Starting phenix.real_space_refine
on Tue Jun 10 01:08:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tfs_25879/06_2025/7tfs_25879.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tfs_25879/06_2025/7tfs_25879.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tfs_25879/06_2025/7tfs_25879.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tfs_25879/06_2025/7tfs_25879.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tfs_25879/06_2025/7tfs_25879.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tfs_25879/06_2025/7tfs_25879.cif"
  }
  resolution = 4.3
  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
-------------------------------------------------------------------------------
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=   0.001 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Fe     28      7.16       5
     S      91      5.16       5
     C    7168      2.51       5
     N    1918      2.21       5
     O    2177      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 11382
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 1454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1454
          Classifications: {'peptide': 202}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 190}
    Chain: "A"
      Number of atoms: 172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 172
          Unusual residues: {'HEC': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
  Restraints were copied for chains:
    C, B, E, D, G, F
  Time building chain proxies: 4.39, per 1000 atoms: 0.39
  Number of scatterers: 11382
  At special positions: 0
  Unit cell: (72.36, 72.36, 267.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Fe     28     26.01
     S      91     16.00
     O    2177      8.00
     N    1918      7.00
     C    7168      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=96, symmetry=0
  Number of additional bonds: simple=96, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 3.55
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2506

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 14 sheets defined
      23.3% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 50 through 54
      removed outlier: 3.937A  pdb=" N   PHE A  53 " --> pdb=" O   ILE A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 77
      removed outlier: 4.006A  pdb=" N   THR A  76 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 3.696A  pdb=" N   LYS A  91 " --> pdb=" O   VAL A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 107
      removed outlier: 3.643A  pdb=" N   PHE A 102 " --> pdb=" O   SER A  98 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   CYS A 106 " --> pdb=" O   PHE A 102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 132
      removed outlier: 3.826A  pdb=" N   ASN A 132 " --> pdb=" O   VAL A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 164
    Processing helix  chain 'A' and resid 223 through 230
      removed outlier: 4.050A  pdb=" N   CYS A 229 " --> pdb=" O   LEU A 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 54
      removed outlier: 3.937A  pdb=" N   PHE B  53 " --> pdb=" O   ILE B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 77
      removed outlier: 4.006A  pdb=" N   THR B  76 " --> pdb=" O   THR B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 91
      removed outlier: 3.696A  pdb=" N   LYS B  91 " --> pdb=" O   VAL B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 107
      removed outlier: 3.644A  pdb=" N   PHE B 102 " --> pdb=" O   SER B  98 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   CYS B 106 " --> pdb=" O   PHE B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 128 through 132
      removed outlier: 3.826A  pdb=" N   ASN B 132 " --> pdb=" O   VAL B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 164
    Processing helix  chain 'B' and resid 223 through 230
      removed outlier: 4.050A  pdb=" N   CYS B 229 " --> pdb=" O   LEU B 225 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 50 through 54
      removed outlier: 3.937A  pdb=" N   PHE C  53 " --> pdb=" O   ILE C  50 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 73 through 77
      removed outlier: 4.006A  pdb=" N   THR C  76 " --> pdb=" O   THR C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.696A  pdb=" N   LYS C  91 " --> pdb=" O   VAL C  88 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 98 through 107
      removed outlier: 3.643A  pdb=" N   PHE C 102 " --> pdb=" O   SER C  98 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   CYS C 106 " --> pdb=" O   PHE C 102 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 128 through 132
      removed outlier: 3.826A  pdb=" N   ASN C 132 " --> pdb=" O   VAL C 129 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 156 through 164
    Processing helix  chain 'C' and resid 223 through 230
      removed outlier: 4.050A  pdb=" N   CYS C 229 " --> pdb=" O   LEU C 225 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 50 through 54
      removed outlier: 3.937A  pdb=" N   PHE D  53 " --> pdb=" O   ILE D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 73 through 77
      removed outlier: 4.007A  pdb=" N   THR D  76 " --> pdb=" O   THR D  73 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 3.696A  pdb=" N   LYS D  91 " --> pdb=" O   VAL D  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 98 through 107
      removed outlier: 3.643A  pdb=" N   PHE D 102 " --> pdb=" O   SER D  98 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   CYS D 106 " --> pdb=" O   PHE D 102 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 128 through 132
      removed outlier: 3.827A  pdb=" N   ASN D 132 " --> pdb=" O   VAL D 129 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 156 through 164
    Processing helix  chain 'D' and resid 223 through 230
      removed outlier: 4.050A  pdb=" N   CYS D 229 " --> pdb=" O   LEU D 225 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 50 through 54
      removed outlier: 3.936A  pdb=" N   PHE E  53 " --> pdb=" O   ILE E  50 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 73 through 77
      removed outlier: 4.007A  pdb=" N   THR E  76 " --> pdb=" O   THR E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 91
      removed outlier: 3.697A  pdb=" N   LYS E  91 " --> pdb=" O   VAL E  88 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 98 through 107
      removed outlier: 3.644A  pdb=" N   PHE E 102 " --> pdb=" O   SER E  98 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   CYS E 106 " --> pdb=" O   PHE E 102 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 128 through 132
      removed outlier: 3.826A  pdb=" N   ASN E 132 " --> pdb=" O   VAL E 129 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 156 through 164
    Processing helix  chain 'E' and resid 223 through 230
      removed outlier: 4.051A  pdb=" N   CYS E 229 " --> pdb=" O   LEU E 225 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 50 through 54
      removed outlier: 3.937A  pdb=" N   PHE F  53 " --> pdb=" O   ILE F  50 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 73 through 77
      removed outlier: 4.006A  pdb=" N   THR F  76 " --> pdb=" O   THR F  73 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 87 through 91
      removed outlier: 3.696A  pdb=" N   LYS F  91 " --> pdb=" O   VAL F  88 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 98 through 107
      removed outlier: 3.643A  pdb=" N   PHE F 102 " --> pdb=" O   SER F  98 " (cutoff:3.500A)
      removed outlier: 4.152A  pdb=" N   CYS F 106 " --> pdb=" O   PHE F 102 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 128 through 132
      removed outlier: 3.826A  pdb=" N   ASN F 132 " --> pdb=" O   VAL F 129 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 156 through 164
    Processing helix  chain 'F' and resid 223 through 230
      removed outlier: 4.050A  pdb=" N   CYS F 229 " --> pdb=" O   LEU F 225 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 50 through 54
      removed outlier: 3.937A  pdb=" N   PHE G  53 " --> pdb=" O   ILE G  50 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 73 through 77
      removed outlier: 4.006A  pdb=" N   THR G  76 " --> pdb=" O   THR G  73 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 87 through 91
      removed outlier: 3.696A  pdb=" N   LYS G  91 " --> pdb=" O   VAL G  88 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 98 through 107
      removed outlier: 3.643A  pdb=" N   PHE G 102 " --> pdb=" O   SER G  98 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   CYS G 106 " --> pdb=" O   PHE G 102 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 128 through 132
      removed outlier: 3.826A  pdb=" N   ASN G 132 " --> pdb=" O   VAL G 129 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 156 through 164
    Processing helix  chain 'G' and resid 223 through 230
      removed outlier: 4.050A  pdb=" N   CYS G 229 " --> pdb=" O   LEU G 225 " (cutoff:3.500A)
    Processing sheet with id=1, first strand: chain 'A' and resid 153 through 154
      removed outlier: 3.844A  pdb=" N   PHE A 153 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
    Processing sheet with id=2, first strand: chain 'A' and resid 168 through 170
      removed outlier: 3.788A  pdb=" N   LEU A 187 " --> pdb=" O   MET A 178 " (cutoff:3.500A)
    Processing sheet with id=3, first strand: chain 'B' and resid 153 through 154
      removed outlier: 3.844A  pdb=" N   PHE B 153 " --> pdb=" O   LEU B 199 " (cutoff:3.500A)
    Processing sheet with id=4, first strand: chain 'B' and resid 168 through 170
      removed outlier: 3.788A  pdb=" N   LEU B 187 " --> pdb=" O   MET B 178 " (cutoff:3.500A)
    Processing sheet with id=5, first strand: chain 'C' and resid 153 through 154
      removed outlier: 3.844A  pdb=" N   PHE C 153 " --> pdb=" O   LEU C 199 " (cutoff:3.500A)
    Processing sheet with id=6, first strand: chain 'C' and resid 168 through 170
      removed outlier: 3.788A  pdb=" N   LEU C 187 " --> pdb=" O   MET C 178 " (cutoff:3.500A)
    Processing sheet with id=7, first strand: chain 'D' and resid 153 through 154
      removed outlier: 3.844A  pdb=" N   PHE D 153 " --> pdb=" O   LEU D 199 " (cutoff:3.500A)
    Processing sheet with id=8, first strand: chain 'D' and resid 168 through 170
      removed outlier: 3.788A  pdb=" N   LEU D 187 " --> pdb=" O   MET D 178 " (cutoff:3.500A)
    Processing sheet with id=9, first strand: chain 'E' and resid 153 through 154
      removed outlier: 3.844A  pdb=" N   PHE E 153 " --> pdb=" O   LEU E 199 " (cutoff:3.500A)
    Processing sheet with id=10, first strand: chain 'E' and resid 168 through 170
      removed outlier: 3.789A  pdb=" N   LEU E 187 " --> pdb=" O   MET E 178 " (cutoff:3.500A)
    Processing sheet with id=11, first strand: chain 'F' and resid 153 through 154
      removed outlier: 3.844A  pdb=" N   PHE F 153 " --> pdb=" O   LEU F 199 " (cutoff:3.500A)
    Processing sheet with id=12, first strand: chain 'F' and resid 168 through 170
      removed outlier: 3.789A  pdb=" N   LEU F 187 " --> pdb=" O   MET F 178 " (cutoff:3.500A)
    Processing sheet with id=13, first strand: chain 'G' and resid 153 through 154
      removed outlier: 3.843A  pdb=" N   PHE G 153 " --> pdb=" O   LEU G 199 " (cutoff:3.500A)
    Processing sheet with id=14, first strand: chain 'G' and resid 168 through 170
      removed outlier: 3.788A  pdb=" N   LEU G 187 " --> pdb=" O   MET G 178 " (cutoff:3.500A)

