Starting phenix.real_space_refine
on Wed Aug  5 20:12:37 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ybj_39119/08_2026/8ybj_39119.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ybj_39119/08_2026/8ybj_39119.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.38
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ybj_39119/08_2026/8ybj_39119.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ybj_39119/08_2026/8ybj_39119.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ybj_39119/08_2026/8ybj_39119.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ybj_39119/08_2026/8ybj_39119.map"
  }
  resolution = 2.38
  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     289      5.49       5
     S      14      5.16       5
     C    6606      2.51       5
     N    2246      2.21       5
     O    2798      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 86 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/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: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 790
          Classifications: {'peptide': 96}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    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: 844
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 844
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    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}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 646
          Classifications: {'peptide': 81}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "G"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    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: 2955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2955
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2987
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
  Time building chain proxies: 2.02, per 1000 atoms: 0.17
  Number of scatterers: 11953
  At special positions: 0
  Unit cell: (75.26, 120.84, 116.6, 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      14     16.00
     P     289     15.00
     O    2798      8.00
     N    2246      7.00
     C    6606      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: 0.74
  Conformation dependent library (CDL) restraints added in 141.5 milliseconds
  

  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:  1412

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 10 sheets defined
      73.4% alpha, 2.9% beta
      144 base pairs and 276 stacking pairs defined.
    Time for finding SS restraints: 1.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.709A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.772A  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 46 through 73
    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 124
      removed outlier: 3.653A  pdb=" N   ALA D 107 " --> pdb=" O   PRO D 103 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (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 132
    Processing helix  chain 'F' and resid 24 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.752A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
    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: 4.558A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.501A  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 '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 103 through 123
      removed outlier: 3.575A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.897A  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
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 6.945A  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 101 through 102
      removed outlier: 6.551A  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: 6.907A  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: 7.095A  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

    414 hydrogen bonds defined for protein.
    1215 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      368 hydrogen bonds
      736 hydrogen bond angles
      0 basepair planarities
      144 basepair parallelities
      276 stacking parallelities
  Total time for adding SS restraints: 1.41

