Starting phenix.real_space_refine
on Sun Dec 29 18:49:35 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tfs_25879/12_2024/7tfs_25879.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tfs_25879/12_2024/7tfs_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_25879/12_2024/7tfs_25879.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tfs_25879/12_2024/7tfs_25879.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tfs_25879/12_2024/7tfs_25879.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tfs_25879/12_2024/7tfs_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-5532/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: 4.26, per 1000 atoms: 0.37
  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: 3.77
  Conformation dependent library (CDL) restraints added in 1.6 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: 1.05
  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: 2.35

  Time building geometry restraints manager: 4.20 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

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:             1.840
  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:         0.070
  Set scattering table:                    0.120
  Process input model:                     24.330
  Find NCS groups from input model:        0.390
  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:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.930
-------------------------------------------------------------------------------
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      :  0.004   0.049  11788  Z= 0.255
  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 

*********************** 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  : 1.310 
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: 0.2246
  time to fit residues: 86.4172
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  : 1.270 
-------------------------------------------------------------------------------
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:    3.9990
   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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
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      :  0.005   0.084  11788  Z= 0.310
  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 

*********************** 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  : 1.165 
Fit side-chains
   revert: symmetry clash
REVERT: B  104 MET cc_start: 0.8266 (mtm) cc_final: 0.8017 (mtm)
REVERT: B  231 LYS cc_start: 0.7496 (pptt) cc_final: 0.6796 (ttmt)
REVERT: C   83 SER cc_start: 0.7995 (p) cc_final: 0.7583 (p)
REVERT: C  148 ASP cc_start: 0.7428 (t70) cc_final: 0.7155 (t70)
REVERT: C  191 LYS cc_start: 0.8365 (tptp) cc_final: 0.8031 (tptp)
REVERT: D   67 TRP cc_start: 0.7474 (t-100) cc_final: 0.6684 (t-100)
REVERT: D   77 PHE cc_start: 0.7456 (m-10) cc_final: 0.6919 (m-10)
REVERT: D  148 ASP cc_start: 0.7220 (t70) cc_final: 0.6913 (t70)
REVERT: D  174 ASN cc_start: 0.7870 (m-40) cc_final: 0.7599 (m-40)
REVERT: D  231 LYS cc_start: 0.7700 (pptt) cc_final: 0.6779 (ttmt)
REVERT: A   83 SER cc_start: 0.7931 (p) cc_final: 0.7679 (p)
REVERT: A  206 LYS cc_start: 0.7873 (tttt) cc_final: 0.7548 (tptt)
REVERT: E   77 PHE cc_start: 0.7420 (m-10) cc_final: 0.7212 (m-10)
REVERT: E  206 LYS cc_start: 0.7958 (tttt) cc_final: 0.7664 (tptp)
REVERT: F  104 MET cc_start: 0.8209 (mtt) cc_final: 0.8001 (mtt)
REVERT: F  174 ASN cc_start: 0.7887 (m-40) cc_final: 0.7672 (m-40)
REVERT: F  206 LYS cc_start: 0.7864 (tttt) cc_final: 0.7663 (tptt)
REVERT: F  231 LYS cc_start: 0.7532 (pptt) cc_final: 0.6739 (tttt)
REVERT: G   67 TRP cc_start: 0.7632 (t-100) cc_final: 0.7405 (t-100)
REVERT: G  148 ASP cc_start: 0.7539 (t70) cc_final: 0.7201 (t70)
REVERT: G  206 LYS cc_start: 0.7810 (tttt) cc_final: 0.7575 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 277
  average time/residue: 0.2237
  time to fit residues: 90.3989
Evaluate side-chains
  220 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 1.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 70 optimal weight:    9.9990
   chunk 39 optimal weight:    3.9990
   chunk 105 optimal weight:    3.9990
   chunk 86 optimal weight:    0.0970
   chunk 35 optimal weight:    4.9990
   chunk 127 optimal weight:    6.9990
   chunk 137 optimal weight:    1.9990
   chunk 113 optimal weight:    4.9990
   chunk 126 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 102 optimal weight:    2.9990
   overall best weight:    1.3584

