Starting phenix.real_space_refine
on Fri Jul  3 14:44:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pey_13361/07_2026/7pey_13361.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pey_13361/07_2026/7pey_13361.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pey_13361/07_2026/7pey_13361.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pey_13361/07_2026/7pey_13361.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pey_13361/07_2026/7pey_13361.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pey_13361/07_2026/7pey_13361.map"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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     342      5.49       5
     S      10      5.16       5
     C    7159      2.51       5
     N    2464      2.21       5
     O    3124      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s

  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: 13099
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "K"
      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: "L"
      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: "M"
      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: "N"
      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: "O"
      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: "P"
      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: "Q"
      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: "R"
      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: 3532
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 3532
          Classifications: {'DNA': 171}
          Link IDs: {'rna3p': 170}
    Chain: "I"
      Number of atoms: 3479
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 3479
          Classifications: {'DNA': 171}
          Link IDs: {'rna3p': 170}
  Time building chain proxies: 2.57, per 1000 atoms: 0.20
  Number of scatterers: 13099
  At special positions: 0
  Unit cell: (150.15, 130.2, 116.55, 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     342     15.00
     O    3124      8.00
     N    2464      7.00
     C    7159      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: 1.18
  Conformation dependent library (CDL) restraints added in 288.1 milliseconds
  

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1432

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 8 sheets defined
      72.0% alpha, 2.1% beta
      166 base pairs and 301 stacking pairs defined.
    Time for finding SS restraints: 1.98
  Creating SS restraints...
    Processing helix  chain 'K' and resid 44 through 57
    Processing helix  chain 'K' and resid 63 through 79
      removed outlier: 3.700A  pdb=" N   PHE K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ASP K  77 " --> pdb=" O   GLU K  73 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   PHE K  78 " --> pdb=" O   ILE K  74 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 85 through 114
    Processing helix  chain 'K' and resid 120 through 132
      removed outlier: 3.819A  pdb=" N   ILE K 124 " --> pdb=" O   MET K 120 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 24 through 29
      removed outlier: 4.055A  pdb=" N   GLN L  27 " --> pdb=" O   ASP L  24 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ILE L  29 " --> pdb=" O   ILE L  26 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 30 through 41
    Processing helix  chain 'L' and resid 50 through 76
    Processing helix  chain 'L' and resid 82 through 93
    Processing helix  chain 'M' and resid 16 through 21
    Processing helix  chain 'M' and resid 26 through 36
    Processing helix  chain 'M' and resid 45 through 73
      removed outlier: 4.079A  pdb=" N   VAL M  49 " --> pdb=" O   ALA M  45 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 79 through 89
    Processing helix  chain 'M' and resid 90 through 97
    Processing helix  chain 'M' and resid 112 through 116
    Processing helix  chain 'N' and resid 37 through 49
      removed outlier: 3.869A  pdb=" N   VAL N  41 " --> pdb=" O   TYR N  37 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 55 through 84
    Processing helix  chain 'N' and resid 90 through 102
      removed outlier: 3.531A  pdb=" N   ILE N  94 " --> pdb=" O   THR N  90 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 103 through 123
    Processing helix  chain 'O' and resid 44 through 57
    Processing helix  chain 'O' and resid 63 through 77
    Processing helix  chain 'O' and resid 85 through 114
    Processing helix  chain 'O' and resid 120 through 131
      removed outlier: 3.580A  pdb=" N   ILE O 124 " --> pdb=" O   MET O 120 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 25 through 29
    Processing helix  chain 'P' and resid 30 through 41
    Processing helix  chain 'P' and resid 49 through 76
      removed outlier: 4.023A  pdb=" N   GLU P  53 " --> pdb=" O   LEU P  49 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASP P  68 " --> pdb=" O   ASN P  64 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 82 through 93
      removed outlier: 3.503A  pdb=" N   VAL P  86 " --> pdb=" O   THR P  82 " (cutoff:3.500A)
      removed outlier: 3.982A  pdb=" N   GLN P  93 " --> pdb=" O   ALA P  89 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 16 through 22
    Processing helix  chain 'Q' and resid 26 through 36
    Processing helix  chain 'Q' and resid 45 through 73
      removed outlier: 4.238A  pdb=" N   VAL Q  49 " --> pdb=" O   ALA Q  45 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 79 through 89
    Processing helix  chain 'Q' and resid 90 through 97
    Processing helix  chain 'Q' and resid 112 through 116
    Processing helix  chain 'R' and resid 37 through 49
    Processing helix  chain 'R' and resid 55 through 84
    Processing helix  chain 'R' and resid 90 through 102
    Processing helix  chain 'R' and resid 104 through 123
      removed outlier: 4.156A  pdb=" N   LYS R 108 " --> pdb=" O   GLY R 104 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'K' and resid 83 through 84
      removed outlier: 6.447A  pdb=" N   ARG K  83 " --> pdb=" O   VAL L  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'K' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'L' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'M' and resid 42 through 43
      removed outlier: 7.475A  pdb=" N   ARG M  42 " --> pdb=" O   ILE N  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'M' and resid 101 through 102
      removed outlier: 7.080A  pdb=" N   THR M 101 " --> pdb=" O   TYR P  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'O' and resid 83 through 84
      removed outlier: 6.669A  pdb=" N   ARG O  83 " --> pdb=" O   VAL P  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'O' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'Q' and resid 42 through 43
      removed outlier: 7.151A  pdb=" N   ARG Q  42 " --> pdb=" O   ILE R  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    400 hydrogen bonds defined for protein.
    1179 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      429 hydrogen bonds
      858 hydrogen bond angles
      0 basepair planarities
      166 basepair parallelities
      301 stacking parallelities
  Total time for adding SS restraints: 2.96

