Starting phenix.real_space_refine
on Fri Jul  3 18:08:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pfe_13373/07_2026/7pfe_13373.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pfe_13373/07_2026/7pfe_13373.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pfe_13373/07_2026/7pfe_13373.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pfe_13373/07_2026/7pfe_13373.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pfe_13373/07_2026/7pfe_13373.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pfe_13373/07_2026/7pfe_13373.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic.
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     354      5.49       5
     S      10      5.16       5
     C    7617      2.51       5
     N    2601      2.21       5
     O    3298      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13880
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "a"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 798
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "b"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "c"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "d"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "e"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 798
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 4, 'TRANS': 92}
    Chain: "f"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "g"
      Number of atoms: 840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 840
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "h"
      Number of atoms: 744
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 744
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "J"
      Number of atoms: 3645
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 177, 3645
          Classifications: {'DNA': 177}
          Link IDs: {'rna3p': 176}
    Chain: "I"
      Number of atoms: 3612
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 177, 3612
          Classifications: {'DNA': 177}
          Link IDs: {'rna3p': 176}
    Chain: "u"
      Number of atoms: 535
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 535
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 2, 'TRANS': 72}
  Time building chain proxies: 2.83, per 1000 atoms: 0.20
  Number of scatterers: 13880
  At special positions: 0
  Unit cell: (133.35, 132.3, 119.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     P     354     15.00
     O    3298      8.00
     N    2601      7.00
     C    7617      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: 1.08
  Conformation dependent library (CDL) restraints added in 414.7 milliseconds
  

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1566

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 10 sheets defined
      70.6% alpha, 3.1% beta
      174 base pairs and 308 stacking pairs defined.
    Time for finding SS restraints: 2.25
  Creating SS restraints...
    Processing helix  chain 'a' and resid 44 through 57
    Processing helix  chain 'a' and resid 63 through 79
      removed outlier: 3.783A  pdb=" N   PHE a  67 " --> pdb=" O   ARG a  63 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ASP a  77 " --> pdb=" O   GLU a  73 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   PHE a  78 " --> pdb=" O   ILE a  74 " (cutoff:3.500A)
    Processing helix  chain 'a' and resid 85 through 114
    Processing helix  chain 'a' and resid 120 through 132
      removed outlier: 3.716A  pdb=" N   ILE a 124 " --> pdb=" O   MET a 120 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 24 through 29
      removed outlier: 3.542A  pdb=" N   GLN b  27 " --> pdb=" O   ASP b  24 " (cutoff:3.500A)
    Processing helix  chain 'b' and resid 30 through 41
    Processing helix  chain 'b' and resid 49 through 74
      removed outlier: 4.607A  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 21
    Processing helix  chain 'c' and resid 26 through 37
    Processing helix  chain 'c' and resid 45 through 73
      removed outlier: 4.205A  pdb=" N   VAL c  49 " --> pdb=" O   ALA c  45 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 79 through 90
      removed outlier: 3.560A  pdb=" N   ASP c  90 " --> pdb=" O   ALA c  86 " (cutoff:3.500A)
    Processing helix  chain 'c' and resid 90 through 97
    Processing helix  chain 'c' and resid 112 through 116
    Processing helix  chain 'd' and resid 37 through 49
      removed outlier: 3.889A  pdb=" N   VAL d  41 " --> pdb=" O   TYR d  37 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 55 through 84
    Processing helix  chain 'd' and resid 90 through 102
      removed outlier: 3.551A  pdb=" N   ILE d  94 " --> pdb=" O   THR d  90 " (cutoff:3.500A)
    Processing helix  chain 'd' and resid 104 through 123
    Processing helix  chain 'e' and resid 44 through 57
    Processing helix  chain 'e' and resid 63 through 76
      removed outlier: 3.531A  pdb=" N   PHE e  67 " --> pdb=" O   ARG e  63 " (cutoff:3.500A)
    Processing helix  chain 'e' and resid 85 through 114
    Processing helix  chain 'e' and resid 120 through 132
    Processing helix  chain 'f' and resid 25 through 29
    Processing helix  chain 'f' and resid 30 through 41
    Processing helix  chain 'f' and resid 49 through 76
      removed outlier: 4.193A  pdb=" N   GLU f  53 " --> pdb=" O   LEU f  49 " (cutoff:3.500A)
    Processing helix  chain 'f' and resid 82 through 93
      removed outlier: 3.547A  pdb=" N   VAL f  86 " --> pdb=" O   THR f  82 " (cutoff:3.500A)
    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: 4.249A  pdb=" N   VAL g  49 " --> pdb=" O   ALA g  45 " (cutoff:3.500A)
    Processing helix  chain 'g' and resid 79 through 89
    Processing helix  chain 'g' and resid 90 through 97
    Processing helix  chain 'g' and resid 112 through 116
    Processing helix  chain 'h' and resid 37 through 49
    Processing helix  chain 'h' and resid 55 through 84
    Processing helix  chain 'h' and resid 90 through 102
    Processing helix  chain 'h' and resid 104 through 124
      removed outlier: 4.177A  pdb=" N   LYS h 108 " --> pdb=" O   GLY h 104 " (cutoff:3.500A)
    Processing helix  chain 'u' and resid 38 through 51
      removed outlier: 4.340A  pdb=" N   LEU u  42 " --> pdb=" O   PRO u  38 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   SER u  50 " --> pdb=" O   ALA u  46 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   LYS u  51 " --> pdb=" O   VAL u  47 " (cutoff:3.500A)
    Processing helix  chain 'u' and resid 58 through 69
    Processing helix  chain 'u' and resid 75 through 89
    Processing sheet with id=AA1, first strand: chain 'a' and resid 83 through 84
      removed outlier: 6.743A  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: 6.347A  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 77 through 78
    Processing sheet with id=AA5, first strand: chain 'c' and resid 101 through 102
      removed outlier: 6.565A  pdb=" N   THR c 101 " --> pdb=" O   TYR f  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'e' and resid 83 through 84
      removed outlier: 6.504A  pdb=" N   ARG e  83 " --> pdb=" O   VAL f  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'e' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'g' and resid 42 through 43
      removed outlier: 7.226A  pdb=" N   ARG g  42 " --> pdb=" O   ILE h  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'g' and resid 77 through 78
    Processing sheet with id=AB1, first strand: chain 'u' and resid 56 through 57

    433 hydrogen bonds defined for protein.
