Starting phenix.real_space_refine
on Wed Sep 17 20:35:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tfs_25879/09_2025/7tfs_25879.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tfs_25879/09_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_25879/09_2025/7tfs_25879.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tfs_25879/09_2025/7tfs_25879.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tfs_25879/09_2025/7tfs_25879.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tfs_25879/09_2025/7tfs_25879.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11382
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      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: "B"
      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, D, A, E, F, G
  Time building chain proxies: 1.67, per 1000 atoms: 0.15
  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: 1.37
  Conformation dependent library (CDL) restraints added in 529.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.36
  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: 1.56

  Time building geometry restraints manager: 1.69 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
  selection = chain 'A'
  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:             2.760
  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:          0.190
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     11.030
  Find NCS groups from input model:        0.100
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.520
-------------------------------------------------------------------------------
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 : 34.30
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.002   0.001   ARG C  69 
 TYR   0.002   0.001   TYR F  80 
 PHE   0.005   0.001   PHE D 215 
 TRP   0.004   0.001   TRP B  67 
 HIS   0.012   0.002   HIS D 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00397 (11788)
  covalent geometry    : angle       0.95684 (16443)
  hydrogen bonds       : bond        0.27741 (  154)
  hydrogen bonds       : angle       8.13248 (  336)
  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  : 0.424 
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: 0.1025
  time to fit residues: 39.8618
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  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:    0.0980
   chunk 107 optimal weight:    0.5980
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    8.9990
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    1.7384

-------------------------------------------------------------------------------
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 152 ASN
E 152 ASN
F 152 ASN
G 152 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.175876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.138355 restraints weight = 18528.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.143284 restraints weight = 13311.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.147136 restraints weight = 10436.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.150112 restraints weight = 8599.790|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.152070 restraints weight = 7378.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.014   0.442  11884  Z= 0.248
  Angle     :  1.074  14.966  16443  Z= 0.390
  Chirality :  0.046   0.222   1631
  Planarity :  0.007   0.069   2065
  Dihedral  : 15.006  89.972   1659
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.00 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.08 (0.20), residues: 1400
  helix:  0.06 (0.37), residues: 154
  sheet: -1.90 (0.47), residues: 70
  loop : -1.71 (0.17), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 217 
 TYR   0.014   0.002   TYR G  80 
 PHE   0.014   0.001   PHE E 215 
 TRP   0.009   0.002   TRP B  67 
 HIS   0.007   0.002   HIS C  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00710 (11788)
  covalent geometry    : angle       1.07371 (16443)
  hydrogen bonds       : bond        0.05012 (  154)
  hydrogen bonds       : angle       7.92051 (  336)
  Misc. bond           : bond        0.13990 (   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
  266 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 0.492 
Fit side-chains
   revert: symmetry clash
REVERT: B  102 PHE cc_start: 0.7889 (m-10) cc_final: 0.7610 (m-10)
REVERT: B  104 MET cc_start: 0.8568 (mtm) cc_final: 0.8368 (mtm)
REVERT: B  231 LYS cc_start: 0.7240 (pptt) cc_final: 0.6753 (ttmt)
REVERT: C   83 SER cc_start: 0.8166 (p) cc_final: 0.7745 (p)
REVERT: C  191 LYS cc_start: 0.8626 (tptp) cc_final: 0.8265 (tptp)
REVERT: D   77 PHE cc_start: 0.7799 (m-10) cc_final: 0.7489 (m-10)
REVERT: D  104 MET cc_start: 0.8501 (mtt) cc_final: 0.8267 (mtt)
REVERT: D  148 ASP cc_start: 0.7568 (t70) cc_final: 0.7299 (t70)
REVERT: D  174 ASN cc_start: 0.8153 (m-40) cc_final: 0.7869 (m-40)
REVERT: D  231 LYS cc_start: 0.7782 (pptt) cc_final: 0.6829 (ttmt)
REVERT: A   56 THR cc_start: 0.9289 (t) cc_final: 0.9044 (p)
REVERT: A   83 SER cc_start: 0.8146 (p) cc_final: 0.7882 (p)
REVERT: A  102 PHE cc_start: 0.7727 (m-10) cc_final: 0.7343 (m-10)
REVERT: A  174 ASN cc_start: 0.8207 (m-40) cc_final: 0.7990 (m-40)
REVERT: A  206 LYS cc_start: 0.7752 (tttt) cc_final: 0.7403 (tptt)
REVERT: E  206 LYS cc_start: 0.7967 (tttt) cc_final: 0.7632 (tptp)
REVERT: F  174 ASN cc_start: 0.8196 (m-40) cc_final: 0.7988 (m-40)
REVERT: F  206 LYS cc_start: 0.7823 (tttt) cc_final: 0.7505 (tptt)
REVERT: F  231 LYS cc_start: 0.7641 (pptt) cc_final: 0.6888 (tttt)
REVERT: G   67 TRP cc_start: 0.7723 (t-100) cc_final: 0.7122 (t-100)
REVERT: G  206 LYS cc_start: 0.7857 (tttt) cc_final: 0.7503 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 266
  average time/residue: 0.1048
  time to fit residues: 40.8730
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  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 135 optimal weight:    6.9990
   chunk 29 optimal weight:    9.9990
   chunk 106 optimal weight:    0.2980
   chunk 115 optimal weight:    5.9990
   chunk 91 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 121 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 113 optimal weight:   20.0000
   chunk 109 optimal weight:    0.8980
   overall best weight:    1.1582