  Time building geometry restraints manager: 1.41 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2792
        1.33 -     1.46: 4997
        1.46 -     1.58: 5541
        1.58 -     1.70: 682
        1.70 -     1.83: 20
  Bond restraints: 14032
  Sorted by residual:
  bond pdb=" C3'  DT J 317 "
       pdb=" C2'  DT J 317 "
    ideal  model  delta    sigma   weight residual
    1.516  1.547 -0.031 8.00e-03 1.56e+04 1.49e+01
  bond pdb=" C3'  DA J 269 "
       pdb=" O3'  DA J 269 "
    ideal  model  delta    sigma   weight residual
    1.435  1.387  0.048 1.30e-02 5.92e+03 1.35e+01
  bond pdb=" C5'  DG I 487 "
       pdb=" C4'  DG I 487 "
    ideal  model  delta    sigma   weight residual
    1.512  1.537 -0.025 7.00e-03 2.04e+04 1.26e+01
  bond pdb=" C3'  DT I 474 "
       pdb=" C2'  DT I 474 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.23e+01
  bond pdb=" C5'  DA I 507 "
       pdb=" C4'  DA I 507 "
    ideal  model  delta    sigma   weight residual
    1.512  1.536 -0.024 7.00e-03 2.04e+04 1.22e+01
  ... (remaining 14027 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.31: 19544
        2.31 -     4.61: 795
        4.61 -     6.92: 62
        6.92 -     9.23: 14
        9.23 -    11.54: 4
  Bond angle restraints: 20419
  Sorted by residual:
  angle pdb=" O4'  DG J 290 "
        pdb=" C1'  DG J 290 "
        pdb=" N9   DG J 290 "
      ideal   model   delta    sigma   weight residual
     108.00  111.37   -3.37 7.00e-01 2.04e+00 2.31e+01
  angle pdb=" CB  LYS R  46 "
        pdb=" CG  LYS R  46 "
        pdb=" CD  LYS R  46 "
      ideal   model   delta    sigma   weight residual
     111.30  122.28  -10.98 2.30e+00 1.89e-01 2.28e+01
  angle pdb=" O5'  DG I 487 "
        pdb=" C5'  DG I 487 "
        pdb=" C4'  DG I 487 "
      ideal   model   delta    sigma   weight residual
     109.40  113.22   -3.82 8.00e-01 1.56e+00 2.28e+01
  angle pdb=" C   GLN O  93 "
        pdb=" CA  GLN O  93 "
        pdb=" CB  GLN O  93 "
      ideal   model   delta    sigma   weight residual
     110.95  118.24   -7.29 1.55e+00 4.16e-01 2.21e+01
  angle pdb=" O4'  DC I 446 "
        pdb=" C4'  DC I 446 "
        pdb=" C3'  DC I 446 "
      ideal   model   delta    sigma   weight residual
     106.00  103.19    2.81 6.00e-01 2.78e+00 2.20e+01
  ... (remaining 20414 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    36.00: 5768
       36.00 -    72.00: 1741
       72.00 -   107.99: 22
      107.99 -   143.99: 3
      143.99 -   179.99: 2
  Dihedral angle restraints: 7536
    sinusoidal: 5314
      harmonic: 2222
  Sorted by residual:
  dihedral pdb=" CA  ILE L  50 "
           pdb=" C   ILE L  50 "
           pdb=" N   TYR L  51 "
           pdb=" CA  TYR L  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.36  -23.64     0      5.00e+00 4.00e-02 2.23e+01
  dihedral pdb=" CA  PRO N 103 "
           pdb=" C   PRO N 103 "
           pdb=" N   GLY N 104 "
           pdb=" CA  GLY N 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.20   22.80     0      5.00e+00 4.00e-02 2.08e+01
  dihedral pdb=" CA  ASP N  51 "
           pdb=" C   ASP N  51 "
           pdb=" N   THR N  52 "
           pdb=" CA  THR N  52 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.05  -20.95     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 7533 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1562
       0.049 -    0.098: 604
       0.098 -    0.148: 136
       0.148 -    0.197: 11
       0.197 -    0.246: 7
  Chirality restraints: 2320
  Sorted by residual:
  chirality pdb=" CG  LEU M  23 "
            pdb=" CB  LEU M  23 "
            pdb=" CD1 LEU M  23 "
            pdb=" CD2 LEU M  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.51e+00
  chirality pdb=" CA  LEU O  92 "
            pdb=" N   LEU O  92 "
            pdb=" C   LEU O  92 "
            pdb=" CB  LEU O  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" CB  VAL O 101 "
            pdb=" CA  VAL O 101 "
            pdb=" CG1 VAL O 101 "
            pdb=" CG2 VAL O 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 2317 not shown)

  Planarity restraints: 1398
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS L  75 "   -0.035 2.00e-02 2.50e+03   2.80e-02 1.18e+01
        pdb=" CG  HIS L  75 "    0.052 2.00e-02 2.50e+03
        pdb=" ND1 HIS L  75 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 HIS L  75 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 HIS L  75 "   -0.024 2.00e-02 2.50e+03
        pdb=" NE2 HIS L  75 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR R  83 "   -0.027 2.00e-02 2.50e+03   2.18e-02 9.48e+00
        pdb=" CG  TYR R  83 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 TYR R  83 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR R  83 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR R  83 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR R  83 "   -0.008 2.00e-02 2.50e+03
        pdb=" CZ  TYR R  83 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR R  83 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE P 100 "   -0.014 2.00e-02 2.50e+03   2.22e-02 8.60e+00
        pdb=" CG  PHE P 100 "    0.050 2.00e-02 2.50e+03
        pdb=" CD1 PHE P 100 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 PHE P 100 "   -0.020 2.00e-02 2.50e+03
        pdb=" CE1 PHE P 100 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE P 100 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  PHE P 100 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1395 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 1084
        2.72 -     3.27: 11922
        3.27 -     3.81: 28286
        3.81 -     4.36: 32152
        4.36 -     4.90: 44433
  Nonbonded interactions: 117877
  Sorted by model distance:
  nonbonded pdb=" OH  TYR Q  39 "
            pdb=" OE1 GLU R  71 "
     model   vdw
     2.177 3.040
  nonbonded pdb=" OG  SER M  40 "
            pdb=" O   ARG M  42 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   LEU O  61 "
            pdb=" NH2 ARG P  36 "
     model   vdw
     2.283 3.120
  nonbonded pdb=" OD2 ASP K 106 "
            pdb=" NH2 ARG K 131 "
     model   vdw
     2.288 3.120
  nonbonded pdb=" O   LEU M  85 "
            pdb=" ND2 ASN M  89 "
     model   vdw
     2.291 3.120
  ... (remaining 117872 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 'K'
  selection = chain 'O'
}
ncs_group {
  reference = chain 'L'
  selection = chain 'P'
}
ncs_group {
  reference = chain 'M'
  selection = chain 'Q'
}
ncs_group {
  reference = chain 'N'
  selection = chain 'R'
}

