Starting phenix.real_space_refine
on Wed Jul 30 13:47:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ktq_23026/07_2025/7ktq_23026.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ktq_23026/07_2025/7ktq_23026.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ktq_23026/07_2025/7ktq_23026.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ktq_23026/07_2025/7ktq_23026.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ktq_23026/07_2025/7ktq_23026.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ktq_23026/07_2025/7ktq_23026.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.001
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
     P     331      5.49       5
     S      12      5.16       5
     C    6973      2.51       5
     N    2384      2.21       5
     O    3045      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12745
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 817
          Classifications: {'peptide': 99}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 809
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "D"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "G"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 800
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "H"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 3343
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 3343
          Classifications: {'DNA': 164}
          Link IDs: {'rna3p': 163}
    Chain: "J"
      Number of atoms: 3441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 167, 3441
          Classifications: {'DNA': 167}
          Link IDs: {'rna3p': 166}
  Time building chain proxies: 7.91, per 1000 atoms: 0.62
  Number of scatterers: 12745
  At special positions: 0
  Unit cell: (76.95, 121.5, 147.15, 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)
     S      12     16.00
     P     331     15.00
     O    3045      8.00
     N    2384      7.00
     C    6973      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.13
  Conformation dependent library (CDL) restraints added in 977.8 milliseconds
  

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1408

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 10 sheets defined
      71.0% alpha, 3.2% beta
      117 base pairs and 288 stacking pairs defined.
    Time for finding SS restraints: 5.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.709A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.551A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.559A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 3.652A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.710A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 101 through 120
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.651A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.552A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.559A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 3.674A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.715A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 101 through 120
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.904A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.310A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.173A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.964A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.192A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78

    400 hydrogen bonds defined for protein.
    1200 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      300 hydrogen bonds
      596 hydrogen bond angles
      0 basepair planarities
      117 basepair parallelities
      288 stacking parallelities
  Total time for adding SS restraints: 4.18

  Time building geometry restraints manager: 3.70 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2203
        1.33 -     1.45: 4715
        1.45 -     1.57: 6049
        1.57 -     1.69: 661
        1.69 -     1.80: 22
  Bond restraints: 13650
  Sorted by residual:
  bond pdb=" O5'  DA J  83 "
       pdb=" C5'  DA J  83 "
    ideal  model  delta    sigma   weight residual
    1.423  1.351  0.072 3.00e-02 1.11e+03 5.72e+00
  bond pdb=" C3'  DT J 106 "
       pdb=" O3'  DT J 106 "
    ideal  model  delta    sigma   weight residual
    1.422  1.487 -0.065 3.00e-02 1.11e+03 4.62e+00
  bond pdb=" O5'  DC I  64 "
       pdb=" C5'  DC I  64 "
    ideal  model  delta    sigma   weight residual
    1.423  1.360  0.063 3.00e-02 1.11e+03 4.41e+00
  bond pdb=" O5'  DG J 102 "
       pdb=" C5'  DG J 102 "
    ideal  model  delta    sigma   weight residual
    1.423  1.363  0.060 3.00e-02 1.11e+03 3.99e+00
  bond pdb=" O5'  DT J  17 "
       pdb=" C5'  DT J  17 "
    ideal  model  delta    sigma   weight residual
    1.423  1.366  0.057 3.00e-02 1.11e+03 3.56e+00
  ... (remaining 13645 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.65: 18537
        1.65 -     3.29: 1229