    154 hydrogen bonds defined for protein.
    336 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: 2.28

  Time building geometry restraints manager: 4.07 seconds

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

  Histogram of bond lengths:
        1.23 -     1.40: 4802
        1.40 -     1.58: 6748
        1.58 -     1.75: 0
        1.75 -     1.93: 126
        1.93 -     2.10: 112
  Bond restraints: 11788
  Sorted by residual:
  bond pdb=" C3B HEC E 301 "
       pdb=" CAB HEC E 301 "
    ideal  model  delta    sigma   weight residual
    1.544  1.562 -0.018 2.00e-02 2.50e+03 7.95e-01
  bond pdb=" C3B HEC G 301 "
       pdb=" CAB HEC G 301 "
    ideal  model  delta    sigma   weight residual
    1.544  1.562 -0.018 2.00e-02 2.50e+03 7.86e-01
  bond pdb=" C3B HEC A 301 "
       pdb=" CAB HEC A 301 "
    ideal  model  delta    sigma   weight residual
    1.544  1.562 -0.018 2.00e-02 2.50e+03 7.66e-01
  bond pdb=" C3B HEC F 301 "
       pdb=" CAB HEC F 301 "
    ideal  model  delta    sigma   weight residual
    1.544  1.561 -0.017 2.00e-02 2.50e+03 7.55e-01
  bond pdb=" C3B HEC D 301 "
       pdb=" CAB HEC D 301 "
    ideal  model  delta    sigma   weight residual
    1.544  1.561 -0.017 2.00e-02 2.50e+03 7.54e-01
  ... (remaining 11783 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.30: 16208
        3.30 -     6.60: 207
        6.60 -     9.90: 7
        9.90 -    13.21: 14
       13.21 -    16.51: 7
  Bond angle restraints: 16443
  Sorted by residual:
  angle pdb=" C   ALA E 213 "
        pdb=" N   PRO E 214 "
        pdb=" CD  PRO E 214 "
      ideal   model   delta    sigma   weight residual
     120.60  104.09   16.51 2.20e+00 2.07e-01 5.63e+01
  angle pdb=" C   ALA B 213 "
        pdb=" N   PRO B 214 "
        pdb=" CD  PRO B 214 "
      ideal   model   delta    sigma   weight residual
     120.60  104.10   16.50 2.20e+00 2.07e-01 5.63e+01
  angle pdb=" C   ALA A 213 "
        pdb=" N   PRO A 214 "
        pdb=" CD  PRO A 214 "
      ideal   model   delta    sigma   weight residual
     120.60  104.12   16.48 2.20e+00 2.07e-01 5.61e+01
  angle pdb=" C   ALA C 213 "
        pdb=" N   PRO C 214 "
        pdb=" CD  PRO C 214 "
      ideal   model   delta    sigma   weight residual
     120.60  104.13   16.47 2.20e+00 2.07e-01 5.61e+01
  angle pdb=" C   ALA F 213 "
        pdb=" N   PRO F 214 "
        pdb=" CD  PRO F 214 "
      ideal   model   delta    sigma   weight residual
     120.60  104.14   16.46 2.20e+00 2.07e-01 5.60e+01
  ... (remaining 16438 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.11: 5733
       17.11 -    34.23: 392
       34.23 -    51.34: 84
       51.34 -    68.46: 84
       68.46 -    85.57: 42
  Dihedral angle restraints: 6335
    sinusoidal: 2415
      harmonic: 3920
  Sorted by residual:
  dihedral pdb=" CA  ILE B  64 "
           pdb=" C   ILE B  64 "
           pdb=" N   PRO B  65 "
           pdb=" CA  PRO B  65 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -143.17  -36.83     0      5.00e+00 4.00e-02 5.43e+01
  dihedral pdb=" CA  ILE E  64 "
           pdb=" C   ILE E  64 "
           pdb=" N   PRO E  65 "
           pdb=" CA  PRO E  65 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -143.17  -36.83     0      5.00e+00 4.00e-02 5.43e+01
  dihedral pdb=" CA  ILE A  64 "
           pdb=" C   ILE A  64 "
           pdb=" N   PRO A  65 "
           pdb=" CA  PRO A  65 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -143.18  -36.82     0      5.00e+00 4.00e-02 5.42e+01
  ... (remaining 6332 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1170
       0.044 -    0.087: 388
       0.087 -    0.131: 59
       0.131 -    0.174: 7
       0.174 -    0.218: 7
  Chirality restraints: 1631
  Sorted by residual:
  chirality pdb=" CA  ILE D  64 "
            pdb=" N   ILE D  64 "
            pdb=" C   ILE D  64 "
            pdb=" CB  ILE D  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  ILE B  64 "
            pdb=" N   ILE B  64 "
            pdb=" C   ILE B  64 "
            pdb=" CB  ILE B  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  ILE A  64 "
            pdb=" N   ILE A  64 "
            pdb=" C   ILE A  64 "
            pdb=" CB  ILE A  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 1628 not shown)