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:             1.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     13.710
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049  14032  Z= 0.629
  Angle     :  1.024  11.536  20419  Z= 0.803
  Chirality :  0.053   0.246   2320
  Planarity :  0.007   0.062   1398
  Dihedral  : 29.812 179.988   6104
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.09 (0.28), residues: 752
  helix:  0.19 (0.21), residues: 536
  sheet:  None (None), residues: 0
  loop : -0.36 (0.37), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG M  42 
 TYR   0.053   0.003   TYR R  83 
 PHE   0.050   0.003   PHE P 100 
 HIS   0.017   0.002   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00715 /  0.63 (14032)
  covalent geometry    : angle       1.02396 /  0.80 (20419)
  hydrogen bonds       : bond        0.10384 /  6.75 (  829)
  hydrogen bonds       : angle       4.31032 /  3.12 ( 2037)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 176
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   50 GLU cc_start: 0.9460 (pm20) cc_final: 0.9031 (pm20)
REVERT: K   85 GLN cc_start: 0.9086 (mt0) cc_final: 0.8802 (mt0)
REVERT: K   90 MET cc_start: 0.9440 (mmp) cc_final: 0.9203 (mmp)
REVERT: K  120 MET cc_start: 0.8702 (mtm) cc_final: 0.8215 (mtt)
REVERT: L   75 HIS cc_start: 0.9443 (t70) cc_final: 0.8943 (t70)
REVERT: M   36 LYS cc_start: 0.9401 (mppt) cc_final: 0.9053 (mmtm)
REVERT: M   64 GLU cc_start: 0.9578 (mm-30) cc_final: 0.9301 (mm-30)
REVERT: M   79 ILE cc_start: 0.9590 (tp) cc_final: 0.9319 (pt)
REVERT: N   96 THR cc_start: 0.9683 (m) cc_final: 0.9463 (m)
REVERT: N   99 ARG cc_start: 0.9334 (mtp85) cc_final: 0.8543 (ttm110)
REVERT: N  102 LEU cc_start: 0.8854 (tp) cc_final: 0.8423 (tt)
REVERT: O   86 SER cc_start: 0.9826 (t) cc_final: 0.9545 (t)
REVERT: O   90 MET cc_start: 0.9660 (mmp) cc_final: 0.9186 (mmm)
REVERT: O  120 MET cc_start: 0.8299 (mtt) cc_final: 0.8035 (mtt)
REVERT: O  125 GLN cc_start: 0.9400 (mt0) cc_final: 0.9195 (mt0)
REVERT: P   72 TYR cc_start: 0.9560 (m-80) cc_final: 0.9259 (m-80)
REVERT: Q   87 ILE cc_start: 0.9480 (mm) cc_final: 0.9159 (mm)
REVERT: Q   90 ASP cc_start: 0.8905 (t70) cc_final: 0.8391 (t0)
REVERT: R   93 GLU cc_start: 0.9067 (mp0) cc_final: 0.8802 (mp0)
REVERT: R  113 GLU cc_start: 0.9357 (mm-30) cc_final: 0.9000 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.1157
  time to fit residues: 29.1652
Evaluate side-chains
  116 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:   20.0000
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:   20.0000
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    3.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K  93 GLN
** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
M  38 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.031365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.023103 restraints weight = 169470.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.023939 restraints weight = 84207.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.024501 restraints weight = 52357.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.024865 restraints weight = 37047.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.025176 restraints weight = 28743.278|
|-----------------------------------------------------------------------------|
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8401
moved from start:          0.1316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.087  14032  Z= 0.176
  Angle     :  0.701   6.912  20419  Z= 0.410
  Chirality :  0.046   0.258   2320
  Planarity :  0.005   0.058   1398
  Dihedral  : 33.034 177.832   4580
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  2.67 %
    Favored  : 96.86 %
  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 (0.30), residues: 752
  helix:  1.05 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop :  0.09 (0.40), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG N  92 
 TYR   0.023   0.002   TYR R  83 
 PHE   0.026   0.002   PHE O 104 
 HIS   0.005   0.001   HIS M  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00304 /  0.18 (14032)
  covalent geometry    : angle       0.70093 /  0.41 (20419)
  hydrogen bonds       : bond        0.05618 /  3.67 (  829)
  hydrogen bonds       : angle       3.43752 /  2.47 ( 2037)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 155
  time to evaluate  : 0.293 
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: K   54 TYR cc_start: 0.9370 (m-10) cc_final: 0.8766 (m-80)
REVERT: K   85 GLN cc_start: 0.9379 (mt0) cc_final: 0.9039 (mt0)
REVERT: K   90 MET cc_start: 0.9278 (mmp) cc_final: 0.8830 (mmp)
REVERT: K   94 GLU cc_start: 0.9495 (mm-30) cc_final: 0.9118 (mm-30)
REVERT: K  120 MET cc_start: 0.8745 (mtm) cc_final: 0.8331 (mtt)
REVERT: K  123 ASP cc_start: 0.9703 (m-30) cc_final: 0.9501 (m-30)
REVERT: L  100 PHE cc_start: 0.8666 (m-80) cc_final: 0.8446 (m-80)
REVERT: M   36 LYS cc_start: 0.9445 (mppt) cc_final: 0.9051 (mmtm)
REVERT: M   38 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8044 (t0)
REVERT: M   56 GLU cc_start: 0.9265 (mt-10) cc_final: 0.8498 (mm-30)
REVERT: M   64 GLU cc_start: 0.9572 (mm-30) cc_final: 0.9320 (mm-30)
REVERT: M   90 ASP cc_start: 0.7335 (t70) cc_final: 0.7097 (t70)
REVERT: M  101 THR cc_start: 0.8806 (m) cc_final: 0.8538 (p)