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7212
moved from start:          0.2234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.071  11788  Z= 0.349
  Angle     :  1.038  17.928  16443  Z= 0.365
  Chirality :  0.045   0.228   1631
  Planarity :  0.005   0.049   2065
  Dihedral  : 14.758  85.269   1659
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  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: -1.91 (0.21), residues: 1400
  helix:  0.45 (0.39), residues: 154
  sheet: -1.95 (0.49), residues: 70
  loop : -1.62 (0.17), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP B  67 
 HIS   0.024   0.002   HIS F 230 
 PHE   0.012   0.001   PHE E 215 
 TYR   0.015   0.002   TYR B  80 
 ARG   0.001   0.000   ARG F 194 

*********************** 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
  261 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 1.146 
Fit side-chains
REVERT: B  128 MET cc_start: 0.6470 (tpt) cc_final: 0.5826 (tpp)
REVERT: C   83 SER cc_start: 0.8020 (p) cc_final: 0.7594 (p)
REVERT: C  191 LYS cc_start: 0.8497 (tptp) cc_final: 0.8106 (tptp)
REVERT: D   77 PHE cc_start: 0.7369 (m-10) cc_final: 0.7079 (m-10)
REVERT: D  170 ASP cc_start: 0.5847 (t0) cc_final: 0.5368 (t0)
REVERT: D  174 ASN cc_start: 0.7839 (m-40) cc_final: 0.7542 (m-40)
REVERT: A   85 MET cc_start: 0.7797 (mtp) cc_final: 0.7534 (mpp)
REVERT: A  206 LYS cc_start: 0.7763 (tttt) cc_final: 0.7499 (tptt)
REVERT: A  231 LYS cc_start: 0.7907 (pptt) cc_final: 0.7626 (pttm)
REVERT: E  148 ASP cc_start: 0.7690 (t70) cc_final: 0.7475 (t70)
REVERT: E  206 LYS cc_start: 0.7990 (tttt) cc_final: 0.7732 (tptp)
REVERT: F   85 MET cc_start: 0.7962 (mtp) cc_final: 0.7450 (mpp)
REVERT: F  104 MET cc_start: 0.8452 (mtt) cc_final: 0.8177 (mtt)
REVERT: F  150 PRO cc_start: 0.8805 (Cg_exo) cc_final: 0.8587 (Cg_endo)
REVERT: F  174 ASN cc_start: 0.7913 (m-40) cc_final: 0.7692 (m-40)
REVERT: F  231 LYS cc_start: 0.7880 (pptt) cc_final: 0.6805 (tttt)
REVERT: G   67 TRP cc_start: 0.7986 (t-100) cc_final: 0.7658 (t-100)
REVERT: G   85 MET cc_start: 0.7944 (mtm) cc_final: 0.7562 (mtm)
REVERT: G  170 ASP cc_start: 0.6460 (t0) cc_final: 0.6092 (t0)
REVERT: G  191 LYS cc_start: 0.8484 (tptp) cc_final: 0.8233 (tptp)
REVERT: G  206 LYS cc_start: 0.7915 (tttt) cc_final: 0.7621 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 261
  average time/residue: 0.2308
  time to fit residues: 86.4627
Evaluate side-chains
  208 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 1.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 125 optimal weight:    0.7980
   chunk 95 optimal weight:    7.9990
   chunk 66 optimal weight:    0.7980
   chunk 14 optimal weight:    5.9990
   chunk 60 optimal weight:    6.9990
   chunk 85 optimal weight:    0.7980
   chunk 127 optimal weight:    3.9990
   chunk 135 optimal weight:    3.9990
   chunk 121 optimal weight:    0.8980
   chunk 36 optimal weight:    0.0570
   chunk 112 optimal weight:    0.6980
   overall best weight:    0.6298