    1272 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      444 hydrogen bonds
      888 hydrogen bond angles
      0 basepair planarities
      174 basepair parallelities
      308 stacking parallelities
  Total time for adding SS restraints: 3.64

  Time building geometry restraints manager: 1.49 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 3118
        1.34 -     1.46: 5388
        1.46 -     1.58: 5614
        1.58 -     1.71: 706
        1.71 -     1.83: 20
  Bond restraints: 14846
  Sorted by residual:
  bond pdb=" C3'  DG I 350 "
       pdb=" O3'  DG I 350 "
    ideal  model  delta    sigma   weight residual
    1.435  1.484 -0.049 1.30e-02 5.92e+03 1.43e+01
  bond pdb=" C3'  DC I 333 "
       pdb=" O3'  DC I 333 "
    ideal  model  delta    sigma   weight residual
    1.435  1.387  0.048 1.30e-02 5.92e+03 1.38e+01
  bond pdb=" C5'  DA I 342 "
       pdb=" C4'  DA I 342 "
    ideal  model  delta    sigma   weight residual
    1.512  1.537 -0.025 7.00e-03 2.04e+04 1.26e+01
  bond pdb=" C3'  DG J 486 "
       pdb=" O3'  DG J 486 "
    ideal  model  delta    sigma   weight residual
    1.435  1.389  0.046 1.30e-02 5.92e+03 1.23e+01
  bond pdb=" C3'  DT I 330 "
       pdb=" C2'  DT I 330 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.13e+01
  ... (remaining 14841 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 19917
        1.93 -     3.85: 1468
        3.85 -     5.78: 122
        5.78 -     7.71: 41
        7.71 -     9.63: 15
  Bond angle restraints: 21563
  Sorted by residual:
  angle pdb=" O4'  DG I 343 "
        pdb=" C4'  DG I 343 "
        pdb=" C3'  DG I 343 "
      ideal   model   delta    sigma   weight residual
     106.00  102.57    3.43 6.00e-01 2.78e+00 3.27e+01
  angle pdb=" O4'  DA I 363 "
        pdb=" C4'  DA I 363 "
        pdb=" C3'  DA I 363 "
      ideal   model   delta    sigma   weight residual
     106.00  102.57    3.43 6.00e-01 2.78e+00 3.27e+01
  angle pdb=" N   GLU e  94 "
        pdb=" CA  GLU e  94 "
        pdb=" CB  GLU e  94 "
      ideal   model   delta    sigma   weight residual
     110.28  118.56   -8.28 1.55e+00 4.16e-01 2.85e+01
  angle pdb=" O4'  DG J 475 "
        pdb=" C4'  DG J 475 "
        pdb=" C3'  DG J 475 "
      ideal   model   delta    sigma   weight residual
     106.00  102.83    3.17 6.00e-01 2.78e+00 2.79e+01
  angle pdb=" O4'  DA I 261 "
        pdb=" C4'  DA I 261 "
        pdb=" C3'  DA I 261 "
      ideal   model   delta    sigma   weight residual
     106.00  102.86    3.14 6.00e-01 2.78e+00 2.74e+01
  ... (remaining 21558 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.97: 6170
       35.97 -    71.93: 1826
       71.93 -   107.90: 25
      107.90 -   143.86: 4
      143.86 -   179.83: 2
  Dihedral angle restraints: 8027
    sinusoidal: 5596
      harmonic: 2431
  Sorted by residual:
  dihedral pdb=" CA  GLU b  74 "
           pdb=" C   GLU b  74 "
           pdb=" N   HIS b  75 "
           pdb=" CA  HIS b  75 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  149.98   30.02     0      5.00e+00 4.00e-02 3.60e+01
  dihedral pdb=" CA  ILE b  50 "
           pdb=" C   ILE b  50 "
           pdb=" N   TYR b  51 "
           pdb=" CA  TYR b  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.25  -22.75     0      5.00e+00 4.00e-02 2.07e+01
  dihedral pdb=" CA  LEU a  60 "
           pdb=" C   LEU a  60 "
           pdb=" N   LEU a  61 "
           pdb=" CA  LEU a  61 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.63  -20.37     0      5.00e+00 4.00e-02 1.66e+01
  ... (remaining 8024 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1964
       0.065 -    0.129: 431
       0.129 -    0.194: 49
       0.194 -    0.259: 11
       0.259 -    0.323: 1
  Chirality restraints: 2456
  Sorted by residual:
  chirality pdb=" CA  PHE e 104 "
            pdb=" N   PHE e 104 "
            pdb=" C   PHE e 104 "
            pdb=" CB  PHE e 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.61e+00
  chirality pdb=" CA  GLU a  94 "
            pdb=" N   GLU a  94 "
            pdb=" C   GLU a  94 "
            pdb=" CB  GLU a  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" C3'  DG I 350 "
            pdb=" C4'  DG I 350 "
            pdb=" O3'  DG I 350 "
            pdb=" C2'  DG I 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.48   -0.25 2.00e-01 2.50e+01 1.51e+00
  ... (remaining 2453 not shown)

  Planarity restraints: 1498
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE a 104 "    0.018 2.00e-02 2.50e+03   2.09e-02 7.62e+00
        pdb=" CG  PHE a 104 "   -0.048 2.00e-02 2.50e+03
        pdb=" CD1 PHE a 104 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 PHE a 104 "    0.014 2.00e-02 2.50e+03
        pdb=" CE1 PHE a 104 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE a 104 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE a 104 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE c  79 "   -0.044 5.00e-02 4.00e+02   6.60e-02 6.98e+00
        pdb=" N   PRO c  80 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO c  80 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO c  80 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG d  99 "    0.214 9.50e-02 1.11e+02   9.63e-02 6.87e+00
        pdb=" NE  ARG d  99 "   -0.019 2.00e-02 2.50e+03
        pdb=" CZ  ARG d  99 "    0.017 2.00e-02 2.50e+03
        pdb=" NH1 ARG d  99 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG d  99 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1495 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 3060
        2.79 -     3.32: 12862
        3.32 -     3.85: 30171
        3.85 -     4.37: 33418
        4.37 -     4.90: 45752
  Nonbonded interactions: 125263
  Sorted by model distance:
  nonbonded pdb=" O   GLN e  93 "
            pdb=" OG  SER e  96 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" OE2 GLU u  52 "
            pdb=" OG  SER u  54 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OG  SER c  40 "
            pdb=" O   ARG c  42 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OG1 THR d  90 "
            pdb=" OE1 GLU d  93 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" NE2 HIS a 113 "
            pdb=" OD1 ASP e 123 "
     model   vdw
     2.312 3.120
  ... (remaining 125258 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'a'
  selection = chain 'e'
}
ncs_group {
  reference = chain 'b'
  selection = chain 'f'
}
ncs_group {
  reference = chain 'c'
