Starting phenix.real_space_refine
on Sat Sep 12 08:02:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pey_13361/09_2026/7pey_13361.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pey_13361/09_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_13361/09_2026/7pey_13361.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pey_13361/09_2026/7pey_13361.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pey_13361/09_2026/7pey_13361.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pey_13361/09_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/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: 2.77, per 1000 atoms: 0.21
  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: 0.97
  Conformation dependent library (CDL) restraints added in 338.7 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: 1.97
  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: 3.21

  Time building geometry restraints manager: 1.31 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: 19537
        2.31 -     4.61: 800
        4.61 -     6.92: 64
        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:             2.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.920
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.910
-------------------------------------------------------------------------------
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     :  1.032  11.536  20419  Z= 0.812
  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       1.03181 /  0.81 (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  : 0.385 
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: 0.8941 (t70)
REVERT: M   36 LYS cc_start: 0.9401 (mppt) cc_final: 0.9054 (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: 0.8542 (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: 0.8999 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 176
  average time/residue: 0.1254
  time to fit residues: 31.8062
Evaluate side-chains
  117 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
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:   30.0000
   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:    8.9990
   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 = 0.031352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.023137 restraints weight = 167881.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.023967 restraints weight = 83468.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.024526 restraints weight = 52033.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.024922 restraints weight = 36794.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2717 r_free = 0.2717 target = 0.025167 restraints weight = 28415.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8403
moved from start:          0.1311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  14032  Z= 0.177
  Angle     :  0.710   7.682  20419  Z= 0.414
  Chirality :  0.046   0.270   2320
  Planarity :  0.005   0.058   1398
  Dihedral  : 32.937 178.226   4580
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.20 %
    Favored  : 98.80 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  2.36 %
    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:  1.11 (0.30), residues: 752
  helix:  1.08 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop :  0.07 (0.40), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG N  92 
 TYR   0.024   0.002   TYR R  83 
 PHE   0.027   0.002   PHE O 104 
 HIS   0.004   0.001   HIS M  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.18 (14032)
  covalent geometry    : angle       0.70985 /  0.41 (20419)
  hydrogen bonds       : bond        0.05585 /  3.65 (  829)
  hydrogen bonds       : angle       3.43521 /  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  : 0.338 
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: 0.9346 (m-10) cc_final: 0.8706 (m-80)
REVERT: K   85 GLN cc_start: 0.9384 (mt0) cc_final: 0.9044 (mt0)
REVERT: K   90 MET cc_start: 0.9276 (mmp) cc_final: 0.8896 (mmp)
REVERT: K   94 GLU cc_start: 0.9492 (mm-30) cc_final: 0.9237 (mm-30)
