Starting phenix.real_space_refine
on Sat Oct 24 03:54:19 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/10go_75157/10_2026/10go_75157.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/10go_75157/10_2026/10go_75157.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/10go_75157/10_2026/10go_75157.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/10go_75157/10_2026/10go_75157.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/10go_75157/10_2026/10go_75157.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/10go_75157/10_2026/10go_75157.map"
  }
  resolution = 2.8
  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     294      5.49       5
     S      10      5.16       5
     C    6649      2.51       5
     N    2257      2.21       5
     O    2826      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12036
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 789
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 789
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 657
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 837
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 789
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 789
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 652
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 652
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 823
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 725
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 2997
      Number of conformers: 1
      Conformer: "B"
        Number of residues, atoms: 147, 2997
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
  Time building chain proxies: 2.49, per 1000 atoms: 0.21
  Number of scatterers: 12036
  At special positions: 0
  Unit cell: (77.964, 115.878, 119.082, 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     294     15.00
     O    2826      8.00
     N    2257      7.00
     C    6649      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: 0.92
  Conformation dependent library (CDL) restraints added in 306.8 milliseconds
  

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1416

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 9 sheets defined
      71.8% alpha, 2.6% beta
      146 base pairs and 258 stacking pairs defined.
    Time for finding SS restraints: 1.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 50 through 57
      removed outlier: 3.674A  pdb=" N   TYR A  54 " --> pdb=" O   GLU A  50 " (cutoff:3.500A)
    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 131
      removed outlier: 3.522A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.511A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   ARG B  55 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ASN B  64 " --> pdb=" O   VAL B  60 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.526A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 27 through 36
    Processing helix  chain 'C' and resid 45 through 74
      removed outlier: 4.436A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 47
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.550A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 124
      removed outlier: 3.592A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ALA D 110 " --> pdb=" O   LEU D 106 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LYS D 116 " --> pdb=" O   SER D 112 " (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
      removed outlier: 3.674A  pdb=" N   GLN F  27 " --> pdb=" O   ASP F  24 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.717A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.508A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.396A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.580A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 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 124
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.185A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.704A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.288A  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 'E' and resid 83 through 84
      removed outlier: 7.216A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.088A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78

    393 hydrogen bonds defined for protein.
    1164 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      373 hydrogen bonds
      746 hydrogen bond angles
      0 basepair planarities
      146 basepair parallelities
      258 stacking parallelities
  Total time for adding SS restraints: 2.44

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2266
        1.33 -     1.45: 4201
        1.45 -     1.57: 5777
        1.57 -     1.69: 585
        1.69 -     1.81: 20