  Planarity restraints: 2065
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA F 213 "   -0.084 5.00e-02 4.00e+02   1.26e-01 2.52e+01
        pdb=" N   PRO F 214 "    0.217 5.00e-02 4.00e+02
        pdb=" CA  PRO F 214 "   -0.079 5.00e-02 4.00e+02
        pdb=" CD  PRO F 214 "   -0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 213 "    0.083 5.00e-02 4.00e+02   1.26e-01 2.52e+01
        pdb=" N   PRO B 214 "   -0.217 5.00e-02 4.00e+02
        pdb=" CA  PRO B 214 "    0.079 5.00e-02 4.00e+02
        pdb=" CD  PRO B 214 "    0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA G 213 "   -0.084 5.00e-02 4.00e+02   1.25e-01 2.52e+01
        pdb=" N   PRO G 214 "    0.216 5.00e-02 4.00e+02
        pdb=" CA  PRO G 214 "   -0.079 5.00e-02 4.00e+02
        pdb=" CD  PRO G 214 "   -0.054 5.00e-02 4.00e+02
  ... (remaining 2062 not shown)

  Histogram of nonbonded interaction distances:
        2.00 -     2.58: 193
        2.58 -     3.16: 9797
        3.16 -     3.74: 17907
        3.74 -     4.32: 23836
        4.32 -     4.90: 37309
  Nonbonded interactions: 89042
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS F  55 "
            pdb="FE   HEC F 301 "
     model   vdw
     2.001 3.080
  nonbonded pdb=" NE2 HIS B  55 "
            pdb="FE   HEC B 301 "
     model   vdw
     2.001 3.080
  nonbonded pdb=" NE2 HIS A  55 "
            pdb="FE   HEC A 301 "
     model   vdw
     2.001 3.080
  nonbonded pdb=" NE2 HIS D  55 "
            pdb="FE   HEC D 301 "
     model   vdw
     2.001 3.080
  nonbonded pdb=" NE2 HIS C  55 "
            pdb="FE   HEC C 301 "
     model   vdw
     2.001 3.080
  ... (remaining 89037 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: 0.09
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.280
  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:          0.440
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     24.720
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7052
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      :  0.017   0.343  11884  Z= 1.475
  Angle     :  0.957  16.507  16443  Z= 0.415
  Chirality :  0.043   0.218   1631
  Planarity :  0.010   0.126   2065
  Dihedral  : 16.802  85.571   3829
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 35.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    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: -2.06 (0.20), residues: 1400
  helix:  0.45 (0.39), residues: 154
  sheet: -1.68 (0.45), residues: 70
  loop : -1.77 (0.17), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  67 
 HIS   0.012   0.002   HIS D 230 
 PHE   0.005   0.001   PHE D 215 
 TYR   0.002   0.001   TYR F  80 
 ARG   0.002   0.001   ARG C  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27741 (  154)
  hydrogen bonds       : angle       8.13248 (  336)
  covalent geometry    : bond        0.00397 (11788)
  covalent geometry    : angle       0.95684 (16443)
  Misc. bond           : bond        0.18545 (   96)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 265
  time to evaluate  : 1.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   77 PHE cc_start: 0.7028 (m-10) cc_final: 0.6749 (m-10)
REVERT: B   83 SER cc_start: 0.8054 (p) cc_final: 0.7792 (p)
REVERT: B  148 ASP cc_start: 0.6455 (t70) cc_final: 0.6247 (t70)
REVERT: B  174 ASN cc_start: 0.7817 (m-40) cc_final: 0.7553 (m-40)
REVERT: C   83 SER cc_start: 0.7994 (p) cc_final: 0.7630 (p)
REVERT: C  200 GLU cc_start: 0.8440 (tp30) cc_final: 0.8231 (tp30)
REVERT: D   77 PHE cc_start: 0.7182 (m-10) cc_final: 0.6692 (m-10)
REVERT: D  104 MET cc_start: 0.7909 (mtt) cc_final: 0.7666 (mtt)
REVERT: D  174 ASN cc_start: 0.7891 (m-40) cc_final: 0.7549 (m-40)
REVERT: D  231 LYS cc_start: 0.7641 (pptt) cc_final: 0.6608 (ttmt)
REVERT: A   77 PHE cc_start: 0.7113 (m-10) cc_final: 0.6603 (m-10)
REVERT: A  148 ASP cc_start: 0.6994 (t70) cc_final: 0.6753 (t70)
REVERT: A  174 ASN cc_start: 0.7974 (m-40) cc_final: 0.7692 (m-40)
REVERT: A  200 GLU cc_start: 0.8475 (tp30) cc_final: 0.8171 (tp30)
REVERT: E   77 PHE cc_start: 0.7214 (m-10) cc_final: 0.6993 (m-10)
REVERT: E   83 SER cc_start: 0.7852 (p) cc_final: 0.7632 (p)
REVERT: E  150 PRO cc_start: 0.8906 (Cg_exo) cc_final: 0.8675 (Cg_endo)
REVERT: F   67 TRP cc_start: 0.7281 (t-100) cc_final: 0.6095 (t-100)
REVERT: F   77 PHE cc_start: 0.7228 (m-10) cc_final: 0.6962 (m-10)
REVERT: F  102 PHE cc_start: 0.7363 (m-10) cc_final: 0.7147 (m-10)
REVERT: F  104 MET cc_start: 0.8001 (mtt) cc_final: 0.7740 (mtt)
REVERT: F  174 ASN cc_start: 0.7917 (m-40) cc_final: 0.7636 (m-40)
REVERT: F  231 LYS cc_start: 0.7545 (pptt) cc_final: 0.6789 (ttmt)
REVERT: G   67 TRP cc_start: 0.7500 (t-100) cc_final: 0.6966 (t-100)
REVERT: G   83 SER cc_start: 0.7925 (p) cc_final: 0.7634 (p)
REVERT: G  141 LEU cc_start: 0.8268 (tp) cc_final: 0.7986 (tp)
REVERT: G  174 ASN cc_start: 0.8111 (m-40) cc_final: 0.7838 (m-40)
REVERT: G  200 GLU cc_start: 0.8451 (tp30) cc_final: 0.8225 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 265
  average time/residue: 0.2343
  time to fit residues: 90.1757
Evaluate side-chains
  215 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 1.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 118 optimal weight:    1.9990
   chunk 106 optimal weight:    0.6980
   chunk 58 optimal weight:    0.4980
   chunk 36 optimal weight:    0.6980
   chunk 71 optimal weight:    7.9990
   chunk 56 optimal weight:    0.8980
   chunk 109 optimal weight:    5.9990
   chunk 42 optimal weight:    8.9990
   chunk 66 optimal weight:    8.9990
   chunk 81 optimal weight:    0.7980
   chunk 127 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
C 152 ASN
D 152 ASN
A 152 ASN
E 152 ASN
G 152 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.182299 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.145742 restraints weight = 18187.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.151092 restraints weight = 12656.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.154721 restraints weight = 9669.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
moved from start:          0.1503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.327  11884  Z= 0.169
  Angle     :  0.930  12.033  16443  Z= 0.353
  Chirality :  0.044   0.210   1631
  Planarity :  0.006   0.067   2065
  Dihedral  : 14.704  82.985   1659
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    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: -1.89 (0.21), residues: 1400
  helix:  0.37 (0.37), residues: 154
  sheet: -1.82 (0.47), residues: 70
  loop : -1.59 (0.17), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  67 
 HIS   0.006   0.002   HIS C  31 
 PHE   0.013   0.001   PHE E 215 
 TYR   0.013   0.002   TYR B  80 
 ARG   0.002   0.000   ARG E 217 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04738 (  154)
  hydrogen bonds       : angle       7.82608 (  336)
  covalent geometry    : bond        0.00484 (11788)
  covalent geometry    : angle       0.93009 (16443)
  Misc. bond           : bond        0.11370 (   96)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 277
  time to evaluate  : 1.285 
Fit side-chains
   revert: symmetry clash
REVERT: B  102 PHE cc_start: 0.7685 (m-10) cc_final: 0.7436 (m-10)
REVERT: B  104 MET cc_start: 0.8433 (mtm) cc_final: 0.8146 (mtm)
REVERT: B  174 ASN cc_start: 0.8234 (m-40) cc_final: 0.8018 (m-40)
REVERT: B  231 LYS cc_start: 0.7546 (pptt) cc_final: 0.6876 (ttmt)
REVERT: C   83 SER cc_start: 0.8222 (p) cc_final: 0.7844 (p)
REVERT: C  113 LEU cc_start: 0.8310 (mt) cc_final: 0.8032 (pp)
REVERT: C  148 ASP cc_start: 0.7642 (t70) cc_final: 0.7380 (t70)
REVERT: C  191 LYS cc_start: 0.8629 (tptp) cc_final: 0.8232 (tptp)
REVERT: D   67 TRP cc_start: 0.7431 (t-100) cc_final: 0.6585 (t-100)
REVERT: D   77 PHE cc_start: 0.7851 (m-10) cc_final: 0.7322 (m-10)
REVERT: D  148 ASP cc_start: 0.7360 (t70) cc_final: 0.7066 (t70)
REVERT: D  174 ASN cc_start: 0.8246 (m-40) cc_final: 0.7956 (m-40)
REVERT: D  231 LYS cc_start: 0.7743 (pptt) cc_final: 0.6836 (ttmt)
REVERT: A   56 THR cc_start: 0.9179 (t) cc_final: 0.8940 (p)
REVERT: A   69 ARG cc_start: 0.7079 (tpp-160) cc_final: 0.6862 (tpp-160)
REVERT: A   83 SER cc_start: 0.8268 (p) cc_final: 0.8050 (p)
REVERT: A  174 ASN cc_start: 0.8285 (m-40) cc_final: 0.8069 (m-40)
REVERT: A  206 LYS cc_start: 0.7762 (tttt) cc_final: 0.7333 (tptt)
REVERT: E   77 PHE cc_start: 0.7765 (m-10) cc_final: 0.7560 (m-10)
REVERT: E  206 LYS cc_start: 0.7910 (tttt) cc_final: 0.7492 (tptp)
REVERT: F  174 ASN cc_start: 0.8250 (m-40) cc_final: 0.8031 (m-40)
REVERT: F  206 LYS cc_start: 0.7792 (tttt) cc_final: 0.7494 (tptt)
REVERT: F  231 LYS cc_start: 0.7573 (pptt) cc_final: 0.6820 (tttt)
REVERT: G   67 TRP cc_start: 0.7541 (t-100) cc_final: 0.7168 (t-100)
REVERT: G  148 ASP cc_start: 0.7703 (t70) cc_final: 0.7399 (t70)
REVERT: G  206 LYS cc_start: 0.7771 (tttt) cc_final: 0.7437 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 277
  average time/residue: 0.2210
  time to fit residues: 88.6609
Evaluate side-chains
  223 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 119 optimal weight:    4.9990
   chunk 139 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0670
   chunk 98 optimal weight:    0.0370
   chunk 83 optimal weight:    0.9990
   chunk 87 optimal weight:    6.9990
   chunk 110 optimal weight:    6.9990
   chunk 58 optimal weight:    0.0000
   chunk 37 optimal weight:    0.0270
   chunk 41 optimal weight:   20.0000
   chunk 23 optimal weight:    2.9990
   overall best weight:    0.2260