REVERT: N  102 LEU cc_start: 0.8706 (tp) cc_final: 0.8355 (tp)
REVERT: O   77 ASP cc_start: 0.9368 (m-30) cc_final: 0.8737 (m-30)
REVERT: O   86 SER cc_start: 0.9782 (t) cc_final: 0.9329 (t)
REVERT: O   94 GLU cc_start: 0.9372 (mp0) cc_final: 0.9033 (mp0)
REVERT: O  104 PHE cc_start: 0.9230 (m-80) cc_final: 0.8710 (m-80)
REVERT: P   72 TYR cc_start: 0.9479 (m-80) cc_final: 0.9278 (m-80)
REVERT: R   83 TYR cc_start: 0.8828 (m-10) cc_final: 0.8587 (m-10)
REVERT: R   88 THR cc_start: 0.9197 (m) cc_final: 0.8950 (p)
REVERT: R   93 GLU cc_start: 0.9108 (mp0) cc_final: 0.8891 (mp0)
REVERT: R  102 LEU cc_start: 0.9299 (tp) cc_final: 0.9070 (tp)
REVERT: R  113 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8928 (mm-30)
  outliers start: 3
  outliers final: 2
  residues processed: 157
  average time/residue: 0.0923
  time to fit residues: 22.2428
Evaluate side-chains
  110 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 107
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 76 optimal weight:   20.0000
   chunk 63 optimal weight:    8.9990
   chunk 38 optimal weight:    9.9990
   chunk 1 optimal weight:    8.9990
   chunk 15 optimal weight:    9.9990
   chunk 16 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 6 optimal weight:   10.0000
   chunk 103 optimal weight:   30.0000
   chunk 31 optimal weight:    5.9990
   overall best weight:    5.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K  55 GLN
M 104 GLN
N 109 HIS
O  55 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2869 r_free = 0.2869 target = 0.028930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2540 r_free = 0.2540 target = 0.021073 restraints weight = 178373.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2580 r_free = 0.2580 target = 0.021855 restraints weight = 88510.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.2604 r_free = 0.2604 target = 0.022372 restraints weight = 55061.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.022709 restraints weight = 39094.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.022998 restraints weight = 30531.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.2625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.082  14032  Z= 0.288
  Angle     :  0.786   8.571  20419  Z= 0.448
  Chirality :  0.048   0.266   2320
  Planarity :  0.006   0.060   1398
  Dihedral  : 33.181 177.620   4580
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 20.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  3.46 %
    Favored  : 96.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.88 (0.28), residues: 752
  helix:  1.00 (0.21), residues: 538
  sheet:  None (None), residues: 0
  loop : -0.27 (0.38), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K  49 
 TYR   0.026   0.003   TYR R  83 
 PHE   0.026   0.003   PHE K  67 
 HIS   0.010   0.002   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00513 /  0.29 (14032)
  covalent geometry    : angle       0.78590 /  0.45 (20419)
  hydrogen bonds       : bond        0.11024 /  7.19 (  829)
  hydrogen bonds       : angle       3.68089 /  2.63 ( 2037)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 132
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9519 (m-10) cc_final: 0.8975 (m-80)
REVERT: K   59 GLU cc_start: 0.8962 (pm20) cc_final: 0.8647 (pm20)
REVERT: K   85 GLN cc_start: 0.9461 (mt0) cc_final: 0.9077 (mt0)
REVERT: K   90 MET cc_start: 0.9238 (mmp) cc_final: 0.8781 (mmp)
REVERT: K   94 GLU cc_start: 0.9456 (mm-30) cc_final: 0.9200 (mm-30)
REVERT: K  104 PHE cc_start: 0.9603 (m-80) cc_final: 0.9400 (m-10)
REVERT: K  120 MET cc_start: 0.8781 (mtm) cc_final: 0.8343 (mtt)
REVERT: K  123 ASP cc_start: 0.9662 (m-30) cc_final: 0.9461 (m-30)
REVERT: L   63 GLU cc_start: 0.9369 (mt-10) cc_final: 0.9167 (mt-10)
REVERT: L   75 HIS cc_start: 0.9299 (t70) cc_final: 0.9097 (t70)
REVERT: M   36 LYS cc_start: 0.9445 (mppt) cc_final: 0.9023 (mmtm)
REVERT: M   41 GLU cc_start: 0.8940 (mp0) cc_final: 0.8243 (tm-30)
REVERT: M   56 GLU cc_start: 0.9351 (mt-10) cc_final: 0.9119 (mt-10)
REVERT: M   64 GLU cc_start: 0.9605 (mm-30) cc_final: 0.9360 (mm-30)
REVERT: M   90 ASP cc_start: 0.7360 (t70) cc_final: 0.7106 (t70)
REVERT: N   62 MET cc_start: 0.9572 (mmp) cc_final: 0.9362 (mmp)
REVERT: N   71 GLU cc_start: 0.9026 (mm-30) cc_final: 0.8631 (mm-30)
REVERT: N  102 LEU cc_start: 0.8724 (tp) cc_final: 0.8408 (tp)
REVERT: O  104 PHE cc_start: 0.9407 (m-80) cc_final: 0.8873 (m-80)
REVERT: O  120 MET cc_start: 0.8364 (mtt) cc_final: 0.8029 (mtt)
REVERT: Q   36 LYS cc_start: 0.9523 (mppt) cc_final: 0.9315 (mmtm)
REVERT: R   93 GLU cc_start: 0.9241 (mp0) cc_final: 0.8967 (mp0)
REVERT: R  113 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8944 (mm-30)
  outliers start: 2
  outliers final: 1
  residues processed: 133
  average time/residue: 0.1039
  time to fit residues: 20.8021
Evaluate side-chains
  99 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 65 optimal weight:    0.8980
   chunk 45 optimal weight:    9.9990
   chunk 38 optimal weight:    8.9990
   chunk 88 optimal weight:   40.0000
   chunk 85 optimal weight:   20.0000
   chunk 43 optimal weight:    5.9990
   chunk 69 optimal weight:    0.8980
   chunk 103 optimal weight:   30.0000
   chunk 99 optimal weight:   20.0000
   chunk 62 optimal weight:    7.9990
   overall best weight:    4.9586