        3.29 -     4.94: 79
        4.94 -     6.58: 16
        6.58 -     8.23: 4
  Bond angle restraints: 19865
  Sorted by residual:
  angle pdb=" C   ARG E  40 "
        pdb=" N   TYR E  41 "
        pdb=" CA  TYR E  41 "
      ideal   model   delta    sigma   weight residual
     122.03  113.80    8.23 2.01e+00 2.48e-01 1.68e+01
  angle pdb=" N   ILE F  26 "
        pdb=" CA  ILE F  26 "
        pdb=" C   ILE F  26 "
      ideal   model   delta    sigma   weight residual
     112.50  107.10    5.40 1.39e+00 5.18e-01 1.51e+01
  angle pdb=" C4'  DC J  82 "
        pdb=" C3'  DC J  82 "
        pdb=" O3'  DC J  82 "
      ideal   model   delta    sigma   weight residual
     110.00  104.27    5.73 1.50e+00 4.44e-01 1.46e+01
  angle pdb=" C3'  DT J 106 "
        pdb=" O3'  DT J 106 "
        pdb=" P    DG J 107 "
      ideal   model   delta    sigma   weight residual
     120.20  125.30   -5.10 1.50e+00 4.44e-01 1.16e+01
  angle pdb=" N   ILE B  26 "
        pdb=" CA  ILE B  26 "
        pdb=" C   ILE B  26 "
      ideal   model   delta    sigma   weight residual
     112.50  107.99    4.51 1.39e+00 5.18e-01 1.05e+01
  ... (remaining 19860 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.95: 5693
       35.95 -    71.89: 1623
       71.89 -   107.84: 21
      107.84 -   143.79: 0
      143.79 -   179.74: 5
  Dihedral angle restraints: 7342
    sinusoidal: 5160
      harmonic: 2182
  Sorted by residual:
  dihedral pdb=" C4'  DC I   3 "
           pdb=" C3'  DC I   3 "
           pdb=" O3'  DC I   3 "
           pdb=" P    DC I   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   39.74 -179.74     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DG I 104 "
           pdb=" C3'  DG I 104 "
           pdb=" O3'  DG I 104 "
           pdb=" P    DC I 105 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   40.45  179.55     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DT J 106 "
           pdb=" C3'  DT J 106 "
           pdb=" O3'  DT J 106 "
           pdb=" P    DG J 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   42.30  177.70     1      3.50e+01 8.16e-04 1.57e+01
  ... (remaining 7339 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1790
       0.059 -    0.118: 418
       0.118 -    0.177: 51
       0.177 -    0.236: 1
       0.236 -    0.295: 2
  Chirality restraints: 2262
  Sorted by residual:
  chirality pdb=" CG  LEU G 115 "
            pdb=" CB  LEU G 115 "
            pdb=" CD1 LEU G 115 "
            pdb=" CD2 LEU G 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.29   -0.30 2.00e-01 2.50e+01 2.18e+00
  chirality pdb=" C1'  DG J  66 "
            pdb=" O4'  DG J  66 "
            pdb=" C2'  DG J  66 "
            pdb=" N9   DG J  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.18    0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" C4'  DA J  83 "
            pdb=" C5'  DA J  83 "
            pdb=" O4'  DA J  83 "
            pdb=" C3'  DA J  83 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.31   -0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 2259 not shown)

  Planarity restraints: 1368
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I 106 "    0.005 2.00e-02 2.50e+03   3.37e-02 2.55e+01
        pdb=" N1   DC I 106 "   -0.025 2.00e-02 2.50e+03
        pdb=" C2   DC I 106 "    0.083 2.00e-02 2.50e+03
        pdb=" O2   DC I 106 "   -0.045 2.00e-02 2.50e+03
        pdb=" N3   DC I 106 "   -0.009 2.00e-02 2.50e+03
        pdb=" C4   DC I 106 "    0.016 2.00e-02 2.50e+03
        pdb=" N4   DC I 106 "   -0.014 2.00e-02 2.50e+03
        pdb=" C5   DC I 106 "   -0.004 2.00e-02 2.50e+03
        pdb=" C6   DC I 106 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  87 "   -0.043 2.00e-02 2.50e+03   2.87e-02 1.86e+01
        pdb=" N1   DC J  87 "    0.068 2.00e-02 2.50e+03
        pdb=" C2   DC J  87 "   -0.027 2.00e-02 2.50e+03
        pdb=" O2   DC J  87 "    0.013 2.00e-02 2.50e+03
        pdb=" N3   DC J  87 "    0.002 2.00e-02 2.50e+03
        pdb=" C4   DC J  87 "   -0.005 2.00e-02 2.50e+03
        pdb=" N4   DC J  87 "   -0.007 2.00e-02 2.50e+03
        pdb=" C5   DC J  87 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6   DC J  87 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS H 106 "   -0.021 2.00e-02 2.50e+03   4.21e-02 1.77e+01
        pdb=" C   HIS H 106 "    0.073 2.00e-02 2.50e+03
        pdb=" O   HIS H 106 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   ALA H 107 "   -0.025 2.00e-02 2.50e+03
  ... (remaining 1365 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1483
        2.74 -     3.28: 10850
        3.28 -     3.82: 24023
        3.82 -     4.36: 29764
        4.36 -     4.90: 41980
  Nonbonded interactions: 108100
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU B  74 "
            pdb=" NH2 ARG D  96 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" OD2 ASP D  65 "