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

Flipped N/Q/H residues before XYZ refinement:
B  62 GLN
E 152 ASN
G  58 HIS
G 152 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.189250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.149090 restraints weight = 17856.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.155566 restraints weight = 11909.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.160564 restraints weight = 8778.325|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7060
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.265  11884  Z= 0.135
  Angle     :  0.851  11.052  16443  Z= 0.323
  Chirality :  0.042   0.206   1631
  Planarity :  0.004   0.044   2065
  Dihedral  : 14.488  89.669   1659
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    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: -1.77 (0.21), residues: 1400
  helix:  0.74 (0.38), residues: 154
  sheet: -1.83 (0.48), residues: 70
  loop : -1.55 (0.18), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  67 
 HIS   0.017   0.002   HIS F 230 
 PHE   0.014   0.001   PHE E 215 
 TYR   0.014   0.001   TYR B  80 
 ARG   0.001   0.000   ARG F 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03253 (  154)
  hydrogen bonds       : angle       7.85776 (  336)
  covalent geometry    : bond        0.00366 (11788)
  covalent geometry    : angle       0.85083 (16443)
  Misc. bond           : bond        0.08461 (   96)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 275
  time to evaluate  : 1.274 
Fit side-chains
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.6916 (tpt) cc_final: 0.6075 (tpp)
REVERT: B  231 LYS cc_start: 0.7848 (pptt) cc_final: 0.6974 (tttt)
REVERT: C   83 SER cc_start: 0.8441 (p) cc_final: 0.8090 (p)
REVERT: C  148 ASP cc_start: 0.7685 (t70) cc_final: 0.7371 (t70)
REVERT: C  170 ASP cc_start: 0.7711 (t0) cc_final: 0.7330 (t0)
REVERT: C  191 LYS cc_start: 0.8804 (tptp) cc_final: 0.8476 (tptp)
REVERT: D   77 PHE cc_start: 0.7937 (m-10) cc_final: 0.7556 (m-10)
REVERT: D  113 LEU cc_start: 0.8003 (mt) cc_final: 0.7622 (pp)
REVERT: D  128 MET cc_start: 0.6985 (tpt) cc_final: 0.6113 (tpp)
REVERT: D  148 ASP cc_start: 0.7349 (t70) cc_final: 0.7006 (t70)
REVERT: D  170 ASP cc_start: 0.7332 (t0) cc_final: 0.6817 (t0)
REVERT: D  174 ASN cc_start: 0.8336 (m-40) cc_final: 0.8016 (m-40)
REVERT: A   56 THR cc_start: 0.9088 (t) cc_final: 0.8887 (p)
REVERT: A   83 SER cc_start: 0.8464 (p) cc_final: 0.8263 (p)
REVERT: A  177 THR cc_start: 0.8810 (t) cc_final: 0.8608 (t)
REVERT: A  231 LYS cc_start: 0.7895 (pptt) cc_final: 0.6969 (ttmt)
REVERT: F   67 TRP cc_start: 0.7345 (t-100) cc_final: 0.7140 (t-100)
REVERT: F  174 ASN cc_start: 0.8334 (m-40) cc_final: 0.8096 (m-40)
REVERT: F  191 LYS cc_start: 0.8820 (tmtt) cc_final: 0.8551 (tptp)
REVERT: F  231 LYS cc_start: 0.7891 (pptt) cc_final: 0.6758 (tttt)
REVERT: G   62 GLN cc_start: 0.6568 (mt0) cc_final: 0.6276 (pt0)
REVERT: G   67 TRP cc_start: 0.7655 (t-100) cc_final: 0.7228 (t-100)
REVERT: G  148 ASP cc_start: 0.7778 (t70) cc_final: 0.7465 (t70)
REVERT: G  170 ASP cc_start: 0.7460 (t0) cc_final: 0.7054 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 275
  average time/residue: 0.2097
  time to fit residues: 84.6118
Evaluate side-chains
  215 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 1.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 63 optimal weight:    0.0870
   chunk 128 optimal weight:    9.9990
   chunk 114 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 59 optimal weight:    4.9990
   chunk 29 optimal weight:    6.9990
   chunk 96 optimal weight:    1.9990
   chunk 118 optimal weight:    0.0670
   overall best weight:    1.2300

