Starting phenix.real_space_refine
on Sat Oct 11 04:18:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8kb5_37070/10_2025/8kb5_37070.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8kb5_37070/10_2025/8kb5_37070.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.26133
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8kb5_37070/10_2025/8kb5_37070.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8kb5_37070/10_2025/8kb5_37070.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8kb5_37070/10_2025/8kb5_37070.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8kb5_37070/10_2025/8kb5_37070.cif"
  }
  resolution = 2.26133
  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
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     288      5.49       5
     S      10      5.16       5
     C    6610      2.51       5
     N    2249      2.21       5
     O    2796      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 85 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11953
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 835
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "E"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 835
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 835
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 719
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 719
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    Chain: "I"
      Number of atoms: 2970
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2970
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2969
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2969
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 2.43, per 1000 atoms: 0.20
  Number of scatterers: 11953
  At special positions: 0
  Unit cell: (117.66, 96.46, 118.72, 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      10     16.00
     P     288     15.00
     O    2796      8.00
     N    2249      7.00
     C    6610      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: 0.90
  Conformation dependent library (CDL) restraints added in 319.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 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:
      36 helices and 10 sheets defined
      73.1% alpha, 2.9% beta
      144 base pairs and 261 stacking pairs defined.
    Time for finding SS restraints: 1.87
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 4.148A  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 132
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.685A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.501A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.705A  pdb=" N   ALA D 107 " --> pdb=" O   PRO D 103 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.766A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.349A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 104 through 123
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.871A  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 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.125A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (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
      removed outlier: 6.673A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.032A  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: 7.071A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (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

    412 hydrogen bonds defined for protein.
    1212 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      370 hydrogen bonds
      740 hydrogen bond angles
      0 basepair planarities
      144 basepair parallelities
      261 stacking parallelities
  Total time for adding SS restraints: 2.05

  Time building geometry restraints manager: 1.24 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: 2323
        1.33 -     1.46: 4297
        1.46 -     1.58: 5543
        1.58 -     1.70: 577
        1.70 -     1.82: 18
  Bond restraints: 12758
  Sorted by residual:
  bond pdb=" CA  GLN F  93 "
       pdb=" C   GLN F  93 "
    ideal  model  delta    sigma   weight residual
    1.522  1.590 -0.068 1.38e-02 5.25e+03 2.43e+01
  bond pdb=" CZ  ARG A 134 "
       pdb=" NH2 ARG A 134 "
    ideal  model  delta    sigma   weight residual
    1.330  1.281  0.049 1.30e-02 5.92e+03 1.45e+01
  bond pdb=" CZ  ARG G  32 "
       pdb=" NH2 ARG G  32 "
    ideal  model  delta    sigma   weight residual
    1.330  1.289  0.041 1.30e-02 5.92e+03 1.01e+01
  bond pdb=" CZ  ARG C  32 "
       pdb=" NH2 ARG C  32 "
    ideal  model  delta    sigma   weight residual