            pdb=" OH  TYR F  98 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" C2'  DA J  20 "
            pdb=" C7   DT J  21 "
     model   vdw
     2.274 3.860
  nonbonded pdb=" OE1 GLU F  74 "
            pdb=" NH2 ARG H  96 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" O6   DG I  44 "
            pdb=" N4   DC J 124 "
     model   vdw
     2.313 3.120
  ... (remaining 108095 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 38 through 133)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 14 through 117)
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.930
  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:          0.500
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     34.290
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
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      :  0.008   0.072  13650  Z= 0.350
  Angle     :  0.840   8.228  19865  Z= 0.523
  Chirality :  0.050   0.295   2262
  Planarity :  0.009   0.043   1368
  Dihedral  : 29.268 179.736   5934
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  5.92 %
    Favored  : 93.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.43 (0.24), residues: 736
  helix: -1.35 (0.18), residues: 532
  sheet:  None (None), residues: 0
  loop : -1.86 (0.34), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.012   0.002   HIS H  46 
 PHE   0.016   0.003   PHE C  25 
 TYR   0.015   0.002   TYR F  98 
 ARG   0.007   0.001   ARG A  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14041 (  700)
  hydrogen bonds       : angle       6.28309 ( 1796)
  covalent geometry    : bond        0.00792 (13650)
  covalent geometry    : angle       0.83954 (19865)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 188
  time to evaluate  : 0.873 
Fit side-chains
REVERT: A   97 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7634 (mt-10)
REVERT: D   30 ARG cc_start: 0.7483 (mtt180) cc_final: 0.7046 (ptm160)
REVERT: D   65 ASP cc_start: 0.8839 (t0) cc_final: 0.8598 (t0)
REVERT: D  113 LYS cc_start: 0.8362 (ttpt) cc_final: 0.8093 (tttp)
REVERT: D  116 THR cc_start: 0.8694 (m) cc_final: 0.8245 (p)
REVERT: D  117 LYS cc_start: 0.8964 (ttmt) cc_final: 0.8656 (ttmt)
REVERT: E   90 MET cc_start: 0.8070 (tpp) cc_final: 0.7567 (mmm)
REVERT: F   35 ARG cc_start: 0.8135 (mtm180) cc_final: 0.7851 (mtm110)
REVERT: G   36 LYS cc_start: 0.8465 (pttp) cc_final: 0.7836 (mmmt)
REVERT: G   75 LYS cc_start: 0.8463 (mttt) cc_final: 0.8194 (mtpt)
REVERT: G   95 LYS cc_start: 0.8683 (tptt) cc_final: 0.8434 (tptt)
REVERT: H   40 LYS cc_start: 0.8557 (mttm) cc_final: 0.8255 (mttt)
REVERT: H   64 ASN cc_start: 0.9031 (m-40) cc_final: 0.8809 (m-40)
REVERT: H  117 LYS cc_start: 0.8649 (ttmt) cc_final: 0.8436 (tppt)
  outliers start: 1
  outliers final: 0
  residues processed: 189
  average time/residue: 0.4307
  time to fit residues: 101.4371
Evaluate side-chains
  134 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 86 optimal weight:   10.0000
   chunk 77 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 79 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 59 optimal weight:    0.6980
   chunk 92 optimal weight:    2.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  25 ASN
B  93 GLN
D  81 ASN
F  27 GLN
G  38 ASN
G 110 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.154775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.104334 restraints weight = 17646.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3102 rms_B_bonded: 1.18
r_work: 0.2933 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2800 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.1821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13650  Z= 0.192
  Angle     :  0.570   5.421  19865  Z= 0.342
  Chirality :  0.034   0.170   2262
  Planarity :  0.005   0.045   1368
  Dihedral  : 32.481 178.973   4452
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.36 %
    Favored  : 98.64 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  :  8.64 %
    Favored  : 89.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.29), residues: 736
  helix:  1.41 (0.21), residues: 540
  sheet:  None (None), residues: 0
  loop : -1.22 (0.37), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.006   0.001   HIS D  46 
 PHE   0.010   0.002   PHE C  25 
 TYR   0.008   0.001   TYR D  34 
 ARG   0.005   0.001   ARG C  42 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05403 (  700)
  hydrogen bonds       : angle       3.08675 ( 1796)
  covalent geometry    : bond        0.00428 (13650)
  covalent geometry    : angle       0.56952 (19865)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 135
  time to evaluate  : 0.957 
Fit side-chains
REVERT: D   30 ARG cc_start: 0.7633 (mtt180) cc_final: 0.6880 (ptm160)
REVERT: D   37 TYR cc_start: 0.9249 (m-80) cc_final: 0.8958 (m-80)
REVERT: D   65 ASP cc_start: 0.9181 (t0) cc_final: 0.8960 (t0)
