_final: 0.7539 (t0)
REVERT: A  139 LYS cc_start: 0.8256 (ttmt) cc_final: 0.7913 (tttm)
REVERT: A  220 ILE cc_start: 0.8640 (tt) cc_final: 0.8439 (tt)
REVERT: C   71 ILE cc_start: 0.8913 (mt) cc_final: 0.8686 (mm)
REVERT: C  105 MET cc_start: 0.7929 (mmm) cc_final: 0.7557 (mmm)
REVERT: C  139 LYS cc_start: 0.8710 (ttmm) cc_final: 0.8492 (mtpt)
REVERT: C  192 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7096 (mpp)
REVERT: D  105 MET cc_start: 0.7298 (mmm) cc_final: 0.7023 (mmm)
REVERT: D  109 PHE cc_start: 0.7687 (m-80) cc_final: 0.7262 (m-80)
REVERT: D  173 ILE cc_start: 0.7487 (tt) cc_final: 0.6872 (mt)
REVERT: D  211 MET cc_start: 0.7112 (mmm) cc_final: 0.6448 (mtm)
REVERT: E  142 MET cc_start: 0.8442 (mtp) cc_final: 0.8206 (mtm)
REVERT: E  209 MET cc_start: 0.4105 (ppp) cc_final: 0.1322 (tpp)
REVERT: F  117 MET cc_start: 0.5641 (pmm) cc_final: 0.5134 (pmm)
REVERT: G   68 TRP cc_start: 0.6764 (p-90) cc_final: 0.5473 (m-90)
REVERT: I   23 ILE cc_start: 0.8923 (mm) cc_final: 0.8675 (mt)
REVERT: K   58 MET cc_start: 0.8107 (tpp) cc_final: 0.7831 (tpp)
REVERT: K   71 LYS cc_start: 0.6190 (tttp) cc_final: 0.5402 (mptt)
  outliers start: 37
  outliers final: 13
  residues processed: 330
  average time/residue: 0.2090
  time to fit residues: 104.6330
Evaluate side-chains
  297 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 283
  time to evaluate  : 1.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  234 ASP
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  192 MET
Chi-restraints excluded: chain D residue   92 ILE
Chi-restraints excluded: chain E residue   58 ILE
Chi-restraints excluded: chain E residue  143 LEU
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain F residue  216 ILE
Chi-restraints excluded: chain H residue   23 ILE
Chi-restraints excluded: chain H residue   34 LEU
Chi-restraints excluded: chain I residue    2 THR
Chi-restraints excluded: chain I residue   87 LEU
Chi-restraints excluded: chain J residue   70 LEU
Chi-restraints excluded: chain K residue   72 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 104 optimal weight:    0.9980
   chunk 30 optimal weight:    0.0970
   chunk 114 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 105 optimal weight:    0.7980
   chunk 122 optimal weight:    0.9980
   overall best weight:    0.7778

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

Flipped N/Q/H residues before XYZ refinement:
** F  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 109 GLN
G  39 GLN
I  39 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.172682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.147901 restraints weight = 15472.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.150744 restraints weight = 10594.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.152132 restraints weight = 8064.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.2638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13117  Z= 0.159
  Angle     :  0.766  13.024  17871  Z= 0.376
  Chirality :  0.044   0.244   2288
  Planarity :  0.006   0.086   2149
  Dihedral  :  6.302  58.035   1725
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 12.45
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.54 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 16.61 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.12 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.21), residues: 1645
  helix:  0.86 (0.15), residues: 1293
  sheet:  None (None), residues: 0
  loop : -3.93 (0.28), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP H  68 
 HIS   0.003   0.001   HIS F 147 
 PHE   0.033   0.002   PHE B 247 
 TYR   0.025   0.002   TYR A 120 
 ARG   0.006   0.000   ARG C 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04235 (  931)
  hydrogen bonds       : angle       4.37445 ( 2793)
  covalent geometry    : bond        0.00355 (13117)
  covalent geometry    : angle       0.76590 (17871)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 287
  time to evaluate  : 1.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 ASN cc_start: 0.7863 (p0) cc_final: 0.7655 (t0)
REVERT: A  139 LYS cc_start: 0.8163 (ttmt) cc_final: 0.7820 (tttm)
REVERT: A  220 ILE cc_start: 0.8579 (tt) cc_final: 0.8360 (tt)
REVERT: B   70 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7783 (ptp-170)
REVERT: B  175 VAL cc_start: 0.9320 (t) cc_final: 0.9042 (t)
REVERT: C   71 ILE cc_start: 0.8918 (mt) cc_final: 0.8630 (mm)
REVERT: C   92 ILE cc_start: 0.7028 (OUTLIER) cc_final: 0.6156 (mt)
REVERT: C  192 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7085 (mpp)
REVERT: D  100 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.7771 (tt)
REVERT: D  109 PHE cc_start: 0.7724 (m-80) cc_final: 0.7382 (m-80)
REVERT: D  209 MET cc_start: 0.8157 (mmm) cc_final: 0.7870 (mmm)
REVERT: D  211 MET cc_start: 0.6875 (mmm) cc_final: 0.6542 (mtm)
REVERT: E  105 MET cc_start: 0.7355 (mmm) cc_final: 0.6486 (mmm)
REVERT: E  142 MET cc_start: 0.8479 (mtp) cc_final: 0.8236 (mtm)
REVERT: E  182 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.6567 (mp0)
REVERT: E  209 MET cc_start: 0.4189 (ppp) cc_final: 0.1920 (tpp)
REVERT: F   78 ILE cc_start: 0.8763 (mt) cc_final: 0.8556 (mt)
REVERT: F  117 MET cc_start: 0.5544 (pmm) cc_final: 0.4789 (pmm)
REVERT: F  187 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8129 (mm)
REVERT: I   23 ILE cc_start: 0.8882 (mm) cc_final: 0.8513 (mt)
REVERT: K   58 MET cc_start: 0.7953 (tpp) cc_final: 0.7669 (tpp)
