Starting phenix.real_space_refine
on Fri May 16 01:25:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8g8b_29845/05_2025/8g8b_29845.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8g8b_29845/05_2025/8g8b_29845.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8g8b_29845/05_2025/8g8b_29845.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8g8b_29845/05_2025/8g8b_29845.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8g8b_29845/05_2025/8g8b_29845.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8g8b_29845/05_2025/8g8b_29845.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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     336      5.49       5
     S      17      5.16       5
     C    7819      2.51       5
     N    2611      2.21       5
     O    3284      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 14067
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      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: "C"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 863
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 863
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "F"
      Number of atoms: 648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 648
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "G"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 834
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 3419
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 168, 3419
          Classifications: {'DNA': 168}
          Link IDs: {'rna3p': 167}
    Chain: "J"
      Number of atoms: 3469
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 168, 3469
          Classifications: {'DNA': 168}
          Link IDs: {'rna3p': 167}
    Chain: "X"
      Number of atoms: 1080
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 132, 1080
          Classifications: {'peptide': 132}
          Link IDs: {'PTRANS': 3, 'TRANS': 128}
          Chain breaks: 1
  Time building chain proxies: 8.45, per 1000 atoms: 0.60
  Number of scatterers: 14067
  At special positions: 0
  Unit cell: (80.5, 119.14, 172.27, 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      17     16.00
     P     336     15.00
     O    3284      8.00
     N    2611      7.00
     C    7819      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.56
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1692

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 10 sheets defined
      74.5% alpha, 2.4% beta
      161 base pairs and 290 stacking pairs defined.
    Time for finding SS restraints: 7.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 4.053A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.736A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.233A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 100 through 121
    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: 3.950A  pdb=" N   GLN F  27 " --> pdb=" O   ASP F  24 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.533A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.363A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
    Processing helix  chain 'X' and resid 141 through 161
    Processing helix  chain 'X' and resid 163 through 176
    Processing helix  chain 'X' and resid 180 through 189
      removed outlier: 3.552A  pdb=" N   ILE X 184 " --> pdb=" O   SER X 180 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 193 through 211
      Proline residue:  X 202  - end of helix
    Processing helix  chain 'X' and resid 215 through 220
    Processing helix  chain 'X' and resid 239 through 249
    Processing helix  chain 'X' and resid 256 through 268
      removed outlier: 3.681A  pdb=" N   HIS X 262 " --> pdb=" O   GLN X 258 " (cutoff:3.500A)
    Processing helix  chain 'X' and resid 270 through 288
      removed outlier: 4.059A  pdb=" N   SER X 288 " --> pdb=" O   LYS X 284 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.928A  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: 6.705A  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: 7.125A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.758A  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: 6.760A  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: 6.981A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78

    491 hydrogen bonds defined for protein.
    1449 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      389 hydrogen bonds
      778 hydrogen bond angles
      0 basepair planarities
      161 basepair parallelities
      290 stacking parallelities
  Total time for adding SS restraints: 6.46

  Time building geometry restraints manager: 4.22 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2622
        1.33 -     1.45: 4963
        1.45 -     1.57: 6717
        1.57 -     1.69: 670
        1.69 -     1.81: 28
  Bond restraints: 15000
  Sorted by residual:
  bond pdb=" N   THR E  32 "
       pdb=" CA  THR E  32 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.29e-02 6.01e+03 7.60e+00
  bond pdb=" N   ARG E  40 "
       pdb=" CA  ARG E  40 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.32e-02 5.74e+03 6.27e+00
  bond pdb=" N   TYR E  41 "
       pdb=" CA  TYR E  41 "
    ideal  model  delta    sigma   weight residual
    1.455  1.486 -0.031 1.27e-02 6.20e+03 5.86e+00
  bond pdb=" C1'  DC J -96 "
       pdb=" N1   DC J -96 "
    ideal  model  delta    sigma   weight residual
    1.490  1.552 -0.062 3.00e-02 1.11e+03 4.20e+00
  bond pdb=" C1'  DC I  83 "
       pdb=" N1   DC I  83 "
    ideal  model  delta    sigma   weight residual
    1.490  1.549 -0.059 3.00e-02 1.11e+03 3.88e+00
  ... (remaining 14995 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 21469
        2.36 -     4.72: 201
        4.72 -     7.08: 20
        7.08 -     9.44: 3
        9.44 -    11.79: 1
  Bond angle restraints: 21694
  Sorted by residual:
  angle pdb=" O3'  DG J -71 "
        pdb=" C3'  DG J -71 "
        pdb=" C2'  DG J -71 "
      ideal   model   delta    sigma   weight residual
     111.50  103.17    8.33 1.50e+00 4.44e-01 3.08e+01
  angle pdb=" O3'  DG J -73 "
        pdb=" C3'  DG J -73 "
        pdb=" C2'  DG J -73 "
      ideal   model   delta    sigma   weight residual
     111.50  104.37    7.13 1.50e+00 4.44e-01 2.26e+01
  angle pdb=" O3'  DA I  78 "
        pdb=" C3'  DA I  78 "
        pdb=" C2'  DA I  78 "
      ideal   model   delta    sigma   weight residual
     111.50  104.62    6.88 1.50e+00 4.44e-01 2.10e+01
  angle pdb=" CB  MET X 197 "
        pdb=" CG  MET X 197 "
        pdb=" SD  MET X 197 "
      ideal   model   delta    sigma   weight residual
     112.70  124.49  -11.79 3.00e+00 1.11e-01 1.55e+01
  angle pdb=" C4'  DC I  75 "
        pdb=" C3'  DC I  75 "
        pdb=" O3'  DC I  75 "
      ideal   model   delta    sigma   weight residual
     110.00  104.22    5.78 1.50e+00 4.44e-01 1.48e+01
  ... (remaining 21689 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.81: 6500
       35.81 -    71.62: 1745
       71.62 -   107.42: 15
      107.42 -   143.23: 2
      143.23 -   179.04: 1
  Dihedral angle restraints: 8263
    sinusoidal: 5648
      harmonic: 2615
  Sorted by residual:
  dihedral pdb=" C4'  DA I  20 "
           pdb=" C3'  DA I  20 "
           pdb=" O3'  DA I  20 "
           pdb=" P    DT I  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   39.04 -179.04     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DA I  82 "
           pdb=" C3'  DA I  82 "
           pdb=" O3'  DA I  82 "
           pdb=" P    DC I  83 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   80.83  139.17     1      3.50e+01 8.16e-04 1.38e+01
  dihedral pdb=" CA  PRO D 100 "
           pdb=" C   PRO D 100 "
           pdb=" N   GLY D 101 "
           pdb=" CA  GLY D 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.49  -18.51     0      5.00e+00 4.00e-02 1.37e+01
  ... (remaining 8260 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1952
       0.041 -    0.083: 438
       0.083 -    0.124: 63
       0.124 -    0.165: 10
       0.165 -    0.206: 5
  Chirality restraints: 2468
  Sorted by residual:
  chirality pdb=" C3'  DC I  75 "
            pdb=" C4'  DC I  75 "
            pdb=" O3'  DC I  75 "
            pdb=" C2'  DC I  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.87    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" C3'  DT J -76 "
            pdb=" C4'  DT J -76 "
            pdb=" O3'  DT J -76 "
            pdb=" C2'  DT J -76 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.85    0.19 2.00e-01 2.50e+01 9.12e-01
  chirality pdb=" C3'  DG J -71 "
            pdb=" C4'  DG J -71 "
            pdb=" O3'  DG J -71 "
            pdb=" C2'  DG J -71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.84    0.18 2.00e-01 2.50e+01 8.50e-01
  ... (remaining 2465 not shown)