    1.330  1.289  0.041 1.30e-02 5.92e+03 1.01e+01
  bond pdb=" CZ  ARG B  95 "
       pdb=" NH2 ARG B  95 "
    ideal  model  delta    sigma   weight residual
    1.330  1.289  0.041 1.30e-02 5.92e+03 1.00e+01
  ... (remaining 12753 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.68: 16896
        1.68 -     3.35: 1286
        3.35 -     5.03: 247
        5.03 -     6.71: 42
        6.71 -     8.38: 8
  Bond angle restraints: 18479
  Sorted by residual:
  angle pdb=" N   GLN F  93 "
        pdb=" CA  GLN F  93 "
        pdb=" C   GLN F  93 "
      ideal   model   delta    sigma   weight residual
     113.01  106.29    6.72 1.20e+00 6.94e-01 3.14e+01
  angle pdb=" C   ARG B  92 "
        pdb=" CA  ARG B  92 "
        pdb=" CB  ARG B  92 "
      ideal   model   delta    sigma   weight residual
     110.88  103.22    7.66 1.57e+00 4.06e-01 2.38e+01
  angle pdb=" N   VAL F  87 "
        pdb=" CA  VAL F  87 "
        pdb=" C   VAL F  87 "
      ideal   model   delta    sigma   weight residual
     110.72  105.89    4.83 1.01e+00 9.80e-01 2.28e+01
  angle pdb=" C   HIS A  39 "
        pdb=" N   ARG A  40 "
        pdb=" CA  ARG A  40 "
      ideal   model   delta    sigma   weight residual
     120.82  127.54   -6.72 1.41e+00 5.03e-01 2.27e+01
  angle pdb=" C   ARG A  40 "
        pdb=" N   TYR A  41 "
        pdb=" CA  TYR A  41 "
      ideal   model   delta    sigma   weight residual
     120.87  126.97   -6.10 1.42e+00 4.96e-01 1.85e+01
  ... (remaining 18474 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.62: 4327
       17.62 -    35.24: 1141
       35.24 -    52.86: 1073
       52.86 -    70.48: 343
       70.48 -    88.11: 16
  Dihedral angle restraints: 6900
    sinusoidal: 4712
      harmonic: 2188
  Sorted by residual:
  dihedral pdb=" CA  PHE A  84 "
           pdb=" C   PHE A  84 "
           pdb=" N   GLN A  85 "
           pdb=" CA  GLN A  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.06   18.94     0      5.00e+00 4.00e-02 1.43e+01
  dihedral pdb=" N   GLN A  76 "
           pdb=" C   GLN A  76 "
           pdb=" CA  GLN A  76 "
           pdb=" CB  GLN A  76 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  131.80   -9.00     0      2.50e+00 1.60e-01 1.30e+01
  dihedral pdb=" CA  PHE E  84 "
           pdb=" C   PHE E  84 "
           pdb=" N   GLN E  85 "
           pdb=" CA  GLN E  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.15   17.85     0      5.00e+00 4.00e-02 1.27e+01
  ... (remaining 6897 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.097: 1983
       0.097 -    0.194: 111
       0.194 -    0.291: 7
       0.291 -    0.388: 2
       0.388 -    0.485: 1
  Chirality restraints: 2104
  Sorted by residual:
  chirality pdb=" P    DT I -17 "
            pdb=" OP1  DT I -17 "
            pdb=" OP2  DT I -17 "
            pdb=" O5'  DT I -17 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.83   -0.48 2.00e-01 2.50e+01 5.87e+00
  chirality pdb=" C4'  DC I  49 "
            pdb=" C5'  DC I  49 "
            pdb=" O4'  DC I  49 "
            pdb=" C3'  DC I  49 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.15   -0.38 2.00e-01 2.50e+01 3.57e+00
  chirality pdb=" CA  GLN A  76 "
            pdb=" N   GLN A  76 "
            pdb=" C   GLN A  76 "
            pdb=" CB  GLN A  76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.20    0.32 2.00e-01 2.50e+01 2.49e+00
  ... (remaining 2101 not shown)

  Planarity restraints: 1336
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG J  56 "    0.119 2.00e-02 2.50e+03   6.39e-02 1.22e+02
        pdb=" N9   DG J  56 "    0.033 2.00e-02 2.50e+03
        pdb=" C8   DG J  56 "   -0.095 2.00e-02 2.50e+03
        pdb=" N7   DG J  56 "   -0.092 2.00e-02 2.50e+03
        pdb=" C5   DG J  56 "   -0.010 2.00e-02 2.50e+03
        pdb=" C6   DG J  56 "    0.041 2.00e-02 2.50e+03
        pdb=" O6   DG J  56 "    0.088 2.00e-02 2.50e+03
        pdb=" N1   DG J  56 "    0.030 2.00e-02 2.50e+03
        pdb=" C2   DG J  56 "   -0.022 2.00e-02 2.50e+03
        pdb=" N2   DG J  56 "   -0.069 2.00e-02 2.50e+03
        pdb=" N3   DG J  56 "   -0.019 2.00e-02 2.50e+03
        pdb=" C4   DG J  56 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I -47 "    0.091 2.00e-02 2.50e+03   6.55e-02 1.07e+02
        pdb=" N1   DT I -47 "    0.042 2.00e-02 2.50e+03
        pdb=" C2   DT I -47 "   -0.016 2.00e-02 2.50e+03
        pdb=" O2   DT I -47 "   -0.122 2.00e-02 2.50e+03
        pdb=" N3   DT I -47 "    0.015 2.00e-02 2.50e+03
        pdb=" C4   DT I -47 "    0.026 2.00e-02 2.50e+03
        pdb=" O4   DT I -47 "    0.092 2.00e-02 2.50e+03