  Bond restraints: 12849
  Sorted by residual:
  bond pdb=" P  B8OG I  55 "
       pdb=" O5'B8OG I  55 "
    ideal  model  delta    sigma   weight residual
    1.708  1.564  0.144 2.00e-02 2.50e+03 5.21e+01
  bond pdb=" C3'  DT J  15 "
       pdb=" C2'  DT J  15 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.59e+00
  bond pdb=" N   LYS D 108 "
       pdb=" CA  LYS D 108 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.036 1.16e-02 7.43e+03 9.52e+00
  bond pdb=" N   LYS C  36 "
       pdb=" CA  LYS C  36 "
    ideal  model  delta    sigma   weight residual
    1.456  1.492 -0.036 1.18e-02 7.18e+03 9.45e+00
  bond pdb=" N   GLU H  35 "
       pdb=" CA  GLU H  35 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.039 1.29e-02 6.01e+03 9.29e+00
  ... (remaining 12844 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.99: 17642
        1.99 -     3.99: 901
        3.99 -     5.98: 61
        5.98 -     7.98: 7
        7.98 -     9.97: 2
  Bond angle restraints: 18613
  Sorted by residual:
  angle pdb=" N   THR G  76 "
        pdb=" CA  THR G  76 "
        pdb=" C   THR G  76 "
      ideal   model   delta    sigma   weight residual
     113.28  107.39    5.89 1.22e+00 6.72e-01 2.33e+01
  angle pdb=" N   VAL E  46 "
        pdb=" CA  VAL E  46 "
        pdb=" C   VAL E  46 "
      ideal   model   delta    sigma   weight residual
     110.62  115.45   -4.83 1.02e+00 9.61e-01 2.24e+01
  angle pdb=" N   TYR E  54 "
        pdb=" CA  TYR E  54 "
        pdb=" C   TYR E  54 "
      ideal   model   delta    sigma   weight residual
     111.28  106.35    4.93 1.09e+00 8.42e-01 2.05e+01
  angle pdb=" C   GLN H  47 "
        pdb=" CA  GLN H  47 "
        pdb=" CB  GLN H  47 "
      ideal   model   delta    sigma   weight residual
     110.79  103.19    7.60 1.68e+00 3.54e-01 2.05e+01
  angle pdb=" N3   DT I  32 "
        pdb=" C4   DT I  32 "
        pdb=" O4   DT I  32 "
      ideal   model   delta    sigma   weight residual
     119.90  122.61   -2.71 6.00e-01 2.78e+00 2.04e+01
  ... (remaining 18608 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.76: 5192
       28.76 -    57.53: 1658
       57.53 -    86.29: 129
       86.29 -   115.05: 1
      115.05 -   143.82: 4
  Dihedral angle restraints: 6984
    sinusoidal: 4787
      harmonic: 2197
  Sorted by residual:
  dihedral pdb=" CD  ARG A  53 "
           pdb=" NE  ARG A  53 "
           pdb=" CZ  ARG A  53 "
           pdb=" NH1 ARG A  53 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   88.82  -88.82     1      1.00e+01 1.00e-02 9.40e+01
  dihedral pdb=" CD  ARG B  92 "
           pdb=" NE  ARG B  92 "
           pdb=" CZ  ARG B  92 "
           pdb=" NH1 ARG B  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -54.37   54.37     1      1.00e+01 1.00e-02 4.01e+01
  dihedral pdb=" CA  GLU A  50 "
           pdb=" C   GLU A  50 "
           pdb=" N   ILE A  51 "
           pdb=" CA  ILE A  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.64   23.36     0      5.00e+00 4.00e-02 2.18e+01
  ... (remaining 6981 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.062: 1736
       0.062 -    0.124: 345
       0.124 -    0.187: 31
       0.187 -    0.249: 3
       0.249 -    0.311: 4
  Chirality restraints: 2119
  Sorted by residual:
  chirality pdb=" CA  ILE C 111 "
            pdb=" N   ILE C 111 "
            pdb=" C   ILE C 111 "
            pdb=" CB  ILE C 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.74   -0.31 2.00e-01 2.50e+01 2.42e+00
  chirality pdb=" CA  GLN H  47 "
            pdb=" N   GLN H  47 "
            pdb=" C   GLN H  47 "
            pdb=" CB  GLN H  47 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.81   -0.30 2.00e-01 2.50e+01 2.24e+00
  chirality pdb=" CA  LYS G  75 "
            pdb=" N   LYS G  75 "
            pdb=" C   LYS G  75 "
            pdb=" CB  LYS G  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.15e+00
  ... (remaining 2116 not shown)

  Planarity restraints: 1334
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A  53 "    1.107 9.50e-02 1.11e+02   4.96e-01 1.48e+02
        pdb=" NE  ARG A  53 "   -0.066 2.00e-02 2.50e+03
        pdb=" CZ  ARG A  53 "   -0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG A  53 "    0.015 2.00e-02 2.50e+03
        pdb=" NH2 ARG A  53 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  92 "   -0.903 9.50e-02 1.11e+02   4.05e-01 9.94e+01
        pdb=" NE  ARG B  92 "    0.053 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  92 "    0.014 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  92 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  92 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G  20 "    0.684 9.50e-02 1.11e+02   3.07e-01 5.74e+01