-------------------------------------------------------------------------------
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
A 152 ASN
E 152 ASN
F 152 ASN
G 152 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.176755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.139190 restraints weight = 18492.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.144244 restraints weight = 13165.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.148181 restraints weight = 10272.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.151243 restraints weight = 8470.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.153332 restraints weight = 7240.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7240
moved from start:          0.2158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.322  11884  Z= 0.182
  Angle     :  0.968  16.524  16443  Z= 0.343
  Chirality :  0.044   0.220   1631
  Planarity :  0.005   0.053   2065
  Dihedral  : 14.861  88.868   1659
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.23 (0.21), residues: 1400
  helix: -0.94 (0.35), residues: 196
  sheet: -1.99 (0.50), residues: 70
  loop : -1.69 (0.18), residues: 1134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 194 
 TYR   0.007   0.001   TYR B  80 
 PHE   0.012   0.001   PHE E 215 
 TRP   0.007   0.002   TRP B  67 
 HIS   0.028   0.002   HIS G 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00529 (11788)
  covalent geometry    : angle       0.96841 (16443)
  hydrogen bonds       : bond        0.03701 (  154)
  hydrogen bonds       : angle       7.76838 (  336)
  Misc. bond           : bond        0.11166 (   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
  261 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 261
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 MET cc_start: 0.7655 (mtp) cc_final: 0.7342 (mpp)
REVERT: B  102 PHE cc_start: 0.7922 (m-10) cc_final: 0.7265 (m-10)
REVERT: B  170 ASP cc_start: 0.7432 (t0) cc_final: 0.6963 (t0)
REVERT: C   83 SER cc_start: 0.8185 (p) cc_final: 0.7852 (p)
REVERT: C  148 ASP cc_start: 0.7779 (t70) cc_final: 0.7540 (t70)
REVERT: C  191 LYS cc_start: 0.8749 (tptp) cc_final: 0.8419 (tptp)
REVERT: D  104 MET cc_start: 0.8530 (mtt) cc_final: 0.8295 (mtt)
REVERT: D  170 ASP cc_start: 0.6770 (t0) cc_final: 0.6291 (t0)
REVERT: D  174 ASN cc_start: 0.8207 (m-40) cc_final: 0.7892 (m-40)
REVERT: D  231 LYS cc_start: 0.7294 (pptt) cc_final: 0.7076 (pttm)
REVERT: A   83 SER cc_start: 0.8256 (p) cc_final: 0.8016 (p)
REVERT: A  206 LYS cc_start: 0.7691 (tttt) cc_final: 0.7370 (tptt)
REVERT: E  148 ASP cc_start: 0.7767 (t70) cc_final: 0.7556 (t70)
REVERT: E  170 ASP cc_start: 0.7224 (t0) cc_final: 0.6888 (t0)
REVERT: E  206 LYS cc_start: 0.7977 (tttt) cc_final: 0.7602 (tptp)
REVERT: F   33 LEU cc_start: 0.9139 (mp) cc_final: 0.8929 (mp)
REVERT: F   80 TYR cc_start: 0.8290 (t80) cc_final: 0.8033 (t80)
REVERT: F   85 MET cc_start: 0.7823 (mtp) cc_final: 0.7376 (mpp)
REVERT: F  150 PRO cc_start: 0.8961 (Cg_exo) cc_final: 0.8584 (Cg_endo)
REVERT: F  174 ASN cc_start: 0.8207 (m-40) cc_final: 0.7977 (m-40)
REVERT: F  206 LYS cc_start: 0.7830 (tttt) cc_final: 0.7500 (tptt)
REVERT: F  231 LYS cc_start: 0.7532 (pptt) cc_final: 0.6746 (tttt)
REVERT: G   67 TRP cc_start: 0.7955 (t-100) cc_final: 0.7396 (t-100)
REVERT: G   85 MET cc_start: 0.7855 (mtm) cc_final: 0.7144 (mtm)
REVERT: G  104 MET cc_start: 0.8522 (mtt) cc_final: 0.8234 (mtt)
REVERT: G  170 ASP cc_start: 0.7389 (t0) cc_final: 0.6969 (t0)
REVERT: G  191 LYS cc_start: 0.8740 (tptp) cc_final: 0.8432 (tptp)
REVERT: G  206 LYS cc_start: 0.7791 (tttt) cc_final: 0.7474 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 261
  average time/residue: 0.1027
  time to fit residues: 39.0538
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  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 73 optimal weight:    0.5980
   chunk 26 optimal weight:    0.9990
   chunk 84 optimal weight:    8.9990
   chunk 1 optimal weight:    5.9990