        pdb=" C5   DT I -47 "   -0.028 2.00e-02 2.50e+03
        pdb=" C7   DT I -47 "   -0.086 2.00e-02 2.50e+03
        pdb=" C6   DT I -47 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I  59 "    0.120 2.00e-02 2.50e+03   6.05e-02 1.01e+02
        pdb=" N9   DA I  59 "    0.007 2.00e-02 2.50e+03
        pdb=" C8   DA I  59 "   -0.070 2.00e-02 2.50e+03
        pdb=" N7   DA I  59 "   -0.062 2.00e-02 2.50e+03
        pdb=" C5   DA I  59 "   -0.019 2.00e-02 2.50e+03
        pdb=" C6   DA I  59 "    0.017 2.00e-02 2.50e+03
        pdb=" N6   DA I  59 "    0.115 2.00e-02 2.50e+03
        pdb=" N1   DA I  59 "   -0.023 2.00e-02 2.50e+03
        pdb=" C2   DA I  59 "   -0.041 2.00e-02 2.50e+03
        pdb=" N3   DA I  59 "   -0.026 2.00e-02 2.50e+03
        pdb=" C4   DA I  59 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1333 not shown)

  Histogram of nonbonded interaction distances:
        2.38 -     2.88: 3664
        2.88 -     3.39: 10210
        3.39 -     3.89: 24290
        3.89 -     4.40: 27833
        4.40 -     4.90: 37547
  Nonbonded interactions: 103544
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN E 125 "
            pdb=" OE2 GLU F  53 "
     model   vdw
     2.377 3.120
  nonbonded pdb=" O   ALA E 114 "
            pdb=" OG1 THR E 115 "
     model   vdw
     2.400 3.040
  nonbonded pdb=" OG  SER A  57 "
            pdb=" OE1 GLU A  59 "
     model   vdw
     2.457 3.040
  nonbonded pdb=" OG  SER G  18 "
            pdb=" O   PHE G  25 "
     model   vdw
     2.488 3.040
  nonbonded pdb=" OD2 ASP E 106 "
            pdb=" NE  ARG E 131 "
     model   vdw
     2.508 3.120
  ... (remaining 103539 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}
ncs_group {
  reference = (chain 'I' and (resid -72 through -1 or resid 1 through 72))
  selection = (chain 'J' and (resid -72 through -1 or resid 1 through 72))
}

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:             1.540
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.160
  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:7.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
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      :  0.007   0.071  12758  Z= 0.369
  Angle     :  0.975   8.383  18479  Z= 0.624
  Chirality :  0.049   0.485   2104
  Planarity :  0.013   0.111   1336
  Dihedral  : 28.085  88.105   5492
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 10.67 %
    Favored  : 89.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  2.15 (0.29), residues: 742
  helix:  1.97 (0.21), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.07 (0.39), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B  92 
 TYR   0.110   0.004   TYR F  51 
 PHE   0.029   0.003   PHE F 100 
 HIS   0.020   0.003   HIS E  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00674 (12758)
  covalent geometry    : angle       0.97520 (18479)
  hydrogen bonds       : bond        0.11620 (  782)
  hydrogen bonds       : angle       3.68069 ( 1952)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.300 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.8294 (tp30) cc_final: 0.8077 (tp30)
REVERT: C   99 ARG cc_start: 0.7357 (mmt180) cc_final: 0.7056 (mmm160)
REVERT: D   36 SER cc_start: 0.8427 (p) cc_final: 0.8202 (p)
REVERT: D   46 LYS cc_start: 0.8907 (mmpt) cc_final: 0.8586 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 1.0145
  time to fit residues: 168.4450
Evaluate side-chains
  148 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:    8.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
C 112 GLN
D  63 ASN
D  84 ASN
F  93 GLN
G  24 GLN
H  47 GLN
H  84 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.165344 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.125548 restraints weight = 10069.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 0.95
r_work: 0.3234 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.0804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029  12758  Z= 0.212
  Angle     :  0.613   8.147  18479  Z= 0.373
  Chirality :  0.038   0.195   2104
  Planarity :  0.005   0.042   1336
  Dihedral  : 30.464  73.918   4006
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 2.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 13.22 %
    Favored  : 85.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  2.68 (0.30), residues: 742
  helix:  2.36 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop :  0.02 (0.41), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  92 
 TYR   0.014   0.002   TYR F  51 
 PHE   0.013   0.002   PHE E  67 