REVERT: K   71 LYS cc_start: 0.6171 (tttp) cc_final: 0.5411 (mptt)
  outliers start: 42
  outliers final: 19
  residues processed: 316
  average time/residue: 0.2169
  time to fit residues: 104.3507
Evaluate side-chains
  297 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 272
  time to evaluate  : 1.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  113 ASN
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  234 ASP
Chi-restraints excluded: chain B residue   70 ARG
Chi-restraints excluded: chain B residue  214 MET
Chi-restraints excluded: chain B residue  234 ASP
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue  192 MET
Chi-restraints excluded: chain D residue   92 ILE
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain E residue   58 ILE
Chi-restraints excluded: chain E residue  143 LEU
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  182 GLU
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  187 LEU
Chi-restraints excluded: chain F residue  216 ILE
Chi-restraints excluded: chain G residue   87 LEU
Chi-restraints excluded: chain H residue   87 LEU
Chi-restraints excluded: chain I residue    2 THR
Chi-restraints excluded: chain I residue   72 ILE
Chi-restraints excluded: chain I residue   87 LEU
Chi-restraints excluded: chain K residue   14 LEU
Chi-restraints excluded: chain K residue   72 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 123 optimal weight:    3.9990
   chunk 51 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9990
   chunk 141 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 121 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0770
   chunk 151 optimal weight:    0.6980
   chunk 154 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.7140

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

Flipped N/Q/H residues before XYZ refinement:
** F  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 109 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.173552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.149318 restraints weight = 15401.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.150246 restraints weight = 10933.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.151306 restraints weight = 9814.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.3035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13117  Z= 0.147
  Angle     :  0.736  13.136  17871  Z= 0.359
  Chirality :  0.043   0.202   2288
  Planarity :  0.006   0.083   2149
  Dihedral  :  6.066  59.267   1723
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.29 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 17.79 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.22), residues: 1645
  helix:  1.02 (0.15), residues: 1314
  sheet:  None (None), residues: 0
  loop : -4.03 (0.29), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP G  68 
 HIS   0.003   0.002   HIS F 147 
 PHE   0.020   0.002   PHE C 154 
 TYR   0.007   0.001   TYR C 120 
 ARG   0.007   0.000   ARG C 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03982 (  931)
  hydrogen bonds       : angle       4.23805 ( 2793)
  covalent geometry    : bond        0.00324 (13117)
  covalent geometry    : angle       0.73588 (17871)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  350 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 291
  time to evaluate  : 1.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 LYS cc_start: 0.8227 (ttmt) cc_final: 0.7878 (tttm)
REVERT: B   70 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7716 (ptp-170)
REVERT: B  175 VAL cc_start: 0.9322 (t) cc_final: 0.9050 (t)
REVERT: B  247 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7540 (m-80)
REVERT: C   71 ILE cc_start: 0.8876 (mt) cc_final: 0.8650 (mm)
REVERT: C   92 ILE cc_start: 0.7017 (OUTLIER) cc_final: 0.6103 (mt)
REVERT: C  192 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7138 (mpp)
REVERT: D  100 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.7889 (tt)
REVERT: D  109 PHE cc_start: 0.7747 (m-80) cc_final: 0.7411 (m-80)
REVERT: D  209 MET cc_start: 0.8132 (mmm) cc_final: 0.7875 (mmm)
REVERT: D  229 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7840 (mm)
REVERT: E  105 MET cc_start: 0.7260 (mmm) cc_final: 0.6417 (mmm)
REVERT: E  142 MET cc_start: 0.8432 (mtp) cc_final: 0.8209 (mtm)
REVERT: E  182 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.6557 (mp0)
REVERT: E  209 MET cc_start: 0.4395 (ppp) cc_final: 0.2509 (tpp)
REVERT: F   94 MET cc_start: 0.8475 (mpp) cc_final: 0.8210 (mpp)
REVERT: F  187 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8168 (mm)
REVERT: H   37 MET cc_start: 0.6203 (ttt) cc_final: 0.5316 (mtt)
REVERT: I   23 ILE cc_start: 0.8836 (mm) cc_final: 0.8473 (mt)
REVERT: K   58 MET cc_start: 0.7868 (tpp) cc_final: 0.7653 (tpp)
  outliers start: 59
  outliers final: 25
  residues processed: 334
  average time/residue: 0.2045
  time to fit residues: 104.1946
Evaluate side-chains
  313 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 280
  time to evaluate  : 1.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  234 ASP
Chi-restraints excluded: chain B residue   70 ARG
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  214 MET
Chi-restraints excluded: chain B residue  234 ASP
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  192 MET
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue   92 ILE
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  163 ILE
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  229 LEU