   chunk 7 optimal weight:    0.6980
   chunk 118 optimal weight:    0.5980
   chunk 13 optimal weight:   10.0000
   chunk 120 optimal weight:    8.9990
   chunk 67 optimal weight:   10.0000
   chunk 33 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 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 = 0.4169 r_free = 0.4169 target = 0.179179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.141856 restraints weight = 18264.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.147137 restraints weight = 12862.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.151282 restraints weight = 9925.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.154364 restraints weight = 8100.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.156692 restraints weight = 6880.411|
|-----------------------------------------------------------------------------|
r_work (final): 0.3916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7195
moved from start:          0.2438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.281  11884  Z= 0.155
  Angle     :  0.917  15.284  16443  Z= 0.329
  Chirality :  0.043   0.227   1631
  Planarity :  0.005   0.054   2065
  Dihedral  : 14.946  88.856   1659
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.64 %
    Favored  : 92.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.16 (0.21), residues: 1400
  helix: -0.94 (0.35), residues: 196
  sheet: -1.86 (0.50), residues: 70
  loop : -1.63 (0.18), residues: 1134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG G  69 
 TYR   0.007   0.001   TYR G  80 
 PHE   0.011   0.001   PHE B  77 
 TRP   0.005   0.001   TRP B  67 
 HIS   0.022   0.001   HIS C 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 (11788)
  covalent geometry    : angle       0.91720 (16443)
  hydrogen bonds       : bond        0.03298 (  154)
  hydrogen bonds       : angle       7.54655 (  336)
  Misc. bond           : bond        0.09146 (   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
  257 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 257
  time to evaluate  : 0.418 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 MET cc_start: 0.7760 (mtp) cc_final: 0.7461 (mpp)
REVERT: B  102 PHE cc_start: 0.7947 (m-10) cc_final: 0.7308 (m-10)
REVERT: B  104 MET cc_start: 0.8599 (mtt) cc_final: 0.8316 (mtm)
REVERT: C   83 SER cc_start: 0.8094 (p) cc_final: 0.7808 (p)
REVERT: C  191 LYS cc_start: 0.8753 (tptp) cc_final: 0.8452 (tptp)
REVERT: D  104 MET cc_start: 0.8411 (mtt) cc_final: 0.8067 (mtm)
REVERT: D  174 ASN cc_start: 0.8159 (m-40) cc_final: 0.7875 (m-40)
REVERT: A   83 SER cc_start: 0.8212 (p) cc_final: 0.8011 (p)
REVERT: A  206 LYS cc_start: 0.7708 (tttt) cc_final: 0.7335 (tptt)
REVERT: E  148 ASP cc_start: 0.7438 (t70) cc_final: 0.7109 (t70)
REVERT: E  206 LYS cc_start: 0.7967 (tttt) cc_final: 0.7623 (tptp)
REVERT: F   80 TYR cc_start: 0.8218 (t80) cc_final: 0.8006 (t80)
REVERT: F   85 MET cc_start: 0.7837 (mtp) cc_final: 0.7455 (mpp)
REVERT: F  174 ASN cc_start: 0.8238 (m-40) cc_final: 0.8011 (m-40)
REVERT: F  191 LYS cc_start: 0.8728 (tmtt) cc_final: 0.8505 (tptp)
REVERT: F  231 LYS cc_start: 0.7283 (pptt) cc_final: 0.6540 (tttt)
REVERT: G   67 TRP cc_start: 0.8100 (t-100) cc_final: 0.7683 (t-100)
REVERT: G  191 LYS cc_start: 0.8745 (tptp) cc_final: 0.8427 (tptp)
REVERT: G  206 LYS cc_start: 0.7745 (tttt) cc_final: 0.7434 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 257
  average time/residue: 0.0975
  time to fit residues: 36.8961
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  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 129 optimal weight:    0.7980
   chunk 73 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9980
   chunk 59 optimal weight:    0.1980
   chunk 115 optimal weight:    5.9990
   chunk 23 optimal weight:    2.9990
   chunk 93 optimal weight:    8.9990
   chunk 84 optimal weight:    2.9990
   chunk 109 optimal weight:    0.0770
   overall best weight:    0.5538