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1548
        1.32 -     1.44: 4687
        1.44 -     1.57: 5915
        1.57 -     1.69: 579
        1.69 -     1.81: 24
  Bond restraints: 12753
  Sorted by residual:
  bond pdb=" C5'  DT I  55 "
       pdb=" C4'  DT I  55 "
    ideal  model  delta    sigma   weight residual
    1.512  1.552 -0.040 7.00e-03 2.04e+04 3.31e+01
  bond pdb=" C5'  DA I  50 "
       pdb=" C4'  DA I  50 "
    ideal  model  delta    sigma   weight residual
    1.512  1.550 -0.038 7.00e-03 2.04e+04 2.89e+01
  bond pdb=" N3   DC I   7 "
       pdb=" C4   DC I   7 "
    ideal  model  delta    sigma   weight residual
    1.335  1.300  0.035 7.00e-03 2.04e+04 2.47e+01
  bond pdb=" C5   DT J -57 "
       pdb=" C6   DT J -57 "
    ideal  model  delta    sigma   weight residual
    1.339  1.372 -0.033 7.00e-03 2.04e+04 2.20e+01
  bond pdb=" N3   DC J   3 "
       pdb=" C4   DC J   3 "
    ideal  model  delta    sigma   weight residual
    1.335  1.302  0.033 7.00e-03 2.04e+04 2.19e+01
  ... (remaining 12748 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 16467
        1.64 -     3.29: 1706
        3.29 -     4.93: 255
        4.93 -     6.58: 31
        6.58 -     8.22: 5
  Bond angle restraints: 18464
  Sorted by residual:
  angle pdb=" O5'  DA I  50 "
        pdb=" C5'  DA I  50 "
        pdb=" C4'  DA I  50 "
      ideal   model   delta    sigma   weight residual
     109.40  115.83   -6.43 8.00e-01 1.56e+00 6.46e+01
  angle pdb=" O5'  DT J -16 "
        pdb=" C5'  DT J -16 "
        pdb=" C4'  DT J -16 "
      ideal   model   delta    sigma   weight residual
     109.40  115.29   -5.89 8.00e-01 1.56e+00 5.42e+01
  angle pdb=" O5'  DT I  55 "
        pdb=" C5'  DT I  55 "
        pdb=" C4'  DT I  55 "
      ideal   model   delta    sigma   weight residual
     109.40  114.36   -4.96 8.00e-01 1.56e+00 3.85e+01
  angle pdb=" O5'  DC I   7 "
        pdb=" C5'  DC I   7 "
        pdb=" C4'  DC I   7 "
      ideal   model   delta    sigma   weight residual
     109.40  114.07   -4.67 8.00e-01 1.56e+00 3.41e+01
  angle pdb=" O5'  DC I  35 "
        pdb=" C5'  DC I  35 "
        pdb=" C4'  DC I  35 "
      ideal   model   delta    sigma   weight residual
     109.40  113.89   -4.49 8.00e-01 1.56e+00 3.15e+01
  ... (remaining 18459 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.67: 4408
       17.67 -    35.33: 1035
       35.33 -    53.00: 1144
       53.00 -    70.67: 319
       70.67 -    88.33: 24
  Dihedral angle restraints: 6930
    sinusoidal: 4738
      harmonic: 2192
  Sorted by residual:
  dihedral pdb=" CA  PRO H 103 "
           pdb=" C   PRO H 103 "
           pdb=" N   GLY H 104 "
           pdb=" CA  GLY H 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.86   28.14     0      5.00e+00 4.00e-02 3.17e+01
  dihedral pdb=" CA  LEU F  22 "
           pdb=" C   LEU F  22 "
           pdb=" N   ARG F  23 "
           pdb=" CA  ARG F  23 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.06  -21.94     0      5.00e+00 4.00e-02 1.93e+01
  dihedral pdb=" CA  PRO D 103 "
           pdb=" C   PRO D 103 "
           pdb=" N   GLY D 104 "
           pdb=" CA  GLY D 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.42   21.58     0      5.00e+00 4.00e-02 1.86e+01
  ... (remaining 6927 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1662
       0.070 -    0.139: 384
       0.139 -    0.209: 38
       0.209 -    0.279: 12
       0.279 -    0.348: 4
  Chirality restraints: 2100
  Sorted by residual:
  chirality pdb=" C4'  DC I -70 "
            pdb=" C5'  DC I -70 "
            pdb=" O4'  DC I -70 "
            pdb=" C3'  DC I -70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.18   -0.35 2.00e-01 2.50e+01 3.03e+00
  chirality pdb=" CA  LYS G  74 "
            pdb=" N   LYS G  74 "
            pdb=" C   LYS G  74 "
            pdb=" CB  LYS G  74 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.96e+00
  chirality pdb=" CA  ASN G  73 "
            pdb=" N   ASN G  73 "
            pdb=" C   ASN G  73 "
            pdb=" CB  ASN G  73 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.21    0.30 2.00e-01 2.50e+01 2.32e+00
  ... (remaining 2097 not shown)