REVERT: D   80 TYR cc_start: 0.8615 (m-10) cc_final: 0.7760 (m-10)
REVERT: D  113 LYS cc_start: 0.8920 (ttpt) cc_final: 0.8577 (tttp)
REVERT: D  116 THR cc_start: 0.8763 (m) cc_final: 0.8209 (p)
REVERT: D  117 LYS cc_start: 0.8874 (ttmt) cc_final: 0.8635 (ttmt)
REVERT: E   90 MET cc_start: 0.8846 (tpp) cc_final: 0.8631 (mmm)
REVERT: E  120 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8083 (mtp)
REVERT: F   35 ARG cc_start: 0.8867 (mtm180) cc_final: 0.8470 (mtm110)
REVERT: F   68 ASP cc_start: 0.9411 (m-30) cc_final: 0.9057 (m-30)
REVERT: G   35 ARG cc_start: 0.8183 (mtp-110) cc_final: 0.7917 (mtm110)
REVERT: G   36 LYS cc_start: 0.8723 (pttp) cc_final: 0.8079 (mmmt)
REVERT: G   75 LYS cc_start: 0.8510 (mttt) cc_final: 0.8253 (mtpt)
REVERT: G   95 LYS cc_start: 0.9091 (tptt) cc_final: 0.8840 (tptt)
REVERT: G  110 ASN cc_start: 0.8544 (t0) cc_final: 0.8231 (t0)
REVERT: H   39 TYR cc_start: 0.8506 (t80) cc_final: 0.7729 (t80)
  outliers start: 9
  outliers final: 5
  residues processed: 138
  average time/residue: 0.3224
  time to fit residues: 59.6370
Evaluate side-chains
  126 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 120
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 100 optimal weight:    5.9990
   chunk 3 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   chunk 44 optimal weight:    0.3980
   chunk 4 optimal weight:    0.7980
   chunk 76 optimal weight:    2.9990
   chunk 27 optimal weight:    0.2980
   chunk 39 optimal weight:    1.9990
   chunk 16 optimal weight:    8.9990
   chunk 75 optimal weight:    3.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
B  93 GLN
F  93 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.154619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.104556 restraints weight = 17761.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 1.13
r_work: 0.2995 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2860 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8520
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  13650  Z= 0.172
  Angle     :  0.529   5.440  19865  Z= 0.321
  Chirality :  0.032   0.135   2262
  Planarity :  0.004   0.041   1368
  Dihedral  : 31.845 178.522   4452
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.49 %
    Favored  : 98.51 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  :  9.12 %
    Favored  : 89.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.30), residues: 736
  helix:  2.36 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -1.01 (0.39), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS D  46 
 PHE   0.010   0.002   PHE F 100 
 TYR   0.008   0.001   TYR G  57 
 ARG   0.004   0.000   ARG A  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04800 (  700)
  hydrogen bonds       : angle       2.89321 ( 1796)
  covalent geometry    : bond        0.00381 (13650)
  covalent geometry    : angle       0.52883 (19865)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 138
  time to evaluate  : 1.014 
Fit side-chains
REVERT: B   26 ILE cc_start: 0.9103 (tp) cc_final: 0.8854 (tp)
REVERT: D   30 ARG cc_start: 0.7857 (mtt180) cc_final: 0.6981 (ptp-170)
REVERT: D   37 TYR cc_start: 0.9272 (m-80) cc_final: 0.9001 (m-80)
REVERT: D   65 ASP cc_start: 0.9169 (t0) cc_final: 0.8902 (t0)
REVERT: D  113 LYS cc_start: 0.8878 (ttpt) cc_final: 0.8494 (tttp)
REVERT: D  116 THR cc_start: 0.8853 (m) cc_final: 0.8241 (p)
REVERT: E   90 MET cc_start: 0.8788 (tpp) cc_final: 0.8555 (mmm)
REVERT: E  129 ARG cc_start: 0.8332 (tpt90) cc_final: 0.7940 (tpt90)
REVERT: F   35 ARG cc_start: 0.8825 (mtm180) cc_final: 0.8445 (mtm110)
REVERT: G   35 ARG cc_start: 0.8212 (mtp-110) cc_final: 0.7984 (mtm110)
REVERT: G   36 LYS cc_start: 0.8621 (pttp) cc_final: 0.8142 (mmmt)
REVERT: G   38 ASN cc_start: 0.8757 (OUTLIER) cc_final: 0.8352 (m110)
REVERT: G   95 LYS cc_start: 0.9020 (tptt) cc_final: 0.8747 (tptt)
REVERT: G  110 ASN cc_start: 0.8588 (t0) cc_final: 0.8293 (t0)
REVERT: H   39 TYR cc_start: 0.8643 (t80) cc_final: 0.7656 (t80)
  outliers start: 11
  outliers final: 6
  residues processed: 142
  average time/residue: 0.3566
  time to fit residues: 66.4254
Evaluate side-chains
  133 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 126
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 70 optimal weight:    9.9990
   chunk 14 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 85 optimal weight:    5.9990
   chunk 94 optimal weight:    2.9990
   chunk 73 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
H  81 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.152363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.102700 restraints weight = 17714.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 1.02
r_work: 0.2954 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2825 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13650  Z= 0.198
  Angle     :  0.550   5.467  19865  Z= 0.330
  Chirality :  0.033   0.147   2262