  Planarity restraints: 1582
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT I  79 "    0.023 2.00e-02 2.50e+03   1.15e-02 3.31e+00
        pdb=" N1   DT I  79 "    0.002 2.00e-02 2.50e+03
        pdb=" C2   DT I  79 "   -0.006 2.00e-02 2.50e+03
        pdb=" O2   DT I  79 "   -0.013 2.00e-02 2.50e+03
        pdb=" N3   DT I  79 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DT I  79 "    0.003 2.00e-02 2.50e+03
        pdb=" O4   DT I  79 "    0.018 2.00e-02 2.50e+03
        pdb=" C5   DT I  79 "   -0.007 2.00e-02 2.50e+03
        pdb=" C7   DT I  79 "   -0.005 2.00e-02 2.50e+03
        pdb=" C6   DT I  79 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY F  56 "    0.009 2.00e-02 2.50e+03   1.79e-02 3.20e+00
        pdb=" C   GLY F  56 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   GLY F  56 "    0.012 2.00e-02 2.50e+03
        pdb=" N   VAL F  57 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "    0.029 5.00e-02 4.00e+02   4.40e-02 3.10e+00
        pdb=" N   PRO G  80 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "    0.025 5.00e-02 4.00e+02
  ... (remaining 1579 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 146
        2.63 -     3.20: 11304
        3.20 -     3.76: 26958
        3.76 -     4.33: 36243
        4.33 -     4.90: 50059
  Nonbonded interactions: 124710
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  85 "
            pdb=" N2   DG J -85 "
     model   vdw
     2.061 3.120
  nonbonded pdb=" N6   DA I  72 "
            pdb=" N3   DT J -72 "
     model   vdw
     2.065 2.560
  nonbonded pdb=" CD  PRO E  30 "
            pdb=" OE1 GLU X 209 "
     model   vdw
     2.132 3.440
  nonbonded pdb=" N1   DA I  72 "
            pdb=" O2   DT J -72 "
     model   vdw
     2.152 2.496
  nonbonded pdb=" O   GLN X 155 "
            pdb=" OG1 THR X 159 "
     model   vdw
     2.276 3.040
  ... (remaining 124705 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 38 through 133)
  selection = (chain 'E' and resid 38 through 133)
}
ncs_group {
  reference = (chain 'B' and resid 22 through 101)
  selection = (chain 'F' and resid 22 through 101)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.96
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.400
  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:          0.470
  Check model and map are aligned:         0.100
  Set scattering table:                    0.130
  Process input model:                     40.120
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
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      :  0.004   0.062  15000  Z= 0.208
  Angle     :  0.639  11.794  21694  Z= 0.388
  Chirality :  0.036   0.206   2468
  Planarity :  0.004   0.044   1582
  Dihedral  : 28.756 179.040   6571
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.81 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 17.15 %
    Favored  : 80.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.27), residues: 882
  helix:  1.93 (0.20), residues: 658
  sheet:  None (None), residues: 0
  loop : -0.64 (0.37), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP X 277 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.012   0.002   PHE E  67 
 TYR   0.013   0.002   TYR H  80 
 ARG   0.004   0.000   ARG H  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12470 (  880)
  hydrogen bonds       : angle       5.37206 ( 2227)
  covalent geometry    : bond        0.00450 (15000)
  covalent geometry    : angle       0.63909 (21694)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  327 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 312
  time to evaluate  : 1.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 LEU cc_start: 0.9228 (mt) cc_final: 0.8846 (tp)
REVERT: A   89 VAL cc_start: 0.9748 (t) cc_final: 0.9395 (m)
REVERT: A   90 MET cc_start: 0.9569 (mmp) cc_final: 0.9326 (mmm)
REVERT: A   99 TYR cc_start: 0.8162 (t80) cc_final: 0.7841 (t80)
REVERT: A  106 ASP cc_start: 0.9386 (m-30) cc_final: 0.8954 (t0)
REVERT: A  110 CYS cc_start: 0.9719 (m) cc_final: 0.9434 (m)
REVERT: B   53 GLU cc_start: 0.9278 (tp30) cc_final: 0.8811 (tt0)
REVERT: B   59 LYS cc_start: 0.9633 (tppp) cc_final: 0.9388 (tppp)
REVERT: B   61 PHE cc_start: 0.9349 (t80) cc_final: 0.8959 (t80)
REVERT: B   66 ILE cc_start: 0.9625 (mt) cc_final: 0.9422 (tt)
REVERT: C   51 LEU cc_start: 0.9717 (tp) cc_final: 0.9504 (tp)
REVERT: C   75 LYS cc_start: 0.8650 (mmtm) cc_final: 0.8343 (mmmt)
REVERT: C   94 ASN cc_start: 0.9568 (t0) cc_final: 0.9177 (m-40)
REVERT: C  101 THR cc_start: 0.9445 (m) cc_final: 0.9047 (t)
REVERT: D   34 TYR cc_start: 0.9188 (m-80) cc_final: 0.8727 (m-80)
REVERT: D   64 ASN cc_start: 0.9598 (m-40) cc_final: 0.8956 (m110)
REVERT: E   65 LEU cc_start: 0.9858 (mt) cc_final: 0.9618 (mt)
REVERT: E   94 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8919 (tp30)
REVERT: E  109 LEU cc_start: 0.9672 (mt) cc_final: 0.9301 (mt)
REVERT: F   26 ILE cc_start: 0.9212 (tp) cc_final: 0.8951 (tp)
REVERT: F   46 ILE cc_start: 0.9314 (mt) cc_final: 0.8878 (tp)
REVERT: F   51 TYR cc_start: 0.8809 (m-80) cc_final: 0.8470 (m-80)
REVERT: F   53 GLU cc_start: 0.9195 (tp30) cc_final: 0.8912 (tt0)
REVERT: F   64 ASN cc_start: 0.9661 (m-40) cc_final: 0.9248 (m-40)
REVERT: F   74 GLU cc_start: 0.9430 (mt-10) cc_final: 0.9102 (mt-10)
REVERT: G   25 PHE cc_start: 0.8966 (m-80) cc_final: 0.8594 (m-10)
REVERT: G   51 LEU cc_start: 0.9900 (tp) cc_final: 0.9654 (tp)
REVERT: G   56 GLU cc_start: 0.8697 (tt0) cc_final: 0.7532 (tt0)
REVERT: G   73 ASN cc_start: 0.9480 (m110) cc_final: 0.9070 (m110)
REVERT: G   93 LEU cc_start: 0.9811 (mt) cc_final: 0.9580 (tp)
REVERT: G   94 ASN cc_start: 0.9749 (t0) cc_final: 0.9359 (m-40)
REVERT: G  101 THR cc_start: 0.9441 (m) cc_final: 0.9144 (p)
REVERT: H   34 TYR cc_start: 0.9144 (m-80) cc_final: 0.8306 (m-10)
REVERT: H   41 VAL cc_start: 0.9742 (t) cc_final: 0.9493 (p)
REVERT: H   58 ILE cc_start: 0.9776 (mt) cc_final: 0.9432 (mt)
REVERT: H   59 MET cc_start: 0.9744 (mmm) cc_final: 0.9533 (mmm)
REVERT: H   64 ASN cc_start: 0.9453 (m-40) cc_final: 0.9223 (m110)
REVERT: H   76 ARG cc_start: 0.9617 (mtm-85) cc_final: 0.9298 (ptp-110)
REVERT: H   90 GLU cc_start: 0.9535 (mp0) cc_final: 0.9034 (mp0)
REVERT: H   98 LEU cc_start: 0.8787 (mt) cc_final: 0.8338 (mt)
REVERT: H  109 SER cc_start: 0.9698 (OUTLIER) cc_final: 0.9445 (p)
  outliers start: 15
  outliers final: 2
  residues processed: 323
  average time/residue: 0.3357
  time to fit residues: 144.5315
Evaluate side-chains
  187 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 184
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:    7.9990
   chunk 89 optimal weight:   20.0000
   chunk 49 optimal weight:    9.9990
   chunk 30 optimal weight:    0.8980
   chunk 60 optimal weight:    5.9990
   chunk 47 optimal weight:    7.9990
   chunk 92 optimal weight:   10.0000
   chunk 35 optimal weight:    0.9990
   chunk 56 optimal weight:    7.9990
   chunk 68 optimal weight:   10.0000
   chunk 107 optimal weight:   30.0000
   overall best weight:    4.7788