 HIS   0.006   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 (12758)
  covalent geometry    : angle       0.61263 (18479)
  hydrogen bonds       : bond        0.05612 (  782)
  hydrogen bonds       : angle       3.01207 ( 1952)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 157
  time to evaluate  : 0.346 
Fit side-chains
REVERT: C   61 GLU cc_start: 0.8179 (tp30) cc_final: 0.7960 (tp30)
REVERT: C   71 ARG cc_start: 0.7205 (ttm110) cc_final: 0.6968 (ttp80)
REVERT: C   99 ARG cc_start: 0.7694 (mmt180) cc_final: 0.7194 (mmm160)
REVERT: G   15 LYS cc_start: 0.8014 (mtpm) cc_final: 0.7631 (mtmt)
  outliers start: 9
  outliers final: 4
  residues processed: 160
  average time/residue: 1.1230
  time to fit residues: 187.5825
Evaluate side-chains
  158 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 154
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain H residue   51 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 42 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 89 optimal weight:    4.9990
   chunk 35 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 23 optimal weight:    6.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
B  25 ASN
D  63 ASN
D  84 ASN
G  24 GLN
G 104 GLN
H  47 GLN
H  84 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.166558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.127041 restraints weight = 10126.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 0.96
r_work: 0.3235 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3063 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.1005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  12758  Z= 0.193
  Angle     :  0.584   7.921  18479  Z= 0.357
  Chirality :  0.036   0.159   2104
  Planarity :  0.005   0.051   1336
  Dihedral  : 30.352  73.730   4006
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 14.81 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  2.88 (0.30), residues: 742
  helix:  2.52 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop :  0.04 (0.41), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  92 
 TYR   0.013   0.002   TYR F  51 
 PHE   0.013   0.002   PHE E  67 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00413 (12758)
  covalent geometry    : angle       0.58422 (18479)
  hydrogen bonds       : bond        0.05191 (  782)
  hydrogen bonds       : angle       2.91954 ( 1952)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 157
  time to evaluate  : 0.334 
Fit side-chains
REVERT: C   71 ARG cc_start: 0.7206 (ttm110) cc_final: 0.6969 (ttp80)
REVERT: C   99 ARG cc_start: 0.7871 (mmt180) cc_final: 0.7376 (mmm160)
REVERT: F   79 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8770 (mtmt)
REVERT: F   92 ARG cc_start: 0.8213 (mmm160) cc_final: 0.7770 (mtp85)
REVERT: G   15 LYS cc_start: 0.8074 (mtpm) cc_final: 0.7688 (mtmt)
  outliers start: 9
  outliers final: 4
  residues processed: 159
  average time/residue: 1.0645
  time to fit residues: 176.9666
Evaluate side-chains
  156 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 151
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain F residue   79 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 72 optimal weight:   20.0000
   chunk 11 optimal weight:    3.9990
   chunk 16 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 85 optimal weight:    8.9990
   chunk 37 optimal weight:    0.7980
   chunk 73 optimal weight:   10.0000
   chunk 95 optimal weight:    3.9990
   chunk 98 optimal weight:    7.9990
   chunk 80 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   overall best weight:    2.3186

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
C 104 GLN
D  63 ASN
D  84 ASN
G  24 GLN
G 104 GLN
H  47 GLN
H  84 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.163834 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.122977 restraints weight = 10093.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 0.90
r_work: 0.3227 rms_B_bonded: 1.89 restraints_weight: 0.5000
r_work: 0.3060 rms_B_bonded: 2.98 restraints_weight: 0.2500
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.0996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.038  12758  Z= 0.267
  Angle     :  0.656   9.046  18479  Z= 0.393
  Chirality :  0.041   0.179   2104
  Planarity :  0.006   0.045   1336
  Dihedral  : 30.680  73.717   4006
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 13.69 %
    Favored  : 83.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.52 (0.29), residues: 742
  helix:  2.24 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.04 (0.41), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  79 