  selection = chain 'g'
}
ncs_group {
  reference = chain 'd'
  selection = chain 'h'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.180
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.064  14846  Z= 0.655
  Angle     :  1.061   9.632  21563  Z= 0.829
  Chirality :  0.054   0.323   2456
  Planarity :  0.008   0.096   1498
  Dihedral  : 29.754 179.829   6461
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.12 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.26), residues: 825
  helix:  0.09 (0.20), residues: 566
  sheet: -2.08 (1.53), residues: 10
  loop : -0.80 (0.32), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG d  99 
 TYR   0.035   0.003   TYR f  72 
 PHE   0.048   0.003   PHE a 104 
 HIS   0.008   0.003   HIS b  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00761 /  0.65 (14846)
  covalent geometry    : angle       1.06121 /  0.83 (21563)
  hydrogen bonds       : bond        0.11466 /  7.28 (  877)
  hydrogen bonds       : angle       4.99610 /  3.59 ( 2160)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   50 GLU cc_start: 0.9307 (mp0) cc_final: 0.9024 (mp0)
REVERT: a   81 ASP cc_start: 0.8781 (t0) cc_final: 0.8269 (p0)
REVERT: a   94 GLU cc_start: 0.9252 (mp0) cc_final: 0.8561 (mp0)
REVERT: c   25 PHE cc_start: 0.8697 (m-80) cc_final: 0.8220 (m-80)
REVERT: c   72 ASP cc_start: 0.9478 (m-30) cc_final: 0.9250 (m-30)
REVERT: d   85 LYS cc_start: 0.9666 (mppt) cc_final: 0.9451 (mmtm)
REVERT: d   99 ARG cc_start: 0.9093 (ttm110) cc_final: 0.8705 (mtp85)
REVERT: d  106 LEU cc_start: 0.9478 (mt) cc_final: 0.9174 (mt)
REVERT: d  113 GLU cc_start: 0.9130 (mp0) cc_final: 0.8823 (mp0)
REVERT: e   50 GLU cc_start: 0.9653 (mp0) cc_final: 0.9278 (mp0)
REVERT: e   54 TYR cc_start: 0.9479 (m-80) cc_final: 0.9278 (m-80)
REVERT: e   90 MET cc_start: 0.9263 (tpt) cc_final: 0.8975 (tpt)
REVERT: e  106 ASP cc_start: 0.9480 (m-30) cc_final: 0.9139 (m-30)
REVERT: e  120 MET cc_start: 0.7446 (mtt) cc_final: 0.7055 (mtt)
REVERT: e  124 ILE cc_start: 0.9539 (mt) cc_final: 0.9047 (mp)
REVERT: f   44 LYS cc_start: 0.9248 (ttmt) cc_final: 0.8998 (ttmt)
REVERT: f   85 ASP cc_start: 0.8626 (m-30) cc_final: 0.8339 (m-30)
REVERT: g   36 LYS cc_start: 0.9016 (mppt) cc_final: 0.8759 (mmtm)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1233
  time to fit residues: 28.4453
Evaluate side-chains
  105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:   20.0000
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:   20.0000
   chunk 106 optimal weight:    0.9990
   overall best weight:    1.3588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
b  75 HIS
d  84 ASN
** e  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** g  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.030707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2595 r_free = 0.2595 target = 0.022723 restraints weight = 156312.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2637 r_free = 0.2637 target = 0.023570 restraints weight = 74535.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.024140 restraints weight = 45867.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.024513 restraints weight = 32499.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.024790 restraints weight = 25517.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.1229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14846  Z= 0.163
  Angle     :  0.702   6.916  21563  Z= 0.415
  Chirality :  0.047   0.293   2456
  Planarity :  0.005   0.059   1498
  Dihedral  : 33.188 176.646   4809
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 12.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  4.47 %
    Favored  : 95.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.61 (0.27), residues: 825
  helix:  0.94 (0.21), residues: 572
  sheet: -2.98 (1.16), residues: 10
  loop : -0.55 (0.33), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG d  99 
 TYR   0.014   0.002   TYR c  39 
 PHE   0.016   0.002   PHE e 104 
 HIS   0.004   0.001   HIS a 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.16 (14846)
  covalent geometry    : angle       0.70184 /  0.42 (21563)
  hydrogen bonds       : bond        0.05133 /  3.37 (  877)
  hydrogen bonds       : angle       3.77485 /  2.69 ( 2160)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 146
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   50 GLU cc_start: 0.9316 (mp0) cc_final: 0.8981 (mp0)
REVERT: a   59 GLU cc_start: 0.8734 (pm20) cc_final: 0.8423 (pm20)
REVERT: a   60 LEU cc_start: 0.8763 (mt) cc_final: 0.8473 (mt)
REVERT: a   94 GLU cc_start: 0.9291 (mp0) cc_final: 0.8956 (mm-30)
REVERT: a  120 MET cc_start: 0.8845 (mpp) cc_final: 0.8628 (mpp)
REVERT: c   25 PHE cc_start: 0.8655 (m-80) cc_final: 0.8428 (m-80)
REVERT: c   34 LEU cc_start: 0.9598 (mt) cc_final: 0.8903 (pp)
REVERT: c   90 ASP cc_start: 0.8607 (t0) cc_final: 0.8357 (t0)
REVERT: c   95 LYS cc_start: 0.9465 (ttmm) cc_final: 0.9011 (mppt)
REVERT: d   85 LYS cc_start: 0.9703 (mppt) cc_final: 0.9495 (mmtm)
REVERT: d   99 ARG cc_start: 0.9061 (ttm110) cc_final: 0.8839 (mtp85)
REVERT: e   50 GLU cc_start: 0.9611 (mp0) cc_final: 0.9283 (mp0)
REVERT: e   54 TYR cc_start: 0.9447 (m-80) cc_final: 0.9154 (m-80)
REVERT: e   90 MET cc_start: 0.9222 (tpt) cc_final: 0.9006 (tpt)
REVERT: e  104 PHE cc_start: 0.9624 (m-10) cc_final: 0.9193 (m-80)
REVERT: e  106 ASP cc_start: 0.9423 (m-30) cc_final: 0.9156 (m-30)
REVERT: f   44 LYS cc_start: 0.9352 (ttmt) cc_final: 0.9096 (ttmt)
REVERT: f   85 ASP cc_start: 0.8718 (m-30) cc_final: 0.8398 (m-30)
REVERT: g   36 LYS cc_start: 0.8825 (mppt) cc_final: 0.8461 (mmtm)
REVERT: g   73 ASN cc_start: 0.9427 (t0) cc_final: 0.9187 (t0)
REVERT: h  105 GLU cc_start: 0.9307 (tp30) cc_final: 0.8859 (tp30)
  outliers start: 3
  outliers final: 1
  residues processed: 147
  average time/residue: 0.1059
  time to fit residues: 23.0574
Evaluate side-chains
  105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:   20.0000
   chunk 60 optimal weight:    0.8980
   chunk 104 optimal weight:   20.0000
   chunk 65 optimal weight:    6.9990
   chunk 106 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 111 optimal weight:   20.0000
   chunk 78 optimal weight:   20.0000
   chunk 82 optimal weight:   20.0000
   chunk 22 optimal weight:    4.9990
   overall best weight:    3.5788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** a  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  68 ASN