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

Flipped N/Q/H residues before XYZ refinement:
B  64 ASN
B  75 HIS
B  93 GLN
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H 106 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.059947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.046172 restraints weight = 160044.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.046996 restraints weight = 97189.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.047312 restraints weight = 66583.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.3734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055  15000  Z= 0.287
  Angle     :  0.696  13.099  21694  Z= 0.409
  Chirality :  0.038   0.207   2468
  Planarity :  0.007   0.150   1582
  Dihedral  : 31.609 178.169   4762
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.27), residues: 882
  helix:  1.68 (0.19), residues: 665
  sheet:  None (None), residues: 0
  loop : -0.37 (0.39), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP X 207 
 HIS   0.009   0.002   HIS F  75 
 PHE   0.018   0.002   PHE X 278 
 TYR   0.028   0.003   TYR H  80 
 ARG   0.013   0.001   ARG X 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08307 (  880)
  hydrogen bonds       : angle       3.73894 ( 2227)
  covalent geometry    : bond        0.00625 (15000)
  covalent geometry    : angle       0.69555 (21694)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 1.022 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 LEU cc_start: 0.9678 (mp) cc_final: 0.9462 (mt)
REVERT: A  106 ASP cc_start: 0.9565 (m-30) cc_final: 0.9197 (t0)
REVERT: A  126 LEU cc_start: 0.9447 (mm) cc_final: 0.9169 (tp)
REVERT: B   53 GLU cc_start: 0.9399 (tp30) cc_final: 0.8932 (tt0)
REVERT: B   97 LEU cc_start: 0.9533 (tp) cc_final: 0.9216 (tp)
REVERT: C   25 PHE cc_start: 0.8486 (m-10) cc_final: 0.8063 (m-10)
REVERT: C   94 ASN cc_start: 0.9253 (t0) cc_final: 0.8930 (t0)
REVERT: C  101 THR cc_start: 0.8759 (m) cc_final: 0.8411 (t)
REVERT: D   59 MET cc_start: 0.9751 (mmm) cc_final: 0.9293 (mmm)
REVERT: D   64 ASN cc_start: 0.9524 (m-40) cc_final: 0.9316 (m-40)
REVERT: D   80 TYR cc_start: 0.9112 (m-10) cc_final: 0.8826 (m-10)
REVERT: E   73 GLU cc_start: 0.9092 (tt0) cc_final: 0.8853 (tt0)
REVERT: E   74 ILE cc_start: 0.9568 (mt) cc_final: 0.9230 (mt)
REVERT: E   94 GLU cc_start: 0.9637 (mm-30) cc_final: 0.9271 (mm-30)
REVERT: E   99 TYR cc_start: 0.9612 (t80) cc_final: 0.9305 (t80)
REVERT: E  130 ILE cc_start: 0.9392 (mt) cc_final: 0.8481 (mt)
REVERT: F   26 ILE cc_start: 0.8901 (tp) cc_final: 0.8640 (tp)
REVERT: F   53 GLU cc_start: 0.8992 (tp30) cc_final: 0.8740 (tt0)
REVERT: F   57 VAL cc_start: 0.9598 (t) cc_final: 0.9290 (p)
REVERT: G   25 PHE cc_start: 0.9396 (m-80) cc_final: 0.8766 (m-10)
REVERT: G   64 GLU cc_start: 0.9645 (mt-10) cc_final: 0.9440 (mm-30)
REVERT: G   73 ASN cc_start: 0.8779 (m110) cc_final: 0.8525 (m110)
REVERT: G   94 ASN cc_start: 0.9383 (t0) cc_final: 0.9073 (t0)
REVERT: G  101 THR cc_start: 0.8752 (m) cc_final: 0.8408 (p)
REVERT: H   34 TYR cc_start: 0.9507 (m-80) cc_final: 0.9296 (m-80)
REVERT: H   73 GLU cc_start: 0.9596 (tp30) cc_final: 0.8695 (tp30)
REVERT: H   91 ILE cc_start: 0.9666 (mm) cc_final: 0.9440 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 237
  average time/residue: 0.3181
  time to fit residues: 102.4723
Evaluate side-chains
  163 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 46 optimal weight:    8.9990
   chunk 59 optimal weight:    0.5980
   chunk 26 optimal weight:    7.9990
   chunk 62 optimal weight:    8.9990
   chunk 61 optimal weight:    0.9990
   chunk 66 optimal weight:    5.9990
   chunk 73 optimal weight:    8.9990
   chunk 37 optimal weight:   20.0000
   chunk 87 optimal weight:   10.0000
   chunk 25 optimal weight:    5.9990
   chunk 57 optimal weight:    9.9990
   overall best weight:    4.3188