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

Flipped N/Q/H residues before XYZ refinement:
C 152 ASN
** F  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  31 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.179726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.142252 restraints weight = 18358.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.147073 restraints weight = 13338.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.150933 restraints weight = 10496.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.2558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.428  11884  Z= 0.184
  Angle     :  0.987  16.131  16443  Z= 0.352
  Chirality :  0.045   0.227   1631
  Planarity :  0.006   0.061   2065
  Dihedral  : 14.666  82.574   1659
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 11.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    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: -2.12 (0.21), residues: 1400
  helix: -0.66 (0.35), residues: 196
  sheet: -1.88 (0.49), residues: 70
  loop : -1.66 (0.18), residues: 1134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B  67 
 HIS   0.014   0.002   HIS G 230 
 PHE   0.012   0.001   PHE B 102 
 TYR   0.017   0.002   TYR E  80 
 ARG   0.007   0.001   ARG A  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03568 (  154)
  hydrogen bonds       : angle       7.50803 (  336)
  covalent geometry    : bond        0.00489 (11788)
  covalent geometry    : angle       0.98681 (16443)
  Misc. bond           : bond        0.10184 (   96)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 1.225 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.6973 (tpt) cc_final: 0.6009 (tpp)
REVERT: B  231 LYS cc_start: 0.7016 (pptt) cc_final: 0.6702 (tttt)
REVERT: C   83 SER cc_start: 0.8119 (p) cc_final: 0.7806 (p)
REVERT: C  191 LYS cc_start: 0.8746 (tptp) cc_final: 0.8429 (tptp)
REVERT: C  231 LYS cc_start: 0.7439 (pptt) cc_final: 0.6513 (ttmt)
REVERT: D  231 LYS cc_start: 0.7870 (pptt) cc_final: 0.6854 (tttt)
REVERT: A   56 THR cc_start: 0.9142 (t) cc_final: 0.8876 (p)
REVERT: A   83 SER cc_start: 0.8126 (p) cc_final: 0.7887 (p)
REVERT: A  102 PHE cc_start: 0.7639 (m-10) cc_final: 0.7364 (m-10)
REVERT: A  231 LYS cc_start: 0.7565 (pptt) cc_final: 0.6897 (ttmt)
REVERT: E  148 ASP cc_start: 0.7878 (t70) cc_final: 0.7677 (t70)
REVERT: E  191 LYS cc_start: 0.8609 (tptp) cc_final: 0.8261 (tptp)
REVERT: E  206 LYS cc_start: 0.7783 (tttt) cc_final: 0.7543 (tptp)
REVERT: F  174 ASN cc_start: 0.8260 (m-40) cc_final: 0.8043 (m-40)
REVERT: F  191 LYS cc_start: 0.8733 (tmtt) cc_final: 0.8505 (tptp)
REVERT: F  231 LYS cc_start: 0.7454 (pptt) cc_final: 0.6924 (tttt)
REVERT: G   67 TRP cc_start: 0.7856 (t-100) cc_final: 0.7388 (t-100)
REVERT: G   85 MET cc_start: 0.7846 (mtm) cc_final: 0.7504 (mtm)
REVERT: G  191 LYS cc_start: 0.8810 (tptm) cc_final: 0.8462 (tptp)
REVERT: G  206 LYS cc_start: 0.7865 (tttt) cc_final: 0.7505 (tptt)
REVERT: G  231 LYS cc_start: 0.7138 (pttm) cc_final: 0.6806 (pttm)
  outliers start: 0
  outliers final: 0
  residues processed: 247
  average time/residue: 0.2195
  time to fit residues: 79.4356
Evaluate side-chains
  213 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 1.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 46 optimal weight:    8.9990
   chunk 136 optimal weight:    1.9990
   chunk 60 optimal weight:    7.9990
   chunk 18 optimal weight:    0.2980
   chunk 111 optimal weight:    0.9980
   chunk 44 optimal weight:    9.9990
   chunk 125 optimal weight:    0.3980
   chunk 39 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 61 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
D 152 ASN
E 152 ASN
** F  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  31 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4167 r_free = 0.4167 target = 0.179270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.141475 restraints weight = 18385.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.146376 restraints weight = 13430.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.149569 restraints weight = 10569.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7336
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.454  11884  Z= 0.171
  Angle     :  0.942  16.995  16443  Z= 0.336
  Chirality :  0.043   0.226   1631
  Planarity :  0.006   0.070   2065
  Dihedral  : 14.777  79.018   1659
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    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: -2.06 (0.22), residues: 1400
  helix: -0.65 (0.36), residues: 196
  sheet: -1.95 (0.50), residues: 70
  loop : -1.59 (0.18), residues: 1134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  67 
 HIS   0.010   0.001   HIS C 230 
 PHE   0.011   0.001   PHE A 102 
 TYR   0.024   0.002   TYR G  80 
 ARG   0.004   0.000   ARG B  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03159 (  154)
  hydrogen bonds       : angle       7.60865 (  336)
  covalent geometry    : bond        0.00465 (11788)
  covalent geometry    : angle       0.94189 (16443)
  Misc. bond           : bond        0.09619 (   96)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 1.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 MET cc_start: 0.7782 (mtp) cc_final: 0.7304 (mpp)
REVERT: B  231 LYS cc_start: 0.6958 (pptt) cc_final: 0.6689 (tttt)
REVERT: C   31 HIS cc_start: 0.8639 (m90) cc_final: 0.8391 (m90)
REVERT: C   83 SER cc_start: 0.8129 (p) cc_final: 0.7828 (p)
REVERT: C  170 ASP cc_start: 0.7537 (t0) cc_final: 0.7121 (t0)
REVERT: C  191 LYS cc_start: 0.8793 (tptp) cc_final: 0.8478 (tptp)
REVERT: C  231 LYS cc_start: 0.7475 (pptt) cc_final: 0.6508 (ttmt)
REVERT: A   85 MET cc_start: 0.7817 (mtp) cc_final: 0.7465 (mpp)
REVERT: A  206 LYS cc_start: 0.7665 (tttt) cc_final: 0.7315 (tptt)
REVERT: A  231 LYS cc_start: 0.7466 (pptt) cc_final: 0.6832 (ttmt)
REVERT: E  148 ASP cc_start: 0.7933 (t70) cc_final: 0.7700 (t70)
REVERT: E  170 ASP cc_start: 0.7428 (t0) cc_final: 0.6986 (t0)
REVERT: E  191 LYS cc_start: 0.8689 (tptp) cc_final: 0.8369 (tptp)
REVERT: F   67 TRP cc_start: 0.7530 (t-100) cc_final: 0.6815 (t-100)
REVERT: F   80 TYR cc_start: 0.8258 (t80) cc_final: 0.7999 (t80)
REVERT: F   85 MET cc_start: 0.7832 (mtp) cc_final: 0.7304 (mpp)
REVERT: F  174 ASN cc_start: 0.8174 (m-40) cc_final: 0.7957 (m-40)
REVERT: F  191 LYS cc_start: 0.8693 (tmtt) cc_final: 0.8493 (tptp)
REVERT: F  231 LYS cc_start: 0.7180 (pptt) cc_final: 0.6725 (tttt)
REVERT: G   67 TRP cc_start: 0.8060 (t-100) cc_final: 0.7500 (t-100)
REVERT: G  170 ASP cc_start: 0.7690 (t0) cc_final: 0.7249 (t0)
REVERT: G  191 LYS cc_start: 0.8825 (tptm) cc_final: 0.8519 (tptp)
REVERT: G  194 ARG cc_start: 0.8815 (mpt-90) cc_final: 0.8594 (mmt90)
REVERT: G  206 LYS cc_start: 0.7772 (tttt) cc_final: 0.7498 (tptt)
REVERT: G  231 LYS cc_start: 0.7054 (pttm) cc_final: 0.6731 (pttm)
  outliers start: 0
  outliers final: 0
  residues processed: 245
  average time/residue: 0.2101
  time to fit residues: 74.7765
Evaluate side-chains
  205 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 135 optimal weight:    0.4980
   chunk 43 optimal weight:    2.9990
   chunk 28 optimal weight:    7.9990
   chunk 69 optimal weight:    2.9990
   chunk 41 optimal weight:    8.9990
   chunk 94 optimal weight:    2.9990
   chunk 75 optimal weight:    0.0870
   chunk 40 optimal weight:    0.7980
   chunk 116 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.6760