  Planarity :  0.004   0.041   1368
  Dihedral  : 31.868 178.867   4452
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 4.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 11.52 %
    Favored  : 87.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.53 (0.30), residues: 736
  helix:  2.55 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -1.00 (0.40), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS D  46 
 PHE   0.009   0.002   PHE C  25 
 TYR   0.014   0.001   TYR F  51 
 ARG   0.005   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05140 (  700)
  hydrogen bonds       : angle       2.92802 ( 1796)
  covalent geometry    : bond        0.00450 (13650)
  covalent geometry    : angle       0.55020 (19865)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 0.926 
Fit side-chains
REVERT: A   76 GLN cc_start: 0.8490 (tt0) cc_final: 0.8236 (tt0)
REVERT: B   26 ILE cc_start: 0.9117 (tp) cc_final: 0.8911 (tp)
REVERT: D   30 ARG cc_start: 0.7804 (mtt180) cc_final: 0.6957 (ptp-170)
REVERT: D   37 TYR cc_start: 0.9285 (m-80) cc_final: 0.9050 (m-80)
REVERT: D   65 ASP cc_start: 0.9138 (t0) cc_final: 0.8891 (t0)
REVERT: E   90 MET cc_start: 0.8746 (tpp) cc_final: 0.8482 (mmm)
REVERT: E  122 LYS cc_start: 0.8465 (mtmt) cc_final: 0.8180 (mtmt)
REVERT: E  129 ARG cc_start: 0.8485 (tpt90) cc_final: 0.8067 (tpt90)
REVERT: F   35 ARG cc_start: 0.8840 (mmm160) cc_final: 0.8464 (mtm110)
REVERT: G   35 ARG cc_start: 0.8183 (mtp-110) cc_final: 0.7938 (mtm110)
REVERT: G   36 LYS cc_start: 0.8515 (pttp) cc_final: 0.8110 (mmmt)
REVERT: H   31 LYS cc_start: 0.8424 (ttpt) cc_final: 0.8214 (ttpt)
REVERT: H   39 TYR cc_start: 0.8839 (t80) cc_final: 0.8467 (t80)
  outliers start: 9
  outliers final: 7
  residues processed: 132
  average time/residue: 0.3525
  time to fit residues: 61.4966
Evaluate side-chains
  132 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 125
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain D residue   49 THR
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 73 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 52 optimal weight:    0.7980
   chunk 62 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   chunk 11 optimal weight:    0.7980
   chunk 61 optimal weight:    0.3980
   chunk 36 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
D  46 HIS
F  93 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.153250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.103713 restraints weight = 17752.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 1.03
r_work: 0.2981 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2854 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8553
moved from start:          0.2857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13650  Z= 0.153
  Angle     :  0.525   5.410  19865  Z= 0.319
  Chirality :  0.032   0.138   2262
  Planarity :  0.004   0.037   1368
  Dihedral  : 31.819 178.768   4452
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.68 %
    Favored  : 86.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.85 (0.31), residues: 736
  helix:  2.80 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.93 (0.40), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D  46 
 PHE   0.011   0.001   PHE A  78 
 TYR   0.012   0.001   TYR F  88 
 ARG   0.006   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04831 (  700)
  hydrogen bonds       : angle       2.86914 ( 1796)
  covalent geometry    : bond        0.00334 (13650)
  covalent geometry    : angle       0.52528 (19865)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.955 
Fit side-chains
REVERT: A   76 GLN cc_start: 0.8433 (tt0) cc_final: 0.8175 (tt0)
REVERT: B   26 ILE cc_start: 0.9117 (tp) cc_final: 0.8885 (tp)
REVERT: B   88 TYR cc_start: 0.9072 (m-10) cc_final: 0.8468 (m-80)
REVERT: D   30 ARG cc_start: 0.7806 (mtt180) cc_final: 0.7065 (ptp-170)
REVERT: D   37 TYR cc_start: 0.9255 (m-80) cc_final: 0.8991 (m-80)
REVERT: D   65 ASP cc_start: 0.9105 (t0) cc_final: 0.8873 (t0)
REVERT: E   90 MET cc_start: 0.8724 (tpp) cc_final: 0.8469 (mmm)
REVERT: E  129 ARG cc_start: 0.8480 (tpt90) cc_final: 0.8075 (tpt90)
REVERT: F   35 ARG cc_start: 0.8816 (mmm160) cc_final: 0.8468 (mtm110)
REVERT: G   35 ARG cc_start: 0.8175 (mtp-110) cc_final: 0.7931 (mtm110)
REVERT: G   36 LYS cc_start: 0.8504 (pttp) cc_final: 0.8162 (mmmt)
REVERT: G   38 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8327 (m110)
REVERT: H   39 TYR cc_start: 0.8823 (t80) cc_final: 0.8455 (t80)
  outliers start: 10
  outliers final: 8
  residues processed: 131
  average time/residue: 0.4278
  time to fit residues: 74.1491
Evaluate side-chains
  134 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 125
  time to evaluate  : 1.091 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 36 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 43 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 44 optimal weight:    0.2980