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.032446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2606 r_free = 0.2606 target = 0.025292 restraints weight = 192646.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.026125 restraints weight = 92556.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.026645 restraints weight = 54871.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.027132 restraints weight = 37703.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.027372 restraints weight = 28199.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8468
moved from start:          0.2644

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  14032  Z= 0.245
  Angle     :  0.723   8.300  20419  Z= 0.420
  Chirality :  0.046   0.271   2320
  Planarity :  0.005   0.060   1398
  Dihedral  : 33.319 177.914   4580
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 16.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  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:  1.02 (0.29), residues: 752
  helix:  1.10 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.24 (0.39), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG P  95 
 TYR   0.016   0.003   TYR P  98 
 PHE   0.018   0.003   PHE K 104 
 HIS   0.008   0.002   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00433 /  0.24 (14032)
  covalent geometry    : angle       0.72311 /  0.42 (20419)
  hydrogen bonds       : bond        0.07659 /  4.98 (  829)
  hydrogen bonds       : angle       3.68848 /  2.67 ( 2037)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9543 (m-10) cc_final: 0.9017 (m-80)
REVERT: K   85 GLN cc_start: 0.9358 (mt0) cc_final: 0.8939 (mt0)
REVERT: K   90 MET cc_start: 0.9337 (mmp) cc_final: 0.8964 (mmp)
REVERT: K   94 GLU cc_start: 0.9491 (mm-30) cc_final: 0.9206 (mm-30)
REVERT: K  120 MET cc_start: 0.8729 (mtm) cc_final: 0.8283 (mtt)
REVERT: L   75 HIS cc_start: 0.9344 (t70) cc_final: 0.9126 (t70)
REVERT: M   41 GLU cc_start: 0.8939 (mp0) cc_final: 0.7975 (tp30)
REVERT: M   56 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8993 (mt-10)
REVERT: M   64 GLU cc_start: 0.9611 (mm-30) cc_final: 0.9392 (mm-30)
REVERT: M   90 ASP cc_start: 0.7263 (t70) cc_final: 0.7024 (t70)
REVERT: N   62 MET cc_start: 0.9578 (mmp) cc_final: 0.9316 (mmp)
REVERT: N   71 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8615 (mm-30)
REVERT: N  102 LEU cc_start: 0.8711 (tp) cc_final: 0.8385 (tp)
REVERT: O   86 SER cc_start: 0.9772 (p) cc_final: 0.9570 (p)
REVERT: O  104 PHE cc_start: 0.9363 (m-80) cc_final: 0.8766 (m-80)
REVERT: O  120 MET cc_start: 0.8297 (mtt) cc_final: 0.7946 (mtt)
REVERT: R   59 MET cc_start: 0.8984 (tpt) cc_final: 0.8451 (tpt)
REVERT: R   71 GLU cc_start: 0.9504 (mm-30) cc_final: 0.9267 (mm-30)
REVERT: R   93 GLU cc_start: 0.9254 (mp0) cc_final: 0.8969 (mp0)
REVERT: R  113 GLU cc_start: 0.9280 (mm-30) cc_final: 0.8969 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0940
  time to fit residues: 19.2719
Evaluate side-chains
  101 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 103 optimal weight:   30.0000
   chunk 70 optimal weight:    0.1980
   chunk 44 optimal weight:    0.7980
   chunk 101 optimal weight:   20.0000
   chunk 105 optimal weight:   30.0000
   chunk 42 optimal weight:    0.9990
   chunk 99 optimal weight:   30.0000
   chunk 94 optimal weight:   20.0000
   chunk 17 optimal weight:    8.9990
   chunk 58 optimal weight:    6.9990
   chunk 76 optimal weight:   30.0000
   overall best weight:    3.5986

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.029209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2543 r_free = 0.2543 target = 0.021299 restraints weight = 174169.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2583 r_free = 0.2583 target = 0.022077 restraints weight = 85594.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.022595 restraints weight = 52900.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.2626 r_free = 0.2626 target = 0.022966 restraints weight = 37398.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.023202 restraints weight = 28921.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.2626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.2939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14032  Z= 0.201
  Angle     :  0.694   8.013  20419  Z= 0.404
  Chirality :  0.046   0.253   2320
  Planarity :  0.005   0.060   1398
  Dihedral  : 33.260 179.391   4580
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 14.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  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:  1.19 (0.29), residues: 752
  helix:  1.25 (0.21), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.26 (0.39), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG K  49 
 TYR   0.014   0.002   TYR N  40 
 PHE   0.014   0.002   PHE O 104 
 HIS   0.006   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.20 (14032)
  covalent geometry    : angle       0.69431 /  0.40 (20419)
  hydrogen bonds       : bond        0.06782 /  4.41 (  829)
  hydrogen bonds       : angle       3.52289 /  2.55 ( 2037)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9561 (m-10) cc_final: 0.9017 (m-80)
REVERT: K   85 GLN cc_start: 0.9383 (mt0) cc_final: 0.8886 (mt0)
REVERT: K   90 MET cc_start: 0.9290 (mmp) cc_final: 0.8893 (mmp)
REVERT: K   94 GLU cc_start: 0.9432 (mm-30) cc_final: 0.9113 (mm-30)
REVERT: K  120 MET cc_start: 0.8780 (mtm) cc_final: 0.8215 (mtt)
REVERT: K  123 ASP cc_start: 0.9667 (m-30) cc_final: 0.9450 (m-30)
REVERT: L   75 HIS cc_start: 0.9290 (t70) cc_final: 0.9052 (t70)
REVERT: M   41 GLU cc_start: 0.8919 (mp0) cc_final: 0.7965 (tp30)
REVERT: M   56 GLU cc_start: 0.9313 (mt-10) cc_final: 0.9090 (mt-10)
REVERT: M   90 ASP cc_start: 0.7506 (t70) cc_final: 0.7280 (t70)
REVERT: N   71 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8613 (mm-30)
REVERT: N  102 LEU cc_start: 0.8711 (tp) cc_final: 0.8381 (tp)
REVERT: N  109 HIS cc_start: 0.9837 (m170) cc_final: 0.9635 (m170)
REVERT: O  104 PHE cc_start: 0.9414 (m-80) cc_final: 0.8757 (m-80)
REVERT: O  120 MET cc_start: 0.8324 (mtt) cc_final: 0.7913 (mtt)
REVERT: P   72 TYR cc_start: 0.9404 (m-80) cc_final: 0.9033 (m-80)
REVERT: Q   36 LYS cc_start: 0.9308 (mmtm) cc_final: 0.9105 (mmtm)
REVERT: R   71 GLU cc_start: 0.9496 (mm-30) cc_final: 0.9233 (mm-30)
REVERT: R  113 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8938 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0890
  time to fit residues: 18.0452
Evaluate side-chains
  100 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 90 optimal weight:   30.0000
   chunk 17 optimal weight:    9.9990
   chunk 94 optimal weight:   20.0000
   chunk 35 optimal weight:    1.9990
   chunk 99 optimal weight:   20.0000
   chunk 102 optimal weight:   30.0000
   chunk 31 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 26 optimal weight:    7.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    2.7186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.029413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2555 r_free = 0.2555 target = 0.021480 restraints weight = 169722.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2595 r_free = 0.2595 target = 0.022260 restraints weight = 83430.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.022767 restraints weight = 51506.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.2637 r_free = 0.2637 target = 0.023142 restraints weight = 36478.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2648 r_free = 0.2648 target = 0.023368 restraints weight = 28196.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.2635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.3113