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

Flipped N/Q/H residues before XYZ refinement:
C 152 ASN
D  31 HIS
D 152 ASN
F  31 HIS
F  59 ASN
G  31 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.181520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.143673 restraints weight = 18216.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.148734 restraints weight = 13140.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.152720 restraints weight = 10281.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7274
moved from start:          0.2953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.321  11884  Z= 0.141
  Angle     :  0.902  16.854  16443  Z= 0.319
  Chirality :  0.042   0.212   1631
  Planarity :  0.005   0.059   2065
  Dihedral  : 14.852  77.084   1659
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    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: -1.66 (0.22), residues: 1400
  helix:  0.75 (0.40), residues: 154
  sheet: -1.93 (0.51), residues: 70
  loop : -1.44 (0.18), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  67 
 HIS   0.007   0.001   HIS C 230 
 PHE   0.011   0.001   PHE B 102 
 TYR   0.020   0.002   TYR G  80 
 ARG   0.002   0.000   ARG E  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02902 (  154)
  hydrogen bonds       : angle       7.46108 (  336)
  covalent geometry    : bond        0.00374 (11788)
  covalent geometry    : angle       0.90170 (16443)
  Misc. bond           : bond        0.08679 (   96)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 1.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 MET cc_start: 0.7854 (mtp) cc_final: 0.7329 (mpp)
REVERT: B  231 LYS cc_start: 0.7302 (pptt) cc_final: 0.6684 (tttt)
REVERT: C   83 SER cc_start: 0.8110 (p) cc_final: 0.7797 (p)
REVERT: C  191 LYS cc_start: 0.8808 (tptp) cc_final: 0.8515 (tptp)
REVERT: D  174 ASN cc_start: 0.8028 (m-40) cc_final: 0.7750 (m-40)
REVERT: D  231 LYS cc_start: 0.6837 (pttm) cc_final: 0.6268 (tttt)
REVERT: A   83 SER cc_start: 0.8271 (p) cc_final: 0.8060 (p)
REVERT: A  206 LYS cc_start: 0.7706 (tttt) cc_final: 0.7358 (tptt)
REVERT: E  148 ASP cc_start: 0.7822 (t70) cc_final: 0.7520 (t70)
REVERT: F   30 LYS cc_start: 0.7159 (mmtt) cc_final: 0.6931 (tptm)
REVERT: F   67 TRP cc_start: 0.7712 (t-100) cc_final: 0.7006 (t-100)
REVERT: F  174 ASN cc_start: 0.8103 (m-40) cc_final: 0.7894 (m-40)
REVERT: F  191 LYS cc_start: 0.8727 (tmtt) cc_final: 0.8513 (tptp)
REVERT: F  231 LYS cc_start: 0.7080 (pptt) cc_final: 0.6651 (tttt)
REVERT: G   67 TRP cc_start: 0.8264 (t-100) cc_final: 0.7615 (t-100)
REVERT: G   83 SER cc_start: 0.8240 (p) cc_final: 0.8036 (p)
REVERT: G  191 LYS cc_start: 0.8855 (tptm) cc_final: 0.8549 (tptp)
REVERT: G  206 LYS cc_start: 0.7764 (tttt) cc_final: 0.7488 (tptt)
REVERT: G  231 LYS cc_start: 0.6991 (pttm) cc_final: 0.6697 (pttm)
  outliers start: 0
  outliers final: 0
  residues processed: 248
  average time/residue: 0.2457
  time to fit residues: 89.5150
Evaluate side-chains
  209 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 1.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 62 optimal weight:    0.0980
   chunk 79 optimal weight:    2.9990
   chunk 120 optimal weight:    7.9990
   chunk 87 optimal weight:    0.7980
   chunk 17 optimal weight:    0.0050
   chunk 94 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 6 optimal weight:    0.2980
   chunk 109 optimal weight:    9.9990
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
D 152 ASN
E  31 HIS
F  31 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.184261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.146607 restraints weight = 18306.686|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.151896 restraints weight = 13095.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.155982 restraints weight = 10125.560|
|-----------------------------------------------------------------------------|
r_work (final): 0.3909
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7217
moved from start:          0.3162

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.266  11884  Z= 0.130
  Angle     :  0.907  17.813  16443  Z= 0.316
  Chirality :  0.042   0.210   1631
  Planarity :  0.005   0.051   2065
  Dihedral  : 14.990  81.326   1659
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    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: -2.00 (0.22), residues: 1400
  helix: -0.63 (0.36), residues: 203
  sheet: -1.98 (0.51), residues: 70
  loop : -1.54 (0.19), residues: 1127