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

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

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.182221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.145289 restraints weight = 18171.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.150734 restraints weight = 12700.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.154912 restraints weight = 9692.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.157602 restraints weight = 7865.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.160342 restraints weight = 6740.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.2622

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= 0.138
  Angle     :  0.883  15.264  16443  Z= 0.317
  Chirality :  0.042   0.213   1631
  Planarity :  0.006   0.068   2065
  Dihedral  : 15.024  87.765   1659
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.07 %
    Favored  : 93.93 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.06 (0.22), residues: 1400
  helix: -0.67 (0.35), residues: 196
  sheet: -1.91 (0.51), residues: 70
  loop : -1.60 (0.18), residues: 1134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG G 194 
 TYR   0.006   0.001   TYR B  80 
 PHE   0.018   0.001   PHE C 102 
 TRP   0.006   0.001   TRP B  67 
 HIS   0.026   0.001   HIS F 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (11788)
  covalent geometry    : angle       0.88266 (16443)
  hydrogen bonds       : bond        0.02902 (  154)
  hydrogen bonds       : angle       7.53303 (  336)
  Misc. bond           : bond        0.08245 (   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
  266 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 266
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   85 MET cc_start: 0.7714 (mtp) cc_final: 0.7473 (mpp)
REVERT: B  102 PHE cc_start: 0.7906 (m-10) cc_final: 0.7349 (m-10)
REVERT: B  104 MET cc_start: 0.8546 (mtt) cc_final: 0.8320 (mtm)
REVERT: C   85 MET cc_start: 0.7888 (mtp) cc_final: 0.7253 (mpp)
REVERT: C  113 LEU cc_start: 0.8370 (mt) cc_final: 0.8102 (pp)
REVERT: C  191 LYS cc_start: 0.8769 (tptp) cc_final: 0.8432 (tptp)
REVERT: C  231 LYS cc_start: 0.6970 (pttm) cc_final: 0.5872 (ttmt)
REVERT: D  104 MET cc_start: 0.8316 (mtt) cc_final: 0.7956 (mtt)
REVERT: D  174 ASN cc_start: 0.8074 (m-40) cc_final: 0.7784 (m-40)
REVERT: A   77 PHE cc_start: 0.7716 (m-10) cc_final: 0.7247 (m-10)
REVERT: A   83 SER cc_start: 0.8215 (p) cc_final: 0.8008 (p)
REVERT: A  206 LYS cc_start: 0.7756 (tttt) cc_final: 0.7361 (tptt)
REVERT: E  148 ASP cc_start: 0.7385 (t70) cc_final: 0.7042 (t70)
REVERT: E  170 ASP cc_start: 0.7093 (t0) cc_final: 0.6652 (t0)
REVERT: E  206 LYS cc_start: 0.7778 (tttt) cc_final: 0.7508 (tptp)
REVERT: F   85 MET cc_start: 0.7721 (mtp) cc_final: 0.7445 (mpp)
REVERT: F  174 ASN cc_start: 0.8064 (m-40) cc_final: 0.7828 (m-40)
REVERT: F  191 LYS cc_start: 0.8713 (tmtt) cc_final: 0.8479 (tptp)
REVERT: G   67 TRP cc_start: 0.8162 (t-100) cc_final: 0.7634 (t-100)
REVERT: G  191 LYS cc_start: 0.8746 (tptp) cc_final: 0.8466 (tptp)
REVERT: G  206 LYS cc_start: 0.7734 (tttt) cc_final: 0.7441 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 266
  average time/residue: 0.0966
  time to fit residues: 38.1991
Evaluate side-chains
  217 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 89 optimal weight:    0.0060
   chunk 40 optimal weight:    3.9990
   chunk 86 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 53 optimal weight:    8.9990
   chunk 18 optimal weight:    0.9990
   chunk 122 optimal weight:    0.9990
   chunk 66 optimal weight:   10.0000
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.7400