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14032  Z= 0.173
  Angle     :  0.673   7.730  20419  Z= 0.391
  Chirality :  0.045   0.254   2320
  Planarity :  0.004   0.058   1398
  Dihedral  : 33.205 179.837   4580
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  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:  1.29 (0.30), residues: 752
  helix:  1.36 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.31 (0.40), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG N  79 
 TYR   0.012   0.002   TYR N  40 
 PHE   0.027   0.002   PHE K 104 
 HIS   0.005   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.17 (14032)
  covalent geometry    : angle       0.67271 /  0.39 (20419)
  hydrogen bonds       : bond        0.05825 /  3.79 (  829)
  hydrogen bonds       : angle       3.48208 /  2.54 ( 2037)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9555 (m-10) cc_final: 0.8969 (m-80)
REVERT: K   90 MET cc_start: 0.9287 (mmp) cc_final: 0.8891 (mmp)
REVERT: K  120 MET cc_start: 0.8771 (mtm) cc_final: 0.8144 (mtt)
REVERT: K  123 ASP cc_start: 0.9651 (m-30) cc_final: 0.9451 (m-30)
REVERT: L   75 HIS cc_start: 0.9294 (t70) cc_final: 0.9058 (t70)
REVERT: M   41 GLU cc_start: 0.8993 (mp0) cc_final: 0.8045 (tp30)
REVERT: M   56 GLU cc_start: 0.9295 (mt-10) cc_final: 0.9022 (mt-10)
REVERT: M   90 ASP cc_start: 0.7459 (t70) cc_final: 0.7244 (t70)
REVERT: N   71 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8623 (mm-30)
REVERT: N  102 LEU cc_start: 0.8665 (tp) cc_final: 0.8349 (tp)
REVERT: O   86 SER cc_start: 0.9783 (p) cc_final: 0.9400 (p)
REVERT: O  104 PHE cc_start: 0.9388 (m-80) cc_final: 0.8846 (m-80)
REVERT: O  120 MET cc_start: 0.8343 (mtt) cc_final: 0.7911 (mtt)
REVERT: P   72 TYR cc_start: 0.9354 (m-80) cc_final: 0.8998 (m-80)
REVERT: Q   36 LYS cc_start: 0.9290 (mmtm) cc_final: 0.8991 (mmtm)
REVERT: R   71 GLU cc_start: 0.9506 (mm-30) cc_final: 0.9161 (mm-30)
REVERT: R   76 GLU cc_start: 0.9411 (tp30) cc_final: 0.9177 (tp30)
REVERT: R  113 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8941 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1021
  time to fit residues: 21.5135
Evaluate side-chains
  99 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 76 optimal weight:   30.0000
   chunk 35 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   chunk 77 optimal weight:   20.0000
   chunk 70 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 38 optimal weight:    0.9980
   chunk 23 optimal weight:    6.9990
   chunk 11 optimal weight:    2.9990
   chunk 88 optimal weight:   40.0000
   overall best weight:    2.3988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
N 109 HIS
** R  63 ASN ** 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 = 0.2893 r_free = 0.2893 target = 0.029491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2559 r_free = 0.2559 target = 0.021631 restraints weight = 169884.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2601 r_free = 0.2601 target = 0.022410 restraints weight = 83226.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.022946 restraints weight = 50918.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.023273 restraints weight = 35623.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.023540 restraints weight = 27608.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.2649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.3256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14032  Z= 0.164
  Angle     :  0.669   7.723  20419  Z= 0.389
  Chirality :  0.044   0.253   2320
  Planarity :  0.004   0.057   1398
  Dihedral  : 33.136 179.128   4580
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  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:  1.46 (0.30), residues: 752
  helix:  1.50 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.31 (0.40), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K  69 
 TYR   0.010   0.001   TYR N  40 
 PHE   0.032   0.002   PHE M  25 
 HIS   0.008   0.001   HIS N 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.16 (14032)
  covalent geometry    : angle       0.66916 /  0.39 (20419)
  hydrogen bonds       : bond        0.05528 /  3.59 (  829)
  hydrogen bonds       : angle       3.50802 /  2.56 ( 2037)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9521 (m-10) cc_final: 0.8933 (m-80)
REVERT: K   90 MET cc_start: 0.9303 (mmp) cc_final: 0.8899 (mmp)
REVERT: K  120 MET cc_start: 0.8709 (mtm) cc_final: 0.8006 (mtt)
REVERT: L   44 LYS cc_start: 0.8742 (pptt) cc_final: 0.8538 (pptt)
REVERT: L   75 HIS cc_start: 0.9302 (t70) cc_final: 0.9087 (t70)
REVERT: M   36 LYS cc_start: 0.9556 (mptt) cc_final: 0.9260 (mmtm)
REVERT: M   41 GLU cc_start: 0.8990 (mp0) cc_final: 0.8065 (tp30)