  Planarity restraints: 1335
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT J -24 "    0.050 2.00e-02 2.50e+03   6.62e-02 1.10e+02
        pdb=" N1   DT J -24 "    0.046 2.00e-02 2.50e+03
        pdb=" C2   DT J -24 "   -0.018 2.00e-02 2.50e+03
        pdb=" O2   DT J -24 "   -0.117 2.00e-02 2.50e+03
        pdb=" N3   DT J -24 "    0.013 2.00e-02 2.50e+03
        pdb=" C4   DT J -24 "    0.027 2.00e-02 2.50e+03
        pdb=" O4   DT J -24 "    0.080 2.00e-02 2.50e+03
        pdb=" C5   DT J -24 "   -0.005 2.00e-02 2.50e+03
        pdb=" C7   DT J -24 "   -0.125 2.00e-02 2.50e+03
        pdb=" C6   DT J -24 "    0.048 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I  55 "    0.095 2.00e-02 2.50e+03   6.04e-02 9.12e+01
        pdb=" N1   DT I  55 "    0.038 2.00e-02 2.50e+03
        pdb=" C2   DT I  55 "   -0.020 2.00e-02 2.50e+03
        pdb=" O2   DT I  55 "   -0.093 2.00e-02 2.50e+03
        pdb=" N3   DT I  55 "   -0.015 2.00e-02 2.50e+03
        pdb=" C4   DT I  55 "    0.021 2.00e-02 2.50e+03
        pdb=" O4   DT I  55 "    0.100 2.00e-02 2.50e+03
        pdb=" C5   DT I  55 "   -0.033 2.00e-02 2.50e+03
        pdb=" C7   DT I  55 "   -0.063 2.00e-02 2.50e+03
        pdb=" C6   DT I  55 "   -0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC I   5 "   -0.101 2.00e-02 2.50e+03   6.31e-02 8.96e+01
        pdb=" N1   DC I   5 "   -0.023 2.00e-02 2.50e+03
        pdb=" C2   DC I   5 "    0.008 2.00e-02 2.50e+03
        pdb=" O2   DC I   5 "    0.067 2.00e-02 2.50e+03
        pdb=" N3   DC I   5 "    0.004 2.00e-02 2.50e+03
        pdb=" C4   DC I   5 "    0.023 2.00e-02 2.50e+03
        pdb=" N4   DC I   5 "   -0.107 2.00e-02 2.50e+03
        pdb=" C5   DC I   5 "    0.078 2.00e-02 2.50e+03
        pdb=" C6   DC I   5 "    0.051 2.00e-02 2.50e+03
  ... (remaining 1332 not shown)

  Histogram of nonbonded interaction distances:
        2.44 -     2.93: 4264
        2.93 -     3.43: 10430
        3.43 -     3.92: 24382
        3.92 -     4.41: 27712
        4.41 -     4.90: 36602
  Nonbonded interactions: 103390
  Sorted by model distance:
  nonbonded pdb=" N   ASP D  51 "
            pdb=" OD1 ASP D  51 "
     model   vdw
     2.443 3.120
  nonbonded pdb=" OG  SER G  18 "
            pdb=" O   PHE G  25 "
     model   vdw
     2.467 3.040
  nonbonded pdb=" OD2 ASP D  68 "
            pdb=" OH  TYR F  98 "
     model   vdw
     2.486 3.040
  nonbonded pdb=" OG  SER C  40 "
            pdb=" O   ARG C  42 "
     model   vdw
     2.504 3.040
  nonbonded pdb=" NH2 ARG G  32 "
            pdb=" OE1 GLU H  35 "
     model   vdw
     2.521 3.120
  ... (remaining 103385 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' and resid 40 through 135)
}
ncs_group {
  reference = (chain 'B' and resid 22 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 11 through 118)
  selection = (chain 'G' and resid 11 through 118)
}
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=0.00 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:             1.140
  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:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.470
  Find NCS groups from input model:        0.110
  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:             0.010
  Load rotamer database and sin/cos tables:6.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
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      :  0.009   0.058  12753  Z= 0.791
  Angle     :  1.030   8.220  18464  Z= 0.921
  Chirality :  0.060   0.348   2100
  Planarity :  0.012   0.112   1335
  Dihedral  : 28.235  88.333   5518
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 0.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 12.28 %
    Favored  : 87.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.32 (0.29), residues: 742
  helix:  2.20 (0.22), residues: 534
  sheet:  None (None), residues: 0
  loop : -0.20 (0.36), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG F  35 
 TYR   0.036   0.003   TYR G  39 
 PHE   0.008   0.002   PHE E  67 
 HIS   0.007   0.002   HIS G  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00858 /  0.79 (12753)
  covalent geometry    : angle       1.02954 /  0.92 (18464)
  hydrogen bonds       : bond        0.12210 /  7.98 (  782)
  hydrogen bonds       : angle       3.69658 /  2.69 ( 1951)