e  55 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.029610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2548 r_free = 0.2548 target = 0.021658 restraints weight = 166406.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2590 r_free = 0.2590 target = 0.022470 restraints weight = 81581.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.023022 restraints weight = 50856.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.023370 restraints weight = 36413.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.023619 restraints weight = 28994.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.2632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.1579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  14846  Z= 0.216
  Angle     :  0.705   9.069  21563  Z= 0.414
  Chirality :  0.045   0.278   2456
  Planarity :  0.005   0.062   1498
  Dihedral  : 33.111 177.756   4809
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 15.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.43 %
    Allowed  :  3.32 %
    Favored  : 96.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.77 (0.27), residues: 825
  helix:  1.04 (0.20), residues: 580
  sheet: -2.76 (1.19), residues: 10
  loop : -0.50 (0.36), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG a  83 
 TYR   0.020   0.002   TYR f  72 
 PHE   0.017   0.002   PHE a 104 
 HIS   0.007   0.002   HIS h 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.22 (14846)
  covalent geometry    : angle       0.70496 /  0.41 (21563)
  hydrogen bonds       : bond        0.07340 /  4.94 (  877)
  hydrogen bonds       : angle       3.74955 /  2.66 ( 2160)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 139
  time to evaluate  : 0.336 
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: a   50 GLU cc_start: 0.9316 (mp0) cc_final: 0.9026 (mp0)
REVERT: a   60 LEU cc_start: 0.8713 (mt) cc_final: 0.8352 (mt)
REVERT: b   58 LEU cc_start: 0.9821 (tp) cc_final: 0.9448 (pp)
REVERT: b   74 GLU cc_start: 0.9142 (pm20) cc_final: 0.8632 (pm20)
REVERT: c   90 ASP cc_start: 0.8841 (t0) cc_final: 0.8350 (t0)
REVERT: c   95 LYS cc_start: 0.9467 (ttmm) cc_final: 0.9023 (mppt)
REVERT: d   85 LYS cc_start: 0.9701 (mppt) cc_final: 0.9453 (mmtm)
REVERT: e   50 GLU cc_start: 0.9638 (mp0) cc_final: 0.9345 (mp0)
REVERT: e  104 PHE cc_start: 0.9647 (m-10) cc_final: 0.9224 (m-80)
REVERT: e  106 ASP cc_start: 0.9434 (m-30) cc_final: 0.9185 (m-30)
REVERT: e  120 MET cc_start: 0.6868 (mtt) cc_final: 0.6585 (mtt)
REVERT: f   44 LYS cc_start: 0.9401 (ttmt) cc_final: 0.9126 (ttmt)
REVERT: f   85 ASP cc_start: 0.8690 (m-30) cc_final: 0.8359 (m-30)
REVERT: g   73 ASN cc_start: 0.9483 (t0) cc_final: 0.9177 (t0)
REVERT: h  105 GLU cc_start: 0.9207 (tp30) cc_final: 0.8925 (tp30)
  outliers start: 3
  outliers final: 2
  residues processed: 140
  average time/residue: 0.1170
  time to fit residues: 23.8893
Evaluate side-chains
  108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 106
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 97 optimal weight:   20.0000
   chunk 37 optimal weight:    5.9990
   chunk 100 optimal weight:   20.0000
   chunk 15 optimal weight:    2.9990
   chunk 91 optimal weight:   30.0000
   chunk 96 optimal weight:   20.0000
   chunk 105 optimal weight:   30.0000
   chunk 44 optimal weight:    0.9990
   chunk 83 optimal weight:   20.0000
   chunk 70 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    3.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** a  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
b  75 HIS
c  68 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.029372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2553 r_free = 0.2553 target = 0.021703 restraints weight = 161407.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2596 r_free = 0.2596 target = 0.022538 restraints weight = 77616.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.023079 restraints weight = 47414.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.023470 restraints weight = 33669.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.023713 restraints weight = 26144.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.2634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.1910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  14846  Z= 0.218
  Angle     :  0.691   8.406  21563  Z= 0.405
  Chirality :  0.044   0.278   2456
  Planarity :  0.005   0.060   1498
  Dihedral  : 33.136 176.948   4809
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.27), residues: 825
  helix:  1.14 (0.20), residues: 580
  sheet: -2.78 (1.29), residues: 10
  loop : -0.55 (0.36), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG f  92 
 TYR   0.021   0.002   TYR h  40 
 PHE   0.018   0.002   PHE c  25 
 HIS   0.006   0.002   HIS a  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.22 (14846)
  covalent geometry    : angle       0.69114 /  0.40 (21563)
  hydrogen bonds       : bond        0.06788 /  4.55 (  877)
  hydrogen bonds       : angle       3.80640 /  2.70 ( 2160)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.344 
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: b   58 LEU cc_start: 0.9831 (tp) cc_final: 0.9466 (pp)
REVERT: c   25 PHE cc_start: 0.8640 (m-80) cc_final: 0.8362 (m-80)
REVERT: c   90 ASP cc_start: 0.8568 (t0) cc_final: 0.8102 (t0)
REVERT: c   91 GLU cc_start: 0.9029 (mp0) cc_final: 0.8757 (mm-30)
REVERT: c   95 LYS cc_start: 0.9469 (ttmm) cc_final: 0.8946 (mppt)
REVERT: d   85 LYS cc_start: 0.9703 (mppt) cc_final: 0.9464 (mmtm)
REVERT: e   90 MET cc_start: 0.9263 (tpt) cc_final: 0.9059 (tpp)
REVERT: e  104 PHE cc_start: 0.9510 (m-10) cc_final: 0.9243 (m-80)
REVERT: e  105 GLU cc_start: 0.9485 (pm20) cc_final: 0.9274 (pm20)
REVERT: e  106 ASP cc_start: 0.9445 (m-30) cc_final: 0.9141 (m-30)
REVERT: f   44 LYS cc_start: 0.9357 (ttmt) cc_final: 0.8906 (ttmt)
REVERT: f   58 LEU cc_start: 0.9840 (tt) cc_final: 0.9572 (pp)
REVERT: f   74 GLU cc_start: 0.9265 (pm20) cc_final: 0.8935 (pm20)
REVERT: f   85 ASP cc_start: 0.8727 (m-30) cc_final: 0.8391 (m-30)
REVERT: g   36 LYS cc_start: 0.8864 (mppt) cc_final: 0.8517 (mmtm)
REVERT: h   71 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8713 (mm-30)
REVERT: h  105 GLU cc_start: 0.9203 (tp30) cc_final: 0.8960 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1132
  time to fit residues: 22.8093
Evaluate side-chains
  102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 93 optimal weight:   20.0000