Chi-restraints excluded: chain E residue   58 ILE
Chi-restraints excluded: chain E residue  143 LEU
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  182 GLU
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  187 LEU
Chi-restraints excluded: chain G residue   55 LEU
Chi-restraints excluded: chain G residue   87 LEU
Chi-restraints excluded: chain H residue   87 LEU
Chi-restraints excluded: chain I residue    2 THR
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain I residue   78 LEU
Chi-restraints excluded: chain I residue   87 LEU
Chi-restraints excluded: chain J residue   62 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 111 optimal weight:    0.0270
   chunk 19 optimal weight:    0.4980
   chunk 149 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 75 optimal weight:    6.9990
   chunk 5 optimal weight:    0.7980
   chunk 98 optimal weight:    0.7980
   chunk 39 optimal weight:    3.9990
   chunk 117 optimal weight:    3.9990
   chunk 54 optimal weight:    0.7980
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
D 188 GLN
** F 109 GLN ** 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 = 0.4004 r_free = 0.4004 target = 0.175160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.150049 restraints weight = 15468.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.152833 restraints weight = 10319.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.154679 restraints weight = 7951.525|
|-----------------------------------------------------------------------------|
r_work (final): 0.3791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.3367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  13117  Z= 0.144
  Angle     :  0.738  14.876  17871  Z= 0.359
  Chirality :  0.043   0.206   2288
  Planarity :  0.006   0.083   2149
  Dihedral  :  5.917  59.264   1723
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.29 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 20.43 %
    Favored  : 76.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.12 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.22), residues: 1645
  helix:  1.24 (0.15), residues: 1298
  sheet:  None (None), residues: 0
  loop : -3.93 (0.28), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP G  68 
 HIS   0.002   0.001   HIS F  97 
 PHE   0.020   0.002   PHE C 154 
 TYR   0.011   0.001   TYR A 120 
 ARG   0.005   0.000   ARG C 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03856 (  931)
  hydrogen bonds       : angle       4.16525 ( 2793)
  covalent geometry    : bond        0.00316 (13117)
  covalent geometry    : angle       0.73838 (17871)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  342 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 291
  time to evaluate  : 1.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 LYS cc_start: 0.8197 (ttmt) cc_final: 0.7839 (tttm)
REVERT: B   70 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.7647 (ptp-170)
REVERT: B  211 MET cc_start: 0.7637 (mpp) cc_final: 0.7430 (mmt)
REVERT: B  247 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.7464 (m-80)
REVERT: C   71 ILE cc_start: 0.8865 (mt) cc_final: 0.8617 (mm)
REVERT: C   92 ILE cc_start: 0.6860 (OUTLIER) cc_final: 0.5990 (mt)
REVERT: C  192 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7161 (mpp)
REVERT: D  100 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.7852 (tt)
REVERT: D  109 PHE cc_start: 0.7763 (m-80) cc_final: 0.7448 (m-80)
REVERT: D  209 MET cc_start: 0.8143 (mmm) cc_final: 0.7905 (mmm)
REVERT: E  105 MET cc_start: 0.7249 (mmm) cc_final: 0.6519 (mmm)
REVERT: E  182 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.6662 (mp0)
REVERT: E  209 MET cc_start: 0.4387 (ppp) cc_final: 0.2790 (tpp)
REVERT: F   94 MET cc_start: 0.8477 (mpp) cc_final: 0.8249 (mpp)
REVERT: F  117 MET cc_start: 0.4874 (pmm) cc_final: 0.4586 (pmm)
REVERT: F  187 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8163 (mm)
REVERT: H   37 MET cc_start: 0.6278 (ttt) cc_final: 0.5570 (mtt)
REVERT: I   23 ILE cc_start: 0.8838 (mm) cc_final: 0.8436 (mt)
REVERT: K   58 MET cc_start: 0.7885 (tpp) cc_final: 0.7643 (tpp)
  outliers start: 51
  outliers final: 31
  residues processed: 325
  average time/residue: 0.2047
  time to fit residues: 102.1698
Evaluate side-chains
  316 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 278
  time to evaluate  : 1.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  234 ASP
Chi-restraints excluded: chain B residue   70 ARG
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  214 MET
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  234 ASP
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  192 MET
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue   92 ILE
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  163 ILE
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain E residue   58 ILE
Chi-restraints excluded: chain E residue  143 LEU
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  161 THR
Chi-restraints excluded: chain E residue  182 GLU
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  187 LEU
Chi-restraints excluded: chain F residue  214 LEU
Chi-restraints excluded: chain F residue  216 ILE
Chi-restraints excluded: chain F residue  257 MET
Chi-restraints excluded: chain G residue   55 LEU
Chi-restraints excluded: chain G residue   87 LEU
Chi-restraints excluded: chain H residue   87 LEU
Chi-restraints excluded: chain I residue    2 THR
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain I residue   78 LEU