*********************** 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
  150 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 ARG cc_start: 0.8516 (ttt180) cc_final: 0.8312 (tpt90)
REVERT: C   15 LYS cc_start: 0.7916 (mtpt) cc_final: 0.7683 (mtmt)
REVERT: C   95 LYS cc_start: 0.8930 (ttmt) cc_final: 0.8498 (tttp)
REVERT: E   97 GLU cc_start: 0.9069 (mt-10) cc_final: 0.8852 (mt-10)
REVERT: G   95 LYS cc_start: 0.8499 (ttmt) cc_final: 0.7913 (tttt)
REVERT: H   93 GLU cc_start: 0.8887 (mp0) cc_final: 0.8483 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 150
  average time/residue: 0.7910
  time to fit residues: 124.3874
Evaluate side-chains
  137 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 137
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  25 ASN
C  38 ASN
D  84 ASN
E  68 GLN
H  82 HIS
H  84 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.165823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.117689 restraints weight = 10869.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.3322 rms_B_bonded: 1.13
r_work: 0.3100 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2942 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2942
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.0837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  12753  Z= 0.149
  Angle     :  0.672   7.399  18464  Z= 0.389
  Chirality :  0.048   0.218   2100
  Planarity :  0.004   0.034   1335
  Dihedral  : 30.855  98.453   4021
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 12.60 %
    Favored  : 85.65 %
  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 are not related in a simple way.
  whole:  2.89 (0.30), residues: 742
  helix:  2.68 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -0.27 (0.37), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG H  92 
 TYR   0.012   0.001   TYR F  51 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00239 /  0.15 (12753)
  covalent geometry    : angle       0.67167 /  0.39 (18464)
  hydrogen bonds       : bond        0.05413 /  3.61 (  782)
  hydrogen bonds       : angle       2.99694 /  2.19 ( 1951)

*********************** 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
  156 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 145
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  134 ARG cc_start: 0.7522 (ttt90) cc_final: 0.7247 (mtt180)
REVERT: C   15 LYS cc_start: 0.7956 (mtpt) cc_final: 0.7459 (mtmt)
REVERT: C   36 LYS cc_start: 0.8752 (mppt) cc_final: 0.8309 (mmtp)
REVERT: E   97 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8674 (mt-10)
REVERT: G   95 LYS cc_start: 0.8421 (ttmt) cc_final: 0.7758 (tttt)
REVERT: H   93 GLU cc_start: 0.8752 (mp0) cc_final: 0.8356 (mp0)
REVERT: H  112 SER cc_start: 0.8756 (m) cc_final: 0.8530 (t)
  outliers start: 11
  outliers final: 2
  residues processed: 148
  average time/residue: 0.8082
  time to fit residues: 125.7118
Evaluate side-chains
  145 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 143
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain G residue   76 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0970
   chunk 52 optimal weight:    3.9990
   chunk 89 optimal weight:   10.0000
   chunk 35 optimal weight:    0.6980
   chunk 92 optimal weight:    9.9990
   chunk 51 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    1.7584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 108 ASN
E  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.163209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.114809 restraints weight = 11098.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3291 rms_B_bonded: 1.14
r_work: 0.3058 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.0979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12753  Z= 0.180
  Angle     :  0.679   6.997  18464  Z= 0.389
  Chirality :  0.050   0.223   2100
  Planarity :  0.005   0.045   1335
  Dihedral  : 31.088 103.202   4021
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 12.44 %
    Favored  : 85.81 %
  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 are not related in a simple way.
  whole:  2.71 (0.30), residues: 742
  helix:  2.58 (0.22), residues: 539
  sheet:  None (None), residues: 0
  loop : -0.42 (0.36), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  92 
 TYR   0.015   0.002   TYR B  88 
 PHE   0.007   0.002   PHE E  67 
 HIS   0.005   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.18 (12753)
  covalent geometry    : angle       0.67919 /  0.39 (18464)
  hydrogen bonds       : bond        0.06212 /  4.17 (  782)
  hydrogen bonds       : angle       2.97296 /  2.16 ( 1951)