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

Flipped N/Q/H residues before XYZ refinement:
A  85 GLN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.057005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.044235 restraints weight = 167845.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.044477 restraints weight = 103545.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.044795 restraints weight = 71337.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.5128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  15000  Z= 0.254
  Angle     :  0.658  12.453  21694  Z= 0.386
  Chirality :  0.036   0.155   2468
  Planarity :  0.005   0.055   1582
  Dihedral  : 32.132 176.872   4762
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 16.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.27), residues: 882
  helix:  1.51 (0.19), residues: 665
  sheet:  None (None), residues: 0
  loop : -0.24 (0.39), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP X 207 
 HIS   0.010   0.002   HIS F  75 
 PHE   0.018   0.002   PHE A  67 
 TYR   0.024   0.003   TYR B  88 
 ARG   0.010   0.001   ARG D  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07158 (  880)
  hydrogen bonds       : angle       3.69840 ( 2227)
  covalent geometry    : bond        0.00549 (15000)
  covalent geometry    : angle       0.65771 (21694)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 1.009 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   62 ILE cc_start: 0.9309 (mm) cc_final: 0.9070 (mm)
REVERT: A   67 PHE cc_start: 0.9451 (t80) cc_final: 0.8988 (t80)
REVERT: A   81 ASP cc_start: 0.9445 (m-30) cc_final: 0.9236 (m-30)
REVERT: A   99 TYR cc_start: 0.9442 (t80) cc_final: 0.9171 (t80)
REVERT: A  126 LEU cc_start: 0.9561 (mm) cc_final: 0.9227 (tp)
REVERT: B   53 GLU cc_start: 0.9449 (tp30) cc_final: 0.9043 (tt0)
REVERT: B   97 LEU cc_start: 0.9512 (tp) cc_final: 0.9133 (tp)
REVERT: C   25 PHE cc_start: 0.8188 (m-10) cc_final: 0.7738 (m-10)
REVERT: C   39 TYR cc_start: 0.9107 (m-10) cc_final: 0.8849 (m-80)
REVERT: C   83 LEU cc_start: 0.9669 (mp) cc_final: 0.9262 (mp)
REVERT: C   94 ASN cc_start: 0.9257 (t0) cc_final: 0.8914 (t0)
REVERT: C  101 THR cc_start: 0.8784 (m) cc_final: 0.8413 (t)
REVERT: C  112 GLN cc_start: 0.9226 (tp40) cc_final: 0.8881 (tp-100)
REVERT: D   64 ASN cc_start: 0.9416 (m-40) cc_final: 0.9169 (m-40)
REVERT: D   65 ASP cc_start: 0.9806 (t0) cc_final: 0.9583 (t0)
REVERT: D   73 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8918 (mm-30)
REVERT: E   94 GLU cc_start: 0.9640 (mm-30) cc_final: 0.9317 (mm-30)
REVERT: E  124 ILE cc_start: 0.9656 (mt) cc_final: 0.9452 (mt)
REVERT: F   97 LEU cc_start: 0.9399 (tp) cc_final: 0.9194 (tp)
REVERT: F  100 PHE cc_start: 0.7088 (m-80) cc_final: 0.6463 (m-80)
REVERT: G   25 PHE cc_start: 0.9166 (m-10) cc_final: 0.8455 (m-10)
REVERT: G   73 ASN cc_start: 0.8559 (m110) cc_final: 0.8273 (m110)
REVERT: G   94 ASN cc_start: 0.9337 (t0) cc_final: 0.9047 (t0)
REVERT: G  101 THR cc_start: 0.8528 (m) cc_final: 0.8135 (p)
REVERT: H   64 ASN cc_start: 0.9325 (m110) cc_final: 0.9111 (m110)
REVERT: H   76 ARG cc_start: 0.9772 (mpt-90) cc_final: 0.9544 (ptp-110)
REVERT: H   91 ILE cc_start: 0.9630 (mm) cc_final: 0.9411 (mm)
REVERT: H  110 GLU cc_start: 0.9721 (mm-30) cc_final: 0.9356 (mm-30)
REVERT: H  113 LYS cc_start: 0.9579 (ptpp) cc_final: 0.9204 (pttm)
REVERT: H  117 LYS cc_start: 0.9729 (ptpp) cc_final: 0.9404 (ptmm)
  outliers start: 0
  outliers final: 0
  residues processed: 202
  average time/residue: 0.2991
  time to fit residues: 82.9368
Evaluate side-chains
  150 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 109 optimal weight:    9.9990
   chunk 110 optimal weight:   30.0000
   chunk 84 optimal weight:    8.9990
   chunk 105 optimal weight:    5.9990
   chunk 82 optimal weight:    8.9990
   chunk 61 optimal weight:    2.9990
   chunk 41 optimal weight:    8.9990
   chunk 37 optimal weight:    5.9990
   chunk 97 optimal weight:    7.9990
   chunk 57 optimal weight:   10.0000
   overall best weight:    5.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
** H  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.043366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2968 r_free = 0.2968 target = 0.030034 restraints weight = 138017.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.031060 restraints weight = 71027.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.031735 restraints weight = 44800.511|
|-----------------------------------------------------------------------------|
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.6338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049  15000  Z= 0.321
  Angle     :  0.717  17.940  21694  Z= 0.418
  Chirality :  0.039   0.139   2468
  Planarity :  0.006   0.070   1582
  Dihedral  : 32.696 177.502   4762
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 23.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.26), residues: 882
  helix:  0.99 (0.19), residues: 659
  sheet:  None (None), residues: 0
  loop : -0.37 (0.38), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP X 207 
 HIS   0.009   0.002   HIS F  75 
 PHE   0.015   0.002   PHE A  67 
 TYR   0.031   0.003   TYR B  88 
 ARG   0.023   0.001   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10107 (  880)
  hydrogen bonds       : angle       4.13432 ( 2227)
  covalent geometry    : bond        0.00692 (15000)
  covalent geometry    : angle       0.71685 (21694)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 TYR cc_start: 0.9481 (t80) cc_final: 0.9228 (t80)
REVERT: A  126 LEU cc_start: 0.9349 (mm) cc_final: 0.9063 (tp)
REVERT: B   53 GLU cc_start: 0.8830 (tp30) cc_final: 0.8400 (tt0)
REVERT: B   98 TYR cc_start: 0.8028 (m-10) cc_final: 0.7629 (m-10)
REVERT: C   25 PHE cc_start: 0.7666 (m-10) cc_final: 0.7136 (m-10)
REVERT: C   83 LEU cc_start: 0.9426 (mp) cc_final: 0.9074 (mp)
REVERT: C   94 ASN cc_start: 0.8862 (t0) cc_final: 0.8601 (t0)
REVERT: C  101 THR cc_start: 0.7921 (m) cc_final: 0.7564 (p)
REVERT: D   73 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8917 (mm-30)
REVERT: E   94 GLU cc_start: 0.9603 (mm-30) cc_final: 0.9344 (mm-30)
REVERT: E  119 ILE cc_start: 0.9074 (pt) cc_final: 0.8873 (pt)
REVERT: F   97 LEU cc_start: 0.8991 (tp) cc_final: 0.8741 (tp)
REVERT: F  100 PHE cc_start: 0.6058 (m-80) cc_final: 0.5821 (m-80)
REVERT: G   25 PHE cc_start: 0.8928 (m-10) cc_final: 0.8404 (m-10)
REVERT: H   97 LEU cc_start: 0.8432 (mt) cc_final: 0.7715 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.3133
  time to fit residues: 78.2655
Evaluate side-chains
  134 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.000 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 89 optimal weight:    9.9990
   chunk 63 optimal weight:   20.0000
   chunk 57 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 116 optimal weight:   30.0000
   chunk 91 optimal weight:   10.0000
   chunk 59 optimal weight:    7.9990
   chunk 11 optimal weight:    9.9990
   chunk 101 optimal weight:    7.9990
   chunk 17 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  81 ASN
D 106 HIS
E 108 ASN
** H  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.051952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.039900 restraints weight = 181914.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.040133 restraints weight = 107613.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.040611 restraints weight = 72265.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.7190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.051  15000  Z= 0.329
  Angle     :  0.729  15.614  21694  Z= 0.423
  Chirality :  0.039   0.145   2468
  Planarity :  0.006   0.058   1582
  Dihedral  : 33.072 176.974   4762
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 24.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.26), residues: 882
  helix:  0.72 (0.19), residues: 666
  sheet:  None (None), residues: 0
  loop : -0.45 (0.38), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.003   TRP X 207 
 HIS   0.011   0.002   HIS D 106 
 PHE   0.023   0.002   PHE F  61 
 TYR   0.033   0.003   TYR H  80 
 ARG   0.010   0.001   ARG H  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10165 (  880)
  hydrogen bonds       : angle       4.22307 ( 2227)
  covalent geometry    : bond        0.00706 (15000)
  covalent geometry    : angle       0.72885 (21694)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 1.026 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 LEU cc_start: 0.9636 (mm) cc_final: 0.9368 (tt)
REVERT: B   53 GLU cc_start: 0.9462 (tp30) cc_final: 0.9009 (tt0)
REVERT: B   97 LEU cc_start: 0.9481 (tp) cc_final: 0.9151 (tp)
REVERT: C   83 LEU cc_start: 0.9639 (mp) cc_final: 0.9309 (mp)
REVERT: C   90 ASP cc_start: 0.7891 (t0) cc_final: 0.7682 (t70)
REVERT: C   94 ASN cc_start: 0.9276 (t0) cc_final: 0.8968 (t0)
REVERT: C  101 THR cc_start: 0.8734 (m) cc_final: 0.8417 (p)
REVERT: D   59 MET cc_start: 0.9819 (mmp) cc_final: 0.9553 (mmm)
REVERT: D   64 ASN cc_start: 0.9307 (m-40) cc_final: 0.9067 (m-40)
REVERT: D   65 ASP cc_start: 0.9708 (t70) cc_final: 0.9463 (t0)
REVERT: D   79 HIS cc_start: 0.9718 (t-90) cc_final: 0.9514 (t-90)
REVERT: E   99 TYR cc_start: 0.9512 (t80) cc_final: 0.9203 (t80)
REVERT: G   25 PHE cc_start: 0.9072 (m-10) cc_final: 0.8036 (m-10)
REVERT: G   56 GLU cc_start: 0.8388 (tt0) cc_final: 0.7024 (tt0)
REVERT: G   94 ASN cc_start: 0.9185 (t0) cc_final: 0.8923 (t0)
REVERT: G  101 THR cc_start: 0.8868 (m) cc_final: 0.8561 (p)
REVERT: H   64 ASN cc_start: 0.9260 (m-40) cc_final: 0.9041 (m110)
REVERT: H   73 GLU cc_start: 0.9166 (mp0) cc_final: 0.8863 (mp0)
REVERT: H   76 ARG cc_start: 0.9725 (ptp-110) cc_final: 0.9477 (ptt-90)
REVERT: H  113 LYS cc_start: 0.9579 (ptpp) cc_final: 0.9180 (pttm)
REVERT: H  117 LYS cc_start: 0.9735 (ptpp) cc_final: 0.9406 (ptmm)
REVERT: H  122 LYS cc_start: 0.9125 (tmmt) cc_final: 0.8905 (pttt)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.3443
  time to fit residues: 78.5943
Evaluate side-chains
  121 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   chunk 31 optimal weight:    0.9990
   chunk 81 optimal weight:    8.9990
   chunk 48 optimal weight:    7.9990
   chunk 19 optimal weight:    7.9990
   chunk 93 optimal weight:    6.9990
   chunk 60 optimal weight:    3.9990
   chunk 95 optimal weight:    6.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.043451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.029747 restraints weight = 138936.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2986 r_free = 0.2986 target = 0.030800 restraints weight = 70212.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.031509 restraints weight = 43996.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.7293