        pdb=" NE  ARG G  20 "   -0.041 2.00e-02 2.50e+03
        pdb=" CZ  ARG G  20 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG G  20 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG G  20 "    0.022 2.00e-02 2.50e+03
  ... (remaining 1331 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 413
        2.69 -     3.24: 9950
        3.24 -     3.79: 23214
        3.79 -     4.35: 29471
        4.35 -     4.90: 41555
  Nonbonded interactions: 104603
  Sorted by model distance:
  nonbonded pdb=" O   ARG F  23 "
            pdb=" OD1 ASP F  24 "
     model   vdw
     2.133 3.040
  nonbonded pdb=" OH  TYR B  98 "
            pdb=" OD2 ASP H  68 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" OG1 THR D  90 "
            pdb=" OE1 GLU D  93 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" N   GLU A  59 "
            pdb=" OE1 GLU A  59 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" NH2 ARG E  42 "
            pdb=" OP1  DG J  69 "
     model   vdw
     2.311 3.120
  ... (remaining 104598 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' and resid 21 through 101)
  selection = (chain 'F' and resid 21 through 101)
}
ncs_group {
  reference = (chain 'C' and resid 11 through 117)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 32 through 124)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             21.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.360
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.100
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.030
  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:7.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.190
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
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   0.144  12849  Z= 0.551
  Angle     :  0.871   9.969  18613  Z= 0.735
  Chirality :  0.050   0.311   2119
  Planarity :  0.024   0.496   1334
  Dihedral  : 27.928 143.818   5568
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 11.92 %
    Favored  : 88.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.00 (0.30), residues: 743
  helix:  1.20 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.67 (0.41), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A  42 
 TYR   0.011   0.002   TYR B  72 
 PHE   0.011   0.001   PHE B  61 
 HIS   0.005   0.001   HIS E  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00650 /  0.55 (12849)
  covalent geometry    : angle       0.87095 /  0.73 (18613)
  hydrogen bonds       : bond        0.10989 /  7.80 (  766)
  hydrogen bonds       : angle       3.95842 /  2.76 ( 1910)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.368 
Fit side-chains
   revert: symmetry clash
REVERT: B   84 MET cc_start: 0.8751 (mmm) cc_final: 0.8393 (tpp)
REVERT: C   36 LYS cc_start: 0.8920 (ptpt) cc_final: 0.8622 (pptt)
REVERT: D   42 TYR cc_start: 0.8087 (t80) cc_final: 0.7840 (t80)
REVERT: D   68 ASP cc_start: 0.9020 (t0) cc_final: 0.8812 (t0)
REVERT: E   59 GLU cc_start: 0.7841 (pm20) cc_final: 0.7368 (pm20)
REVERT: G   15 LYS cc_start: 0.7255 (tttp) cc_final: 0.6878 (ttpt)
REVERT: G   73 ASN cc_start: 0.8872 (t0) cc_final: 0.8341 (t0)
REVERT: G  110 ASN cc_start: 0.8616 (t0) cc_final: 0.8033 (p0)
REVERT: H   33 ARG cc_start: 0.8070 (mmt90) cc_final: 0.7786 (mmt-90)
REVERT: H   63 ASN cc_start: 0.8237 (t0) cc_final: 0.8007 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.7823
  time to fit residues: 123.3786
Evaluate side-chains
  140 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 38, 61, 45]
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  85 GLN
A 113 HIS
D  84 ASN
E  68 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.099860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.063946 restraints weight = 23119.583|
|-----------------------------------------------------------------------------|
r_work (start): 0.2950 rms_B_bonded: 1.76
r_work: 0.2782 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2781
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2781 r_free = 0.2781    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2781 r_free = 0.2781    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.99   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.2781
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8724
moved from start:          0.0735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12849  Z= 0.167
  Angle     :  0.635   6.233  18613  Z= 0.378
  Chirality :  0.043   0.212   2119
  Planarity :  0.006   0.116   1334
  Dihedral  : 30.616 144.372   4072
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 14.94 %
    Favored  : 83.94 %
  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:  2.05 (0.31), residues: 743