*********************** 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
  154 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 143
  time to evaluate  : 0.298 
Fit side-chains
REVERT: A  134 ARG cc_start: 0.7404 (ttt90) cc_final: 0.7190 (mtt180)
REVERT: B   93 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7648 (mt0)
REVERT: C   15 LYS cc_start: 0.8010 (mtpt) cc_final: 0.7506 (mtmt)
REVERT: E   97 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8793 (mt-10)
REVERT: G   95 LYS cc_start: 0.8439 (ttmt) cc_final: 0.7769 (tttt)
  outliers start: 11
  outliers final: 5
  residues processed: 146
  average time/residue: 0.8752
  time to fit residues: 134.0710
Evaluate side-chains
  147 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 141
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain G residue   76 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 72 optimal weight:   50.0000
   chunk 11 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 85 optimal weight:   30.0000
   chunk 37 optimal weight:    1.9990
   chunk 73 optimal weight:   20.0000
   chunk 95 optimal weight:    9.9990
   chunk 98 optimal weight:   10.0000
   chunk 80 optimal weight:    9.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    3.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  84 ASN
E  68 GLN
H  82 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.161111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.112638 restraints weight = 10958.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 1.12
r_work: 0.3020 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2857 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
moved from start:          0.1224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  12753  Z= 0.274
  Angle     :  0.792   7.361  18464  Z= 0.435
  Chirality :  0.058   0.240   2100
  Planarity :  0.006   0.045   1335
  Dihedral  : 31.364 106.081   4021
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 3.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.08 %
    Favored  : 98.92 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 12.28 %
    Favored  : 85.49 %
  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 are not related in a simple way.
  whole:  1.96 (0.29), residues: 742
  helix:  2.05 (0.21), residues: 539
  sheet:  None (None), residues: 0
  loop : -0.78 (0.35), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG H  79 
 TYR   0.026   0.003   TYR B  88 
 PHE   0.011   0.002   PHE E  67 
 HIS   0.007   0.002   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00585 /  0.27 (12753)
  covalent geometry    : angle       0.79248 /  0.43 (18464)
  hydrogen bonds       : bond        0.07936 /  5.34 (  782)
  hydrogen bonds       : angle       3.15135 /  2.29 ( 1951)

*********************** 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
  151 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 137
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7539 (mt0)
REVERT: C   15 LYS cc_start: 0.8107 (mtpt) cc_final: 0.7592 (mtmt)
REVERT: C   36 LYS cc_start: 0.8563 (mptt) cc_final: 0.8201 (mmtp)
REVERT: D   82 HIS cc_start: 0.8153 (t-90) cc_final: 0.7713 (m-70)
REVERT: G   95 LYS cc_start: 0.8429 (ttmt) cc_final: 0.7737 (tttt)
REVERT: H   93 GLU cc_start: 0.8775 (mp0) cc_final: 0.8425 (mp0)
  outliers start: 14
  outliers final: 7
  residues processed: 141
  average time/residue: 0.8512
  time to fit residues: 125.9007
Evaluate side-chains
  144 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 136
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain G residue   76 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 94 optimal weight:    9.9990
   chunk 4 optimal weight:    0.5980
   chunk 54 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 72 optimal weight:   50.0000
   chunk 15 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E  68 GLN
F  25 ASN
H  82 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.163229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.114838 restraints weight = 10911.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 1.13
r_work: 0.3055 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.1227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12753  Z= 0.149
  Angle     :  0.690   6.692  18464  Z= 0.389
  Chirality :  0.050   0.230   2100
  Planarity :  0.005   0.048   1335
  Dihedral  : 31.294 107.705   4021
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 12.28 %
    Favored  : 85.65 %
  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 are not related in a simple way.
  whole:  2.43 (0.30), residues: 742
  helix:  2.40 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -0.65 (0.36), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  92 
 TYR   0.014   0.002   TYR B  88 
 PHE   0.008   0.001   PHE E  67 
 HIS   0.005   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.15 (12753)
  covalent geometry    : angle       0.68988 /  0.39 (18464)
  hydrogen bonds       : bond        0.05618 /  3.75 (  782)
  hydrogen bonds       : angle       3.09724 /  2.26 ( 1951)