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  15000  Z= 0.207
  Angle     :  0.650  10.846  21694  Z= 0.379
  Chirality :  0.036   0.134   2468
  Planarity :  0.004   0.052   1582
  Dihedral  : 32.547 176.643   4762
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 16.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.27), residues: 882
  helix:  1.11 (0.19), residues: 663
  sheet:  None (None), residues: 0
  loop : -0.39 (0.39), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP X 207 
 HIS   0.007   0.001   HIS F  75 
 PHE   0.011   0.002   PHE A  67 
 TYR   0.022   0.002   TYR B  88 
 ARG   0.004   0.000   ARG D  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06203 (  880)
  hydrogen bonds       : angle       3.81706 ( 2227)
  covalent geometry    : bond        0.00447 (15000)
  covalent geometry    : angle       0.64996 (21694)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 TYR cc_start: 0.9559 (t80) cc_final: 0.9324 (t80)
REVERT: A  126 LEU cc_start: 0.9498 (mm) cc_final: 0.9209 (tt)
REVERT: B   53 GLU cc_start: 0.9386 (tp30) cc_final: 0.8987 (tt0)
REVERT: B   97 LEU cc_start: 0.9346 (tp) cc_final: 0.9085 (tp)
REVERT: C   25 PHE cc_start: 0.8174 (m-10) cc_final: 0.7503 (m-10)
REVERT: C   83 LEU cc_start: 0.9520 (mp) cc_final: 0.9159 (mp)
REVERT: C  101 THR cc_start: 0.8517 (m) cc_final: 0.8286 (p)
REVERT: D   59 MET cc_start: 0.9740 (mmp) cc_final: 0.9525 (mmm)
REVERT: E   99 TYR cc_start: 0.9528 (t80) cc_final: 0.9283 (t80)
REVERT: G   25 PHE cc_start: 0.8864 (m-10) cc_final: 0.7902 (m-10)
REVERT: G   56 GLU cc_start: 0.8254 (tt0) cc_final: 0.7247 (tt0)
REVERT: G   94 ASN cc_start: 0.9189 (t0) cc_final: 0.8973 (m-40)
REVERT: G  101 THR cc_start: 0.8475 (m) cc_final: 0.8220 (p)
REVERT: H  110 GLU cc_start: 0.9562 (mm-30) cc_final: 0.9353 (mm-30)
REVERT: H  113 LYS cc_start: 0.9663 (ptpp) cc_final: 0.9376 (pttm)
REVERT: H  117 LYS cc_start: 0.9721 (ptpp) cc_final: 0.9446 (ptmm)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.3247
  time to fit residues: 80.6295
Evaluate side-chains
  127 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 106 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   chunk 64 optimal weight:   10.0000
   chunk 45 optimal weight:    4.9990
   chunk 95 optimal weight:    8.9990
   chunk 32 optimal weight:   10.0000
   chunk 68 optimal weight:    1.9990
   chunk 28 optimal weight:   10.0000
   chunk 77 optimal weight:    8.9990
   chunk 108 optimal weight:    0.0870
   chunk 99 optimal weight:    8.9990
   overall best weight:    3.4166