Chi-restraints excluded: chain I residue   87 LEU
Chi-restraints excluded: chain J residue   14 LEU
Chi-restraints excluded: chain J residue   62 LEU
Chi-restraints excluded: chain K residue   72 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 105 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 153 optimal weight:    7.9990
   chunk 111 optimal weight:    0.6980
   chunk 36 optimal weight:    0.5980
   chunk 80 optimal weight:    3.9990
   chunk 132 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 93 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 137 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** F 109 GLN ** 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 = 0.4001 r_free = 0.4001 target = 0.175031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.150322 restraints weight = 15640.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.151937 restraints weight = 11223.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.153636 restraints weight = 8709.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
moved from start:          0.3602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13117  Z= 0.144
  Angle     :  0.740  15.536  17871  Z= 0.357
  Chirality :  0.042   0.219   2288
  Planarity :  0.006   0.083   2149
  Dihedral  :  5.795  58.636   1723
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 12.11
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.36 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 21.20 %
    Favored  : 74.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.12 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.22), residues: 1645
  helix:  1.34 (0.15), residues: 1300
  sheet:  None (None), residues: 0
  loop : -3.88 (0.28), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP H  68 
 HIS   0.002   0.001   HIS F  97 
 PHE   0.018   0.001   PHE C 154 
 TYR   0.006   0.001   TYR C 120 
 ARG   0.005   0.000   ARG C 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03768 (  931)
  hydrogen bonds       : angle       4.09788 ( 2793)
  covalent geometry    : bond        0.00322 (13117)
  covalent geometry    : angle       0.74027 (17871)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  345 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 290
  time to evaluate  : 1.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 LEU cc_start: 0.4193 (OUTLIER) cc_final: 0.3506 (mm)
REVERT: A  139 LYS cc_start: 0.8229 (ttmt) cc_final: 0.7851 (tttt)
REVERT: B   70 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7679 (ptp-170)
REVERT: B   80 GLN cc_start: 0.7845 (mt0) cc_final: 0.7626 (mt0)
REVERT: C   92 ILE cc_start: 0.6864 (OUTLIER) cc_final: 0.5991 (mt)
REVERT: C  192 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7205 (mpp)
REVERT: D  100 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.7903 (tt)
REVERT: D  109 PHE cc_start: 0.7756 (m-80) cc_final: 0.7422 (m-80)
REVERT: D  229 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7609 (mm)
REVERT: E  105 MET cc_start: 0.7234 (mmm) cc_final: 0.6534 (mmm)
REVERT: E  209 MET cc_start: 0.4590 (ppp) cc_final: 0.3565 (tpp)
REVERT: F  187 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8119 (mm)
REVERT: F  252 GLN cc_start: 0.7761 (tp40) cc_final: 0.7546 (tp-100)
REVERT: H   37 MET cc_start: 0.6350 (ttt) cc_final: 0.5644 (mtt)
REVERT: I   23 ILE cc_start: 0.8817 (mm) cc_final: 0.8438 (mt)
REVERT: K   58 MET cc_start: 0.7784 (tpp) cc_final: 0.7546 (tpp)
  outliers start: 55
  outliers final: 29
  residues processed: 325
  average time/residue: 0.2084
  time to fit residues: 103.8216
Evaluate side-chains
  319 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 283
  time to evaluate  : 1.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  234 ASP
Chi-restraints excluded: chain B residue   70 ARG
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  192 MET
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue   92 ILE
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  163 ILE
Chi-restraints excluded: chain D residue  182 GLU
Chi-restraints excluded: chain D residue  229 LEU
Chi-restraints excluded: chain E residue   58 ILE
Chi-restraints excluded: chain E residue  143 LEU
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  161 THR
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  187 LEU
Chi-restraints excluded: chain F residue  214 LEU
Chi-restraints excluded: chain F residue  216 ILE
Chi-restraints excluded: chain F residue  257 MET
Chi-restraints excluded: chain G residue   55 LEU
Chi-restraints excluded: chain G residue   74 MET
Chi-restraints excluded: chain G residue   87 LEU
Chi-restraints excluded: chain H residue   87 LEU
Chi-restraints excluded: chain I residue    2 THR
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain I residue   78 LEU
Chi-restraints excluded: chain I residue   87 LEU
Chi-restraints excluded: chain J residue   62 LEU
Chi-restraints excluded: chain K residue   72 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 71 optimal weight:    0.8980
   chunk 100 optimal weight:    3.9990
   chunk 116 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 103 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 16 optimal weight:    0.4980
   chunk 104 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   chunk 154 optimal weight:    0.5980