*********************** 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
  153 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 140
  time to evaluate  : 0.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   15 LYS cc_start: 0.8094 (mtpt) cc_final: 0.7572 (mtmt)
REVERT: C   36 LYS cc_start: 0.8544 (mptt) cc_final: 0.8170 (mmtp)
REVERT: D   71 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8180 (mt-10)
REVERT: G   95 LYS cc_start: 0.8455 (ttmt) cc_final: 0.7765 (tttt)
REVERT: H   93 GLU cc_start: 0.8754 (mp0) cc_final: 0.8391 (mp0)
REVERT: H  112 SER cc_start: 0.8790 (m) cc_final: 0.8553 (t)
  outliers start: 13
  outliers final: 5
  residues processed: 144
  average time/residue: 0.7889
  time to fit residues: 119.1765
Evaluate side-chains
  145 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 139
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain G residue   76 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 32 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   chunk 17 optimal weight:    0.8980
   chunk 80 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 54 optimal weight:    3.9990
   chunk 87 optimal weight:   40.0000
   chunk 97 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    1.7786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3919 r_free = 0.3919 target = 0.162843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.114403 restraints weight = 10934.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3278 rms_B_bonded: 1.13
r_work: 0.3050 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2889 rms_B_bonded: 3.47 restraints_weight: 0.2500
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.1257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12753  Z= 0.179
  Angle     :  0.680   7.053  18464  Z= 0.384
  Chirality :  0.050   0.215   2100
  Planarity :  0.005   0.044   1335
  Dihedral  : 31.153 113.889   4021
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 3.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 13.08 %
    Favored  : 85.01 %
  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 are not related in a simple way.
  whole:  2.50 (0.30), residues: 742
  helix:  2.45 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -0.61 (0.36), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 129 
 TYR   0.018   0.002   TYR B  88 
 PHE   0.008   0.002   PHE E  67 
 HIS   0.006   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00350 /  0.18 (12753)
  covalent geometry    : angle       0.68035 /  0.38 (18464)
  hydrogen bonds       : bond        0.06046 /  4.05 (  782)
  hydrogen bonds       : angle       2.97547 /  2.17 ( 1951)

*********************** 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
  151 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 139
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: C   15 LYS cc_start: 0.8094 (mtpt) cc_final: 0.7560 (mtmt)
REVERT: C   36 LYS cc_start: 0.8528 (OUTLIER) cc_final: 0.8221 (mptm)
REVERT: D   68 ASP cc_start: 0.9170 (t0) cc_final: 0.8838 (t0)
REVERT: D   71 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.8105 (mt-10)
REVERT: G   95 LYS cc_start: 0.8459 (ttmt) cc_final: 0.7768 (tttt)
  outliers start: 12
  outliers final: 8
  residues processed: 142
  average time/residue: 0.8183
  time to fit residues: 121.9586
Evaluate side-chains
  148 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 138
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   95 LYS
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain G residue   76 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 71 optimal weight:    1.9990
   chunk 98 optimal weight:   20.0000
   chunk 41 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 91 optimal weight:    9.9990
   chunk 18 optimal weight:    0.7980
   chunk 84 optimal weight:   30.0000
   overall best weight:    1.0582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
G  24 GLN
H  82 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.163312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.115049 restraints weight = 10890.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 1.12
r_work: 0.3058 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2899 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8394
moved from start:          0.1259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070  12753  Z= 0.153
  Angle     :  0.666   7.146  18464  Z= 0.378
  Chirality :  0.048   0.214   2100
  Planarity :  0.005   0.061   1335
  Dihedral  : 31.148 113.879   4021
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 13.24 %
    Favored  : 84.69 %
  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 are not related in a simple way.
  whole:  2.55 (0.30), residues: 742
  helix:  2.49 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -0.59 (0.36), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  79 
 TYR   0.012   0.002   TYR F  51 
 PHE   0.009   0.001   PHE E  67 
 HIS   0.005   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.15 (12753)
  covalent geometry    : angle       0.66639 /  0.38 (18464)
  hydrogen bonds       : bond        0.05719 /  3.83 (  782)
  hydrogen bonds       : angle       2.96342 /  2.16 ( 1951)