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP B  67 
 HIS   0.039   0.001   HIS E 230 
 PHE   0.009   0.001   PHE E 215 
 TYR   0.018   0.002   TYR G  80 
 ARG   0.002   0.000   ARG D  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02873 (  154)
  hydrogen bonds       : angle       7.36252 (  336)
  covalent geometry    : bond        0.00334 (11788)
  covalent geometry    : angle       0.90698 (16443)
  Misc. bond           : bond        0.07837 (   96)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 1.558 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 MET cc_start: 0.8110 (mtp) cc_final: 0.7523 (mpp)
REVERT: B  231 LYS cc_start: 0.7232 (pptt) cc_final: 0.6626 (tttt)
REVERT: C   83 SER cc_start: 0.8239 (p) cc_final: 0.7884 (p)
REVERT: C  170 ASP cc_start: 0.7591 (t0) cc_final: 0.7273 (t0)
REVERT: C  191 LYS cc_start: 0.8833 (tptp) cc_final: 0.8543 (tptp)
REVERT: C  231 LYS cc_start: 0.6862 (pttm) cc_final: 0.5764 (tttt)
REVERT: D   83 SER cc_start: 0.8330 (p) cc_final: 0.7944 (t)
REVERT: D  104 MET cc_start: 0.8421 (mtt) cc_final: 0.8185 (mtm)
REVERT: D  174 ASN cc_start: 0.7980 (m-40) cc_final: 0.7709 (m-40)
REVERT: D  231 LYS cc_start: 0.6778 (pttm) cc_final: 0.6076 (tttt)
REVERT: A   67 TRP cc_start: 0.8529 (t-100) cc_final: 0.7810 (t-100)
REVERT: A   85 MET cc_start: 0.7861 (mtp) cc_final: 0.7331 (mpp)
REVERT: E  148 ASP cc_start: 0.7754 (t70) cc_final: 0.7422 (t70)
REVERT: E  170 ASP cc_start: 0.7235 (t0) cc_final: 0.6860 (t0)
REVERT: F  231 LYS cc_start: 0.7092 (pptt) cc_final: 0.6606 (tttt)
REVERT: G   67 TRP cc_start: 0.8312 (t-100) cc_final: 0.7581 (t-100)
REVERT: G   83 SER cc_start: 0.8175 (p) cc_final: 0.7953 (p)
REVERT: G  191 LYS cc_start: 0.8872 (tptm) cc_final: 0.8576 (tptp)
REVERT: G  231 LYS cc_start: 0.7246 (pttm) cc_final: 0.6912 (pttm)
  outliers start: 0
  outliers final: 0
  residues processed: 248
  average time/residue: 0.2097
  time to fit residues: 76.3740
Evaluate side-chains
  201 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 1.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 90 optimal weight:   10.0000
   chunk 74 optimal weight:    0.5980
   chunk 56 optimal weight:    3.9990
   chunk 114 optimal weight:    0.9990
   chunk 79 optimal weight:    5.9990
   chunk 45 optimal weight:    5.9990
   chunk 119 optimal weight:    0.9990
   chunk 126 optimal weight:    3.9990
   chunk 99 optimal weight:    3.9990
   chunk 98 optimal weight:    0.9990
   chunk 67 optimal weight:    3.9990
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
C 152 ASN
D 152 ASN
A  31 HIS
A 152 ASN
E  31 HIS
E 152 ASN
F  31 HIS
F 152 ASN
G  31 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.177292 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.138980 restraints weight = 18823.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.143558 restraints weight = 13926.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.147194 restraints weight = 11089.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.3377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.411  11884  Z= 0.207
  Angle     :  1.078  22.890  16443  Z= 0.363
  Chirality :  0.045   0.235   1631
  Planarity :  0.005   0.052   2065
  Dihedral  : 15.171  88.780   1659
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.50 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.07 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 6.49 %
    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: -2.16 (0.22), residues: 1400
  helix: -0.76 (0.36), residues: 196
  sheet: -1.98 (0.52), residues: 70
  loop : -1.66 (0.18), residues: 1134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  67 
 HIS   0.041   0.002   HIS D 230 
 PHE   0.011   0.001   PHE C 190 
 TYR   0.022   0.003   TYR G  80 
 ARG   0.002   0.000   ARG D  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03492 (  154)
  hydrogen bonds       : angle       7.44169 (  336)
  covalent geometry    : bond        0.00553 (11788)
  covalent geometry    : angle       1.07782 (16443)
  Misc. bond           : bond        0.10200 (   96)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 240
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
REVERT: B  191 LYS cc_start: 0.8766 (tmtt) cc_final: 0.8512 (tptp)
REVERT: B  231 LYS cc_start: 0.7226 (pptt) cc_final: 0.6795 (tttt)
REVERT: C   83 SER cc_start: 0.8276 (p) cc_final: 0.7892 (p)
REVERT: C  191 LYS cc_start: 0.8817 (tptp) cc_final: 0.8545 (tptp)
REVERT: D  174 ASN cc_start: 0.8097 (m-40) cc_final: 0.7844 (m-40)
REVERT: D  191 LYS cc_start: 0.8891 (tmtt) cc_final: 0.8662 (tptp)
REVERT: A  102 PHE cc_start: 0.7766 (m-10) cc_final: 0.7432 (m-10)
REVERT: A  104 MET cc_start: 0.8511 (mtt) cc_final: 0.8223 (mtt)
REVERT: A  206 LYS cc_start: 0.7731 (tttt) cc_final: 0.7412 (tptt)
REVERT: E  148 ASP cc_start: 0.7984 (t70) cc_final: 0.7712 (t70)
REVERT: E  191 LYS cc_start: 0.8676 (tptp) cc_final: 0.8395 (tptp)
REVERT: F   67 TRP cc_start: 0.7646 (t-100) cc_final: 0.6690 (t-100)
REVERT: F   80 TYR cc_start: 0.8550 (t80) cc_final: 0.8247 (t80)
REVERT: F  231 LYS cc_start: 0.7253 (pptt) cc_final: 0.6753 (tttt)
REVERT: G   67 TRP cc_start: 0.8499 (t-100) cc_final: 0.7806 (t-100)
REVERT: G   83 SER cc_start: 0.8282 (p) cc_final: 0.8036 (p)
REVERT: G  191 LYS cc_start: 0.8880 (tptm) cc_final: 0.8599 (tptp)
REVERT: G  231 LYS cc_start: 0.7340 (pttm) cc_final: 0.7010 (pttm)
  outliers start: 1
  outliers final: 0
  residues processed: 240
  average time/residue: 0.2161
  time to fit residues: 74.6258
Evaluate side-chains
  200 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 1.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 126 optimal weight:    7.9990
   chunk 100 optimal weight:    8.9990
   chunk 48 optimal weight:    3.9990
   chunk 28 optimal weight:    6.9990
   chunk 4 optimal weight:   10.0000
   chunk 18 optimal weight:    4.9990
   chunk 70 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 88 optimal weight:   10.0000
   overall best weight:    3.1586