REVERT: K  120 MET cc_start: 0.8751 (mtm) cc_final: 0.8333 (mtt)
REVERT: K  123 ASP cc_start: 0.9697 (m-30) cc_final: 0.9492 (m-30)
REVERT: M   36 LYS cc_start: 0.9447 (mppt) cc_final: 0.9054 (mmtm)
REVERT: M   38 ASN cc_start: 0.8642 (OUTLIER) cc_final: 0.8020 (t0)
REVERT: M   56 GLU cc_start: 0.9262 (mt-10) cc_final: 0.8499 (mm-30)
REVERT: M   64 GLU cc_start: 0.9572 (mm-30) cc_final: 0.9310 (mm-30)
REVERT: M   90 ASP cc_start: 0.7377 (t70) cc_final: 0.7122 (t70)
REVERT: M  101 THR cc_start: 0.8802 (m) cc_final: 0.8537 (p)
REVERT: N  102 LEU cc_start: 0.8730 (tp) cc_final: 0.8389 (tp)
REVERT: O   77 ASP cc_start: 0.9368 (m-30) cc_final: 0.8740 (m-30)
REVERT: O   86 SER cc_start: 0.9785 (t) cc_final: 0.9503 (t)
REVERT: O   93 GLN cc_start: 0.9536 (pt0) cc_final: 0.9160 (pt0)
REVERT: O  104 PHE cc_start: 0.9231 (m-80) cc_final: 0.8714 (m-80)
REVERT: R   83 TYR cc_start: 0.8824 (m-10) cc_final: 0.8556 (m-10)
REVERT: R   88 THR cc_start: 0.9199 (m) cc_final: 0.8949 (p)
REVERT: R   93 GLU cc_start: 0.9101 (mp0) cc_final: 0.8886 (mp0)
REVERT: R  102 LEU cc_start: 0.9274 (tp) cc_final: 0.9028 (tp)
REVERT: R  113 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8928 (mm-30)
  outliers start: 3
  outliers final: 2
  residues processed: 157
  average time/residue: 0.1025
  time to fit residues: 24.7133
Evaluate side-chains
  109 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 106
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 38 optimal weight:    4.9990
   chunk 1 optimal weight:   10.0000
   chunk 15 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 6 optimal weight:    9.9990
   chunk 103 optimal weight:   30.0000
   chunk 31 optimal weight:    4.9990
   overall best weight:    3.9988

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.033622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.026356 restraints weight = 190348.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.027207 restraints weight = 90698.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.027729 restraints weight = 53916.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.2738 r_free = 0.2738 target = 0.028213 restraints weight = 37304.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.028431 restraints weight = 27949.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8428
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  14032  Z= 0.211
  Angle     :  0.712   8.385  20419  Z= 0.412
  Chirality :  0.045   0.281   2320
  Planarity :  0.005   0.059   1398
  Dihedral  : 32.902 177.993   4580
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 15.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.99 %
    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:  1.26 (0.29), residues: 752
  helix:  1.27 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.12 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG K  49 
 TYR   0.022   0.002   TYR R  83 
 PHE   0.026   0.003   PHE K  67 
 HIS   0.007   0.002   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.21 (14032)
  covalent geometry    : angle       0.71205 /  0.41 (20419)
  hydrogen bonds       : bond        0.07498 /  4.87 (  829)
  hydrogen bonds       : angle       3.44195 /  2.47 ( 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
  144 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 143
  time to evaluate  : 0.380 
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: 0.9477 (m-10) cc_final: 0.8955 (m-80)
REVERT: K   59 GLU cc_start: 0.8966 (pm20) cc_final: 0.8668 (pm20)
REVERT: K   85 GLN cc_start: 0.9406 (mt0) cc_final: 0.9038 (mt0)
REVERT: K   90 MET cc_start: 0.9235 (mmp) cc_final: 0.8895 (mmp)
REVERT: K   94 GLU cc_start: 0.9472 (mm-30) cc_final: 0.9180 (mm-30)
REVERT: K  120 MET cc_start: 0.8746 (mtm) cc_final: 0.8299 (mtt)
REVERT: K  123 ASP cc_start: 0.9693 (m-30) cc_final: 0.9480 (m-30)
REVERT: L   63 GLU cc_start: 0.9369 (mt-10) cc_final: 0.9169 (mt-10)
REVERT: L  100 PHE cc_start: 0.8619 (m-80) cc_final: 0.8399 (m-80)
REVERT: M   36 LYS cc_start: 0.9444 (mppt) cc_final: 0.9026 (mmtm)