*********************** 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
  152 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 139
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   15 LYS cc_start: 0.8090 (mtpt) cc_final: 0.7547 (mtmt)
REVERT: C   36 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8180 (mptm)
REVERT: D   71 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8107 (mt-10)
REVERT: G   95 LYS cc_start: 0.8443 (ttmt) cc_final: 0.7746 (tttt)
REVERT: H  112 SER cc_start: 0.8807 (m) cc_final: 0.8569 (t)
  outliers start: 13
  outliers final: 7
  residues processed: 143
  average time/residue: 0.7913
  time to fit residues: 118.9040
Evaluate side-chains
  147 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 138
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain G residue   76 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 1 optimal weight:    0.8980
   chunk 63 optimal weight:    4.9990
   chunk 50 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 73 optimal weight:   20.0000
   chunk 71 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 82 optimal weight:   10.0000
   overall best weight:    1.1382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.163438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.115266 restraints weight = 10897.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3287 rms_B_bonded: 1.11
r_work: 0.3061 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2903 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2903
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.1296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12753  Z= 0.155
  Angle     :  0.663   6.336  18464  Z= 0.377
  Chirality :  0.048   0.215   2100
  Planarity :  0.005   0.068   1335
  Dihedral  : 31.135 114.510   4021
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 14.04 %
    Favored  : 84.53 %
  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 are not related in a simple way.
  whole:  2.59 (0.30), residues: 742
  helix:  2.51 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -0.58 (0.36), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG D  92 
 TYR   0.013   0.002   TYR F  51 
 PHE   0.010   0.001   PHE E  67 
 HIS   0.005   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.15 (12753)
  covalent geometry    : angle       0.66329 /  0.38 (18464)
  hydrogen bonds       : bond        0.05649 /  3.78 (  782)
  hydrogen bonds       : angle       2.94758 /  2.15 ( 1951)

*********************** 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
  149 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 140
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   15 LYS cc_start: 0.8086 (mtpt) cc_final: 0.7545 (mtmt)
REVERT: C   36 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8184 (mptm)
REVERT: D   71 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8100 (mt-10)
REVERT: G   95 LYS cc_start: 0.8447 (ttmt) cc_final: 0.7751 (tttt)
REVERT: H  112 SER cc_start: 0.8810 (m) cc_final: 0.8576 (t)
  outliers start: 9
  outliers final: 7
  residues processed: 143
  average time/residue: 0.8302
  time to fit residues: 124.4535
Evaluate side-chains
  149 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 140
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain G residue   76 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 68 optimal weight:    6.9990
   chunk 91 optimal weight:    9.9990
   chunk 78 optimal weight:   10.0000
   chunk 62 optimal weight:    5.9990
   chunk 73 optimal weight:   20.0000
   chunk 88 optimal weight:   30.0000
   chunk 39 optimal weight:    0.4980
   chunk 86 optimal weight:   50.0000
   chunk 14 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    2.0986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.162392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.113988 restraints weight = 10911.358|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 1.12
r_work: 0.3041 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2881 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8416
moved from start:          0.1328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12753  Z= 0.199
  Angle     :  0.698   7.053  18464  Z= 0.391
  Chirality :  0.051   0.214   2100
  Planarity :  0.005   0.039   1335
  Dihedral  : 31.183 118.789   4021
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 13.88 %
    Favored  : 84.37 %
  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 are not related in a simple way.
  whole:  2.36 (0.30), residues: 742
  helix:  2.34 (0.22), residues: 541
  sheet:  None (None), residues: 0
  loop : -0.65 (0.36), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG H  92 
 TYR   0.022   0.002   TYR B  88 
 PHE   0.009   0.002   PHE E  67 
 HIS   0.005   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00406 /  0.20 (12753)
  covalent geometry    : angle       0.69783 /  0.39 (18464)
  hydrogen bonds       : bond        0.06379 /  4.28 (  782)
  hydrogen bonds       : angle       2.99522 /  2.18 ( 1951)