  helix:  2.03 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.55 (0.42), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  42 
 TYR   0.009   0.001   TYR H  40 
 PHE   0.009   0.001   PHE E  67 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.17 (12849)
  covalent geometry    : angle       0.63473 /  0.38 (18613)
  hydrogen bonds       : bond        0.04833 /  3.24 (  766)
  hydrogen bonds       : angle       3.10692 /  2.16 ( 1910)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 147
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: B   93 GLN cc_start: 0.8418 (OUTLIER) cc_final: 0.7438 (mp10)
REVERT: C   36 LYS cc_start: 0.8926 (ptpt) cc_final: 0.8616 (pptt)
REVERT: C   92 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8285 (mt-10)
REVERT: D   42 TYR cc_start: 0.8060 (t80) cc_final: 0.7760 (t80)
REVERT: D   86 ARG cc_start: 0.8799 (mmt-90) cc_final: 0.8591 (mmt-90)
REVERT: E   87 SER cc_start: 0.8889 (m) cc_final: 0.8633 (p)
REVERT: G   15 LYS cc_start: 0.7296 (tttp) cc_final: 0.6885 (ttpt)
REVERT: G   73 ASN cc_start: 0.8692 (t0) cc_final: 0.8198 (t0)
REVERT: G  110 ASN cc_start: 0.8668 (t0) cc_final: 0.8098 (p0)
REVERT: H   63 ASN cc_start: 0.8255 (t0) cc_final: 0.8017 (m-40)
  outliers start: 7
  outliers final: 1
  residues processed: 149
  average time/residue: 0.8376
  time to fit residues: 131.5184
Evaluate side-chains
  143 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 140
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   92 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks: [71, 39, 93, 95, 86, 83, 62, 27, 54, 40, 3]
   chunk 71 optimal weight:    3.9990
   chunk 39 optimal weight:    2.9990
   chunk 93 optimal weight:    9.9990
   chunk 95 optimal weight:    9.9990
   chunk 86 optimal weight:   20.0000
   chunk 83 optimal weight:   10.0000
   chunk 62 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 3 optimal weight:    0.4980
   overall best weight:    2.8988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  75 HIS
H  47 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.096268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.059193 restraints weight = 23064.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 1.70
r_work: 0.2664 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2683
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.99   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2683 r_free = 0.2683    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2683
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8772
moved from start:          0.1513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.056  12849  Z= 0.321
  Angle     :  0.718   7.189  18613  Z= 0.399
  Chirality :  0.050   0.264   2119
  Planarity :  0.005   0.048   1334
  Dihedral  : 31.365 145.878   4072
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.63 %
    Favored  : 83.31 %
  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:  2.05 (0.31), residues: 743
  helix:  2.09 (0.22), residues: 539
  sheet:  None (None), residues: 0
  loop : -0.62 (0.40), residues: 204

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  53 
 TYR   0.019   0.002   TYR E  54 
 PHE   0.016   0.002   PHE G  25 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00702 /  0.32 (12849)
  covalent geometry    : angle       0.71808 /  0.40 (18613)
  hydrogen bonds       : bond        0.05863 /  3.93 (  766)
  hydrogen bonds       : angle       2.98246 /  2.09 ( 1910)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 138
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.8920 (ptpt) cc_final: 0.8570 (pptt)
REVERT: C   73 ASN cc_start: 0.8393 (t0) cc_final: 0.7781 (t160)
REVERT: C   92 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8219 (mt-10)
REVERT: D   42 TYR cc_start: 0.8213 (t80) cc_final: 0.8005 (t80)
REVERT: G   15 LYS cc_start: 0.7217 (tttp) cc_final: 0.6891 (ttpt)
REVERT: G   56 GLU cc_start: 0.8716 (tt0) cc_final: 0.8495 (tt0)
REVERT: G   73 ASN cc_start: 0.8632 (t0) cc_final: 0.8151 (t0)
REVERT: G   90 ASP cc_start: 0.8300 (t0) cc_final: 0.8040 (t0)
  outliers start: 13
  outliers final: 3
  residues processed: 142
  average time/residue: 0.8562
  time to fit residues: 128.1695
Evaluate side-chains
  138 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 134
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain H residue  122 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks: [45, 31, 98, 81, 25, 3, 10, 50, 7, 91, 73]
   chunk 45 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 98 optimal weight:   10.0000
   chunk 81 optimal weight:   10.9990
   chunk 25 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 91 optimal weight:   10.0000
   chunk 73 optimal weight:   20.0000