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.2464

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  11788  Z= 0.241
  Angle     :  0.883  13.997  16443  Z= 0.323
  Chirality :  0.043   0.222   1631
  Planarity :  0.006   0.067   2065
  Dihedral  : 14.607  79.440   1659
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  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: -2.11 (0.21), residues: 1400
  helix: -0.77 (0.35), residues: 196
  sheet: -1.94 (0.49), residues: 70
  loop : -1.62 (0.18), residues: 1134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  67 
 HIS   0.015   0.001   HIS G 230 
 PHE   0.014   0.001   PHE B 102 
 TYR   0.007   0.001   TYR B  80 
 ARG   0.003   0.000   ARG D  69 

*********************** 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
  254 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 254
  time to evaluate  : 1.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 MET cc_start: 0.7848 (mtp) cc_final: 0.7377 (mpp)
REVERT: B  104 MET cc_start: 0.8135 (mtm) cc_final: 0.7935 (mtm)
REVERT: B  128 MET cc_start: 0.6365 (tpt) cc_final: 0.5676 (tpp)
REVERT: C   83 SER cc_start: 0.7911 (p) cc_final: 0.7567 (p)
REVERT: C  148 ASP cc_start: 0.7553 (t70) cc_final: 0.7338 (t70)
REVERT: C  191 LYS cc_start: 0.8534 (tptp) cc_final: 0.8231 (tptp)
REVERT: C  231 LYS cc_start: 0.7495 (pptt) cc_final: 0.7269 (pttm)
REVERT: D  104 MET cc_start: 0.8168 (mtt) cc_final: 0.7927 (mtt)
REVERT: D  174 ASN cc_start: 0.7867 (m-40) cc_final: 0.7572 (m-40)
REVERT: A  206 LYS cc_start: 0.7724 (tttt) cc_final: 0.7487 (tptt)
REVERT: E  148 ASP cc_start: 0.7717 (t70) cc_final: 0.7398 (t70)
REVERT: F  174 ASN cc_start: 0.7882 (m-40) cc_final: 0.7656 (m-40)
REVERT: F  231 LYS cc_start: 0.7247 (pptt) cc_final: 0.6838 (tttt)
REVERT: G   67 TRP cc_start: 0.8046 (t-100) cc_final: 0.7649 (t-100)
REVERT: G  141 LEU cc_start: 0.8348 (tp) cc_final: 0.8132 (tp)
REVERT: G  191 LYS cc_start: 0.8543 (tptp) cc_final: 0.8256 (tptp)
REVERT: G  206 LYS cc_start: 0.7789 (tttt) cc_final: 0.7573 (tptt)
REVERT: G  231 LYS cc_start: 0.6817 (pttm) cc_final: 0.6521 (pttm)
  outliers start: 0
  outliers final: 0
  residues processed: 254
  average time/residue: 0.2282
  time to fit residues: 84.4960
Evaluate side-chains
  207 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 1.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 1 optimal weight:    8.9990
   chunk 100 optimal weight:    8.9990
   chunk 55 optimal weight:    0.0270
   chunk 115 optimal weight:    2.9990
   chunk 93 optimal weight:    6.9990
   chunk 0 optimal weight:    7.9990
   chunk 69 optimal weight:    8.9990
   chunk 121 optimal weight:   20.0000
   chunk 34 optimal weight:    7.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    3.6046

-------------------------------------------------------------------------------
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  31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  62 GLN
D 152 ASN
A 152 ASN
E 152 ASN
F  31 HIS
F 152 ASN
G  31 HIS
G 152 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.3641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.163  11788  Z= 0.674
  Angle     :  1.473  21.871  16443  Z= 0.505
  Chirality :  0.054   0.277   1631
  Planarity :  0.008   0.098   2065
  Dihedral  : 16.143  88.154   1659
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 19.69
  Ramachandran Plot:
    Outliers :  0.64 %
    Allowed  : 11.21 %
    Favored  : 88.14 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  4.20 %
    Favored  : 95.71 %
  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: -2.22 (0.22), residues: 1400
  helix: -0.33 (0.39), residues: 154
  sheet: -1.91 (0.51), residues: 70
  loop : -1.78 (0.18), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B  67 
 HIS   0.025   0.003   HIS C 230 
 PHE   0.017   0.002   PHE C 190 
 TYR   0.021   0.004   TYR F  80 
 ARG   0.006   0.001   ARG D  69 