 TYR   0.015   0.003   TYR F  51 
 PHE   0.015   0.002   PHE E  67 
 HIS   0.006   0.002   HIS A 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00588 (12758)
  covalent geometry    : angle       0.65604 (18479)
  hydrogen bonds       : bond        0.06336 (  782)
  hydrogen bonds       : angle       3.05778 ( 1952)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 154
  time to evaluate  : 0.288 
Fit side-chains
REVERT: C   99 ARG cc_start: 0.7844 (mmt180) cc_final: 0.7322 (mmm160)
REVERT: D   47 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8362 (tt0)
REVERT: E   59 GLU cc_start: 0.8499 (pm20) cc_final: 0.7948 (pm20)
REVERT: F   79 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8714 (mtmm)
REVERT: G   15 LYS cc_start: 0.8058 (mtpm) cc_final: 0.7625 (mtmt)
  outliers start: 15
  outliers final: 6
  residues processed: 158
  average time/residue: 1.0067
  time to fit residues: 166.2095
Evaluate side-chains
  159 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 151
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain D residue   47 GLN
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain H residue   46 LYS
Chi-restraints excluded: chain H residue  112 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 17 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   chunk 4 optimal weight:    0.0770
   chunk 54 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 72 optimal weight:   20.0000
   chunk 15 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.7138

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

Flipped N/Q/H residues before XYZ refinement:
C 112 GLN
D  63 ASN
D  84 ASN
G  24 GLN
G 104 GLN
H  47 GLN
H  82 HIS
H  84 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.166569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.126039 restraints weight = 10052.855|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 0.91
r_work: 0.3260 rms_B_bonded: 1.92 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.1016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12758  Z= 0.171
  Angle     :  0.593   7.865  18479  Z= 0.362
  Chirality :  0.036   0.164   2104
  Planarity :  0.005   0.089   1336
  Dihedral  : 30.639  73.645   4006
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 3.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 14.33 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  2.77 (0.30), residues: 742
  helix:  2.45 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.04 (0.41), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  79 
 TYR   0.014   0.002   TYR D  83 
 PHE   0.013   0.001   PHE E  67 
 HIS   0.004   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (12758)
  covalent geometry    : angle       0.59335 (18479)
  hydrogen bonds       : bond        0.05159 (  782)
  hydrogen bonds       : angle       3.01932 ( 1952)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 155
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   99 ARG cc_start: 0.7750 (mmt180) cc_final: 0.7159 (mmm160)
REVERT: E   59 GLU cc_start: 0.8460 (pm20) cc_final: 0.7876 (pm20)
REVERT: F   79 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8707 (mtmm)
REVERT: G   15 LYS cc_start: 0.7998 (mtpm) cc_final: 0.7586 (mtmt)
REVERT: G   77 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7611 (mtp180)
  outliers start: 14
  outliers final: 6
  residues processed: 160
  average time/residue: 1.0095
  time to fit residues: 169.0090
Evaluate side-chains
  160 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 152
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain F residue   63 GLU
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain G residue   77 ARG
Chi-restraints excluded: chain H residue  112 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 32 optimal weight:    6.9990
   chunk 28 optimal weight:    4.9990
   chunk 52 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 80 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    1.9990
   chunk 87 optimal weight:    7.9990
   chunk 97 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
D  63 ASN
D  84 ASN
G 104 GLN
H  47 GLN
H  82 HIS
H  84 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.166927 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.126363 restraints weight = 10124.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 0.91
r_work: 0.3264 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3100 rms_B_bonded: 3.01 restraints_weight: 0.2500
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.1107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025  12758  Z= 0.180