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.053111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.040370 restraints weight = 176936.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.041082 restraints weight = 106631.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.041514 restraints weight = 73571.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.7602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  15000  Z= 0.223
  Angle     :  0.657  11.076  21694  Z= 0.384
  Chirality :  0.037   0.175   2468
  Planarity :  0.005   0.052   1582
  Dihedral  : 32.469 177.474   4762
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 18.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.27), residues: 882
  helix:  1.04 (0.19), residues: 665
  sheet:  None (None), residues: 0
  loop : -0.38 (0.40), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP X 207 
 HIS   0.008   0.001   HIS F  75 
 PHE   0.012   0.002   PHE A  67 
 TYR   0.021   0.002   TYR H  34 
 ARG   0.006   0.001   ARG X 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07051 (  880)
  hydrogen bonds       : angle       3.91018 ( 2227)
  covalent geometry    : bond        0.00483 (15000)
  covalent geometry    : angle       0.65673 (21694)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 174
  time to evaluate  : 1.052 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.9367 (m-30) cc_final: 0.9124 (m-30)
REVERT: A   97 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8784 (mt-10)
REVERT: A  126 LEU cc_start: 0.9658 (mm) cc_final: 0.9376 (tt)
REVERT: B   49 LEU cc_start: 0.9701 (mp) cc_final: 0.9330 (mp)
REVERT: B   97 LEU cc_start: 0.9432 (tp) cc_final: 0.9150 (tp)
REVERT: C   25 PHE cc_start: 0.8044 (m-10) cc_final: 0.7380 (m-10)
REVERT: C   83 LEU cc_start: 0.9637 (mp) cc_final: 0.9269 (mp)
REVERT: C   94 ASN cc_start: 0.9106 (t0) cc_final: 0.8692 (m-40)
REVERT: C  101 THR cc_start: 0.8911 (m) cc_final: 0.8652 (p)
REVERT: D   59 MET cc_start: 0.9825 (mmp) cc_final: 0.9495 (mmm)
REVERT: D   64 ASN cc_start: 0.9272 (m-40) cc_final: 0.9026 (m-40)
REVERT: E   99 TYR cc_start: 0.9610 (t80) cc_final: 0.9304 (t80)
REVERT: F   61 PHE cc_start: 0.9563 (t80) cc_final: 0.9329 (t80)
REVERT: F   72 TYR cc_start: 0.9345 (m-80) cc_final: 0.8907 (m-80)
REVERT: G   25 PHE cc_start: 0.8865 (m-10) cc_final: 0.7889 (m-10)
REVERT: G   56 GLU cc_start: 0.8338 (tt0) cc_final: 0.6877 (tt0)
REVERT: G   94 ASN cc_start: 0.9376 (t0) cc_final: 0.9113 (m-40)
REVERT: G  101 THR cc_start: 0.8617 (m) cc_final: 0.8242 (p)
REVERT: H   34 TYR cc_start: 0.9347 (m-80) cc_final: 0.9144 (m-80)
REVERT: H   64 ASN cc_start: 0.9169 (m-40) cc_final: 0.8927 (m-40)
REVERT: H  110 GLU cc_start: 0.9699 (mm-30) cc_final: 0.9339 (mm-30)
REVERT: H  113 LYS cc_start: 0.9575 (ptpp) cc_final: 0.9151 (pttm)
REVERT: H  117 LYS cc_start: 0.9776 (ptpp) cc_final: 0.9513 (ptmm)
  outliers start: 0
  outliers final: 0
  residues processed: 174
  average time/residue: 0.3086
  time to fit residues: 73.8874
Evaluate side-chains
  126 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 98 optimal weight:    7.9990
   chunk 38 optimal weight:    0.9990
   chunk 95 optimal weight:    8.9990
   chunk 45 optimal weight:    1.9990
   chunk 90 optimal weight:   10.0000
   chunk 24 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 71 optimal weight:    5.9990
   chunk 69 optimal weight:    8.9990
   chunk 77 optimal weight:    8.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.053413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.040592 restraints weight = 174912.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.041317 restraints weight = 103133.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 17)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.041707 restraints weight = 69764.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.7837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  15000  Z= 0.210
  Angle     :  0.647  11.497  21694  Z= 0.377
  Chirality :  0.036   0.173   2468
  Planarity :  0.005   0.054   1582
  Dihedral  : 32.395 177.233   4762
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.27), residues: 882
  helix:  1.13 (0.19), residues: 665
  sheet:  None (None), residues: 0
  loop : -0.31 (0.40), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP X 207 
 HIS   0.006   0.001   HIS F  75 
 PHE   0.012   0.002   PHE A  67 
 TYR   0.018   0.002   TYR F  88 
 ARG   0.009   0.000   ARG X 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06391 (  880)
  hydrogen bonds       : angle       3.84261 ( 2227)
  covalent geometry    : bond        0.00451 (15000)
  covalent geometry    : angle       0.64689 (21694)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 177
  time to evaluate  : 1.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.9378 (m-30) cc_final: 0.9155 (m-30)
REVERT: A  126 LEU cc_start: 0.9605 (mm) cc_final: 0.9347 (tt)
REVERT: B   72 TYR cc_start: 0.9040 (m-10) cc_final: 0.8663 (m-10)
REVERT: B   97 LEU cc_start: 0.9470 (tp) cc_final: 0.9203 (tp)
REVERT: C   25 PHE cc_start: 0.7871 (m-10) cc_final: 0.7321 (m-10)
REVERT: C   83 LEU cc_start: 0.9611 (mp) cc_final: 0.9241 (mp)
REVERT: C   94 ASN cc_start: 0.9088 (t0) cc_final: 0.8810 (t0)
REVERT: C  101 THR cc_start: 0.8839 (m) cc_final: 0.8581 (p)
REVERT: D   59 MET cc_start: 0.9824 (mmp) cc_final: 0.9473 (mmm)
REVERT: D   64 ASN cc_start: 0.9283 (m-40) cc_final: 0.9071 (m-40)
REVERT: E   99 TYR cc_start: 0.9590 (t80) cc_final: 0.9298 (t80)
REVERT: F   61 PHE cc_start: 0.9534 (t80) cc_final: 0.9274 (t80)
REVERT: F   68 ASP cc_start: 0.9468 (m-30) cc_final: 0.9004 (m-30)
REVERT: F   72 TYR cc_start: 0.9372 (m-80) cc_final: 0.9017 (m-80)
REVERT: G   25 PHE cc_start: 0.8852 (m-10) cc_final: 0.7903 (m-10)
REVERT: G   56 GLU cc_start: 0.8325 (tt0) cc_final: 0.6990 (tt0)
REVERT: G   94 ASN cc_start: 0.9416 (t0) cc_final: 0.9197 (m-40)
REVERT: G  101 THR cc_start: 0.8575 (m) cc_final: 0.8201 (p)
REVERT: H   64 ASN cc_start: 0.9253 (m-40) cc_final: 0.9035 (m-40)
REVERT: H   76 ARG cc_start: 0.9756 (mtm110) cc_final: 0.9396 (ptp-110)
REVERT: H  110 GLU cc_start: 0.9667 (mm-30) cc_final: 0.9437 (mm-30)
REVERT: H  113 LYS cc_start: 0.9580 (ptpp) cc_final: 0.9233 (pttp)
REVERT: H  117 LYS cc_start: 0.9780 (ptpp) cc_final: 0.9537 (ptmm)
  outliers start: 0
  outliers final: 0
  residues processed: 177
  average time/residue: 0.3242
  time to fit residues: 78.5355
Evaluate side-chains
  128 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 1.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 109 optimal weight:    9.9990
   chunk 53 optimal weight:    0.7980
   chunk 97 optimal weight:    7.9990
   chunk 113 optimal weight:    8.9990
   chunk 117 optimal weight:   20.0000
   chunk 32 optimal weight:    9.9990
   chunk 75 optimal weight:    8.9990
   chunk 63 optimal weight:    0.0270
   chunk 70 optimal weight:    0.7980
   chunk 59 optimal weight:    5.9990
   chunk 112 optimal weight:    7.9990
   overall best weight:    3.1242