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
F  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.153467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.103869 restraints weight = 18027.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 1.03
r_work: 0.2984 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2856 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.2895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  13650  Z= 0.158
  Angle     :  0.519   5.355  19865  Z= 0.315
  Chirality :  0.032   0.140   2262
  Planarity :  0.004   0.036   1368
  Dihedral  : 31.750 178.701   4452
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.00 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.96 (0.31), residues: 736
  helix:  2.89 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.89 (0.41), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.002   0.001   HIS E  39 
 PHE   0.007   0.001   PHE A  78 
 TYR   0.011   0.001   TYR F  51 
 ARG   0.007   0.001   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04713 (  700)
  hydrogen bonds       : angle       2.82860 ( 1796)
  covalent geometry    : bond        0.00345 (13650)
  covalent geometry    : angle       0.51893 (19865)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 0.939 
Fit side-chains
REVERT: A   76 GLN cc_start: 0.8433 (tt0) cc_final: 0.8187 (tt0)
REVERT: B   26 ILE cc_start: 0.9090 (tp) cc_final: 0.8853 (tp)
REVERT: B   88 TYR cc_start: 0.9078 (m-10) cc_final: 0.8467 (m-80)
REVERT: D   30 ARG cc_start: 0.7873 (mtt180) cc_final: 0.6887 (ptp-170)
REVERT: D   37 TYR cc_start: 0.9249 (m-80) cc_final: 0.8991 (m-80)
REVERT: D   65 ASP cc_start: 0.9098 (t0) cc_final: 0.8874 (t0)
REVERT: E   90 MET cc_start: 0.8716 (tpp) cc_final: 0.8471 (mmm)
REVERT: E  129 ARG cc_start: 0.8488 (tpt90) cc_final: 0.8092 (tpt90)
REVERT: F   35 ARG cc_start: 0.8814 (mmm160) cc_final: 0.8462 (mtm110)
REVERT: G   35 ARG cc_start: 0.8190 (mtp-110) cc_final: 0.7943 (mtm110)
REVERT: G   36 LYS cc_start: 0.8476 (pttp) cc_final: 0.8134 (mmmt)
REVERT: G   38 ASN cc_start: 0.8722 (OUTLIER) cc_final: 0.8325 (m110)
REVERT: H   39 TYR cc_start: 0.8832 (t80) cc_final: 0.8445 (t80)
  outliers start: 9
  outliers final: 7
  residues processed: 132
  average time/residue: 0.3592
  time to fit residues: 62.7438
Evaluate side-chains
  131 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 123
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 101 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 0 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 48 optimal weight:    0.5980
   chunk 77 optimal weight:    2.9990
   chunk 55 optimal weight:    2.9990
   chunk 86 optimal weight:   10.0000
   chunk 89 optimal weight:    4.9990
   chunk 4 optimal weight:    0.4980
   overall best weight:    1.1782

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
D  92 GLN
F  93 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.151923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.102275 restraints weight = 17663.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 1.01
r_work: 0.2959 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2833 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.3104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  13650  Z= 0.202
  Angle     :  0.545   5.406  19865  Z= 0.328
  Chirality :  0.034   0.138   2262
  Planarity :  0.004   0.034   1368
  Dihedral  : 31.706 179.070   4452
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 5.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 12.00 %
    Favored  : 86.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.81 (0.31), residues: 736
  helix:  2.77 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.92 (0.41), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS D  46 
 PHE   0.007   0.001   PHE D  62 
 TYR   0.016   0.001   TYR F  51 
 ARG   0.006   0.001   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05124 (  700)
  hydrogen bonds       : angle       2.91520 ( 1796)
  covalent geometry    : bond        0.00460 (13650)
  covalent geometry    : angle       0.54540 (19865)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 124
  time to evaluate  : 0.869 
Fit side-chains
REVERT: A   76 GLN cc_start: 0.8409 (tt0) cc_final: 0.8161 (tt0)
REVERT: B   26 ILE cc_start: 0.9173 (tp) cc_final: 0.8957 (tp)
REVERT: D   30 ARG cc_start: 0.7968 (mtt180) cc_final: 0.6988 (ptp-170)
REVERT: D   37 TYR cc_start: 0.9239 (m-80) cc_final: 0.9002 (m-80)
REVERT: E   90 MET cc_start: 0.8762 (tpp) cc_final: 0.8504 (mmm)
REVERT: E  129 ARG cc_start: 0.8558 (tpt90) cc_final: 0.8180 (tpt90)
REVERT: F   35 ARG cc_start: 0.8853 (mmm160) cc_final: 0.8487 (mtm110)
REVERT: G   35 ARG cc_start: 0.8171 (mtp-110) cc_final: 0.7911 (mtm110)
REVERT: G   36 LYS cc_start: 0.8534 (pttp) cc_final: 0.8176 (mmmt)