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** F 109 GLN ** 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 = 0.3994 r_free = 0.3994 target = 0.174380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.150127 restraints weight = 15366.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.151570 restraints weight = 10999.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.153045 restraints weight = 8721.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.3791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  13117  Z= 0.145
  Angle     :  0.743  13.495  17871  Z= 0.359
  Chirality :  0.043   0.214   2288
  Planarity :  0.006   0.085   2149
  Dihedral  :  5.734  56.839   1723
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.17 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 21.61 %
    Favored  : 74.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.12 %
    Twisted General : 0.06 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.22), residues: 1645
  helix:  1.41 (0.15), residues: 1300
  sheet:  None (None), residues: 0
  loop : -3.81 (0.29), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP I  68 
 HIS   0.002   0.001   HIS F 147 
 PHE   0.020   0.001   PHE B 247 
 TYR   0.006   0.001   TYR C 120 
 ARG   0.005   0.000   ARG B  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03813 (  931)
  hydrogen bonds       : angle       4.07505 ( 2793)
  covalent geometry    : bond        0.00324 (13117)
  covalent geometry    : angle       0.74338 (17871)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  344 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 294
  time to evaluate  : 1.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  139 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7972 (tttm)
REVERT: B   70 ARG cc_start: 0.8584 (OUTLIER) cc_final: 0.7668 (ptp-170)
REVERT: B   80 GLN cc_start: 0.7836 (mt0) cc_final: 0.7613 (mt0)
REVERT: C   92 ILE cc_start: 0.6880 (OUTLIER) cc_final: 0.6023 (mt)
REVERT: C  192 MET cc_start: 0.7869 (OUTLIER) cc_final: 0.7179 (mpp)
REVERT: D  100 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.7949 (tt)
REVERT: D  109 PHE cc_start: 0.7750 (m-80) cc_final: 0.7429 (m-80)
REVERT: D  139 LYS cc_start: 0.8265 (ttpt) cc_final: 0.7943 (ttmm)
REVERT: D  201 ASP cc_start: 0.8042 (t0) cc_final: 0.7782 (t0)
REVERT: D  229 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7780 (mm)
REVERT: E  105 MET cc_start: 0.7159 (mmm) cc_final: 0.6454 (mmm)
REVERT: E  209 MET cc_start: 0.5017 (ppp) cc_final: 0.3667 (tpp)
REVERT: F  252 GLN cc_start: 0.7717 (tp40) cc_final: 0.7516 (tp-100)
REVERT: H   37 MET cc_start: 0.6197 (ttt) cc_final: 0.5672 (mtt)
REVERT: I   23 ILE cc_start: 0.8847 (mm) cc_final: 0.8450 (mt)
REVERT: K   58 MET cc_start: 0.7823 (tpp) cc_final: 0.7592 (tpp)
  outliers start: 50
  outliers final: 34
  residues processed: 324
  average time/residue: 0.2102
  time to fit residues: 104.2804
Evaluate side-chains
  320 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 281
  time to evaluate  : 1.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  234 ASP
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain B residue   70 ARG
Chi-restraints excluded: chain B residue  214 MET
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  234 ASP
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain C residue   65 MET
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  192 MET
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue   92 ILE
Chi-restraints excluded: chain D residue  100 LEU
Chi-restraints excluded: chain D residue  229 LEU
Chi-restraints excluded: chain E residue   58 ILE
Chi-restraints excluded: chain E residue  104 ILE
Chi-restraints excluded: chain E residue  143 LEU
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  161 THR
Chi-restraints excluded: chain E residue  173 ILE
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  214 LEU
Chi-restraints excluded: chain F residue  216 ILE
Chi-restraints excluded: chain F residue  217 PHE
Chi-restraints excluded: chain G residue   55 LEU
Chi-restraints excluded: chain G residue   68 TRP
Chi-restraints excluded: chain G residue   74 MET
Chi-restraints excluded: chain G residue   87 LEU
Chi-restraints excluded: chain H residue   50 SER
Chi-restraints excluded: chain H residue   87 LEU
Chi-restraints excluded: chain I residue    2 THR
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain I residue   78 LEU
Chi-restraints excluded: chain I residue   87 LEU
Chi-restraints excluded: chain J residue   62 LEU
Chi-restraints excluded: chain K residue   72 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 132 optimal weight:    6.9990
   chunk 4 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 136 optimal weight:    8.9990
   chunk 2 optimal weight:    1.9990
   chunk 123 optimal weight:    0.9980
   chunk 152 optimal weight:    5.9990
   chunk 114 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
** B  80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F 109 GLN ** 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 = 0.3926 r_free = 0.3926 target = 0.167636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.143388 restraints weight = 15529.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.144777 restraints weight = 11090.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.146608 restraints weight = 8899.238|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.3867

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075  13117  Z= 0.201
  Angle     :  0.809  12.091  17871  Z= 0.390
  Chirality :  0.046   0.248   2288
  Planarity :  0.006   0.093   2149