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.053213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.040405 restraints weight = 173906.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.041143 restraints weight = 102471.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.041588 restraints weight = 69311.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.7982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045  15000  Z= 0.209
  Angle     :  0.649   8.714  21694  Z= 0.377
  Chirality :  0.036   0.149   2468
  Planarity :  0.005   0.054   1582
  Dihedral  : 32.340 177.329   4762
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 16.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.27), residues: 882
  helix:  1.16 (0.19), residues: 665
  sheet:  None (None), residues: 0
  loop : -0.41 (0.39), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP X 207 
 HIS   0.006   0.001   HIS F  75 
 PHE   0.013   0.002   PHE A  67 
 TYR   0.017   0.002   TYR C  50 
 ARG   0.010   0.001   ARG X 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06410 (  880)
  hydrogen bonds       : angle       3.80466 ( 2227)
  covalent geometry    : bond        0.00452 (15000)
  covalent geometry    : angle       0.64857 (21694)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 1.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.9364 (m-30) cc_final: 0.9127 (m-30)
REVERT: A   97 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8885 (mt-10)
REVERT: A  126 LEU cc_start: 0.9628 (mm) cc_final: 0.9368 (tt)
REVERT: B   97 LEU cc_start: 0.9484 (tp) cc_final: 0.9204 (tp)
REVERT: C   25 PHE cc_start: 0.7989 (m-10) cc_final: 0.7670 (m-10)
REVERT: C   56 GLU cc_start: 0.9354 (pp20) cc_final: 0.8859 (tt0)
REVERT: C   83 LEU cc_start: 0.9629 (mp) cc_final: 0.9263 (mp)
REVERT: C   94 ASN cc_start: 0.9137 (t0) cc_final: 0.8837 (t0)
REVERT: C  101 THR cc_start: 0.8945 (m) cc_final: 0.8680 (p)
REVERT: D   59 MET cc_start: 0.9833 (mmp) cc_final: 0.9468 (mmm)
REVERT: D   64 ASN cc_start: 0.9305 (m-40) cc_final: 0.9072 (m-40)
REVERT: D   65 ASP cc_start: 0.9674 (t0) cc_final: 0.9370 (t0)
REVERT: D   69 ARG cc_start: 0.9329 (mtt180) cc_final: 0.8970 (ptp-110)
REVERT: D   98 LEU cc_start: 0.8781 (mt) cc_final: 0.8379 (mt)
REVERT: E   99 TYR cc_start: 0.9613 (t80) cc_final: 0.9303 (t80)
REVERT: F   61 PHE cc_start: 0.9542 (t80) cc_final: 0.9318 (t80)
REVERT: G   25 PHE cc_start: 0.9001 (m-10) cc_final: 0.7923 (m-10)
REVERT: G   56 GLU cc_start: 0.8483 (tt0) cc_final: 0.7089 (tt0)
REVERT: G   94 ASN cc_start: 0.9377 (t0) cc_final: 0.9144 (m-40)
REVERT: G  101 THR cc_start: 0.8754 (m) cc_final: 0.8379 (p)
REVERT: H   64 ASN cc_start: 0.9301 (m-40) cc_final: 0.9085 (m-40)
REVERT: H   76 ARG cc_start: 0.9744 (mtm110) cc_final: 0.9347 (ptp-110)
REVERT: H  110 GLU cc_start: 0.9655 (mm-30) cc_final: 0.9394 (mm-30)
REVERT: H  113 LYS cc_start: 0.9579 (ptpp) cc_final: 0.9233 (pttp)
REVERT: H  117 LYS cc_start: 0.9749 (ptpp) cc_final: 0.9490 (ptmm)
  outliers start: 0
  outliers final: 0
  residues processed: 175
  average time/residue: 0.3314
  time to fit residues: 79.4539
Evaluate side-chains
  134 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 25 optimal weight:    7.9990
   chunk 23 optimal weight:    4.9990
   chunk 80 optimal weight:    7.9990
   chunk 116 optimal weight:    0.0050
   chunk 71 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0970
   chunk 30 optimal weight:    4.9990
   chunk 99 optimal weight:    8.9990
   chunk 76 optimal weight:    8.9990
   chunk 57 optimal weight:    9.9990
   chunk 19 optimal weight:    4.9990
   overall best weight:    2.6198