REVERT: M   56 GLU cc_start: 0.9290 (mt-10) cc_final: 0.9000 (mt-10)
REVERT: M   64 GLU cc_start: 0.9607 (mm-30) cc_final: 0.9405 (mm-30)
REVERT: M   90 ASP cc_start: 0.7270 (t70) cc_final: 0.7020 (t70)
REVERT: M  101 THR cc_start: 0.8752 (m) cc_final: 0.8457 (p)
REVERT: N   62 MET cc_start: 0.9547 (mmp) cc_final: 0.9330 (mmp)
REVERT: N  102 LEU cc_start: 0.8683 (tp) cc_final: 0.8380 (tp)
REVERT: O   86 SER cc_start: 0.9809 (t) cc_final: 0.9457 (t)
REVERT: O   97 GLU cc_start: 0.9379 (OUTLIER) cc_final: 0.9177 (mp0)
REVERT: O  100 LEU cc_start: 0.9735 (mt) cc_final: 0.9519 (mt)
REVERT: O  104 PHE cc_start: 0.9318 (m-80) cc_final: 0.8802 (m-80)
REVERT: O  120 MET cc_start: 0.8427 (mtt) cc_final: 0.8081 (mtt)
REVERT: R   93 GLU cc_start: 0.9256 (mp0) cc_final: 0.8973 (mp0)
REVERT: R  102 LEU cc_start: 0.9319 (tp) cc_final: 0.9080 (tp)
REVERT: R  113 GLU cc_start: 0.9299 (mm-30) cc_final: 0.8972 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 143
  average time/residue: 0.1068
  time to fit residues: 22.9149
Evaluate side-chains
  104 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 45 optimal weight:    4.9990
   chunk 38 optimal weight:   10.0000
   chunk 88 optimal weight:   40.0000
   chunk 85 optimal weight:   20.0000
   chunk 43 optimal weight:    3.9990
   chunk 69 optimal weight:    0.8980
   chunk 103 optimal weight:   30.0000
   chunk 99 optimal weight:   20.0000
   chunk 62 optimal weight:    1.9990
   overall best weight:    3.1788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
O  55 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.030230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2584 r_free = 0.2584 target = 0.022145 restraints weight = 169890.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.022963 restraints weight = 84078.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2648 r_free = 0.2648 target = 0.023531 restraints weight = 51660.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2666 r_free = 0.2666 target = 0.023889 restraints weight = 36203.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.2677 r_free = 0.2677 target = 0.024188 restraints weight = 27986.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.2251

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= 0.183
  Angle     :  0.685  11.838  20419  Z= 0.396
  Chirality :  0.044   0.276   2320
  Planarity :  0.005   0.060   1398
  Dihedral  : 32.926 177.719   4580
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 13.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  2.52 %
    Favored  : 97.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.41 (0.29), residues: 752
  helix:  1.44 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.24 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K  49 
 TYR   0.018   0.002   TYR P  72 
 PHE   0.030   0.003   PHE K 104 
 HIS   0.005   0.001   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00312 /  0.18 (14032)
  covalent geometry    : angle       0.68531 /  0.40 (20419)
  hydrogen bonds       : bond        0.05614 /  3.64 (  829)
  hydrogen bonds       : angle       3.38810 /  2.44 ( 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
  143 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.275 
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: 0.9520 (m-10) cc_final: 0.8990 (m-80)
REVERT: K   59 GLU cc_start: 0.8922 (pm20) cc_final: 0.8613 (pm20)
REVERT: K   85 GLN cc_start: 0.9396 (mt0) cc_final: 0.9019 (mt0)
REVERT: K   90 MET cc_start: 0.9211 (mmp) cc_final: 0.8869 (mmp)
REVERT: K   94 GLU cc_start: 0.9413 (mm-30) cc_final: 0.9084 (mm-30)
REVERT: K  120 MET cc_start: 0.8731 (mtm) cc_final: 0.8262 (mtt)
REVERT: L   63 GLU cc_start: 0.9384 (mt-10) cc_final: 0.9163 (mt-10)
REVERT: L   75 HIS cc_start: 0.9214 (t70) cc_final: 0.8830 (t70)
REVERT: M   36 LYS cc_start: 0.9428 (mppt) cc_final: 0.8967 (mmtm)
REVERT: M   41 GLU cc_start: 0.8929 (mp0) cc_final: 0.7975 (tp30)
REVERT: M   56 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8943 (mt-10)
REVERT: M   64 GLU cc_start: 0.9617 (mm-30) cc_final: 0.9377 (mm-30)