*********************** 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
  229 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 228
  time to evaluate  : 1.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  148 ASP cc_start: 0.4386 (OUTLIER) cc_final: 0.3970 (m-30)
REVERT: C   83 SER cc_start: 0.7951 (p) cc_final: 0.7646 (p)
REVERT: C   85 MET cc_start: 0.7993 (mtp) cc_final: 0.7595 (mtp)
REVERT: C  104 MET cc_start: 0.8637 (mtt) cc_final: 0.8257 (ttm)
REVERT: C  191 LYS cc_start: 0.8656 (tptp) cc_final: 0.8386 (tptp)
REVERT: C  194 ARG cc_start: 0.8704 (mpt-90) cc_final: 0.8457 (mmt90)
REVERT: C  206 LYS cc_start: 0.7912 (tttt) cc_final: 0.7655 (tptt)
REVERT: D   80 TYR cc_start: 0.8813 (t80) cc_final: 0.8498 (t80)
REVERT: D  104 MET cc_start: 0.8607 (mtt) cc_final: 0.8289 (mtt)
REVERT: D  135 ILE cc_start: 0.8934 (tp) cc_final: 0.8619 (tp)
REVERT: A  206 LYS cc_start: 0.7872 (tttt) cc_final: 0.7558 (tptt)
REVERT: E  102 PHE cc_start: 0.8072 (m-10) cc_final: 0.7566 (m-80)
REVERT: G   67 TRP cc_start: 0.8642 (t-100) cc_final: 0.8039 (t-100)
REVERT: G  170 ASP cc_start: 0.6753 (t0) cc_final: 0.6389 (t0)
REVERT: G  191 LYS cc_start: 0.8595 (tptp) cc_final: 0.8324 (tptp)
REVERT: G  206 LYS cc_start: 0.7974 (tttt) cc_final: 0.7688 (tptt)
  outliers start: 1
  outliers final: 0
  residues processed: 229
  average time/residue: 0.2369
  time to fit residues: 77.5451
Evaluate side-chains
  196 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 195
  time to evaluate  : 1.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 121 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 79 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 135 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9980
   chunk 62 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 44 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 130 optimal weight:    0.0020
   overall best weight:    0.7190

-------------------------------------------------------------------------------
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
A 152 ASN
F  31 HIS
F 152 ASN
G  31 HIS
G 152 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7263
moved from start:          0.3450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  11788  Z= 0.271
  Angle     :  0.982  16.869  16443  Z= 0.343
  Chirality :  0.043   0.223   1631
  Planarity :  0.006   0.076   2065
  Dihedral  : 15.691  87.751   1659
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  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: -2.39 (0.21), residues: 1400
  helix: -1.40 (0.34), residues: 196
  sheet: -2.09 (0.50), residues: 70
  loop : -1.74 (0.18), residues: 1134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  67 
 HIS   0.009   0.001   HIS E 230 
 PHE   0.009   0.001   PHE B 102 
 TYR   0.009   0.002   TYR E  80 
 ARG   0.009   0.000   ARG B  69 