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

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

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.182486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.142953 restraints weight = 18371.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.148580 restraints weight = 12917.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.152817 restraints weight = 9903.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.155560 restraints weight = 8057.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.158484 restraints weight = 6916.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.2833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.320  11884  Z= 0.145
  Angle     :  0.917  16.566  16443  Z= 0.319
  Chirality :  0.042   0.215   1631
  Planarity :  0.005   0.059   2065
  Dihedral  : 15.168  88.137   1659
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 9.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.75 (0.22), residues: 1400
  helix:  0.59 (0.39), residues: 154
  sheet: -1.97 (0.51), residues: 70
  loop : -1.49 (0.18), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G 194 
 TYR   0.011   0.001   TYR B  80 
 PHE   0.015   0.001   PHE D 102 
 TRP   0.014   0.002   TRP B  67 
 HIS   0.013   0.001   HIS F 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (11788)
  covalent geometry    : angle       0.91726 (16443)
  hydrogen bonds       : bond        0.02959 (  154)
  hydrogen bonds       : angle       7.27732 (  336)
  Misc. bond           : bond        0.09364 (   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
  255 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 255
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  102 PHE cc_start: 0.7953 (m-10) cc_final: 0.7413 (m-10)
REVERT: B  104 MET cc_start: 0.8569 (mtt) cc_final: 0.8343 (mtm)
REVERT: B  231 LYS cc_start: 0.7037 (pttm) cc_final: 0.6396 (tttt)
REVERT: C   83 SER cc_start: 0.8202 (p) cc_final: 0.7906 (p)
REVERT: C  113 LEU cc_start: 0.8350 (mt) cc_final: 0.8101 (pp)
REVERT: C  191 LYS cc_start: 0.8847 (tptp) cc_final: 0.8538 (tptp)
REVERT: C  231 LYS cc_start: 0.6691 (pttm) cc_final: 0.5640 (ttmt)
REVERT: D  104 MET cc_start: 0.8328 (mtt) cc_final: 0.8019 (mtt)
REVERT: D  174 ASN cc_start: 0.8180 (m-40) cc_final: 0.7890 (m-40)
REVERT: D  191 LYS cc_start: 0.8902 (tmtt) cc_final: 0.8693 (tptp)
REVERT: A   83 SER cc_start: 0.8272 (p) cc_final: 0.8034 (p)
REVERT: A  102 PHE cc_start: 0.7653 (m-10) cc_final: 0.7370 (m-10)
REVERT: A  153 PHE cc_start: 0.7426 (p90) cc_final: 0.7193 (p90)
REVERT: A  206 LYS cc_start: 0.7764 (tttt) cc_final: 0.7327 (tptt)
REVERT: E  148 ASP cc_start: 0.7510 (t70) cc_final: 0.7172 (t70)
REVERT: E  206 LYS cc_start: 0.7710 (tttt) cc_final: 0.7452 (tptp)
REVERT: F  174 ASN cc_start: 0.8144 (m-40) cc_final: 0.7930 (m-40)
REVERT: F  191 LYS cc_start: 0.8801 (tmtt) cc_final: 0.8518 (tptp)
REVERT: G   67 TRP cc_start: 0.8322 (t-100) cc_final: 0.7650 (t-100)
REVERT: G   83 SER cc_start: 0.8226 (p) cc_final: 0.8016 (p)
REVERT: G  191 LYS cc_start: 0.8804 (tptp) cc_final: 0.8530 (tptp)
REVERT: G  206 LYS cc_start: 0.7726 (tttt) cc_final: 0.7410 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 255
  average time/residue: 0.0982
  time to fit residues: 36.9258
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  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 29 optimal weight:    0.0980
   chunk 41 optimal weight:    6.9990
   chunk 57 optimal weight:    5.9990
   chunk 116 optimal weight:    1.9990
   chunk 118 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 121 optimal weight:    4.9990
   overall best weight:    1.4188

-------------------------------------------------------------------------------
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
E 152 ASN
F  31 HIS
F 152 ASN
G  31 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 = 0.4136 r_free = 0.4136 target = 0.175358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.136956 restraints weight = 18760.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.141821 restraints weight = 13637.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.145564 restraints weight = 10735.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.148046 restraints weight = 8951.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.150532 restraints weight = 7828.607|
|-----------------------------------------------------------------------------|
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7325
moved from start:          0.3097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.409  11884  Z= 0.199
  Angle     :  1.033  19.313  16443  Z= 0.354
  Chirality :  0.044   0.241   1631
  Planarity :  0.005   0.074   2065
  Dihedral  : 15.435  88.142   1659
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 10.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.86 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.80 (0.22), residues: 1400
  helix:  0.44 (0.40), residues: 154
  sheet: -1.95 (0.53), residues: 70
  loop : -1.51 (0.19), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C  69 
 TYR   0.009   0.002   TYR G  80 
 PHE   0.018   0.001   PHE B 102 
 TRP   0.010   0.001   TRP A  67 
 HIS   0.012   0.001   HIS F 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00544 (11788)
  covalent geometry    : angle       1.03308 (16443)
  hydrogen bonds       : bond        0.03435 (  154)
  hydrogen bonds       : angle       7.48821 (  336)
  Misc. bond           : bond        0.11268 (   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  : 0.429 
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: B  104 MET cc_start: 0.8670 (mtt) cc_final: 0.8441 (mtm)
REVERT: C   85 MET cc_start: 0.7997 (mtp) cc_final: 0.7437 (mpp)
REVERT: C  191 LYS cc_start: 0.8805 (tptp) cc_final: 0.8505 (tptp)
REVERT: D  104 MET cc_start: 0.8471 (mtt) cc_final: 0.8150 (mtt)
REVERT: D  174 ASN cc_start: 0.8094 (m-40) cc_final: 0.7824 (m-40)
REVERT: D  191 LYS cc_start: 0.8880 (tmtt) cc_final: 0.8668 (tptp)
REVERT: A   77 PHE cc_start: 0.7951 (m-10) cc_final: 0.7694 (m-10)
REVERT: A   83 SER cc_start: 0.8140 (p) cc_final: 0.7934 (p)
REVERT: A  206 LYS cc_start: 0.7779 (tttt) cc_final: 0.7444 (tptt)
REVERT: E  148 ASP cc_start: 0.7722 (t70) cc_final: 0.7433 (t70)
REVERT: E  170 ASP cc_start: 0.7076 (t0) cc_final: 0.6721 (t0)
REVERT: E  206 LYS cc_start: 0.7802 (tttt) cc_final: 0.7501 (tptp)
REVERT: F   80 TYR cc_start: 0.8477 (t80) cc_final: 0.8194 (t80)
REVERT: F  206 LYS cc_start: 0.7846 (tttt) cc_final: 0.7592 (tptt)
REVERT: G   67 TRP cc_start: 0.8538 (t-100) cc_final: 0.7821 (t-100)
REVERT: G  191 LYS cc_start: 0.8750 (tptp) cc_final: 0.8470 (tptp)
REVERT: G  194 ARG cc_start: 0.8572 (mmt90) cc_final: 0.8244 (mmt90)
REVERT: G  206 LYS cc_start: 0.7873 (tttt) cc_final: 0.7576 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 248
  average time/residue: 0.0913
  time to fit residues: 33.3986
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  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 40 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   chunk 0 optimal weight:    5.9990
   chunk 52 optimal weight:    0.3980
   chunk 127 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 96 optimal weight:    0.0000
   chunk 76 optimal weight:    3.9990
   chunk 121 optimal weight:    8.9990
   chunk 86 optimal weight:    0.8980
   overall best weight:    0.6186