REVERT: M   90 ASP cc_start: 0.7341 (t70) cc_final: 0.7083 (t70)
REVERT: M  101 THR cc_start: 0.9033 (m) cc_final: 0.8813 (p)
REVERT: N   62 MET cc_start: 0.9563 (mmp) cc_final: 0.9330 (mmp)
REVERT: N   71 GLU cc_start: 0.9000 (mm-30) cc_final: 0.8789 (mm-30)
REVERT: N   96 THR cc_start: 0.9647 (m) cc_final: 0.9426 (p)
REVERT: N  102 LEU cc_start: 0.8664 (tp) cc_final: 0.8362 (tp)
REVERT: O   86 SER cc_start: 0.9810 (t) cc_final: 0.9535 (t)
REVERT: O  100 LEU cc_start: 0.9732 (mt) cc_final: 0.9478 (mt)
REVERT: O  104 PHE cc_start: 0.9352 (m-80) cc_final: 0.8787 (m-80)
REVERT: O  120 MET cc_start: 0.8424 (mtt) cc_final: 0.8051 (mtt)
REVERT: P   72 TYR cc_start: 0.9319 (m-80) cc_final: 0.9066 (m-80)
REVERT: Q   92 GLU cc_start: 0.9035 (tt0) cc_final: 0.8718 (tp30)
REVERT: Q  118 LYS cc_start: 0.8771 (mttt) cc_final: 0.8324 (mtmm)
REVERT: R   93 GLU cc_start: 0.9243 (mp0) cc_final: 0.8984 (mp0)
REVERT: R  113 GLU cc_start: 0.9272 (mm-30) cc_final: 0.8953 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1010
  time to fit residues: 21.8767
Evaluate side-chains
  113 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 113
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
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:    9.9990
   chunk 44 optimal weight:    0.9980
   chunk 101 optimal weight:   30.0000
   chunk 105 optimal weight:   40.0000
   chunk 42 optimal weight:    1.9990
   chunk 99 optimal weight:   20.0000
   chunk 94 optimal weight:   30.0000
   chunk 17 optimal weight:    8.9990
   chunk 58 optimal weight:    0.7980
   chunk 76 optimal weight:   30.0000
   overall best weight:    4.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
K  55 GLN
** K  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  75 HIS ** 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 = 0.2867 r_free = 0.2867 target = 0.028912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2541 r_free = 0.2541 target = 0.021090 restraints weight = 177340.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2580 r_free = 0.2580 target = 0.021860 restraints weight = 87550.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2605 r_free = 0.2605 target = 0.022348 restraints weight = 54349.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.022732 restraints weight = 38803.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2633 r_free = 0.2633 target = 0.022964 restraints weight = 30163.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.2623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.2842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  14032  Z= 0.239
  Angle     :  0.742   8.193  20419  Z= 0.420
  Chirality :  0.046   0.271   2320
  Planarity :  0.005   0.058   1398
  Dihedral  : 33.003 177.109   4580
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 17.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  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:  1.25 (0.29), residues: 752
  helix:  1.33 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.35 (0.40), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG K  49 
 TYR   0.025   0.002   TYR L  98 
 PHE   0.034   0.003   PHE K 104 
 HIS   0.008   0.002   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00420 /  0.24 (14032)
  covalent geometry    : angle       0.74209 /  0.42 (20419)
  hydrogen bonds       : bond        0.09110 /  5.92 (  829)
  hydrogen bonds       : angle       3.58162 /  2.58 ( 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
  135 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9575 (m-10) cc_final: 0.9054 (m-80)
REVERT: K   85 GLN cc_start: 0.9456 (mt0) cc_final: 0.8983 (mt0)
REVERT: K   90 MET cc_start: 0.9203 (mmp) cc_final: 0.8823 (mmp)
REVERT: K   94 GLU cc_start: 0.9402 (mm-30) cc_final: 0.9154 (mm-30)
REVERT: K  104 PHE cc_start: 0.9565 (m-80) cc_final: 0.9360 (m-10)
REVERT: K  120 MET cc_start: 0.8700 (mtm) cc_final: 0.8060 (mtt)
REVERT: K  123 ASP cc_start: 0.9646 (m-30) cc_final: 0.9397 (m-30)
REVERT: L   63 GLU cc_start: 0.9380 (mt-10) cc_final: 0.9158 (mt-10)