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  47 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.098022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.061298 restraints weight = 22986.867|
|-----------------------------------------------------------------------------|
r_work (start): 0.2894 rms_B_bonded: 1.71
r_work: 0.2715 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (13 function evaluations)
r_final: 0.2733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8727
moved from start:          0.1462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12849  Z= 0.151
  Angle     :  0.618   6.722  18613  Z= 0.357
  Chirality :  0.043   0.286   2119
  Planarity :  0.004   0.045   1334
  Dihedral  : 31.208 144.932   4072
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 16.22 %
    Favored  : 82.03 %
  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 (0.31), residues: 743
  helix:  2.35 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.55 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  86 
 TYR   0.011   0.001   TYR H  40 
 PHE   0.009   0.002   PHE A  67 
 HIS   0.002   0.001   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.15 (12849)
  covalent geometry    : angle       0.61836 /  0.36 (18613)
  hydrogen bonds       : bond        0.04137 /  2.75 (  766)
  hydrogen bonds       : angle       2.75745 /  1.92 ( 1910)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 142
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.8876 (ptpt) cc_final: 0.8583 (pptt)
REVERT: C   73 ASN cc_start: 0.8383 (t0) cc_final: 0.7809 (t160)
REVERT: C   92 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8168 (mt-10)
REVERT: D   42 TYR cc_start: 0.8029 (t80) cc_final: 0.7700 (t80)
REVERT: F   77 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8666 (mtmp)
REVERT: G   15 LYS cc_start: 0.7146 (tttp) cc_final: 0.6816 (ttpt)
REVERT: G   73 ASN cc_start: 0.8568 (t0) cc_final: 0.8112 (t0)
REVERT: G   90 ASP cc_start: 0.8331 (t0) cc_final: 0.8039 (t0)
REVERT: H   63 ASN cc_start: 0.8361 (OUTLIER) cc_final: 0.8039 (m-40)
  outliers start: 11
  outliers final: 2
  residues processed: 147
  average time/residue: 0.8167
  time to fit residues: 126.5697
Evaluate side-chains
  142 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 137
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   63 ASN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks: [6, 41, 99, 40, 69, 52, 22, 74, 36, 38, 1]
   chunk 6 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 99 optimal weight:   20.0000
   chunk 40 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 74 optimal weight:   10.0000
   chunk 36 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   overall best weight:    1.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 104 GLN
E  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.097473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.060651 restraints weight = 23079.665|
|-----------------------------------------------------------------------------|
r_work (start): 0.2886 rms_B_bonded: 1.70
r_work: 0.2710 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2723
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2723 r_free = 0.2723    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2723 r_free = 0.2723    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2723
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8729
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12849  Z= 0.190
  Angle     :  0.628   6.872  18613  Z= 0.361
  Chirality :  0.044   0.295   2119
  Planarity :  0.004   0.045   1334
  Dihedral  : 31.214 145.238   4072
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 16.69 %
    Favored  : 81.40 %
  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:  2.52 (0.31), residues: 743
  helix:  2.43 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.58 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  79 
 TYR   0.010   0.001   TYR C  50 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.19 (12849)
  covalent geometry    : angle       0.62810 /  0.36 (18613)
  hydrogen bonds       : bond        0.04419 /  2.96 (  766)
  hydrogen bonds       : angle       2.71895 /  1.89 ( 1910)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.8866 (ptpt) cc_final: 0.8571 (pptt)
REVERT: C   73 ASN cc_start: 0.8452 (t0) cc_final: 0.7893 (t160)
REVERT: C   92 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8283 (mt-10)
REVERT: D   42 TYR cc_start: 0.8087 (t80) cc_final: 0.7816 (t80)
REVERT: G   15 LYS cc_start: 0.7178 (tttp) cc_final: 0.6836 (ttpt)
REVERT: G   73 ASN cc_start: 0.8537 (t0) cc_final: 0.8081 (t0)
REVERT: G   90 ASP cc_start: 0.8353 (t0) cc_final: 0.8049 (t0)