   chunk 105 optimal weight:   30.0000
   chunk 70 optimal weight:    0.9990
   chunk 7 optimal weight:    8.9990
   chunk 100 optimal weight:   30.0000
   chunk 103 optimal weight:   20.0000
   chunk 27 optimal weight:    1.9990
   chunk 67 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    2.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** a  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  68 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.029576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2557 r_free = 0.2557 target = 0.021850 restraints weight = 161083.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2598 r_free = 0.2598 target = 0.022633 restraints weight = 77443.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2626 r_free = 0.2626 target = 0.023185 restraints weight = 47767.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.023529 restraints weight = 33990.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2657 r_free = 0.2657 target = 0.023782 restraints weight = 26943.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.2633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.2142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.074  14846  Z= 0.187
  Angle     :  0.671   7.744  21563  Z= 0.394
  Chirality :  0.044   0.279   2456
  Planarity :  0.005   0.058   1498
  Dihedral  : 33.071 176.727   4809
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 13.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  2.16 %
    Favored  : 97.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.27), residues: 825
  helix:  1.23 (0.20), residues: 582
  sheet: -2.50 (1.50), residues: 10
  loop : -0.65 (0.35), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG b  23 
 TYR   0.029   0.002   TYR f  98 
 PHE   0.013   0.002   PHE c  25 
 HIS   0.006   0.002   HIS b  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.19 (14846)
  covalent geometry    : angle       0.67053 /  0.39 (21563)
  hydrogen bonds       : bond        0.05811 /  3.86 (  877)
  hydrogen bonds       : angle       3.69878 /  2.61 ( 2160)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 149
  time to evaluate  : 0.341 
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: a  106 ASP cc_start: 0.9047 (m-30) cc_final: 0.8816 (m-30)
REVERT: b   58 LEU cc_start: 0.9830 (tp) cc_final: 0.9449 (pp)
REVERT: c   25 PHE cc_start: 0.8626 (m-80) cc_final: 0.8346 (m-80)
REVERT: c   90 ASP cc_start: 0.8530 (t0) cc_final: 0.8097 (t0)
REVERT: c   95 LYS cc_start: 0.9497 (ttmm) cc_final: 0.9043 (mppt)
REVERT: d   59 MET cc_start: 0.8268 (tpt) cc_final: 0.8057 (tpt)
REVERT: d   85 LYS cc_start: 0.9702 (mppt) cc_final: 0.9450 (mmtm)
REVERT: d   99 ARG cc_start: 0.9234 (mtp85) cc_final: 0.8966 (ttm110)
REVERT: e   50 GLU cc_start: 0.9704 (mp0) cc_final: 0.9359 (mp0)
REVERT: e  104 PHE cc_start: 0.9604 (m-10) cc_final: 0.9140 (m-80)
REVERT: e  106 ASP cc_start: 0.9427 (m-30) cc_final: 0.9192 (m-30)
REVERT: f   44 LYS cc_start: 0.9356 (ttmt) cc_final: 0.9065 (ttmt)
REVERT: f   58 LEU cc_start: 0.9838 (tt) cc_final: 0.9566 (pp)
REVERT: f   74 GLU cc_start: 0.9215 (pm20) cc_final: 0.8896 (pm20)
REVERT: f   85 ASP cc_start: 0.8700 (m-30) cc_final: 0.8394 (m-30)
REVERT: h   71 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8679 (mm-30)
REVERT: h  105 GLU cc_start: 0.9143 (tp30) cc_final: 0.8940 (tp30)
REVERT: h  116 LYS cc_start: 0.9668 (mtmm) cc_final: 0.9425 (ptpp)
  outliers start: 2
  outliers final: 1
  residues processed: 150
  average time/residue: 0.1108
  time to fit residues: 24.5361
Evaluate side-chains
  107 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 96 optimal weight:   30.0000
   chunk 48 optimal weight:    5.9990
   chunk 68 optimal weight:    0.8980
   chunk 18 optimal weight:    9.9990
   chunk 29 optimal weight:    6.9990
   chunk 36 optimal weight:   20.0000
   chunk 75 optimal weight:   20.0000
   chunk 59 optimal weight:    0.4980
   chunk 38 optimal weight:    0.9990
   chunk 106 optimal weight:   20.0000
   chunk 46 optimal weight:    0.9990
   overall best weight:    1.8786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** a  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  68 ASN
f  75 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.029779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2565 r_free = 0.2565 target = 0.021964 restraints weight = 158360.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2607 r_free = 0.2607 target = 0.022776 restraints weight = 76132.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.023335 restraints weight = 46881.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.023699 restraints weight = 33311.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.023941 restraints weight = 26176.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.2310

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14846  Z= 0.160
  Angle     :  0.660   7.624  21563  Z= 0.388
  Chirality :  0.044   0.277   2456
  Planarity :  0.004   0.064   1498
  Dihedral  : 32.969 177.597   4809
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.28), residues: 825
  helix:  1.28 (0.21), residues: 586
  sheet: -2.25 (1.60), residues: 10
  loop : -0.68 (0.35), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG f  92 
 TYR   0.018   0.002   TYR f  98 
 PHE   0.012   0.001   PHE c  25 
 HIS   0.006   0.001   HIS b  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.16 (14846)
  covalent geometry    : angle       0.65982 /  0.39 (21563)
  hydrogen bonds       : bond        0.04994 /  3.31 (  877)
  hydrogen bonds       : angle       3.63346 /  2.57 ( 2160)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 0.340 
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: a   50 GLU cc_start: 0.9304 (mp0) cc_final: 0.9035 (mp0)
REVERT: a  105 GLU cc_start: 0.9453 (mm-30) cc_final: 0.9250 (mm-30)
REVERT: a  106 ASP cc_start: 0.9025 (m-30) cc_final: 0.8807 (m-30)
REVERT: b   58 LEU cc_start: 0.9792 (tp) cc_final: 0.9437 (pp)
REVERT: c   25 PHE cc_start: 0.8598 (m-80) cc_final: 0.8376 (m-80)
REVERT: c   34 LEU cc_start: 0.9556 (mt) cc_final: 0.8899 (pp)
REVERT: c   90 ASP cc_start: 0.8525 (t0) cc_final: 0.8026 (t0)
REVERT: c   95 LYS cc_start: 0.9479 (ttmm) cc_final: 0.9025 (mppt)
REVERT: d   62 MET cc_start: 0.8605 (mmp) cc_final: 0.8395 (mmp)
REVERT: d   85 LYS cc_start: 0.9701 (mppt) cc_final: 0.9444 (mmtm)