  Angle     :  0.578   7.377  18479  Z= 0.353
  Chirality :  0.036   0.160   2104
  Planarity :  0.004   0.041   1336
  Dihedral  : 30.464  73.454   4006
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 3.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.49 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  2.89 (0.30), residues: 742
  helix:  2.54 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop :  0.02 (0.42), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  79 
 TYR   0.013   0.002   TYR F  88 
 PHE   0.013   0.002   PHE E  67 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (12758)
  covalent geometry    : angle       0.57788 (18479)
  hydrogen bonds       : bond        0.05025 (  782)
  hydrogen bonds       : angle       2.90409 ( 1952)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 152
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A   39 HIS cc_start: 0.5675 (OUTLIER) cc_final: 0.5103 (p-80)
REVERT: B   79 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8885 (mmtm)
REVERT: C   99 ARG cc_start: 0.7741 (mmt180) cc_final: 0.7155 (mmm160)
REVERT: F   79 LYS cc_start: 0.9002 (OUTLIER) cc_final: 0.8723 (mtmt)
REVERT: G   15 LYS cc_start: 0.7965 (mtpm) cc_final: 0.7568 (mtmt)
REVERT: G   77 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.7621 (mtp180)
  outliers start: 13
  outliers final: 4
  residues processed: 157
  average time/residue: 1.0536
  time to fit residues: 172.9422
Evaluate side-chains
  158 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 150
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain G residue   77 ARG
Chi-restraints excluded: chain H residue  112 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 71 optimal weight:    1.9990
   chunk 98 optimal weight:    8.9990
   chunk 41 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 91 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 84 optimal weight:    5.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
D  63 ASN
G  24 GLN
G 104 GLN
H  47 GLN
H  84 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.165865 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.126040 restraints weight = 10041.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 0.95
r_work: 0.3233 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 3.20 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.1112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.028  12758  Z= 0.209
  Angle     :  0.602   8.117  18479  Z= 0.364
  Chirality :  0.037   0.164   2104
  Planarity :  0.005   0.042   1336
  Dihedral  : 30.469  72.931   4006
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.33 %
    Favored  : 83.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  2.77 (0.30), residues: 742
  helix:  2.45 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.03 (0.41), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  86 
 TYR   0.016   0.002   TYR F  88 
 PHE   0.013   0.002   PHE E  67 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 (12758)
  covalent geometry    : angle       0.60205 (18479)
  hydrogen bonds       : bond        0.05497 (  782)
  hydrogen bonds       : angle       2.93109 ( 1952)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 153
  time to evaluate  : 0.266 
Fit side-chains
REVERT: C   99 ARG cc_start: 0.7774 (mmt180) cc_final: 0.7208 (mmm160)
REVERT: E   64 LYS cc_start: 0.8570 (mtpm) cc_final: 0.8273 (mppt)
REVERT: F   79 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8762 (mtmt)
REVERT: G   15 LYS cc_start: 0.7993 (mtpm) cc_final: 0.7615 (mtmt)
REVERT: G   77 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7713 (mtp180)
  outliers start: 13
  outliers final: 7
  residues processed: 158
  average time/residue: 1.0917
  time to fit residues: 180.2399
Evaluate side-chains
  160 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 151
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain D residue   57 LYS
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain G residue   77 ARG
Chi-restraints excluded: chain H residue   46 LYS
Chi-restraints excluded: chain H residue  112 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 50 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 73 optimal weight:   10.0000
   chunk 71 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
C 104 GLN
D  63 ASN
G  24 GLN
G 104 GLN
H  47 GLN
H  84 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.165932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.126389 restraints weight = 10042.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 0.90