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.053705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.040935 restraints weight = 173873.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.041691 restraints weight = 102897.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.042102 restraints weight = 68860.365|
|-----------------------------------------------------------------------------|
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.8115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  15000  Z= 0.190
  Angle     :  0.639   7.922  21694  Z= 0.372
  Chirality :  0.036   0.152   2468
  Planarity :  0.004   0.055   1582
  Dihedral  : 32.175 177.048   4762
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 15.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.27), residues: 882
  helix:  1.23 (0.20), residues: 665
  sheet:  None (None), residues: 0
  loop : -0.37 (0.40), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP X 207 
 HIS   0.004   0.001   HIS F  75 
 PHE   0.013   0.001   PHE A  67 
 TYR   0.019   0.002   TYR C  50 
 ARG   0.008   0.000   ARG X 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05516 (  880)
  hydrogen bonds       : angle       3.71420 ( 2227)
  covalent geometry    : bond        0.00408 (15000)
  covalent geometry    : angle       0.63924 (21694)

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

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

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1764 Ramachandran restraints generated.
    882 Oldfield, 0 Emsley, 882 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 178
  time to evaluate  : 1.142 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.9331 (m-30) cc_final: 0.8885 (m-30)
REVERT: A   97 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8902 (mt-10)
REVERT: A  126 LEU cc_start: 0.9643 (mm) cc_final: 0.9419 (tt)
REVERT: B   72 TYR cc_start: 0.8946 (m-10) cc_final: 0.8601 (m-10)
REVERT: B   74 GLU cc_start: 0.9259 (mt-10) cc_final: 0.9043 (mt-10)
REVERT: B   97 LEU cc_start: 0.9474 (tp) cc_final: 0.9178 (tp)
REVERT: C   25 PHE cc_start: 0.8293 (m-10) cc_final: 0.7448 (m-10)
REVERT: C   83 LEU cc_start: 0.9663 (mp) cc_final: 0.9287 (mp)
REVERT: C   94 ASN cc_start: 0.9274 (t0) cc_final: 0.8960 (t0)
REVERT: C  101 THR cc_start: 0.9029 (m) cc_final: 0.8751 (p)
REVERT: D   59 MET cc_start: 0.9864 (mmp) cc_final: 0.9492 (mmm)
REVERT: D   64 ASN cc_start: 0.9351 (m-40) cc_final: 0.8983 (m110)
REVERT: D   65 ASP cc_start: 0.9671 (t0) cc_final: 0.9304 (t0)
REVERT: D   69 ARG cc_start: 0.9344 (mtt180) cc_final: 0.8941 (ptp-110)
REVERT: D   79 HIS cc_start: 0.9764 (t-90) cc_final: 0.9501 (t-90)
REVERT: D   97 LEU cc_start: 0.8801 (mm) cc_final: 0.8584 (mm)
REVERT: D   98 LEU cc_start: 0.8812 (mt) cc_final: 0.8429 (mt)
REVERT: E   99 TYR cc_start: 0.9618 (t80) cc_final: 0.9273 (t80)
REVERT: F   61 PHE cc_start: 0.9563 (t80) cc_final: 0.9328 (t80)
REVERT: G   25 PHE cc_start: 0.8965 (m-10) cc_final: 0.7920 (m-10)
REVERT: G   56 GLU cc_start: 0.8571 (tt0) cc_final: 0.7117 (tt0)
REVERT: G   94 ASN cc_start: 0.9489 (t0) cc_final: 0.9246 (m-40)
REVERT: G  101 THR cc_start: 0.8824 (m) cc_final: 0.8440 (p)
REVERT: H   59 MET cc_start: 0.9811 (mmp) cc_final: 0.9593 (mmm)
REVERT: H   64 ASN cc_start: 0.9240 (m-40) cc_final: 0.8935 (m-40)
REVERT: H   76 ARG cc_start: 0.9738 (mtm110) cc_final: 0.9280 (ptp-110)
REVERT: H  113 LYS cc_start: 0.9547 (ptpp) cc_final: 0.9233 (pttm)
REVERT: H  117 LYS cc_start: 0.9752 (ptpp) cc_final: 0.9497 (ptmm)
  outliers start: 0
  outliers final: 0
  residues processed: 178
  average time/residue: 0.3211
  time to fit residues: 78.1889
Evaluate side-chains
  134 residues out of total 758 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.033 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 38 optimal weight:    5.9990
   chunk 88 optimal weight:   20.0000
   chunk 52 optimal weight:    0.7980
   chunk 82 optimal weight:   10.0000
   chunk 69 optimal weight:    8.9990
   chunk 41 optimal weight:   10.0000
   chunk 35 optimal weight:    9.9990
   chunk 11 optimal weight:    9.9990
   chunk 46 optimal weight:   10.0000
   chunk 104 optimal weight:   10.0000
   chunk 63 optimal weight:    1.9990
   overall best weight:    5.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  44 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.050916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.038640 restraints weight = 184938.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.039194 restraints weight = 111137.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.039570 restraints weight = 76174.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.8597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  15000  Z= 0.295
  Angle     :  0.713  12.616  21694  Z= 0.412
  Chirality :  0.039   0.144   2468
  Planarity :  0.005   0.051   1582
  Dihedral  : 32.629 177.382   4762
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 23.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.27), residues: 882
  helix:  0.94 (0.19), residues: 659
  sheet:  None (None), residues: 0
  loop : -0.24 (0.41), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP X 207 
 HIS   0.007   0.002   HIS F  75 
 PHE   0.013   0.002   PHE A  67 
 TYR   0.026   0.003   TYR C  50 
 ARG   0.010   0.001   ARG X 282 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.09335 (  880)
  hydrogen bonds       : angle       4.13871 ( 2227)
  covalent geometry    : bond        0.00639 (15000)
  covalent geometry    : angle       0.71272 (21694)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4197.93 seconds
wall clock time: 74 minutes 13.57 seconds (4453.57 seconds total)