REVERT: L   75 HIS cc_start: 0.9155 (t70) cc_final: 0.8773 (t70)
REVERT: M   41 GLU cc_start: 0.8904 (mp0) cc_final: 0.8004 (tp30)
REVERT: M   56 GLU cc_start: 0.9319 (mt-10) cc_final: 0.9014 (mt-10)
REVERT: M   64 GLU cc_start: 0.9620 (mm-30) cc_final: 0.9375 (mm-30)
REVERT: N   71 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8632 (mm-30)
REVERT: N  102 LEU cc_start: 0.8712 (tp) cc_final: 0.8401 (tp)
REVERT: O   86 SER cc_start: 0.9805 (t) cc_final: 0.9541 (p)
REVERT: O  100 LEU cc_start: 0.9757 (mt) cc_final: 0.9512 (mt)
REVERT: O  104 PHE cc_start: 0.9418 (m-80) cc_final: 0.8884 (m-80)
REVERT: O  120 MET cc_start: 0.8354 (mtt) cc_final: 0.7929 (mtt)
REVERT: P   72 TYR cc_start: 0.9365 (m-80) cc_final: 0.9028 (m-80)
REVERT: Q   36 LYS cc_start: 0.9584 (mptt) cc_final: 0.9381 (mmtm)
REVERT: R   76 GLU cc_start: 0.9429 (tp30) cc_final: 0.9031 (mt-10)
REVERT: R  101 LEU cc_start: 0.9325 (tt) cc_final: 0.8906 (tt)
REVERT: R  113 GLU cc_start: 0.9217 (mm-30) cc_final: 0.8937 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.0983
  time to fit residues: 20.4478
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  : 0.335 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 99 optimal weight:   30.0000
   chunk 102 optimal weight:   30.0000
   chunk 31 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 26 optimal weight:   10.0000
   chunk 6 optimal weight:    1.9990
   overall best weight:    2.3588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** K  93 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 = 0.2894 r_free = 0.2894 target = 0.029750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2565 r_free = 0.2565 target = 0.021736 restraints weight = 171224.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2605 r_free = 0.2605 target = 0.022539 restraints weight = 84512.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.023090 restraints weight = 52051.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2647 r_free = 0.2647 target = 0.023466 restraints weight = 36615.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2659 r_free = 0.2659 target = 0.023697 restraints weight = 28412.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.2649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.2949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14032  Z= 0.164
  Angle     :  0.666   7.400  20419  Z= 0.386
  Chirality :  0.044   0.280   2320
  Planarity :  0.004   0.059   1398
  Dihedral  : 33.024 178.632   4580
  Min Nonbonded Distance : 2.373

Molprobity Statistics.
  All-atom Clashscore : 12.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  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:  1.41 (0.30), residues: 752
  helix:  1.47 (0.22), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.33 (0.40), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG N  79 
 TYR   0.029   0.002   TYR M  57 
 PHE   0.024   0.002   PHE K 104 
 HIS   0.005   0.001   HIS L  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00272 /  0.16 (14032)
  covalent geometry    : angle       0.66582 /  0.39 (20419)
  hydrogen bonds       : bond        0.05350 /  3.49 (  829)
  hydrogen bonds       : angle       3.44245 /  2.49 ( 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
  142 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.355 
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: 0.9533 (m-10) cc_final: 0.8981 (m-80)
REVERT: K   85 GLN cc_start: 0.9383 (mt0) cc_final: 0.8839 (mt0)
REVERT: K   90 MET cc_start: 0.9202 (mmp) cc_final: 0.8798 (mmp)
REVERT: K   94 GLU cc_start: 0.9391 (mm-30) cc_final: 0.9097 (mm-30)
REVERT: K  120 MET cc_start: 0.8743 (mtm) cc_final: 0.8137 (mtt)
REVERT: L   63 GLU cc_start: 0.9368 (mt-10) cc_final: 0.9146 (mt-10)
REVERT: L   75 HIS cc_start: 0.9231 (t70) cc_final: 0.8776 (t70)
REVERT: M   41 GLU cc_start: 0.8940 (mp0) cc_final: 0.8070 (tp30)
REVERT: M   56 GLU cc_start: 0.9313 (mt-10) cc_final: 0.9001 (mt-10)
REVERT: M   90 ASP cc_start: 0.7358 (t0) cc_final: 0.6978 (t0)
REVERT: N   71 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8619 (mm-30)