*********************** 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
  258 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   67 TRP cc_start: 0.8395 (t-100) cc_final: 0.7764 (t-100)
REVERT: B  102 PHE cc_start: 0.7924 (m-10) cc_final: 0.7645 (m-10)
REVERT: C   80 TYR cc_start: 0.8252 (t80) cc_final: 0.7366 (t80)
REVERT: C   83 SER cc_start: 0.7899 (p) cc_final: 0.7639 (p)
REVERT: C  174 ASN cc_start: 0.7939 (m-40) cc_final: 0.7680 (m-40)
REVERT: C  191 LYS cc_start: 0.8679 (tptp) cc_final: 0.8391 (tptp)
REVERT: D  170 ASP cc_start: 0.5861 (t0) cc_final: 0.5282 (t0)
REVERT: D  174 ASN cc_start: 0.7814 (m-40) cc_final: 0.7547 (m-40)
REVERT: A   80 TYR cc_start: 0.8592 (t80) cc_final: 0.8392 (t80)
REVERT: A  177 THR cc_start: 0.8533 (t) cc_final: 0.8321 (t)
REVERT: A  206 LYS cc_start: 0.7831 (tttt) cc_final: 0.7590 (tptt)
REVERT: E   77 PHE cc_start: 0.7627 (m-10) cc_final: 0.6978 (m-10)
REVERT: E  148 ASP cc_start: 0.7762 (t70) cc_final: 0.7537 (t70)
REVERT: E  170 ASP cc_start: 0.6651 (t0) cc_final: 0.6264 (t0)
REVERT: F   67 TRP cc_start: 0.7960 (t-100) cc_final: 0.7270 (t-100)
REVERT: F  170 ASP cc_start: 0.6197 (t0) cc_final: 0.5630 (t0)
REVERT: F  174 ASN cc_start: 0.7930 (m-40) cc_final: 0.7707 (m-40)
REVERT: G   67 TRP cc_start: 0.8667 (t-100) cc_final: 0.8016 (t-100)
REVERT: G  141 LEU cc_start: 0.8446 (tp) cc_final: 0.8225 (tp)
REVERT: G  191 LYS cc_start: 0.8609 (tptp) cc_final: 0.8342 (tptp)
REVERT: G  194 ARG cc_start: 0.8787 (mpt-90) cc_final: 0.8518 (mmt90)
REVERT: G  206 LYS cc_start: 0.7924 (tttt) cc_final: 0.7662 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 258
  average time/residue: 0.2330
  time to fit residues: 87.5127
Evaluate side-chains
  216 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 1.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 77 optimal weight:    1.9990
   chunk 98 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 114 optimal weight:    3.9990
   chunk 75 optimal weight:    0.0470
   chunk 134 optimal weight:    3.9990
   chunk 84 optimal weight:    0.0050
   chunk 82 optimal weight:    0.4980
   chunk 62 optimal weight:    0.8980
   chunk 83 optimal weight:    4.9990
   overall best weight:    0.6894

-------------------------------------------------------------------------------
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
G 152 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7246
moved from start:          0.3593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  11788  Z= 0.254
  Angle     :  0.970  16.019  16443  Z= 0.336
  Chirality :  0.043   0.228   1631
  Planarity :  0.006   0.071   2065
  Dihedral  : 15.429  82.856   1659
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.50 %
    Favored  : 90.50 %
  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 : 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: -1.92 (0.22), residues: 1400
  helix: -0.11 (0.39), residues: 154
  sheet: -2.27 (0.50), residues: 70
  loop : -1.51 (0.19), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  67 
 HIS   0.008   0.001   HIS C 230 
 PHE   0.008   0.001   PHE E 215 
 TYR   0.019   0.002   TYR F  80 
 ARG   0.002   0.000   ARG D  69 