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

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.179318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.141635 restraints weight = 18348.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.146676 restraints weight = 13288.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.150541 restraints weight = 10394.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.153021 restraints weight = 8601.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.155764 restraints weight = 7446.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7228
moved from start:          0.3203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.293  11884  Z= 0.139
  Angle     :  0.913  16.953  16443  Z= 0.317
  Chirality :  0.042   0.217   1631
  Planarity :  0.005   0.066   2065
  Dihedral  : 15.230  82.225   1659
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.71 (0.22), residues: 1400
  helix:  0.65 (0.40), residues: 154
  sheet: -2.00 (0.51), residues: 70
  loop : -1.47 (0.18), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  69 
 TYR   0.005   0.001   TYR C  80 
 PHE   0.010   0.001   PHE E 215 
 TRP   0.012   0.001   TRP B  67 
 HIS   0.006   0.001   HIS C 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00378 (11788)
  covalent geometry    : angle       0.91273 (16443)
  hydrogen bonds       : bond        0.02986 (  154)
  hydrogen bonds       : angle       7.32264 (  336)
  Misc. bond           : bond        0.08877 (   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
  251 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 251
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   83 SER cc_start: 0.8074 (p) cc_final: 0.7763 (p)
REVERT: C  191 LYS cc_start: 0.8829 (tptp) cc_final: 0.8570 (tptp)
REVERT: C  231 LYS cc_start: 0.6353 (pttm) cc_final: 0.5931 (pttt)
REVERT: D  174 ASN cc_start: 0.8030 (m-40) cc_final: 0.7759 (m-40)
REVERT: A   83 SER cc_start: 0.8062 (p) cc_final: 0.7861 (p)
REVERT: A  206 LYS cc_start: 0.7764 (tttt) cc_final: 0.7414 (tptt)
REVERT: E  206 LYS cc_start: 0.7909 (tttt) cc_final: 0.7564 (tptp)
REVERT: F  104 MET cc_start: 0.8239 (mtt) cc_final: 0.8011 (tpp)
REVERT: F  174 ASN cc_start: 0.8174 (m-40) cc_final: 0.7949 (m-40)
REVERT: G   67 TRP cc_start: 0.8493 (t-100) cc_final: 0.7835 (t-100)
REVERT: G  170 ASP cc_start: 0.7491 (t0) cc_final: 0.7105 (t0)
REVERT: G  191 LYS cc_start: 0.8748 (tptp) cc_final: 0.8455 (tptp)
REVERT: G  206 LYS cc_start: 0.7911 (tttt) cc_final: 0.7599 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 251
  average time/residue: 0.0972
  time to fit residues: 35.8029
Evaluate side-chains
  206 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 2 optimal weight:    0.0970
   chunk 132 optimal weight:    3.9990
   chunk 128 optimal weight:   10.0000
   chunk 85 optimal weight:    5.9990
   chunk 44 optimal weight:    8.9990
   chunk 34 optimal weight:    1.9990
   chunk 117 optimal weight:    1.9990
   overall best weight:    0.9980