REVERT: d   99 ARG cc_start: 0.9243 (mtp85) cc_final: 0.8995 (ttm110)
REVERT: e   50 GLU cc_start: 0.9667 (mp0) cc_final: 0.9385 (mp0)
REVERT: e   60 LEU cc_start: 0.8580 (mp) cc_final: 0.8004 (mt)
REVERT: e   82 LEU cc_start: 0.8840 (mt) cc_final: 0.8507 (mt)
REVERT: e   90 MET cc_start: 0.9335 (tpp) cc_final: 0.9004 (tpt)
REVERT: e  100 LEU cc_start: 0.9578 (mm) cc_final: 0.9219 (mm)
REVERT: e  104 PHE cc_start: 0.9448 (m-10) cc_final: 0.9152 (m-80)
REVERT: e  105 GLU cc_start: 0.9502 (pm20) cc_final: 0.9253 (pm20)
REVERT: e  106 ASP cc_start: 0.9440 (m-30) cc_final: 0.9074 (m-30)
REVERT: f   58 LEU cc_start: 0.9824 (tt) cc_final: 0.9432 (pp)
REVERT: f   59 LYS cc_start: 0.9825 (ptmm) cc_final: 0.9553 (ptmm)
REVERT: f   72 TYR cc_start: 0.9603 (m-80) cc_final: 0.9289 (m-80)
REVERT: f   85 ASP cc_start: 0.8653 (m-30) cc_final: 0.8256 (m-30)
REVERT: g   61 GLU cc_start: 0.9495 (tm-30) cc_final: 0.9105 (tm-30)
REVERT: h   71 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8688 (mm-30)
REVERT: h  105 GLU cc_start: 0.9154 (tp30) cc_final: 0.8946 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 149
  average time/residue: 0.1112
  time to fit residues: 24.6443
Evaluate side-chains
  106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 111 optimal weight:   20.0000
   chunk 50 optimal weight:    0.9980
   chunk 94 optimal weight:   20.0000
   chunk 25 optimal weight:    3.9990
   chunk 88 optimal weight:   30.0000
   chunk 87 optimal weight:   20.0000
   chunk 49 optimal weight:    3.9990
   chunk 81 optimal weight:   30.0000
   chunk 100 optimal weight:   30.0000
   chunk 1 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   overall best weight:    2.3786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** a  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  68 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.029495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2557 r_free = 0.2557 target = 0.021815 restraints weight = 163625.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2599 r_free = 0.2599 target = 0.022611 restraints weight = 78337.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.023167 restraints weight = 48354.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.023544 restraints weight = 34408.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2661 r_free = 0.2661 target = 0.023792 restraints weight = 26849.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14846  Z= 0.172
  Angle     :  0.663   7.746  21563  Z= 0.387
  Chirality :  0.043   0.275   2456
  Planarity :  0.004   0.066   1498
  Dihedral  : 32.886 178.116   4809
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 13.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.01 %
    Favored  : 98.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.05 (0.28), residues: 825
  helix:  1.32 (0.20), residues: 586
  sheet: -2.14 (1.70), residues: 10
  loop : -0.69 (0.36), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG b  23 
 TYR   0.016   0.002   TYR f  98 
 PHE   0.012   0.001   PHE f 100 
 HIS   0.006   0.001   HIS b  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.17 (14846)
  covalent geometry    : angle       0.66311 /  0.39 (21563)
  hydrogen bonds       : bond        0.05554 /  3.69 (  877)
  hydrogen bonds       : angle       3.69792 /  2.59 ( 2160)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.348 
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  105 GLU cc_start: 0.9459 (mm-30) cc_final: 0.9218 (mm-30)
REVERT: a  106 ASP cc_start: 0.9010 (m-30) cc_final: 0.8798 (m-30)
REVERT: b   58 LEU cc_start: 0.9803 (tp) cc_final: 0.9423 (pp)
REVERT: c   25 PHE cc_start: 0.8653 (m-80) cc_final: 0.8428 (m-80)
REVERT: c   34 LEU cc_start: 0.9603 (mt) cc_final: 0.8951 (pp)
REVERT: c   90 ASP cc_start: 0.8539 (t0) cc_final: 0.8013 (t0)
REVERT: c   95 LYS cc_start: 0.9462 (ttmm) cc_final: 0.9006 (mppt)
REVERT: d   62 MET cc_start: 0.8620 (mmp) cc_final: 0.8382 (mmp)
REVERT: d   85 LYS cc_start: 0.9708 (mppt) cc_final: 0.9455 (mmtm)
REVERT: d   99 ARG cc_start: 0.9292 (mtp85) cc_final: 0.8992 (ttm110)
REVERT: e   50 GLU cc_start: 0.9711 (mp0) cc_final: 0.9402 (mp0)
REVERT: e   60 LEU cc_start: 0.8581 (mp) cc_final: 0.8253 (mt)
REVERT: e   82 LEU cc_start: 0.8812 (mt) cc_final: 0.8488 (mt)
REVERT: e  104 PHE cc_start: 0.9531 (m-10) cc_final: 0.8953 (m-80)
REVERT: e  106 ASP cc_start: 0.9522 (m-30) cc_final: 0.9315 (m-30)
REVERT: e  120 MET cc_start: 0.6832 (mtt) cc_final: 0.6356 (mtt)
REVERT: f   58 LEU cc_start: 0.9837 (tt) cc_final: 0.9581 (pp)
REVERT: f   85 ASP cc_start: 0.8669 (m-30) cc_final: 0.8315 (m-30)
REVERT: g   61 GLU cc_start: 0.9491 (tm-30) cc_final: 0.9105 (tm-30)
REVERT: h   52 THR cc_start: 0.8262 (m) cc_final: 0.7977 (p)
REVERT: h   71 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8683 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.1102
  time to fit residues: 23.5757
Evaluate side-chains
  101 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 62 optimal weight:    0.3980
   chunk 17 optimal weight:    0.9980
   chunk 73 optimal weight:   30.0000
   chunk 74 optimal weight:   30.0000
   chunk 51 optimal weight:    0.9980
   chunk 85 optimal weight:   20.0000
   chunk 47 optimal weight:    8.9990
   chunk 55 optimal weight:    9.9990
   chunk 37 optimal weight:    2.9990
   chunk 63 optimal weight:    9.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    1.8784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** a  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
c  68 ASN
e 108 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.029770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2570 r_free = 0.2570 target = 0.022020 restraints weight = 158470.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2611 r_free = 0.2611 target = 0.022824 restraints weight = 76611.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.023370 restraints weight = 47228.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2659 r_free = 0.2659 target = 0.023748 restraints weight = 33657.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.023997 restraints weight = 26297.311|
|-----------------------------------------------------------------------------|
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14846  Z= 0.157
  Angle     :  0.650   9.460  21563  Z= 0.380
  Chirality :  0.043   0.281   2456
  Planarity :  0.004   0.067   1498
  Dihedral  : 32.802 178.330   4809