r_work: 0.3235 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 3.18 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.1116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  12758  Z= 0.211
  Angle     :  0.603   8.207  18479  Z= 0.365
  Chirality :  0.037   0.165   2104
  Planarity :  0.005   0.062   1336
  Dihedral  : 30.471  73.007   4006
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.97 %
    Favored  : 82.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  2.75 (0.30), residues: 742
  helix:  2.43 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.02 (0.41), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E  86 
 TYR   0.013   0.002   TYR D  83 
 PHE   0.014   0.002   PHE E  67 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 (12758)
  covalent geometry    : angle       0.60267 (18479)
  hydrogen bonds       : bond        0.05468 (  782)
  hydrogen bonds       : angle       2.92362 ( 1952)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 152
  time to evaluate  : 0.310 
Fit side-chains
REVERT: B   79 LYS cc_start: 0.9175 (OUTLIER) cc_final: 0.8914 (mmtm)
REVERT: C   99 ARG cc_start: 0.7768 (mmt180) cc_final: 0.7180 (mmm160)
REVERT: F   79 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8760 (mtmt)
REVERT: G   15 LYS cc_start: 0.8001 (mtpm) cc_final: 0.7626 (mtmt)
REVERT: G   77 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7730 (mtp180)
  outliers start: 13
  outliers final: 6
  residues processed: 155
  average time/residue: 1.1592
  time to fit residues: 187.5362
Evaluate side-chains
  160 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 151
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain D residue   57 LYS
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain G residue   77 ARG
Chi-restraints excluded: chain H residue  112 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 68 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 73 optimal weight:   10.0000
   chunk 88 optimal weight:    5.9990
   chunk 39 optimal weight:    0.6980
   chunk 86 optimal weight:   10.0000
   chunk 14 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
D  63 ASN
G  24 GLN
G 104 GLN
H  47 GLN
H  82 HIS
H  84 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.166663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.126083 restraints weight = 10007.817|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 0.91
r_work: 0.3261 rms_B_bonded: 1.91 restraints_weight: 0.5000
r_work: 0.3098 rms_B_bonded: 3.00 restraints_weight: 0.2500
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.1143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12758  Z= 0.176
  Angle     :  0.592   9.331  18479  Z= 0.358
  Chirality :  0.035   0.161   2104
  Planarity :  0.005   0.068   1336
  Dihedral  : 30.468  73.302   4006
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 15.61 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  2.84 (0.30), residues: 742
  helix:  2.50 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.01 (0.42), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  92 
 TYR   0.015   0.002   TYR D  83 
 PHE   0.013   0.002   PHE E  67 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 (12758)
  covalent geometry    : angle       0.59200 (18479)
  hydrogen bonds       : bond        0.05141 (  782)
  hydrogen bonds       : angle       2.91062 ( 1952)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 154
  time to evaluate  : 0.260 
Fit side-chains
REVERT: A   39 HIS cc_start: 0.5719 (OUTLIER) cc_final: 0.5198 (p-80)
REVERT: B   79 LYS cc_start: 0.9152 (OUTLIER) cc_final: 0.8881 (mmtm)
REVERT: C   99 ARG cc_start: 0.7713 (mmt180) cc_final: 0.7136 (mmm160)
REVERT: F   79 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8726 (mtmt)
REVERT: G   15 LYS cc_start: 0.7973 (mtpm) cc_final: 0.7585 (mtmt)
REVERT: G   77 ARG cc_start: 0.8532 (OUTLIER) cc_final: 0.7669 (mtp180)
  outliers start: 12
  outliers final: 6
  residues processed: 158
  average time/residue: 1.0884
  time to fit residues: 179.7345
Evaluate side-chains
  161 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 151
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain D residue   57 LYS
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain G residue   77 ARG
Chi-restraints excluded: chain H residue  112 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0040
   chunk 70 optimal weight:    8.9990
   chunk 81 optimal weight:    3.9990
   chunk 79 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 72 optimal weight:   20.0000
   chunk 91 optimal weight:    3.9990