REVERT: N   71 GLU cc_start: 0.9046 (mm-30) cc_final: 0.8603 (mm-30)
REVERT: N  102 LEU cc_start: 0.8669 (tp) cc_final: 0.8318 (tp)
REVERT: N  105 GLU cc_start: 0.9620 (mp0) cc_final: 0.9391 (pm20)
REVERT: N  109 HIS cc_start: 0.9801 (m90) cc_final: 0.9501 (m170)
REVERT: O   94 GLU cc_start: 0.9419 (mp0) cc_final: 0.9179 (mp0)
REVERT: O  100 LEU cc_start: 0.9742 (mt) cc_final: 0.9481 (mt)
REVERT: O  104 PHE cc_start: 0.9438 (m-80) cc_final: 0.8846 (m-80)
REVERT: P   72 TYR cc_start: 0.9370 (m-80) cc_final: 0.8969 (m-80)
REVERT: Q   36 LYS cc_start: 0.9340 (mmtm) cc_final: 0.9031 (mmtm)
REVERT: R   59 MET cc_start: 0.8672 (tpt) cc_final: 0.8419 (tpt)
REVERT: R  113 GLU cc_start: 0.9239 (mm-30) cc_final: 0.8957 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1030
  time to fit residues: 21.8329
Evaluate side-chains
  108 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 73 optimal weight:   30.0000
   chunk 33 optimal weight:    0.9980
   chunk 98 optimal weight:   30.0000
   chunk 87 optimal weight:   30.0000
   chunk 27 optimal weight:    9.9990
   chunk 44 optimal weight:    5.9990
   chunk 74 optimal weight:   30.0000
   chunk 97 optimal weight:   20.0000
   chunk 92 optimal weight:   20.0000
   chunk 85 optimal weight:   20.0000
   chunk 25 optimal weight:    1.9990
   overall best weight:    7.7990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  95 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.030507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2545 r_free = 0.2545 target = 0.023784 restraints weight = 200060.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2588 r_free = 0.2588 target = 0.024507 restraints weight = 96578.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.025040 restraints weight = 58517.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2633 r_free = 0.2633 target = 0.025313 restraints weight = 39679.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.025634 restraints weight = 31475.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.2597
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.4007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.066  14032  Z= 0.350
  Angle     :  0.855   9.451  20419  Z= 0.477
  Chirality :  0.051   0.274   2320
  Planarity :  0.007   0.063   1398
  Dihedral  : 33.436 178.568   4580
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 26.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  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:  0.36 (0.29), residues: 752
  helix:  0.62 (0.21), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.52 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG K  49 
 TYR   0.021   0.003   TYR R  40 
 PHE   0.023   0.003   PHE M  25 
 HIS   0.025   0.004   HIS N 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00625 /  0.35 (14032)
  covalent geometry    : angle       0.85465 /  0.48 (20419)
  hydrogen bonds       : bond        0.13074 /  8.51 (  829)
  hydrogen bonds       : angle       4.20326 /  3.06 ( 2037)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9592 (m-10) cc_final: 0.8913 (m-80)
REVERT: K   90 MET cc_start: 0.9322 (mmp) cc_final: 0.8989 (mmp)
REVERT: K  120 MET cc_start: 0.8806 (mtm) cc_final: 0.8068 (mtt)
REVERT: K  123 ASP cc_start: 0.9640 (m-30) cc_final: 0.9430 (m-30)
REVERT: M   36 LYS cc_start: 0.9501 (mptt) cc_final: 0.9206 (mmtm)
REVERT: M   90 ASP cc_start: 0.7241 (t0) cc_final: 0.6854 (t0)
REVERT: N   71 GLU cc_start: 0.9100 (mm-30) cc_final: 0.8647 (mm-30)
REVERT: N   99 ARG cc_start: 0.9322 (mtp85) cc_final: 0.9105 (mtp-110)
REVERT: N  102 LEU cc_start: 0.8706 (tp) cc_final: 0.8182 (tt)
REVERT: N  105 GLU cc_start: 0.9595 (mp0) cc_final: 0.9346 (pm20)
REVERT: N  109 HIS cc_start: 0.9768 (m90) cc_final: 0.9427 (m170)
REVERT: O  100 LEU cc_start: 0.9755 (mt) cc_final: 0.9509 (mt)
REVERT: O  104 PHE cc_start: 0.9537 (m-80) cc_final: 0.8963 (m-80)
REVERT: O  120 MET cc_start: 0.8289 (mtt) cc_final: 0.7918 (mtt)
REVERT: P   72 TYR cc_start: 0.9561 (m-80) cc_final: 0.9167 (m-80)
REVERT: Q   36 LYS cc_start: 0.9400 (mmtm) cc_final: 0.9122 (mmtm)
REVERT: R   59 MET cc_start: 0.8777 (tpt) cc_final: 0.8557 (tpt)
REVERT: R  113 GLU cc_start: 0.9263 (mm-30) cc_final: 0.9024 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1035
  time to fit residues: 18.8450
Evaluate side-chains
  92 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 82 optimal weight:   20.0000
   chunk 19 optimal weight:    7.9990
   chunk 101 optimal weight:   20.0000
   chunk 79 optimal weight:   20.0000
   chunk 60 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0060
   chunk 86 optimal weight:   30.0000
   chunk 45 optimal weight:    7.9990
   chunk 41 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   overall best weight:    1.3800