-------------------------------------------------------------------------------
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
E 152 ASN
F  31 HIS
F 152 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4163 r_free = 0.4163 target = 0.178517 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.138581 restraints weight = 18425.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.143768 restraints weight = 13159.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.147874 restraints weight = 10219.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.150559 restraints weight = 8400.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.153067 restraints weight = 7287.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3853
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7226
moved from start:          0.3395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.340  11884  Z= 0.164
  Angle     :  0.971  17.905  16443  Z= 0.335
  Chirality :  0.043   0.224   1631
  Planarity :  0.005   0.064   2065
  Dihedral  : 15.277  88.585   1659
  Min Nonbonded Distance : 2.356

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.14 %
    Favored  : 89.86 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.77 (0.22), residues: 1400
  helix:  0.60 (0.40), residues: 154
  sheet: -2.05 (0.52), residues: 70
  loop : -1.50 (0.18), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  69 
 TYR   0.021   0.002   TYR A  80 
 PHE   0.027   0.001   PHE A 102 
 TRP   0.018   0.002   TRP B  67 
 HIS   0.008   0.001   HIS F 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (11788)
  covalent geometry    : angle       0.97098 (16443)
  hydrogen bonds       : bond        0.02980 (  154)
  hydrogen bonds       : angle       7.36006 (  336)
  Misc. bond           : bond        0.09809 (   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
  241 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 241
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
REVERT: B  104 MET cc_start: 0.8520 (mtt) cc_final: 0.8253 (mtm)
REVERT: B  191 LYS cc_start: 0.8797 (tmtt) cc_final: 0.8522 (tptp)
REVERT: C   83 SER cc_start: 0.8207 (p) cc_final: 0.7922 (p)
REVERT: C  191 LYS cc_start: 0.8877 (tptp) cc_final: 0.8597 (tptp)
REVERT: D  174 ASN cc_start: 0.8220 (m-40) cc_final: 0.7955 (m-40)
REVERT: D  191 LYS cc_start: 0.8982 (tmtt) cc_final: 0.8723 (tptp)
REVERT: A   77 PHE cc_start: 0.7955 (m-10) cc_final: 0.7683 (m-10)
REVERT: A   83 SER cc_start: 0.8351 (p) cc_final: 0.8139 (p)
REVERT: A  206 LYS cc_start: 0.7729 (tttt) cc_final: 0.7330 (tptt)
REVERT: E  170 ASP cc_start: 0.7437 (t0) cc_final: 0.7055 (t0)
REVERT: E  206 LYS cc_start: 0.7763 (tttt) cc_final: 0.7355 (tptp)
REVERT: F  104 MET cc_start: 0.8421 (mtt) cc_final: 0.8129 (tpp)
REVERT: F  174 ASN cc_start: 0.8263 (m-40) cc_final: 0.8057 (m-40)
REVERT: F  191 LYS cc_start: 0.8833 (tmtt) cc_final: 0.8577 (tptp)
REVERT: G   67 TRP cc_start: 0.8530 (t-100) cc_final: 0.7790 (t-100)
REVERT: G  191 LYS cc_start: 0.8807 (tptp) cc_final: 0.8521 (tptp)
REVERT: G  206 LYS cc_start: 0.7899 (tttt) cc_final: 0.7518 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 241
  average time/residue: 0.0966
  time to fit residues: 34.3315
Evaluate side-chains
  211 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 133 optimal weight:    7.9990
   chunk 73 optimal weight:    7.9990
   chunk 134 optimal weight:    5.9990
   chunk 76 optimal weight:    1.9990
   chunk 120 optimal weight:    6.9990
   chunk 89 optimal weight:    9.9990
   chunk 88 optimal weight:    8.9990
   chunk 20 optimal weight:    5.9990
   chunk 16 optimal weight:    0.6980
   chunk 64 optimal weight:    4.9990
   overall best weight:    3.9388

-------------------------------------------------------------------------------
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
E 152 ASN
F  31 HIS
F 152 ASN
G 152 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.164229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.125609 restraints weight = 18825.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.130111 restraints weight = 13493.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.133528 restraints weight = 10605.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.136073 restraints weight = 8863.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.137483 restraints weight = 7720.817|
|-----------------------------------------------------------------------------|
r_work (final): 0.3710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.4078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.020   0.665  11884  Z= 0.458
  Angle     :  1.453  21.089  16443  Z= 0.522
  Chirality :  0.055   0.283   1631
  Planarity :  0.007   0.070   2065
  Dihedral  : 15.469  89.512   1659
  Min Nonbonded Distance : 2.159

Molprobity Statistics.
  All-atom Clashscore : 19.65
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  : 12.71 %
    Favored  : 87.21 %
  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 : 6.49 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.45 (0.21), residues: 1400
  helix: -0.43 (0.40), residues: 154
  sheet: -2.18 (0.52), residues: 70
  loop : -1.94 (0.17), residues: 1176