   chunk 73 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9980
   chunk 77 optimal weight:    3.9990
   overall best weight:    2.3998

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
D  63 ASN
G  24 GLN
H  47 GLN
H  84 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.164416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.124298 restraints weight = 10084.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 0.92
r_work: 0.3212 rms_B_bonded: 2.02 restraints_weight: 0.5000
r_work: 0.3046 rms_B_bonded: 3.16 restraints_weight: 0.2500
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8314
moved from start:          0.1126

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039  12758  Z= 0.272
  Angle     :  0.664   9.363  18479  Z= 0.395
  Chirality :  0.041   0.180   2104
  Planarity :  0.006   0.055   1336
  Dihedral  : 30.640  73.199   4006
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 3.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 15.13 %
    Favored  : 82.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  2.44 (0.29), residues: 742
  helix:  2.18 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.04 (0.41), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  79 
 TYR   0.018   0.003   TYR F  88 
 PHE   0.015   0.002   PHE E  67 
 HIS   0.006   0.002   HIS A 129 

Details of bonding type rmsd
  covalent geometry    : bond        0.00601 (12758)
  covalent geometry    : angle       0.66427 (18479)
  hydrogen bonds       : bond        0.06409 (  782)
  hydrogen bonds       : angle       3.04258 ( 1952)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 151
  time to evaluate  : 0.311 
Fit side-chains
REVERT: A   39 HIS cc_start: 0.5829 (OUTLIER) cc_final: 0.5341 (p-80)
REVERT: B   79 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8928 (mmtm)
REVERT: C   99 ARG cc_start: 0.7783 (mmt180) cc_final: 0.7194 (mmm160)
REVERT: E   59 GLU cc_start: 0.8481 (pm20) cc_final: 0.7944 (pm20)
REVERT: E   64 LYS cc_start: 0.8617 (mtpm) cc_final: 0.8246 (mppt)
REVERT: F   79 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8748 (mtmm)
REVERT: G   15 LYS cc_start: 0.8044 (mtpm) cc_final: 0.7650 (mtmt)
REVERT: G   77 ARG cc_start: 0.8571 (OUTLIER) cc_final: 0.7717 (mtp180)
  outliers start: 12
  outliers final: 6
  residues processed: 155
  average time/residue: 1.0446
  time to fit residues: 169.1489
Evaluate side-chains
  160 residues out of total 628 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 150
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 HIS
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   79 LYS
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain F residue   79 LYS
Chi-restraints excluded: chain G residue   77 ARG
Chi-restraints excluded: chain H residue   46 LYS
Chi-restraints excluded: chain H residue  112 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9980
   chunk 82 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 95 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9980
   chunk 88 optimal weight:    4.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C 104 GLN
D  63 ASN
G  24 GLN
G 104 GLN
H  47 GLN
H  84 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.166334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.125905 restraints weight = 10012.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 0.89
r_work: 0.3265 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.3103 rms_B_bonded: 2.95 restraints_weight: 0.2500
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.1143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  12758  Z= 0.174
  Angle     :  0.600   7.989  18479  Z= 0.363
  Chirality :  0.036   0.164   2104
  Planarity :  0.005   0.072   1336
  Dihedral  : 30.602  73.540   4006
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.61 %
    Favored  : 82.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    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:  2.66 (0.30), residues: 742
  helix:  2.36 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop : -0.03 (0.42), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H  79 
 TYR   0.019   0.002   TYR F  88 
 PHE   0.013   0.002   PHE E  67 
 HIS   0.003   0.001   HIS H  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 (12758)
  covalent geometry    : angle       0.59981 (18479)
  hydrogen bonds       : bond        0.05166 (  782)
  hydrogen bonds       : angle       2.97571 ( 1952)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6307.16 seconds
wall clock time: 107 minutes 28.86 seconds (6448.86 seconds total)