*********************** 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
  150 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 139
  time to evaluate  : 0.293 
Fit side-chains
   revert: symmetry clash
REVERT: C   15 LYS cc_start: 0.8147 (mtpt) cc_final: 0.7573 (mtmt)
REVERT: C   36 LYS cc_start: 0.8574 (OUTLIER) cc_final: 0.8149 (mmtp)
REVERT: D   68 ASP cc_start: 0.9151 (t0) cc_final: 0.8838 (t0)
REVERT: D   71 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8112 (mt-10)
REVERT: D   79 ARG cc_start: 0.8391 (mtt90) cc_final: 0.8143 (mtt-85)
REVERT: G   95 LYS cc_start: 0.8443 (ttmt) cc_final: 0.7744 (tttt)
REVERT: H   93 GLU cc_start: 0.8688 (mp0) cc_final: 0.8273 (mp0)
  outliers start: 11
  outliers final: 7
  residues processed: 142
  average time/residue: 0.8302
  time to fit residues: 123.9538
Evaluate side-chains
  145 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 136
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain C residue   36 LYS
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain G residue   76 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 58 optimal weight:    0.6980
   chunk 18 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 81 optimal weight:    9.9990
   chunk 79 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 72 optimal weight:   50.0000
   chunk 91 optimal weight:   10.0000
   chunk 73 optimal weight:   20.0000
   chunk 23 optimal weight:    0.9990
   chunk 77 optimal weight:   10.0000
   overall best weight:    2.5388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.162238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.113389 restraints weight = 10960.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3264 rms_B_bonded: 1.12
r_work: 0.3033 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2874 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2874
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.1454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12753  Z= 0.222
  Angle     :  0.732   8.161  18464  Z= 0.405
  Chirality :  0.053   0.223   2100
  Planarity :  0.005   0.048   1335
  Dihedral  : 31.288 126.955   4021
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 13.40 %
    Favored  : 84.37 %
  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 are not related in a simple way.
  whole:  2.14 (0.29), residues: 742
  helix:  2.22 (0.22), residues: 539
  sheet:  None (None), residues: 0
  loop : -0.80 (0.36), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  52 
 TYR   0.035   0.003   TYR B  88 
 PHE   0.009   0.002   PHE E  67 
 HIS   0.005   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00464 /  0.22 (12753)
  covalent geometry    : angle       0.73198 /  0.40 (18464)
  hydrogen bonds       : bond        0.06863 /  4.61 (  782)
  hydrogen bonds       : angle       3.05068 /  2.22 ( 1951)

********************** 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
  151 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 137
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   52 ARG cc_start: 0.8035 (ttp80) cc_final: 0.7643 (tmt170)
REVERT: C   15 LYS cc_start: 0.8179 (mtpt) cc_final: 0.7595 (mtmt)
REVERT: C  104 GLN cc_start: 0.8644 (mt0) cc_final: 0.8424 (mt0)
REVERT: D   71 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8109 (mt-10)
REVERT: G   64 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8266 (tt0)
REVERT: G   95 LYS cc_start: 0.8476 (ttmt) cc_final: 0.7779 (tttt)
REVERT: H   92 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7582 (ttm-80)
REVERT: H   93 GLU cc_start: 0.8677 (mp0) cc_final: 0.8325 (mp0)
  outliers start: 14
  outliers final: 6
  residues processed: 141
  average time/residue: 0.7972
  time to fit residues: 118.0458
Evaluate side-chains
  143 residues out of total 627 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 135
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   71 GLU
Chi-restraints excluded: chain D residue  112 SER
Chi-restraints excluded: chain E residue   65 LEU
Chi-restraints excluded: chain E residue   76 GLN
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue   76 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 52 optimal weight:    2.9990
   chunk 82 optimal weight:    9.9990
   chunk 56 optimal weight:    0.8980
   chunk 27 optimal weight:    3.9990
   chunk 95 optimal weight:    9.9990
   chunk 18 optimal weight:    0.9980
   chunk 88 optimal weight:   30.0000
   overall best weight:    1.1384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.163303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.114650 restraints weight = 10945.559|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 1.11
r_work: 0.3050 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2891 rms_B_bonded: 3.45 restraints_weight: 0.2500
r_work (final): 0.2891
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  12753  Z= 0.153
  Angle     :  0.693   7.610  18464  Z= 0.387
  Chirality :  0.049   0.218   2100
  Planarity :  0.005   0.045   1335
  Dihedral  : 31.251 127.443   4021
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.67 %
    Favored  : 99.33 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 13.88 %
    Favored  : 84.53 %
  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 are not related in a simple way.
  whole:  2.38 (0.30), residues: 742
  helix:  2.36 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.68 (0.36), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  52 
 TYR   0.026   0.002   TYR B  88 
 PHE   0.010   0.001   PHE E  67 
 HIS   0.005   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00277 /  0.15 (12753)
  covalent geometry    : angle       0.69325 /  0.39 (18464)
  hydrogen bonds       : bond        0.05963 /  3.99 (  782)
  hydrogen bonds       : angle       3.02453 /  2.21 ( 1951)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4561.43 seconds
wall clock time: 77 minutes 50.70 seconds (4670.70 seconds total)