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

Flipped N/Q/H residues before XYZ refinement:
B 152 ASN
C 152 ASN
D 152 ASN
A  31 HIS
A 152 ASN
E  31 HIS
E 152 ASN
F  31 HIS
F 152 ASN
G  31 HIS
G 118 HIS
G 152 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.167177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.128615 restraints weight = 19548.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.132603 restraints weight = 15045.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.135685 restraints weight = 12377.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
moved from start:          0.4045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.017   0.606  11884  Z= 0.377
  Angle     :  1.363  23.281  16443  Z= 0.482
  Chirality :  0.053   0.270   1631
  Planarity :  0.007   0.071   2065
  Dihedral  : 15.981  89.314   1659
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 18.51
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 11.43 %
    Favored  : 88.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 7.79 %
    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: -2.74 (0.21), residues: 1400
  helix: -1.44 (0.35), residues: 196
  sheet: -2.18 (0.52), residues: 70
  loop : -2.05 (0.17), residues: 1134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP B  67 
 HIS   0.036   0.003   HIS D 230 
 PHE   0.043   0.002   PHE F 102 
 TYR   0.039   0.005   TYR A  80 
 ARG   0.003   0.001   ARG E  69 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05192 (  154)
  hydrogen bonds       : angle       8.20405 (  336)
  covalent geometry    : bond        0.01012 (11788)
  covalent geometry    : angle       1.36319 (16443)
  Misc. bond           : bond        0.14974 (   96)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 1.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  224 LYS cc_start: 0.8416 (pttm) cc_final: 0.8184 (ptpp)
REVERT: C   83 SER cc_start: 0.8208 (p) cc_final: 0.7871 (p)
REVERT: C  191 LYS cc_start: 0.8807 (tptp) cc_final: 0.8542 (tptp)
REVERT: D   67 TRP cc_start: 0.8344 (t-100) cc_final: 0.8039 (t-100)
REVERT: D   80 TYR cc_start: 0.8907 (t80) cc_final: 0.8684 (t80)
REVERT: D  174 ASN cc_start: 0.8038 (m-40) cc_final: 0.7813 (m-40)
REVERT: A   83 SER cc_start: 0.8120 (p) cc_final: 0.7860 (p)
REVERT: A  206 LYS cc_start: 0.7845 (tttt) cc_final: 0.7583 (tptt)
REVERT: F  174 ASN cc_start: 0.8253 (m-40) cc_final: 0.8035 (m-40)
REVERT: G   67 TRP cc_start: 0.8662 (t-100) cc_final: 0.8113 (t-100)
REVERT: G  135 ILE cc_start: 0.9299 (tp) cc_final: 0.8752 (tp)
REVERT: G  191 LYS cc_start: 0.8868 (tptm) cc_final: 0.8636 (tptp)
REVERT: G  231 LYS cc_start: 0.7142 (pttm) cc_final: 0.6940 (pttm)
  outliers start: 0
  outliers final: 0
  residues processed: 233
  average time/residue: 0.2270
  time to fit residues: 75.7100
Evaluate side-chains
  198 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 1.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 34 optimal weight:    0.7980
   chunk 104 optimal weight:    0.0870
   chunk 14 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 2 optimal weight:    0.6980
   chunk 5 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 128 optimal weight:    0.8980
   chunk 44 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9980
   chunk 103 optimal weight:    0.7980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
C 152 ASN
D 152 ASN
A  31 HIS
A 152 ASN
E  31 HIS
E 152 ASN
F  31 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.176885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.139246 restraints weight = 18645.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.144045 restraints weight = 13697.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.147687 restraints weight = 10867.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.3958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.344  11884  Z= 0.151
  Angle     :  0.970  17.863  16443  Z= 0.341
  Chirality :  0.043   0.224   1631
  Planarity :  0.006   0.065   2065
  Dihedral  : 15.611  89.854   1659
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 11.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    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: -2.51 (0.21), residues: 1400
  helix: -1.29 (0.34), residues: 196
  sheet: -2.37 (0.50), residues: 70
  loop : -1.86 (0.18), residues: 1134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  67 
 HIS   0.015   0.001   HIS E 230 
 PHE   0.012   0.001   PHE B  77 
 TYR   0.021   0.003   TYR G  80 
 ARG   0.003   0.000   ARG D 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03384 (  154)
  hydrogen bonds       : angle       7.94208 (  336)
  covalent geometry    : bond        0.00397 (11788)
  covalent geometry    : angle       0.96960 (16443)
  Misc. bond           : bond        0.09092 (   96)

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

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

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2800 Ramachandran restraints generated.
    1400 Oldfield, 0 Emsley, 1400 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 1.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 MET cc_start: 0.8092 (mtp) cc_final: 0.7463 (mtm)
REVERT: B  128 MET cc_start: 0.7285 (tpp) cc_final: 0.6992 (tpt)
REVERT: C   83 SER cc_start: 0.8115 (p) cc_final: 0.7812 (p)
REVERT: C  191 LYS cc_start: 0.8841 (tptp) cc_final: 0.8569 (tptp)
REVERT: C  194 ARG cc_start: 0.8552 (mmt90) cc_final: 0.8254 (mmt90)
REVERT: D  174 ASN cc_start: 0.8024 (m-40) cc_final: 0.7787 (m-40)
REVERT: D  191 LYS cc_start: 0.8794 (tptp) cc_final: 0.8591 (tptp)
REVERT: A   83 SER cc_start: 0.8044 (p) cc_final: 0.7814 (p)
REVERT: A  177 THR cc_start: 0.8432 (t) cc_final: 0.8225 (t)
REVERT: A  206 LYS cc_start: 0.7770 (tttt) cc_final: 0.7532 (tptt)
REVERT: F  174 ASN cc_start: 0.8211 (m-40) cc_final: 0.7963 (m-40)
REVERT: G   67 TRP cc_start: 0.8601 (t-100) cc_final: 0.7864 (t-100)
REVERT: G   85 MET cc_start: 0.7863 (mtp) cc_final: 0.7453 (mpp)
REVERT: G  191 LYS cc_start: 0.8884 (tptm) cc_final: 0.8617 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 244
  average time/residue: 0.2123
  time to fit residues: 74.8337
Evaluate side-chains
  209 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 1.163 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 44 optimal weight:    0.0170
   chunk 20 optimal weight:    8.9990
   chunk 35 optimal weight:    4.9990
   chunk 28 optimal weight:    0.0970
   chunk 72 optimal weight:    2.9990
   chunk 51 optimal weight:    0.5980
   chunk 107 optimal weight:    2.9990
   chunk 134 optimal weight:    3.9990
   chunk 3 optimal weight:    0.6980
   chunk 64 optimal weight:    9.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    0.6818

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

Flipped N/Q/H residues before XYZ refinement:
C 152 ASN
D 152 ASN
A  31 HIS
A 152 ASN
E  31 HIS
E 152 ASN
F  31 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.178742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.139007 restraints weight = 18634.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.144100 restraints weight = 13550.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.147941 restraints weight = 10660.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7323
moved from start:          0.4025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.345  11884  Z= 0.145
  Angle     :  0.971  18.462  16443  Z= 0.337
  Chirality :  0.043   0.223   1631
  Planarity :  0.006   0.065   2065
  Dihedral  : 15.155  87.992   1659
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.57 %
    Favored  : 90.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 7.79 %
    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: -2.41 (0.21), residues: 1400
  helix: -1.10 (0.34), residues: 196
  sheet: -2.36 (0.51), residues: 70
  loop : -1.79 (0.18), residues: 1134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP F  67 
 HIS   0.010   0.001   HIS C 230 
 PHE   0.007   0.001   PHE F 102 
 TYR   0.021   0.003   TYR A  80 
 ARG   0.003   0.000   ARG D 194 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03130 (  154)
  hydrogen bonds       : angle       7.89221 (  336)
  covalent geometry    : bond        0.00387 (11788)
  covalent geometry    : angle       0.97113 (16443)
  Misc. bond           : bond        0.08930 (   96)

===============================================================================
Job complete
usr+sys time: 3921.10 seconds
wall clock time: 69 minutes 30.16 seconds (4170.16 seconds total)