REVERT: H   63 ASN cc_start: 0.8335 (OUTLIER) cc_final: 0.8004 (m-40)
  outliers start: 12
  outliers final: 6
  residues processed: 140
  average time/residue: 0.8269
  time to fit residues: 122.1402
Evaluate side-chains
  142 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 134
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   63 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks: [6, 14, 51, 82, 27, 91, 24, 70, 38, 87, 18]
   chunk 6 optimal weight:    0.5980
   chunk 14 optimal weight:    0.7980
   chunk 51 optimal weight:    1.9990
   chunk 82 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 91 optimal weight:   10.0000
   chunk 24 optimal weight:    0.6980
   chunk 70 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 87 optimal weight:    9.9990
   chunk 18 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.098058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.061175 restraints weight = 23010.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.2889 rms_B_bonded: 1.71
r_work: 0.2711 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (7 function evaluations)
r_final: 0.2733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8721
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12849  Z= 0.142
  Angle     :  0.618   6.901  18613  Z= 0.356
  Chirality :  0.043   0.295   2119
  Planarity :  0.004   0.042   1334
  Dihedral  : 31.203 145.007   4072
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 16.85 %
    Favored  : 81.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.64 (0.31), residues: 743
  helix:  2.53 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.56 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  86 
 TYR   0.011   0.001   TYR H  40 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.14 (12849)
  covalent geometry    : angle       0.61812 /  0.36 (18613)
  hydrogen bonds       : bond        0.04152 /  2.78 (  766)
  hydrogen bonds       : angle       2.69824 /  1.88 ( 1910)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 141
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.8855 (ptpt) cc_final: 0.8559 (pptt)
REVERT: C   73 ASN cc_start: 0.8438 (t0) cc_final: 0.7871 (t160)
REVERT: C   92 GLU cc_start: 0.8561 (OUTLIER) cc_final: 0.8263 (mt-10)
REVERT: D   42 TYR cc_start: 0.8061 (t80) cc_final: 0.7755 (t80)
REVERT: D   93 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.7670 (mp0)
REVERT: F   77 LYS cc_start: 0.8987 (OUTLIER) cc_final: 0.8604 (mtmp)
REVERT: G   15 LYS cc_start: 0.7151 (tttp) cc_final: 0.6813 (ttpt)
REVERT: G   73 ASN cc_start: 0.8505 (t0) cc_final: 0.8057 (t0)
REVERT: G   90 ASP cc_start: 0.8348 (t0) cc_final: 0.8050 (t0)
REVERT: H   63 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.7987 (m-40)
  outliers start: 13
  outliers final: 5
  residues processed: 146
  average time/residue: 0.7957
  time to fit residues: 122.7664
Evaluate side-chains
  146 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 137
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain D residue   93 GLU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   63 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks: [93, 99, 91, 37, 84, 55, 72, 43, 95, 80, 4]
   chunk 93 optimal weight:    9.9990
   chunk 99 optimal weight:   20.0000
   chunk 91 optimal weight:   10.0000
   chunk 37 optimal weight:    0.9990
   chunk 84 optimal weight:    9.9990
   chunk 55 optimal weight:    1.9990
   chunk 72 optimal weight:   20.0000
   chunk 43 optimal weight:    2.9990
   chunk 95 optimal weight:   10.0000
   chunk 80 optimal weight:    9.9990
   chunk 4 optimal weight:    3.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 104 GLN
G  31 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.094312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.057485 restraints weight = 22933.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.2809 rms_B_bonded: 1.69
r_work: 0.2629 rms_B_bonded: 3.28 restraints_weight: 0.5000
r_work (final): 0.2629
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2645
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2645 r_free = 0.2645    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2645 r_free = 0.2645    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2645
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8805
moved from start:          0.2011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.072  12849  Z= 0.434
  Angle     :  0.788   7.501  18613  Z= 0.424
  Chirality :  0.053   0.312   2119
  Planarity :  0.006   0.066   1334
  Dihedral  : 31.691 146.489   4072
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.69 %
    Favored  : 80.92 %
  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 are not related in a simple way.