REVERT: N   96 THR cc_start: 0.9705 (m) cc_final: 0.9496 (m)
REVERT: N   99 ARG cc_start: 0.9304 (mtp85) cc_final: 0.9018 (mtp-110)
REVERT: N  102 LEU cc_start: 0.8733 (tp) cc_final: 0.8413 (tp)
REVERT: O   86 SER cc_start: 0.9812 (t) cc_final: 0.9321 (p)
REVERT: O   94 GLU cc_start: 0.9571 (mp0) cc_final: 0.9319 (mp0)
REVERT: O  100 LEU cc_start: 0.9766 (mt) cc_final: 0.9482 (mt)
REVERT: O  104 PHE cc_start: 0.9390 (m-80) cc_final: 0.8832 (m-80)
REVERT: O  120 MET cc_start: 0.8363 (mtt) cc_final: 0.7916 (mtt)
REVERT: P   72 TYR cc_start: 0.9185 (m-80) cc_final: 0.8863 (m-80)
REVERT: Q   36 LYS cc_start: 0.9573 (mptt) cc_final: 0.9363 (mmtm)
REVERT: Q   92 GLU cc_start: 0.8907 (tt0) cc_final: 0.8623 (tp30)
REVERT: R   76 GLU cc_start: 0.9406 (tp30) cc_final: 0.9063 (tp30)
REVERT: R   93 GLU cc_start: 0.9213 (mp0) cc_final: 0.8940 (mp0)
REVERT: R  113 GLU cc_start: 0.9252 (mm-30) cc_final: 0.8952 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.1044
  time to fit residues: 22.4897
Evaluate side-chains
  112 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 77 optimal weight:   20.0000
   chunk 70 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 37 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 23 optimal weight:    4.9990
   chunk 11 optimal weight:    6.9990
   chunk 88 optimal weight:   40.0000
   overall best weight:    3.3990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
N  95 GLN
N 109 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.029276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2554 r_free = 0.2554 target = 0.021433 restraints weight = 171866.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2594 r_free = 0.2594 target = 0.022211 restraints weight = 85370.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.022733 restraints weight = 52745.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.023098 restraints weight = 37330.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2648 r_free = 0.2648 target = 0.023341 restraints weight = 29041.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.2638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.3151

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= 0.193
  Angle     :  0.702   7.810  20419  Z= 0.399
  Chirality :  0.045   0.274   2320
  Planarity :  0.005   0.057   1398
  Dihedral  : 32.972 179.113   4580
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 15.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  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:  1.37 (0.30), residues: 752
  helix:  1.41 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.26 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG O  72 
 TYR   0.012   0.002   TYR N  40 
 PHE   0.017   0.002   PHE R  65 
 HIS   0.009   0.002   HIS N 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.19 (14032)
  covalent geometry    : angle       0.70218 /  0.40 (20419)
  hydrogen bonds       : bond        0.06735 /  4.37 (  829)
  hydrogen bonds       : angle       3.56457 /  2.58 ( 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
  140 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9550 (m-10) cc_final: 0.8975 (m-80)
REVERT: K   85 GLN cc_start: 0.9407 (mt0) cc_final: 0.8815 (mt0)
REVERT: K   90 MET cc_start: 0.9209 (mmp) cc_final: 0.8879 (mmp)
REVERT: K  104 PHE cc_start: 0.9624 (m-10) cc_final: 0.9309 (m-10)
REVERT: K  120 MET cc_start: 0.8688 (mtm) cc_final: 0.7933 (mtt)
REVERT: L   63 GLU cc_start: 0.9382 (mt-10) cc_final: 0.9150 (mt-10)
REVERT: L   75 HIS cc_start: 0.9224 (t70) cc_final: 0.8758 (t70)
REVERT: M   36 LYS cc_start: 0.9566 (mptt) cc_final: 0.9274 (mmtm)
REVERT: M   41 GLU cc_start: 0.8961 (mp0) cc_final: 0.8098 (tp30)
REVERT: M   56 GLU cc_start: 0.9301 (mt-10) cc_final: 0.9027 (mt-10)
REVERT: M   90 ASP cc_start: 0.7304 (t0) cc_final: 0.6799 (t0)
REVERT: N   71 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8619 (mm-30)
REVERT: N   96 THR cc_start: 0.9703 (m) cc_final: 0.9483 (m)
REVERT: N   99 ARG cc_start: 0.9278 (mtp85) cc_final: 0.9039 (mtp-110)