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 13.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.73 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.08 (0.28), residues: 825
  helix:  1.34 (0.21), residues: 586
  sheet: -2.12 (1.73), residues: 10
  loop : -0.67 (0.36), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG b  23 
 TYR   0.028   0.002   TYR h  40 
 PHE   0.010   0.001   PHE f 100 
 HIS   0.006   0.001   HIS f  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.16 (14846)
  covalent geometry    : angle       0.64971 /  0.38 (21563)
  hydrogen bonds       : bond        0.04786 /  3.15 (  877)
  hydrogen bonds       : angle       3.62653 /  2.54 ( 2160)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 0.360 
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: a   50 GLU cc_start: 0.9297 (mp0) cc_final: 0.9018 (mp0)
REVERT: a  105 GLU cc_start: 0.9476 (mm-30) cc_final: 0.9123 (mm-30)
REVERT: a  106 ASP cc_start: 0.9004 (m-30) cc_final: 0.8799 (m-30)
REVERT: b   58 LEU cc_start: 0.9785 (tp) cc_final: 0.9432 (pp)
REVERT: b   63 GLU cc_start: 0.9484 (mp0) cc_final: 0.9267 (mp0)
REVERT: c   25 PHE cc_start: 0.8658 (m-80) cc_final: 0.8416 (m-80)
REVERT: c   34 LEU cc_start: 0.9597 (mt) cc_final: 0.8969 (pp)
REVERT: c   90 ASP cc_start: 0.8517 (t0) cc_final: 0.7929 (t0)
REVERT: c   91 GLU cc_start: 0.8923 (mp0) cc_final: 0.8708 (mm-30)
REVERT: c   95 LYS cc_start: 0.9456 (ttmm) cc_final: 0.8935 (mppt)
REVERT: d   62 MET cc_start: 0.8516 (mmp) cc_final: 0.8247 (mmp)
REVERT: d   85 LYS cc_start: 0.9707 (mppt) cc_final: 0.9453 (mmtm)
REVERT: d   99 ARG cc_start: 0.9267 (mtp85) cc_final: 0.8979 (ttm110)
REVERT: e   50 GLU cc_start: 0.9670 (mp0) cc_final: 0.9335 (mp0)
REVERT: e   82 LEU cc_start: 0.8886 (mt) cc_final: 0.8515 (mt)
REVERT: e   90 MET cc_start: 0.9295 (mmp) cc_final: 0.8727 (mmt)
REVERT: e  104 PHE cc_start: 0.9531 (m-10) cc_final: 0.8911 (m-80)
REVERT: e  106 ASP cc_start: 0.9495 (m-30) cc_final: 0.9287 (m-30)
REVERT: f   58 LEU cc_start: 0.9828 (tt) cc_final: 0.9407 (pp)
REVERT: f   59 LYS cc_start: 0.9825 (ptmm) cc_final: 0.9541 (ptmm)
REVERT: f   85 ASP cc_start: 0.8656 (m-30) cc_final: 0.8334 (m-30)
REVERT: g   61 GLU cc_start: 0.9488 (tm-30) cc_final: 0.9070 (tm-30)
REVERT: h   52 THR cc_start: 0.8226 (m) cc_final: 0.7823 (p)
REVERT: h   68 ASP cc_start: 0.9307 (t0) cc_final: 0.9091 (t0)
REVERT: h   71 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8699 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1159
  time to fit residues: 24.8949
Evaluate side-chains
  105 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 90 optimal weight:   30.0000
   chunk 103 optimal weight:   20.0000
   chunk 62 optimal weight:    0.8980
   chunk 8 optimal weight:    8.9990
   chunk 23 optimal weight:    0.9980
   chunk 41 optimal weight:    0.8980
   chunk 98 optimal weight:   30.0000
   chunk 76 optimal weight:   20.0000
   overall best weight:    1.3182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** a  93 GLN ** 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 = 0.2943 r_free = 0.2943 target = 0.030002 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2574 r_free = 0.2574 target = 0.022090 restraints weight = 161291.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.022916 restraints weight = 78025.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.023467 restraints weight = 48031.375|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2665 r_free = 0.2665 target = 0.023851 restraints weight = 34304.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.024112 restraints weight = 26876.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.2657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8476
moved from start:          0.2808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14846  Z= 0.148
  Angle     :  0.662   8.256  21563  Z= 0.386
  Chirality :  0.043   0.283   2456
  Planarity :  0.004   0.067   1498
  Dihedral  : 32.707 179.313   4809
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 12.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.72 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.10 (0.28), residues: 825
  helix:  1.36 (0.21), residues: 586
  sheet: -2.19 (1.63), residues: 10
  loop : -0.65 (0.36), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG g  29 
 TYR   0.029   0.002   TYR e  54 
 PHE   0.010   0.001   PHE d  65 
 HIS   0.006   0.001   HIS f  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.15 (14846)
  covalent geometry    : angle       0.66232 /  0.39 (21563)
  hydrogen bonds       : bond        0.04502 /  2.95 (  877)
  hydrogen bonds       : angle       3.68869 /  2.63 ( 2160)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 0.332 
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: a   50 GLU cc_start: 0.9288 (mp0) cc_final: 0.9005 (mp0)
REVERT: a  105 GLU cc_start: 0.9483 (mm-30) cc_final: 0.9126 (mm-30)
REVERT: b   58 LEU cc_start: 0.9821 (tp) cc_final: 0.9440 (pp)
REVERT: b   63 GLU cc_start: 0.9437 (mp0) cc_final: 0.9196 (mp0)
REVERT: c   25 PHE cc_start: 0.8655 (m-80) cc_final: 0.8408 (m-80)
REVERT: c   34 LEU cc_start: 0.9590 (mt) cc_final: 0.8953 (pp)
REVERT: c   90 ASP cc_start: 0.8430 (t0) cc_final: 0.7857 (t0)
REVERT: c   91 GLU cc_start: 0.8923 (mp0) cc_final: 0.8709 (mm-30)
REVERT: c   95 LYS cc_start: 0.9447 (ttmm) cc_final: 0.8931 (mppt)
REVERT: d   62 MET cc_start: 0.8524 (mmp) cc_final: 0.8247 (mmp)
REVERT: d   85 LYS cc_start: 0.9708 (mppt) cc_final: 0.9455 (mmtm)
REVERT: d   99 ARG cc_start: 0.9275 (mtp85) cc_final: 0.8980 (ttm110)
REVERT: e   50 GLU cc_start: 0.9663 (mp0) cc_final: 0.9348 (mp0)
REVERT: e   82 LEU cc_start: 0.8894 (mt) cc_final: 0.8563 (mt)
REVERT: e   90 MET cc_start: 0.9339 (mmp) cc_final: 0.9124 (mmm)
REVERT: e  104 PHE cc_start: 0.9497 (m-10) cc_final: 0.8896 (m-80)
REVERT: e  105 GLU cc_start: 0.9569 (pm20) cc_final: 0.9357 (pm20)
REVERT: e  106 ASP cc_start: 0.9503 (m-30) cc_final: 0.9130 (m-30)
REVERT: e  120 MET cc_start: 0.6764 (mtt) cc_final: 0.6294 (mtt)
REVERT: e  125 GLN cc_start: 0.9449 (mp10) cc_final: 0.9177 (mp10)
REVERT: f   58 LEU cc_start: 0.9826 (tt) cc_final: 0.9437 (pp)
REVERT: f   59 LYS cc_start: 0.9821 (ptmm) cc_final: 0.9548 (ptmm)
REVERT: f   85 ASP cc_start: 0.8657 (m-30) cc_final: 0.8339 (m-30)
REVERT: g   61 GLU cc_start: 0.9490 (tm-30) cc_final: 0.9072 (tm-30)
REVERT: h   52 THR cc_start: 0.8147 (m) cc_final: 0.7741 (p)