  whole:  1.93 (0.30), residues: 743
  helix:  2.04 (0.22), residues: 544
  sheet:  None (None), residues: 0
  loop : -0.90 (0.39), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  86 
 TYR   0.021   0.002   TYR C  50 
 PHE   0.012   0.002   PHE G  25 
 HIS   0.003   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00969 /  0.43 (12849)
  covalent geometry    : angle       0.78825 /  0.42 (18613)
  hydrogen bonds       : bond        0.06486 /  4.36 (  766)
  hydrogen bonds       : angle       2.97286 /  2.09 ( 1910)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 131
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.8945 (ptpt) cc_final: 0.8605 (pptt)
REVERT: C   73 ASN cc_start: 0.8584 (t0) cc_final: 0.8004 (t160)
REVERT: C   92 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8306 (mt-10)
REVERT: E   59 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8080 (pm20)
REVERT: G   15 LYS cc_start: 0.7357 (tttp) cc_final: 0.6969 (ttpt)
REVERT: G   73 ASN cc_start: 0.8607 (t0) cc_final: 0.8137 (t0)
REVERT: G   90 ASP cc_start: 0.8410 (t0) cc_final: 0.8067 (t0)
  outliers start: 15
  outliers final: 8
  residues processed: 136
  average time/residue: 0.8304
  time to fit residues: 119.0209
Evaluate side-chains
  140 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain C residue  114 VAL
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   59 GLU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain G residue  110 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks: [38, 12, 49, 33, 34, 91, 88, 64, 20, 57, 14]
   chunk 38 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 91 optimal weight:    9.9990
   chunk 88 optimal weight:   10.0000
   chunk 64 optimal weight:    0.6980
   chunk 20 optimal weight:    0.8980
   chunk 57 optimal weight:    0.6980
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 104 GLN
H  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.096718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.059897 restraints weight = 22757.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 1.69
r_work: 0.2688 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2689
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2689 r_free = 0.2689    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2689 r_free = 0.2689    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (17 function evaluations)
r_final: 0.2689
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8747
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12849  Z= 0.160
  Angle     :  0.652   7.198  18613  Z= 0.367
  Chirality :  0.045   0.324   2119
  Planarity :  0.004   0.048   1334
  Dihedral  : 31.495 145.300   4072
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 17.97 %
    Favored  : 80.76 %
  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 are not related in a simple way.
  whole:  2.47 (0.31), residues: 743
  helix:  2.43 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.70 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  86 
 TYR   0.012   0.001   TYR H  40 
 PHE   0.008   0.001   PHE A  67 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00309 /  0.16 (12849)
  covalent geometry    : angle       0.65194 /  0.37 (18613)
  hydrogen bonds       : bond        0.04247 /  2.82 (  766)
  hydrogen bonds       : angle       2.77113 /  1.93 ( 1910)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 139
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.8866 (ptpt) cc_final: 0.8570 (pptt)
REVERT: C   73 ASN cc_start: 0.8511 (t0) cc_final: 0.7948 (t160)
REVERT: C   92 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.8280 (mt-10)
REVERT: C   95 LYS cc_start: 0.9061 (ttmt) cc_final: 0.8837 (ttmt)
REVERT: G   15 LYS cc_start: 0.7247 (tttp) cc_final: 0.6879 (ttpt)
REVERT: G   73 ASN cc_start: 0.8526 (t0) cc_final: 0.8066 (t0)
REVERT: G   90 ASP cc_start: 0.8404 (t0) cc_final: 0.8075 (t0)
  outliers start: 8
  outliers final: 4
  residues processed: 141
  average time/residue: 0.8392
  time to fit residues: 124.6896
Evaluate side-chains
  141 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 136
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue  110 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks: [13, 38, 75, 59, 34, 94, 81, 89, 56, 16, 48]
   chunk 13 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 75 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 94 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   chunk 89 optimal weight:   10.0000
   chunk 56 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 104 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.097443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.060786 restraints weight = 22707.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.2887 rms_B_bonded: 1.69
r_work: 0.2712 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2726
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2726 r_free = 0.2726    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2726 r_free = 0.2726    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2726
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8724
moved from start:          0.1890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068  12849  Z= 0.143
  Angle     :  0.631   7.286  18613  Z= 0.361
  Chirality :  0.044   0.325   2119
  Planarity :  0.004   0.050   1334
  Dihedral  : 31.334 145.027   4072
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 18.76 %
    Favored  : 80.13 %
  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:  2.57 (0.31), residues: 743
  helix:  2.50 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.67 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D  86 
 TYR   0.014   0.001   TYR B  51 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.14 (12849)
  covalent geometry    : angle       0.63080 /  0.36 (18613)
  hydrogen bonds       : bond        0.04082 /  2.72 (  766)
  hydrogen bonds       : angle       2.70214 /  1.88 ( 1910)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 137
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.8849 (ptpt) cc_final: 0.8569 (pptt)