REVERT: G   73 ASN cc_start: 0.8795 (t0) cc_final: 0.8574 (t0)
REVERT: H   39 TYR cc_start: 0.8914 (t80) cc_final: 0.8416 (t80)
  outliers start: 9
  outliers final: 9
  residues processed: 128
  average time/residue: 0.3359
  time to fit residues: 56.5774
Evaluate side-chains
  129 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 98 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 80 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 88 optimal weight:    3.9990
   overall best weight:    1.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
B  93 GLN
F  93 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.150190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.100469 restraints weight = 17986.321|
|-----------------------------------------------------------------------------|
r_work (start): 0.3091 rms_B_bonded: 1.03
r_work: 0.2927 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2799 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.3388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  13650  Z= 0.237
  Angle     :  0.575   5.555  19865  Z= 0.343
  Chirality :  0.035   0.133   2262
  Planarity :  0.004   0.034   1368
  Dihedral  : 31.861 179.970   4452
  Min Nonbonded Distance : 2.123

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 12.00 %
    Favored  : 86.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.58 (0.31), residues: 736
  helix:  2.61 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -1.07 (0.41), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H  46 
 PHE   0.010   0.002   PHE D  62 
 TYR   0.015   0.002   TYR F  51 
 ARG   0.004   0.001   ARG A  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05570 (  700)
  hydrogen bonds       : angle       3.01742 ( 1796)
  covalent geometry    : bond        0.00548 (13650)
  covalent geometry    : angle       0.57524 (19865)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 125
  time to evaluate  : 0.956 
Fit side-chains
REVERT: D   30 ARG cc_start: 0.8018 (mtt180) cc_final: 0.7291 (ptm-80)
REVERT: E   90 MET cc_start: 0.8835 (tpp) cc_final: 0.8534 (mmm)
REVERT: E  129 ARG cc_start: 0.8605 (tpt90) cc_final: 0.8239 (tpt90)
REVERT: F   35 ARG cc_start: 0.8842 (mmm160) cc_final: 0.8454 (mtm110)
REVERT: G   35 ARG cc_start: 0.8143 (mtp-110) cc_final: 0.7877 (mtm110)
REVERT: G   36 LYS cc_start: 0.8526 (pttp) cc_final: 0.8130 (mmmt)
  outliers start: 11
  outliers final: 9
  residues processed: 129
  average time/residue: 0.3598
  time to fit residues: 61.0222
Evaluate side-chains
  129 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.894 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain E residue  122 LYS
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 26 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   chunk 84 optimal weight:    5.9990
   chunk 10 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 53 optimal weight:    0.5980
   chunk 90 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0010
   chunk 28 optimal weight:    0.6980
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.5386

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
F  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.151834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.102600 restraints weight = 17794.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 1.01
r_work: 0.2963 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2837 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.3415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13650  Z= 0.150
  Angle     :  0.543   8.417  19865  Z= 0.328
  Chirality :  0.033   0.134   2262
  Planarity :  0.005   0.101   1368
  Dihedral  : 31.805 179.818   4452
  Min Nonbonded Distance : 2.113

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 12.16 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.79 (0.31), residues: 736
  helix:  2.77 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.99 (0.41), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.007   0.001   PHE A  67 
 TYR   0.031   0.002   TYR F  88 
 ARG   0.007   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05030 (  700)
  hydrogen bonds       : angle       2.92607 ( 1796)
  covalent geometry    : bond        0.00323 (13650)
  covalent geometry    : angle       0.54335 (19865)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 128
  time to evaluate  : 0.882 
Fit side-chains
REVERT: D   30 ARG cc_start: 0.8032 (mtt180) cc_final: 0.7269 (ptm-80)
REVERT: E   90 MET cc_start: 0.8773 (tpp) cc_final: 0.8478 (mmm)
REVERT: E  129 ARG cc_start: 0.8575 (tpt90) cc_final: 0.8226 (tpt90)
REVERT: F   35 ARG cc_start: 0.8812 (mmm160) cc_final: 0.8471 (mtm110)
REVERT: G   35 ARG cc_start: 0.8147 (mtp-110) cc_final: 0.7891 (mtm110)
REVERT: G   36 LYS cc_start: 0.8505 (pttp) cc_final: 0.8160 (mmmt)
REVERT: G   38 ASN cc_start: 0.8831 (OUTLIER) cc_final: 0.8417 (m110)
  outliers start: 11