REVERT: h   68 ASP cc_start: 0.9308 (t0) cc_final: 0.9094 (t0)
REVERT: h   71 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8688 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1161
  time to fit residues: 24.9395
Evaluate side-chains
  109 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 109
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 82 optimal weight:   20.0000
   chunk 111 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 38 optimal weight:    6.9990
   chunk 11 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 98 optimal weight:   30.0000
   chunk 7 optimal weight:    4.9990
   chunk 72 optimal weight:   50.0000
   overall best weight:    3.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** a  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
e 108 ASN
** h  95 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 = 0.2913 r_free = 0.2913 target = 0.029263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2535 r_free = 0.2535 target = 0.021309 restraints weight = 168273.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2575 r_free = 0.2575 target = 0.022084 restraints weight = 84578.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2603 r_free = 0.2603 target = 0.022629 restraints weight = 53679.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.022988 restraints weight = 38951.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.023226 restraints weight = 31122.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.2616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8523
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  14846  Z= 0.202
  Angle     :  0.685   8.029  21563  Z= 0.397
  Chirality :  0.043   0.276   2456
  Planarity :  0.005   0.070   1498
  Dihedral  : 32.761 179.328   4809
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 16.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.29 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.99 (0.28), residues: 825
  helix:  1.25 (0.21), residues: 586
  sheet: -2.21 (1.71), residues: 10
  loop : -0.63 (0.37), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG f  92 
 TYR   0.018   0.002   TYR b  88 
 PHE   0.013   0.001   PHE f 100 
 HIS   0.006   0.002   HIS a  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00366 /  0.20 (14846)
  covalent geometry    : angle       0.68527 /  0.40 (21563)
  hydrogen bonds       : bond        0.06573 /  4.39 (  877)
  hydrogen bonds       : angle       3.91281 /  2.78 ( 2160)

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: a   50 GLU cc_start: 0.9281 (mp0) cc_final: 0.8990 (mp0)
REVERT: a  105 GLU cc_start: 0.9453 (mm-30) cc_final: 0.9143 (mm-30)
REVERT: b   58 LEU cc_start: 0.9815 (tp) cc_final: 0.9447 (pp)
REVERT: b   63 GLU cc_start: 0.9489 (mp0) cc_final: 0.9248 (mp0)
REVERT: c   25 PHE cc_start: 0.8654 (m-80) cc_final: 0.8410 (m-80)
REVERT: c   90 ASP cc_start: 0.8549 (t0) cc_final: 0.7982 (t0)
REVERT: c   95 LYS cc_start: 0.9449 (ttmm) cc_final: 0.8938 (mppt)
REVERT: d   85 LYS cc_start: 0.9708 (mppt) cc_final: 0.9432 (mmtm)
REVERT: d   99 ARG cc_start: 0.9275 (mtp85) cc_final: 0.9002 (ttm110)
REVERT: e   50 GLU cc_start: 0.9644 (mp0) cc_final: 0.9325 (mp0)
REVERT: e   82 LEU cc_start: 0.8893 (mt) cc_final: 0.8519 (mt)
REVERT: e   90 MET cc_start: 0.9372 (mmp) cc_final: 0.9155 (mmm)
REVERT: e  104 PHE cc_start: 0.9505 (m-10) cc_final: 0.8902 (m-80)
REVERT: e  106 ASP cc_start: 0.9444 (m-30) cc_final: 0.9031 (m-30)
REVERT: e  120 MET cc_start: 0.6568 (mtt) cc_final: 0.5958 (mtt)
REVERT: f   58 LEU cc_start: 0.9838 (tt) cc_final: 0.9478 (pp)
REVERT: f   72 TYR cc_start: 0.9665 (m-80) cc_final: 0.9421 (m-80)
REVERT: f   85 ASP cc_start: 0.8718 (m-30) cc_final: 0.8284 (m-30)
REVERT: g   61 GLU cc_start: 0.9459 (tm-30) cc_final: 0.9054 (tm-30)
REVERT: h   52 THR cc_start: 0.8183 (m) cc_final: 0.7783 (p)
REVERT: h   68 ASP cc_start: 0.9293 (t0) cc_final: 0.9064 (t0)
REVERT: h   71 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8715 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1068
  time to fit residues: 21.9090
Evaluate side-chains
  100 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 106 optimal weight:    6.9990
   chunk 81 optimal weight:   30.0000
   chunk 103 optimal weight:   20.0000
   chunk 48 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   chunk 100 optimal weight:   30.0000
   chunk 89 optimal weight:   50.0000
   chunk 94 optimal weight:   20.0000
   chunk 46 optimal weight:    0.7980
   chunk 79 optimal weight:   20.0000
   overall best weight:    4.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
a  55 GLN
** a  93 GLN ** 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 = 0.2883 r_free = 0.2883 target = 0.028488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2521 r_free = 0.2521 target = 0.020927 restraints weight = 168043.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2563 r_free = 0.2563 target = 0.021721 restraints weight = 82245.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2592 r_free = 0.2592 target = 0.022270 restraints weight = 51060.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.022619 restraints weight = 36442.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.022847 restraints weight = 28705.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.2603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.3200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.098  14846  Z= 0.240
  Angle     :  0.723   8.863  21563  Z= 0.416
  Chirality :  0.044   0.279   2456
  Planarity :  0.005   0.069   1498
  Dihedral  : 32.879 179.093   4809
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 18.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.14 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.28), residues: 825
  helix:  1.08 (0.20), residues: 586
  sheet: -2.24 (1.83), residues: 10
  loop : -0.59 (0.38), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG b  23 
 TYR   0.026   0.002   TYR e  54 
 PHE   0.015   0.002   PHE f 100 
 HIS   0.017   0.003   HIS h 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00450 /  0.24 (14846)
  covalent geometry    : angle       0.72325 /  0.42 (21563)
  hydrogen bonds       : bond        0.07345 /  4.93 (  877)
  hydrogen bonds       : angle       4.09164 /  2.88 ( 2160)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1886.58 seconds
wall clock time: 33 minutes 44.65 seconds (2024.65 seconds total)