REVERT: C   73 ASN cc_start: 0.8499 (t0) cc_final: 0.7936 (t160)
REVERT: C   92 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8289 (mt-10)
REVERT: C   95 LYS cc_start: 0.9069 (ttmt) cc_final: 0.8848 (ttmt)
REVERT: F   77 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8598 (mtmp)
REVERT: G   15 LYS cc_start: 0.7221 (tttp) cc_final: 0.6853 (ttpt)
REVERT: G   73 ASN cc_start: 0.8523 (t0) cc_final: 0.8079 (t0)
REVERT: G   90 ASP cc_start: 0.8402 (t0) cc_final: 0.8083 (t0)
  outliers start: 7
  outliers final: 4
  residues processed: 140
  average time/residue: 0.8548
  time to fit residues: 126.1272
Evaluate side-chains
  142 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 136
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain F residue   77 LYS
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   63 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks: [88, 99, 92, 26, 33, 8, 42, 37, 7, 24, 83]
   chunk 88 optimal weight:   10.0000
   chunk 99 optimal weight:   20.0000
   chunk 92 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 33 optimal weight:    0.5980
   chunk 8 optimal weight:    0.5980
   chunk 42 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 24 optimal weight:    0.7980
   chunk 83 optimal weight:   10.0000
   overall best weight:    0.7782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 104 GLN
H  47 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.097885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.061558 restraints weight = 23080.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.2908 rms_B_bonded: 1.63
r_work: 0.2736 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2747
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2747 r_free = 0.2747    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2747 r_free = 0.2747    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (7 function evaluations)
r_final: 0.2747
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8810
moved from start:          0.1908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12849  Z= 0.145
  Angle     :  0.605   7.345  18613  Z= 0.352
  Chirality :  0.042   0.327   2119
  Planarity :  0.004   0.049   1334
  Dihedral  : 31.182 145.153   4072
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.69 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 18.92 %
    Favored  : 79.65 %
  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:  2.73 (0.31), residues: 743
  helix:  2.63 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.65 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  86 
 TYR   0.011   0.001   TYR H  40 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.14 (12849)
  covalent geometry    : angle       0.60531 /  0.35 (18613)
  hydrogen bonds       : bond        0.03936 /  2.62 (  766)
  hydrogen bonds       : angle       2.60953 /  1.81 ( 1910)

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

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

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1486 Ramachandran restraints generated.
    743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 141
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
REVERT: C   73 ASN cc_start: 0.8544 (t0) cc_final: 0.7990 (t160)
REVERT: C   92 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8313 (mt-10)
REVERT: C   95 LYS cc_start: 0.9120 (ttmt) cc_final: 0.8898 (ttmt)
REVERT: G   15 LYS cc_start: 0.7373 (tttp) cc_final: 0.6991 (ttpt)
REVERT: G   73 ASN cc_start: 0.8498 (t0) cc_final: 0.8027 (t0)
REVERT: G   90 ASP cc_start: 0.8481 (t0) cc_final: 0.8186 (t0)
  outliers start: 9
  outliers final: 4
  residues processed: 145
  average time/residue: 0.8442
  time to fit residues: 129.0679
Evaluate side-chains
  142 residues out of total 629 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 137
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain C residue   92 GLU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain G residue  110 ASN
Chi-restraints excluded: chain H residue   63 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks: [36, 57, 18, 16, 31, 67, 38, 21, 42, 49, 12]
   chunk 36 optimal weight:    4.9990
   chunk 57 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 38 optimal weight:    0.2980
   chunk 21 optimal weight:    0.6980
   chunk 42 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 104 GLN
H  47 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.097939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.061504 restraints weight = 22870.506|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 1.63
r_work: 0.2734 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2731
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2731 r_free = 0.2731    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2731 r_free = 0.2731    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (7 function evaluations)
r_final: 0.2731
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8862
moved from start:          0.1953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12849  Z= 0.154
  Angle     :  0.612   7.185  18613  Z= 0.353
  Chirality :  0.042   0.325   2119
  Planarity :  0.004   0.049   1334
  Dihedral  : 31.177 145.292   4072
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.27
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.42 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 19.55 %
    Favored  : 79.33 %
  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 are not related in a simple way.
  whole:  2.74 (0.31), residues: 743
  helix:  2.64 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -0.65 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  86 
 TYR   0.010   0.001   TYR H  40 
 PHE   0.010   0.001   PHE A  67 
 HIS   0.004   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.15 (12849)
  covalent geometry    : angle       0.61220 /  0.35 (18613)
  hydrogen bonds       : bond        0.03982 /  2.66 (  766)
  hydrogen bonds       : angle       2.61260 /  1.82 ( 1910)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4306.14 seconds
wall clock time: 73 minutes 56.73 seconds (4436.73 seconds total)