*********************** 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
  258 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 258
  time to evaluate  : 1.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   67 TRP cc_start: 0.8456 (t-100) cc_final: 0.7764 (t-100)
REVERT: C   83 SER cc_start: 0.7941 (p) cc_final: 0.7617 (p)
REVERT: C  148 ASP cc_start: 0.7678 (t70) cc_final: 0.7267 (t70)
REVERT: C  174 ASN cc_start: 0.7909 (m-40) cc_final: 0.7689 (m-40)
REVERT: C  191 LYS cc_start: 0.8687 (tptp) cc_final: 0.8400 (tptp)
REVERT: D   85 MET cc_start: 0.7834 (mtp) cc_final: 0.7055 (mtp)
REVERT: D  174 ASN cc_start: 0.7749 (m-40) cc_final: 0.7521 (m-40)
REVERT: A   80 TYR cc_start: 0.8594 (t80) cc_final: 0.8338 (t80)
REVERT: A  177 THR cc_start: 0.8468 (t) cc_final: 0.8242 (t)
REVERT: A  206 LYS cc_start: 0.7796 (tttt) cc_final: 0.7568 (tptt)
REVERT: E  148 ASP cc_start: 0.7861 (t70) cc_final: 0.7587 (t70)
REVERT: F   67 TRP cc_start: 0.8128 (t-100) cc_final: 0.7362 (t-100)
REVERT: F  104 MET cc_start: 0.8329 (mtt) cc_final: 0.8019 (mtt)
REVERT: G   67 TRP cc_start: 0.8633 (t-100) cc_final: 0.7894 (t-100)
REVERT: G  191 LYS cc_start: 0.8633 (tptp) cc_final: 0.8346 (tptp)
REVERT: G  206 LYS cc_start: 0.8004 (tttt) cc_final: 0.7796 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 258
  average time/residue: 0.2190
  time to fit residues: 82.4785
Evaluate side-chains
  210 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 1.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 80 optimal weight:    8.9990
   chunk 40 optimal weight:    7.9990
   chunk 26 optimal weight:   10.0000
   chunk 85 optimal weight:    0.8980
   chunk 91 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 122 optimal weight:    0.7980
   chunk 129 optimal weight:    0.1980
   overall best weight:    0.9784

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

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

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7266
moved from start:          0.3709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  11788  Z= 0.288
  Angle     :  0.990  17.397  16443  Z= 0.342
  Chirality :  0.044   0.226   1631
  Planarity :  0.006   0.066   2065
  Dihedral  : 15.315  86.554   1659
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.79 %
    Favored  : 91.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  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: -1.85 (0.22), residues: 1400
  helix: -0.07 (0.41), residues: 154
  sheet: -2.32 (0.52), residues: 70
  loop : -1.45 (0.19), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  67 
 HIS   0.009   0.001   HIS C 230 
 PHE   0.009   0.001   PHE B 102 
 TYR   0.020   0.002   TYR F  80 
 ARG   0.005   0.000   ARG B  69 

*********************** 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
  251 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 1.247 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   67 TRP cc_start: 0.8419 (t-100) cc_final: 0.8037 (t-100)
REVERT: C   83 SER cc_start: 0.8006 (p) cc_final: 0.7682 (p)
REVERT: C  148 ASP cc_start: 0.7781 (t70) cc_final: 0.7384 (t70)
REVERT: C  191 LYS cc_start: 0.8691 (tptp) cc_final: 0.8452 (tptp)
REVERT: D   85 MET cc_start: 0.7889 (mtp) cc_final: 0.7103 (mtp)
REVERT: D  174 ASN cc_start: 0.7667 (m-40) cc_final: 0.7446 (m-40)
REVERT: A   83 SER cc_start: 0.7893 (p) cc_final: 0.7656 (p)
REVERT: A  177 THR cc_start: 0.8536 (t) cc_final: 0.8332 (t)
REVERT: A  206 LYS cc_start: 0.7769 (tttt) cc_final: 0.7567 (tptt)
REVERT: E  148 ASP cc_start: 0.7931 (t70) cc_final: 0.7652 (t70)
REVERT: F   67 TRP cc_start: 0.8259 (t-100) cc_final: 0.7601 (t-100)
REVERT: F  104 MET cc_start: 0.8324 (mtt) cc_final: 0.8004 (mtt)
REVERT: F  113 LEU cc_start: 0.8146 (mt) cc_final: 0.7597 (pp)
REVERT: F  174 ASN cc_start: 0.7811 (m-40) cc_final: 0.7611 (m-40)
REVERT: G   67 TRP cc_start: 0.8624 (t-100) cc_final: 0.7894 (t-100)
REVERT: G  191 LYS cc_start: 0.8649 (tptp) cc_final: 0.8380 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 251
  average time/residue: 0.2214
  time to fit residues: 81.2600
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  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 117 optimal weight:    3.9990
   chunk 125 optimal weight:    0.7980
   chunk 129 optimal weight:    4.9990
   chunk 75 optimal weight:    0.6980
   chunk 54 optimal weight:    8.9990
   chunk 98 optimal weight:    0.0370
   chunk 38 optimal weight:    6.9990
   chunk 113 optimal weight:    0.7980
   chunk 118 optimal weight:    0.0370
   chunk 82 optimal weight:    0.6980
   chunk 132 optimal weight:    0.4980
   overall best weight:    0.3936