  Dihedral  :  5.963  57.726   1723
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 13.54
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.72 %
    Favored  : 92.22 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 22.86 %
    Favored  : 73.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.22), residues: 1645
  helix:  1.27 (0.15), residues: 1305
  sheet:  None (None), residues: 0
  loop : -3.73 (0.30), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP F 181 
 HIS   0.004   0.002   HIS F  97 
 PHE   0.024   0.002   PHE G  10 
 TYR   0.007   0.001   TYR C 120 
 ARG   0.004   0.001   ARG B  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04283 (  931)
  hydrogen bonds       : angle       4.23453 ( 2793)
  covalent geometry    : bond        0.00494 (13117)
  covalent geometry    : angle       0.80881 (17871)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  339 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 289
  time to evaluate  : 1.367 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 LYS cc_start: 0.8429 (ttmt) cc_final: 0.7972 (tttm)
REVERT: B   70 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7772 (ptp-170)
REVERT: B   80 GLN cc_start: 0.7905 (mt0) cc_final: 0.7702 (mt0)
REVERT: C   69 THR cc_start: 0.9399 (p) cc_final: 0.9182 (m)
REVERT: C   92 ILE cc_start: 0.7080 (OUTLIER) cc_final: 0.6143 (mt)
REVERT: C  192 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7288 (mpp)
REVERT: D  143 LEU cc_start: 0.8193 (tp) cc_final: 0.7991 (tp)
REVERT: D  173 ILE cc_start: 0.7600 (tt) cc_final: 0.6987 (mt)
REVERT: D  229 LEU cc_start: 0.8319 (OUTLIER) cc_final: 0.7951 (mm)
REVERT: E   90 ASN cc_start: 0.7401 (p0) cc_final: 0.7017 (p0)
REVERT: E  105 MET cc_start: 0.7404 (mmm) cc_final: 0.6623 (mmm)
REVERT: E  109 PHE cc_start: 0.7143 (m-80) cc_final: 0.6929 (m-80)
REVERT: E  209 MET cc_start: 0.5857 (ppp) cc_final: 0.5415 (tpp)
REVERT: E  214 MET cc_start: 0.5903 (ptt) cc_final: 0.5696 (mmt)
REVERT: F  117 MET cc_start: 0.4600 (pmm) cc_final: 0.4178 (ppp)
REVERT: F  252 GLN cc_start: 0.7776 (tp40) cc_final: 0.7558 (tp-100)
REVERT: G   68 TRP cc_start: 0.7321 (OUTLIER) cc_final: 0.6098 (m-90)
REVERT: H   34 LEU cc_start: 0.7863 (mt) cc_final: 0.7513 (tt)
REVERT: H   37 MET cc_start: 0.6136 (ttt) cc_final: 0.5809 (mtt)
REVERT: I   23 ILE cc_start: 0.8874 (mm) cc_final: 0.8567 (mt)
REVERT: K   58 MET cc_start: 0.7853 (tpp) cc_final: 0.7639 (tpp)
  outliers start: 50
  outliers final: 33
  residues processed: 323
  average time/residue: 0.2109
  time to fit residues: 103.9916
Evaluate side-chains
  322 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 284
  time to evaluate  : 1.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  234 ASP
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain B residue   70 ARG
Chi-restraints excluded: chain B residue  161 THR
Chi-restraints excluded: chain B residue  220 ILE
Chi-restraints excluded: chain B residue  234 ASP
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue   98 LEU
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  192 MET
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue  163 ILE
Chi-restraints excluded: chain D residue  182 GLU
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  229 LEU
Chi-restraints excluded: chain E residue   58 ILE
Chi-restraints excluded: chain E residue  104 ILE
Chi-restraints excluded: chain E residue  143 LEU
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  161 THR
Chi-restraints excluded: chain E residue  173 ILE
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  216 ILE
Chi-restraints excluded: chain G residue   55 LEU
Chi-restraints excluded: chain G residue   68 TRP
Chi-restraints excluded: chain G residue   74 MET
Chi-restraints excluded: chain G residue   87 LEU
Chi-restraints excluded: chain H residue   50 SER
Chi-restraints excluded: chain H residue   86 THR
Chi-restraints excluded: chain H residue   87 LEU
Chi-restraints excluded: chain I residue    2 THR
Chi-restraints excluded: chain I residue   74 MET
Chi-restraints excluded: chain I residue   78 LEU
Chi-restraints excluded: chain J residue   62 LEU
Chi-restraints excluded: chain J residue   88 ILE
Chi-restraints excluded: chain K residue   72 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 66 optimal weight:    6.9990
   chunk 125 optimal weight:    0.9990
   chunk 73 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 95 optimal weight:    0.4980
   chunk 79 optimal weight:    0.0770
   chunk 5 optimal weight:    0.8980
   chunk 120 optimal weight:    0.6980
   chunk 156 optimal weight:    8.9990
   chunk 76 optimal weight:    2.9990
   chunk 138 optimal weight:    3.9990
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  39 GLN ** 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 = 0.3978 r_free = 0.3978 target = 0.172784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.147816 restraints weight = 15383.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.150541 restraints weight = 10352.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.152317 restraints weight = 8032.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.4115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  13117  Z= 0.148
  Angle     :  0.766  12.785  17871  Z= 0.370
  Chirality :  0.043   0.220   2288
  Planarity :  0.006   0.088   2149
  Dihedral  :  5.743  56.652   1723
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.23 %