  outliers final: 9
  residues processed: 132
  average time/residue: 0.3414
  time to fit residues: 59.5342
Evaluate side-chains
  134 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 0.869 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 18 optimal weight:    0.7980
   chunk 90 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 88 optimal weight:    4.9990
   chunk 93 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 43 optimal weight:    0.4980
   chunk 100 optimal weight:    5.9990
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
F  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.151834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.102696 restraints weight = 17783.934|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 0.99
r_work: 0.2964 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.3445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13650  Z= 0.170
  Angle     :  0.536   5.330  19865  Z= 0.324
  Chirality :  0.032   0.131   2262
  Planarity :  0.004   0.034   1368
  Dihedral  : 31.687 179.730   4452
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 5.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 12.16 %
    Favored  : 86.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.88 (0.31), residues: 736
  helix:  2.82 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.89 (0.42), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS B  75 
 PHE   0.007   0.001   PHE D  62 
 TYR   0.021   0.002   TYR F  88 
 ARG   0.007   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04911 (  700)
  hydrogen bonds       : angle       2.90266 ( 1796)
  covalent geometry    : bond        0.00378 (13650)
  covalent geometry    : angle       0.53630 (19865)

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

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

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1472 Ramachandran restraints generated.
    736 Oldfield, 0 Emsley, 736 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 124
  time to evaluate  : 1.042 
Fit side-chains
REVERT: D   30 ARG cc_start: 0.7967 (mtt180) cc_final: 0.7213 (ptm-80)
REVERT: E   90 MET cc_start: 0.8764 (tpp) cc_final: 0.8479 (mmm)
REVERT: E  129 ARG cc_start: 0.8591 (tpt90) cc_final: 0.8245 (tpt90)
REVERT: F   35 ARG cc_start: 0.8802 (mmm160) cc_final: 0.8462 (mtm110)
REVERT: G   35 ARG cc_start: 0.8141 (mtp-110) cc_final: 0.7879 (mtm110)
REVERT: G   36 LYS cc_start: 0.8560 (pttp) cc_final: 0.8243 (mmmt)
REVERT: G   38 ASN cc_start: 0.8793 (OUTLIER) cc_final: 0.8361 (m110)
  outliers start: 10
  outliers final: 9
  residues processed: 128
  average time/residue: 0.3449
  time to fit residues: 58.2816
Evaluate side-chains
  131 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 121
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue   80 THR
Chi-restraints excluded: chain C residue  110 ASN
Chi-restraints excluded: chain D residue   33 SER
Chi-restraints excluded: chain E residue   58 THR
Chi-restraints excluded: chain G residue   38 ASN
Chi-restraints excluded: chain G residue  100 VAL
Chi-restraints excluded: chain H residue   48 ASP
Chi-restraints excluded: chain H residue  119 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 102
   random chunks:
   chunk 76 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 50 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 83 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 73 optimal weight:    5.9990
   chunk 63 optimal weight:    0.0980
   chunk 4 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
F  93 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.152052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.101489 restraints weight = 17908.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 1.17
r_work: 0.2944 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2810 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.3498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  13650  Z= 0.181
  Angle     :  0.536   5.440  19865  Z= 0.323
  Chirality :  0.033   0.133   2262
  Planarity :  0.004   0.035   1368
  Dihedral  : 31.545 179.798   4452
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 12.16 %
    Favored  : 85.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.89 (0.31), residues: 736
  helix:  2.83 (0.22), residues: 543
  sheet:  None (None), residues: 0
  loop : -0.89 (0.41), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H  46 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.020   0.002   TYR F  88 
 ARG   0.007   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04861 (  700)
  hydrogen bonds       : angle       2.88140 ( 1796)
  covalent geometry    : bond        0.00408 (13650)
  covalent geometry    : angle       0.53606 (19865)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7374.68 seconds
wall clock time: 127 minutes 25.22 seconds (7645.22 seconds total)