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C  69 
 TYR   0.036   0.004   TYR A  80 
 PHE   0.020   0.002   PHE E  77 
 TRP   0.021   0.003   TRP B  67 
 HIS   0.067   0.003   HIS D 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.01255 (11788)
  covalent geometry    : angle       1.45266 (16443)
  hydrogen bonds       : bond        0.05652 (  154)
  hydrogen bonds       : angle       8.15349 (  336)
  Misc. bond           : bond        0.17810 (   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
  237 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  224 LYS cc_start: 0.8594 (pttm) cc_final: 0.8328 (ptpp)
REVERT: C   83 SER cc_start: 0.8278 (p) cc_final: 0.8003 (p)
REVERT: C  174 ASN cc_start: 0.8319 (m-40) cc_final: 0.7791 (p0)
REVERT: C  191 LYS cc_start: 0.8898 (tptp) cc_final: 0.8613 (tptp)
REVERT: C  194 ARG cc_start: 0.8762 (mpt-90) cc_final: 0.8539 (mmt90)
REVERT: C  206 LYS cc_start: 0.7920 (tttt) cc_final: 0.7470 (tptt)
REVERT: D   67 TRP cc_start: 0.8401 (t-100) cc_final: 0.8056 (t-100)
REVERT: D   80 TYR cc_start: 0.8915 (t80) cc_final: 0.8606 (t80)
REVERT: D  174 ASN cc_start: 0.8146 (m-40) cc_final: 0.7902 (m-40)
REVERT: A   83 SER cc_start: 0.8232 (p) cc_final: 0.7944 (p)
REVERT: A  206 LYS cc_start: 0.7881 (tttt) cc_final: 0.7490 (tptt)
REVERT: E  191 LYS cc_start: 0.9078 (tmtt) cc_final: 0.8852 (tptp)
REVERT: E  206 LYS cc_start: 0.8039 (tttt) cc_final: 0.7645 (tptp)
REVERT: F  174 ASN cc_start: 0.8330 (m-40) cc_final: 0.8129 (m-40)
REVERT: F  206 LYS cc_start: 0.7922 (tttt) cc_final: 0.7572 (tptt)
REVERT: G   67 TRP cc_start: 0.8692 (t-100) cc_final: 0.8077 (t-100)
REVERT: G  104 MET cc_start: 0.8767 (mtt) cc_final: 0.8523 (mtt)
REVERT: G  135 ILE cc_start: 0.9355 (tp) cc_final: 0.8867 (tp)
REVERT: G  191 LYS cc_start: 0.8833 (tptp) cc_final: 0.8600 (tptp)
REVERT: G  206 LYS cc_start: 0.8002 (tttt) cc_final: 0.7660 (tptt)
  outliers start: 0
  outliers final: 0
  residues processed: 237
  average time/residue: 0.1026
  time to fit residues: 35.1052
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  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 140
   random chunks:
   chunk 134 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 77 optimal weight:    6.9990
   chunk 12 optimal weight:    0.0050
   chunk 82 optimal weight:    0.6980
   chunk 42 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 115 optimal weight:    6.9990
   chunk 119 optimal weight:    0.7980
   chunk 49 optimal weight:    4.9990
   chunk 104 optimal weight:    0.9980
   overall best weight:    0.5994

-------------------------------------------------------------------------------
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
E 152 ASN
F  31 HIS
F 152 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.175005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.137145 restraints weight = 18531.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.142118 restraints weight = 13419.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.145209 restraints weight = 10519.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.148515 restraints weight = 8866.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.150709 restraints weight = 7646.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.3892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.336  11884  Z= 0.154
  Angle     :  0.980  16.175  16443  Z= 0.347
  Chirality :  0.043   0.237   1631
  Planarity :  0.006   0.088   2065
  Dihedral  : 15.329  80.123   1659
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.57 %
    Favored  : 92.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 18.18 %
    Cis-general     : 0.00 %
    Twisted Proline : 7.79 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.55 (0.21), residues: 1400
  helix: -1.28 (0.35), residues: 196
  sheet: -2.25 (0.51), residues: 70
  loop : -1.90 (0.18), residues: 1134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 194 
 TYR   0.023   0.002   TYR A  80 
 PHE   0.016   0.001   PHE E 215 
 TRP   0.022   0.003   TRP A  67 
 HIS   0.039   0.002   HIS D 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 (11788)
  covalent geometry    : angle       0.97980 (16443)
  hydrogen bonds       : bond        0.03438 (  154)
  hydrogen bonds       : angle       7.89476 (  336)
  Misc. bond           : bond        0.10087 (   96)

===============================================================================
Job complete
usr+sys time: 1897.68 seconds
wall clock time: 33 minutes 45.34 seconds (2025.34 seconds total)