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

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

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7179
moved from start:          0.3843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  11788  Z= 0.228
  Angle     :  0.926  15.644  16443  Z= 0.324
  Chirality :  0.042   0.217   1631
  Planarity :  0.006   0.062   2065
  Dihedral  : 15.154  86.376   1659
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.07 %
    Favored  : 91.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.54 %
    Favored  : 99.46 %
  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: -1.78 (0.22), residues: 1400
  helix:  0.11 (0.41), residues: 154
  sheet: -2.47 (0.50), residues: 70
  loop : -1.40 (0.19), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  67 
 HIS   0.005   0.001   HIS C 230 
 PHE   0.012   0.001   PHE F 102 
 TYR   0.021   0.002   TYR F  80 
 ARG   0.003   0.000   ARG A  69 

*********************** 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
  260 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.6945 (tpp) cc_final: 0.6521 (tpt)
REVERT: C   83 SER cc_start: 0.8041 (p) cc_final: 0.7686 (p)
REVERT: C  148 ASP cc_start: 0.7613 (t70) cc_final: 0.7285 (t0)
REVERT: C  191 LYS cc_start: 0.8725 (tptp) cc_final: 0.8447 (tptp)
REVERT: D  170 ASP cc_start: 0.5965 (t0) cc_final: 0.5411 (t0)
REVERT: D  174 ASN cc_start: 0.7785 (m-40) cc_final: 0.7531 (m-40)
REVERT: A   77 PHE cc_start: 0.7604 (m-10) cc_final: 0.7301 (m-10)
REVERT: A  177 THR cc_start: 0.8463 (t) cc_final: 0.8179 (t)
REVERT: E  128 MET cc_start: 0.6586 (tpp) cc_final: 0.6125 (tpt)
REVERT: E  148 ASP cc_start: 0.7828 (t70) cc_final: 0.7351 (t70)
REVERT: F  104 MET cc_start: 0.8214 (mtt) cc_final: 0.7918 (mtt)
REVERT: G   67 TRP cc_start: 0.8564 (t-100) cc_final: 0.7733 (t-100)
REVERT: G  191 LYS cc_start: 0.8647 (tptp) cc_final: 0.8380 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 260
  average time/residue: 0.2222
  time to fit residues: 83.5714
Evaluate side-chains
  204 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 1.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 81 optimal weight:    6.9990
   chunk 63 optimal weight:    0.6980
   chunk 92 optimal weight:    0.7980
   chunk 139 optimal weight:    4.9990
   chunk 128 optimal weight:    0.0770
   chunk 111 optimal weight:    0.0980
   chunk 11 optimal weight:    5.9990
   chunk 85 optimal weight:    1.9990
   chunk 68 optimal weight:    8.9990
   chunk 88 optimal weight:   20.0000
   chunk 118 optimal weight:    0.0770
   overall best weight:    0.3496

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

Flipped N/Q/H residues before XYZ refinement:
D  31 HIS
D 140 ASN
D 152 ASN
A  31 HIS
F  31 HIS
G  31 HIS
G 152 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7158
moved from start:          0.3992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  11788  Z= 0.214
  Angle     :  0.925  16.262  16443  Z= 0.320
  Chirality :  0.042   0.209   1631
  Planarity :  0.005   0.061   2065
  Dihedral  : 15.011  88.325   1659
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.21 %
    Favored  : 92.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  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: -1.77 (0.22), residues: 1400
  helix:  0.26 (0.42), residues: 154
  sheet: -2.55 (0.49), residues: 70
  loop : -1.42 (0.19), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B  67 
 HIS   0.006   0.001   HIS G  31 
 PHE   0.014   0.001   PHE E  77 
 TYR   0.020   0.002   TYR F  80 
 ARG   0.002   0.000   ARG E  69 