    Favored  : 92.71 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 24.53 %
    Favored  : 72.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.22), residues: 1645
  helix:  1.43 (0.15), residues: 1307
  sheet:  None (None), residues: 0
  loop : -3.68 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP H  68 
 HIS   0.002   0.001   HIS F  97 
 PHE   0.032   0.002   PHE A 247 
 TYR   0.016   0.001   TYR H  76 
 ARG   0.004   0.000   ARG C 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03896 (  931)
  hydrogen bonds       : angle       4.14923 ( 2793)
  covalent geometry    : bond        0.00329 (13117)
  covalent geometry    : angle       0.76564 (17871)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 286
  time to evaluate  : 1.518 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 LYS cc_start: 0.8301 (ttmt) cc_final: 0.7902 (tttm)
REVERT: B   70 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7726 (ptp-170)
REVERT: B   80 GLN cc_start: 0.7786 (mt0) cc_final: 0.7571 (mt0)
REVERT: C   69 THR cc_start: 0.9393 (p) cc_final: 0.9190 (m)
REVERT: C   92 ILE cc_start: 0.6853 (OUTLIER) cc_final: 0.5903 (mt)
REVERT: C  192 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7227 (mpp)
REVERT: D  109 PHE cc_start: 0.7715 (m-80) cc_final: 0.7186 (m-80)
REVERT: D  139 LYS cc_start: 0.8237 (ttpt) cc_final: 0.7856 (ttmm)
REVERT: D  173 ILE cc_start: 0.7491 (tt) cc_final: 0.6866 (mt)
REVERT: D  229 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7804 (mm)
REVERT: E   90 ASN cc_start: 0.7114 (p0) cc_final: 0.6845 (p0)
REVERT: E  105 MET cc_start: 0.7175 (mmm) cc_final: 0.6582 (mmm)
REVERT: E  209 MET cc_start: 0.5869 (ppp) cc_final: 0.5243 (tpp)
REVERT: E  247 PHE cc_start: 0.8347 (t80) cc_final: 0.8078 (t80)
REVERT: F  252 GLN cc_start: 0.7637 (tp40) cc_final: 0.7431 (tp-100)
REVERT: G   37 MET cc_start: 0.6404 (ttp) cc_final: 0.6192 (ttt)
REVERT: G   68 TRP cc_start: 0.7271 (OUTLIER) cc_final: 0.6068 (m-90)
REVERT: H   34 LEU cc_start: 0.7817 (mt) cc_final: 0.7497 (tt)
REVERT: H   37 MET cc_start: 0.6141 (ttt) cc_final: 0.5879 (mtt)
REVERT: I   23 ILE cc_start: 0.8823 (mm) cc_final: 0.8446 (mt)
  outliers start: 39
  outliers final: 26
  residues processed: 310
  average time/residue: 0.2172
  time to fit residues: 103.8971
Evaluate side-chains
  306 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 275
  time to evaluate  : 1.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 ILE
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  234 ASP
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain B residue   70 ARG
Chi-restraints excluded: chain B residue  234 ASP
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  192 MET
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue   92 ILE
Chi-restraints excluded: chain D residue  163 ILE
Chi-restraints excluded: chain D residue  182 GLU
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  229 LEU
Chi-restraints excluded: chain E residue   58 ILE
Chi-restraints excluded: chain E residue  143 LEU
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  161 THR
Chi-restraints excluded: chain E residue  173 ILE
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  187 LEU
Chi-restraints excluded: chain F residue  216 ILE
Chi-restraints excluded: chain F residue  217 PHE
Chi-restraints excluded: chain G residue   68 TRP
Chi-restraints excluded: chain H residue   87 LEU
Chi-restraints excluded: chain I residue    2 THR
Chi-restraints excluded: chain I residue   78 LEU
Chi-restraints excluded: chain J residue   62 LEU
Chi-restraints excluded: chain K residue   72 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 92 optimal weight:    3.9990
   chunk 158 optimal weight:    3.9990
   chunk 144 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 137 optimal weight:    0.6980
   chunk 109 optimal weight:    2.9990
   chunk 122 optimal weight:    0.0970
   chunk 89 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  39 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.178445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.153445 restraints weight = 15282.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.156195 restraints weight = 10296.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.158023 restraints weight = 8013.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7692
moved from start:          0.4230

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  13117  Z= 0.155
  Angle     :  0.793  13.416  17871  Z= 0.379
  Chirality :  0.045   0.366   2288
  Planarity :  0.006   0.087   2149
  Dihedral  :  5.705  55.998   1723
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.66 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 25.23 %
    Favored  : 72.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.22), residues: 1645
  helix:  1.45 (0.15), residues: 1307
  sheet:  None (None), residues: 0
  loop : -3.67 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP I  68 
 HIS   0.002   0.001   HIS F  97 
 PHE   0.030   0.002   PHE A 247 
 TYR   0.016   0.001   TYR H  76 
 ARG   0.004   0.000   ARG C 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03914 (  931)
  hydrogen bonds       : angle       4.15119 ( 2793)
  covalent geometry    : bond        0.00358 (13117)
  covalent geometry    : angle       0.79310 (17871)

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

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

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3290 Ramachandran restraints generated.