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
L  75 HIS
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  73 ASN
R 109 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.032495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2601 r_free = 0.2601 target = 0.025405 restraints weight = 191162.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.026245 restraints weight = 88649.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2677 r_free = 0.2677 target = 0.026755 restraints weight = 51947.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.027169 restraints weight = 35474.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.027492 restraints weight = 27010.135|
|-----------------------------------------------------------------------------|
r_work (final): 0.2646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.3864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  14032  Z= 0.160
  Angle     :  0.705   8.498  20419  Z= 0.406
  Chirality :  0.047   0.264   2320
  Planarity :  0.005   0.054   1398
  Dihedral  : 33.443 176.228   4580
  Min Nonbonded Distance : 2.327

Molprobity Statistics.
  All-atom Clashscore : 13.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.00 (0.30), residues: 752
  helix:  1.10 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.30 (0.41), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG N  31 
 TYR   0.012   0.002   TYR R  37 
 PHE   0.022   0.003   PHE P 100 
 HIS   0.007   0.001   HIS O  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.16 (14032)
  covalent geometry    : angle       0.70540 /  0.41 (20419)
  hydrogen bonds       : bond        0.05357 /  3.52 (  829)
  hydrogen bonds       : angle       3.73262 /  2.74 ( 2037)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9506 (m-10) cc_final: 0.8956 (m-80)
REVERT: K   85 GLN cc_start: 0.9205 (mt0) cc_final: 0.8722 (mt0)
REVERT: K   90 MET cc_start: 0.9360 (mmp) cc_final: 0.8809 (mmp)
REVERT: K  104 PHE cc_start: 0.9594 (m-10) cc_final: 0.9346 (m-10)
REVERT: K  120 MET cc_start: 0.8848 (mtm) cc_final: 0.8051 (mtt)
REVERT: L   75 HIS cc_start: 0.9297 (t-90) cc_final: 0.8853 (t70)
REVERT: M   36 LYS cc_start: 0.9474 (mptt) cc_final: 0.9151 (mmtm)
REVERT: M   41 GLU cc_start: 0.8993 (mp0) cc_final: 0.8199 (tp30)
REVERT: M   79 ILE cc_start: 0.9546 (tp) cc_final: 0.9279 (pt)
REVERT: M   90 ASP cc_start: 0.7170 (t0) cc_final: 0.6774 (t0)
REVERT: N   71 GLU cc_start: 0.9134 (mm-30) cc_final: 0.8621 (mm-30)
REVERT: N   99 ARG cc_start: 0.9302 (mtp85) cc_final: 0.8753 (ttm110)
REVERT: N  102 LEU cc_start: 0.8619 (tp) cc_final: 0.8273 (tp)
REVERT: N  105 GLU cc_start: 0.9637 (mp0) cc_final: 0.9368 (pm20)
REVERT: N  109 HIS cc_start: 0.9792 (m90) cc_final: 0.9470 (m170)
REVERT: O  100 LEU cc_start: 0.9741 (mt) cc_final: 0.9520 (mt)
REVERT: O  104 PHE cc_start: 0.9457 (m-80) cc_final: 0.8904 (m-80)
REVERT: O  120 MET cc_start: 0.8139 (mtt) cc_final: 0.7770 (mtt)
REVERT: Q   36 LYS cc_start: 0.9375 (mmtm) cc_final: 0.9048 (mmtm)
REVERT: R  113 GLU cc_start: 0.9305 (mm-30) cc_final: 0.9001 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 0.1129
  time to fit residues: 23.9237
Evaluate side-chains
  111 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 38 optimal weight:    8.9990
   chunk 86 optimal weight:   30.0000
   chunk 85 optimal weight:   20.0000
   chunk 97 optimal weight:   20.0000
   chunk 26 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9990
   chunk 16 optimal weight:    3.9990
   chunk 98 optimal weight:   30.0000
   chunk 95 optimal weight:   20.0000
   chunk 17 optimal weight:    9.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    4.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.027973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2516 r_free = 0.2516 target = 0.020520 restraints weight = 175677.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2558 r_free = 0.2558 target = 0.021263 restraints weight = 86110.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2582 r_free = 0.2582 target = 0.021771 restraints weight = 52867.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2601 r_free = 0.2601 target = 0.022118 restraints weight = 37109.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.022366 restraints weight = 28878.400|
|-----------------------------------------------------------------------------|
r_work (final): 0.2600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8493
moved from start:          0.4068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14032  Z= 0.223
  Angle     :  0.730   7.466  20419  Z= 0.418
  Chirality :  0.046   0.264   2320
  Planarity :  0.005   0.056   1398
  Dihedral  : 33.346 177.176   4580
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 17.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  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:  0.94 (0.30), residues: 752
  helix:  1.06 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.32 (0.41), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG N  31 
 TYR   0.013   0.002   TYR N  40 
 PHE   0.019   0.002   PHE M  25 
 HIS   0.007   0.002   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00396 /  0.22 (14032)
  covalent geometry    : angle       0.73028 /  0.42 (20419)
  hydrogen bonds       : bond        0.07727 /  5.03 (  829)
  hydrogen bonds       : angle       3.90500 /  2.87 ( 2037)

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

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

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1504 Ramachandran restraints generated.
    752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9570 (m-10) cc_final: 0.9036 (m-80)
REVERT: K   85 GLN cc_start: 0.9284 (mt0) cc_final: 0.8782 (mt0)
REVERT: K   94 GLU cc_start: 0.8979 (mp0) cc_final: 0.8680 (pm20)
REVERT: K  120 MET cc_start: 0.8851 (mtm) cc_final: 0.8020 (mtt)
REVERT: L   59 LYS cc_start: 0.9735 (tppt) cc_final: 0.9426 (tppt)
REVERT: L   75 HIS cc_start: 0.9184 (t-90) cc_final: 0.8883 (t70)
REVERT: L   97 LEU cc_start: 0.9520 (tp) cc_final: 0.9156 (tp)
REVERT: M   36 LYS cc_start: 0.9467 (mptt) cc_final: 0.9132 (mmtm)
REVERT: M   41 GLU cc_start: 0.8939 (mp0) cc_final: 0.8182 (tp30)
REVERT: M   90 ASP cc_start: 0.7191 (t0) cc_final: 0.6781 (t0)
REVERT: N   71 GLU cc_start: 0.9124 (mm-30) cc_final: 0.8624 (mm-30)
REVERT: N   99 ARG cc_start: 0.9323 (mtp85) cc_final: 0.8733 (ttm110)
REVERT: N  102 LEU cc_start: 0.8709 (tp) cc_final: 0.8338 (tp)
REVERT: N  105 GLU cc_start: 0.9608 (mp0) cc_final: 0.9333 (pm20)
REVERT: N  109 HIS cc_start: 0.9786 (m90) cc_final: 0.9452 (m170)
REVERT: O   86 SER cc_start: 0.9805 (p) cc_final: 0.9411 (p)
REVERT: O  100 LEU cc_start: 0.9755 (mt) cc_final: 0.9479 (mt)
REVERT: O  104 PHE cc_start: 0.9511 (m-80) cc_final: 0.8913 (m-80)
REVERT: O  120 MET cc_start: 0.8322 (mtt) cc_final: 0.7924 (mtt)
REVERT: R  113 GLU cc_start: 0.9231 (mm-30) cc_final: 0.8985 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1134
  time to fit residues: 22.7427
Evaluate side-chains
  102 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 53 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 96 optimal weight:   20.0000
   chunk 61 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 86 optimal weight:   30.0000
   overall best weight:    2.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.032385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2603 r_free = 0.2603 target = 0.025392 restraints weight = 189797.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.026219 restraints weight = 90200.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.026750 restraints weight = 53069.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.027233 restraints weight = 35920.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.027377 restraints weight = 26725.036|
|-----------------------------------------------------------------------------|
r_work (final): 0.2646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8459
moved from start:          0.4114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  14032  Z= 0.165
  Angle     :  0.692   8.132  20419  Z= 0.399
  Chirality :  0.046   0.256   2320
  Planarity :  0.004   0.055   1398
  Dihedral  : 33.289 176.433   4580
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.30), residues: 752
  helix:  1.14 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.25 (0.41), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG L  78 
 TYR   0.012   0.002   TYR O  99 
 PHE   0.018   0.002   PHE M  25 
 HIS   0.007   0.001   HIS O  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.16 (14032)
  covalent geometry    : angle       0.69213 /  0.40 (20419)
  hydrogen bonds       : bond        0.05303 /  3.49 (  829)
  hydrogen bonds       : angle       3.75101 /  2.77 ( 2037)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1777.94 seconds
wall clock time: 32 minutes 2.24 seconds (1922.24 seconds total)