********************** 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
  250 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 250
  time to evaluate  : 1.202 
Fit side-chains
REVERT: B  128 MET cc_start: 0.6844 (tpp) cc_final: 0.6453 (tpt)
REVERT: C   83 SER cc_start: 0.8053 (p) cc_final: 0.7720 (p)
REVERT: C  174 ASN cc_start: 0.7880 (m-40) cc_final: 0.7573 (m-40)
REVERT: C  191 LYS cc_start: 0.8718 (tptp) cc_final: 0.8475 (tptp)
REVERT: D  174 ASN cc_start: 0.7768 (m-40) cc_final: 0.7515 (m-40)
REVERT: D  178 MET cc_start: 0.7791 (ttm) cc_final: 0.7541 (ttt)
REVERT: D  231 LYS cc_start: 0.6034 (pttm) cc_final: 0.5737 (tttt)
REVERT: A   77 PHE cc_start: 0.7547 (m-10) cc_final: 0.7189 (m-10)
REVERT: A   83 SER cc_start: 0.7881 (p) cc_final: 0.7630 (p)
REVERT: A  187 LEU cc_start: 0.9133 (mm) cc_final: 0.8754 (mt)
REVERT: E   83 SER cc_start: 0.7849 (p) cc_final: 0.7630 (p)
REVERT: E  128 MET cc_start: 0.6560 (tpp) cc_final: 0.6079 (tpt)
REVERT: E  148 ASP cc_start: 0.7957 (t70) cc_final: 0.7519 (t70)
REVERT: F   67 TRP cc_start: 0.7590 (t-100) cc_final: 0.6811 (t-100)
REVERT: F  104 MET cc_start: 0.8232 (mtt) cc_final: 0.7888 (mtt)
REVERT: G   62 GLN cc_start: 0.7383 (mp10) cc_final: 0.7071 (mt0)
REVERT: G   67 TRP cc_start: 0.8556 (t-100) cc_final: 0.7886 (t-100)
REVERT: G  191 LYS cc_start: 0.8662 (tptp) cc_final: 0.8420 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 250
  average time/residue: 0.2066
  time to fit residues: 75.9692
Evaluate side-chains
  193 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.228 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 102 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 30 optimal weight:    9.9990
   chunk 111 optimal weight:    4.9990
   chunk 46 optimal weight:    7.9990
   chunk 114 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 20 optimal weight:    8.9990
   chunk 97 optimal weight:    0.3980
   chunk 6 optimal weight:    5.9990
   overall best weight:    2.2788

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

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

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.169715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.130890 restraints weight = 19055.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.135176 restraints weight = 14473.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.138379 restraints weight = 11792.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7539
moved from start:          0.4310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.096  11788  Z= 0.482
  Angle     :  1.214  22.113  16443  Z= 0.420
  Chirality :  0.049   0.265   1631
  Planarity :  0.006   0.064   2065
  Dihedral  : 15.136  81.753   1659
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 13.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.00 %
    Favored  : 88.00 %
  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 : 2.60 %
    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: -2.04 (0.22), residues: 1400
  helix: -0.34 (0.40), residues: 154
  sheet: -2.64 (0.51), residues: 70
  loop : -1.55 (0.18), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.003   TRP A  67 
 HIS   0.015   0.002   HIS C 230 
 PHE   0.020   0.001   PHE A 102 
 TYR   0.028   0.004   TYR F  80 
 ARG   0.008   0.001   ARG E  69 

===============================================================================
Job complete
usr+sys time: 2551.02 seconds
wall clock time: 47 minutes 41.64 seconds (2861.64 seconds total)