    1645 Oldfield, 0 Emsley, 1645 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  324 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 288
  time to evaluate  : 1.280 
Fit side-chains
   revert: symmetry clash
REVERT: A  139 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7874 (tttm)
REVERT: B   70 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7805 (ptp-170)
REVERT: B   80 GLN cc_start: 0.7788 (mt0) cc_final: 0.7577 (mt0)
REVERT: C   92 ILE cc_start: 0.6857 (OUTLIER) cc_final: 0.5907 (mt)
REVERT: C  192 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.7197 (mpp)
REVERT: D  109 PHE cc_start: 0.7726 (m-80) cc_final: 0.7157 (m-80)
REVERT: D  139 LYS cc_start: 0.8239 (ttpt) cc_final: 0.7856 (ttmm)
REVERT: D  173 ILE cc_start: 0.7548 (tt) cc_final: 0.6939 (mt)
REVERT: D  229 LEU cc_start: 0.8228 (OUTLIER) cc_final: 0.7811 (mm)
REVERT: E   90 ASN cc_start: 0.7041 (p0) cc_final: 0.6757 (p0)
REVERT: E  105 MET cc_start: 0.7141 (mmm) cc_final: 0.6473 (mmm)
REVERT: E  109 PHE cc_start: 0.7070 (m-80) cc_final: 0.6792 (m-80)
REVERT: E  209 MET cc_start: 0.6054 (ppp) cc_final: 0.5478 (tpp)
REVERT: E  247 PHE cc_start: 0.8342 (t80) cc_final: 0.8051 (t80)
REVERT: G   37 MET cc_start: 0.6403 (ttp) cc_final: 0.6141 (ttt)
REVERT: G   68 TRP cc_start: 0.7263 (OUTLIER) cc_final: 0.6042 (m-90)
REVERT: H   34 LEU cc_start: 0.7812 (mt) cc_final: 0.7529 (tt)
REVERT: I   23 ILE cc_start: 0.8843 (mm) cc_final: 0.8464 (mt)
  outliers start: 36
  outliers final: 29
  residues processed: 311
  average time/residue: 0.2021
  time to fit residues: 96.7573
Evaluate side-chains
  314 residues out of total 1439 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 280
  time to evaluate  : 1.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  234 ASP
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain B residue   70 ARG
Chi-restraints excluded: chain B residue  234 ASP
Chi-restraints excluded: chain B residue  242 THR
Chi-restraints excluded: chain C residue   61 PHE
Chi-restraints excluded: chain C residue   92 ILE
Chi-restraints excluded: chain C residue  100 LEU
Chi-restraints excluded: chain C residue  192 MET
Chi-restraints excluded: chain D residue   84 LEU
Chi-restraints excluded: chain D residue   92 ILE
Chi-restraints excluded: chain D residue  163 ILE
Chi-restraints excluded: chain D residue  182 GLU
Chi-restraints excluded: chain D residue  216 LEU
Chi-restraints excluded: chain D residue  229 LEU
Chi-restraints excluded: chain E residue   58 ILE
Chi-restraints excluded: chain E residue  143 LEU
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  161 THR
Chi-restraints excluded: chain E residue  173 ILE
Chi-restraints excluded: chain F residue   67 VAL
Chi-restraints excluded: chain F residue  187 LEU
Chi-restraints excluded: chain F residue  214 LEU
Chi-restraints excluded: chain F residue  216 ILE
Chi-restraints excluded: chain F residue  217 PHE
Chi-restraints excluded: chain G residue   68 TRP
Chi-restraints excluded: chain G residue   74 MET
Chi-restraints excluded: chain H residue   86 THR
Chi-restraints excluded: chain H residue   87 LEU
Chi-restraints excluded: chain I residue    2 THR
Chi-restraints excluded: chain I residue   78 LEU
Chi-restraints excluded: chain J residue   62 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 159
   random chunks:
   chunk 61 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 141 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 148 optimal weight:    2.9990
   chunk 121 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0370
   chunk 97 optimal weight:    0.1980
   chunk 96 optimal weight:    0.9980
   chunk 100 optimal weight:    0.0170
   overall best weight:    0.3896

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

Flipped N/Q/H residues before XYZ refinement:
** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  39 GLN ** 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 = 0.4010 r_free = 0.4010 target = 0.175758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.151146 restraints weight = 15291.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.153867 restraints weight = 10311.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.155697 restraints weight = 7975.103|
|-----------------------------------------------------------------------------|
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.4474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  13117  Z= 0.144
  Angle     :  0.784  16.957  17871  Z= 0.373
  Chirality :  0.044   0.389   2288
  Planarity :  0.006   0.084   2149
  Dihedral  :  5.556  55.697   1723
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.11 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 25.85 %
    Favored  : 71.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.12 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.22), residues: 1645
  helix:  1.54 (0.15), residues: 1304
  sheet:  None (None), residues: 0
  loop : -3.58 (0.30), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP H  68 
 HIS   0.002   0.001   HIS F  97 
 PHE   0.028   0.002   PHE A 247 
 TYR   0.013   0.001   TYR H  76 
 ARG   0.004   0.000   ARG C 111 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03769 (  931)
  hydrogen bonds       : angle       4.12065 ( 2793)
  covalent geometry    : bond        0.00314 (13117)
  covalent geometry    : angle       0.78364 (17871)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4395.82 seconds
wall clock time: 77 minutes 2.82 seconds (4622.82 seconds total)