REVERT: N  102 LEU cc_start: 0.8699 (tp) cc_final: 0.8373 (tp)
REVERT: N  105 GLU cc_start: 0.9631 (mp0) cc_final: 0.9401 (pm20)
REVERT: N  109 HIS cc_start: 0.9794 (m90) cc_final: 0.9484 (m170)
REVERT: O   94 GLU cc_start: 0.9610 (mp0) cc_final: 0.9286 (mp0)
REVERT: O  100 LEU cc_start: 0.9749 (mt) cc_final: 0.9455 (mt)
REVERT: O  104 PHE cc_start: 0.9430 (m-80) cc_final: 0.8869 (m-80)
REVERT: O  120 MET cc_start: 0.8376 (mtt) cc_final: 0.7908 (mtt)
REVERT: P   72 TYR cc_start: 0.9294 (m-80) cc_final: 0.8951 (m-80)
REVERT: Q   36 LYS cc_start: 0.9571 (mptt) cc_final: 0.9369 (mmtm)
REVERT: R  113 GLU cc_start: 0.9228 (mm-30) cc_final: 0.8935 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1021
  time to fit residues: 21.6540
Evaluate side-chains
  106 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 98 optimal weight:   30.0000
   chunk 87 optimal weight:   20.0000
   chunk 27 optimal weight:    7.9990
   chunk 44 optimal weight:    5.9990
   chunk 74 optimal weight:   40.0000
   chunk 97 optimal weight:   20.0000
   chunk 92 optimal weight:   30.0000
   chunk 85 optimal weight:   20.0000
   chunk 25 optimal weight:    1.9990
   overall best weight:    7.3992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** K  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  95 GLN
Q  73 ASN
R  47 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.030314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2539 r_free = 0.2539 target = 0.023622 restraints weight = 200469.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2580 r_free = 0.2580 target = 0.024300 restraints weight = 97278.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2614 r_free = 0.2614 target = 0.024864 restraints weight = 59559.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.025130 restraints weight = 40277.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 54)----------------|
| r_work = 0.2639 r_free = 0.2639 target = 0.025487 restraints weight = 31919.074|
|-----------------------------------------------------------------------------|
r_work (final): 0.2585
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
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      :  0.006   0.056  14032  Z= 0.349
  Angle     :  0.887   9.542  20419  Z= 0.490
  Chirality :  0.052   0.303   2320
  Planarity :  0.007   0.066   1398
  Dihedral  : 33.388 177.144   4580
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 27.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.19 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  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:  0.17 (0.28), residues: 752
  helix:  0.50 (0.21), residues: 540
  sheet:  None (None), residues: 0
  loop : -0.63 (0.39), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG L  45 
 TYR   0.029   0.003   TYR M  57 
 PHE   0.019   0.003   PHE P  61 
 HIS   0.013   0.003   HIS P  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00628 /  0.35 (14032)
  covalent geometry    : angle       0.88713 /  0.49 (20419)
  hydrogen bonds       : bond        0.13365 /  8.71 (  829)
  hydrogen bonds       : angle       4.35986 /  3.15 ( 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  : 0.469 
Fit side-chains
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9585 (m-10) cc_final: 0.8958 (m-80)
REVERT: K   90 MET cc_start: 0.9205 (mmp) cc_final: 0.8901 (mmp)
REVERT: K  120 MET cc_start: 0.8795 (mtm) cc_final: 0.8041 (mtt)
REVERT: K  123 ASP cc_start: 0.9640 (m-30) cc_final: 0.9427 (m-30)
REVERT: L   54 THR cc_start: 0.9574 (p) cc_final: 0.9368 (p)
REVERT: L   63 GLU cc_start: 0.9355 (mt-10) cc_final: 0.9078 (mp0)
REVERT: L   75 HIS cc_start: 0.9201 (t70) cc_final: 0.8726 (t70)
REVERT: M   36 LYS cc_start: 0.9489 (mptt) cc_final: 0.9191 (mmtm)
REVERT: M   41 GLU cc_start: 0.8942 (mp0) cc_final: 0.8236 (tp30)
REVERT: M   90 ASP cc_start: 0.7254 (t0) cc_final: 0.6748 (t70)
REVERT: N   62 MET cc_start: 0.9535 (mmp) cc_final: 0.9333 (mmp)
REVERT: N   71 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8643 (mm-30)
REVERT: N   99 ARG cc_start: 0.9309 (mtp85) cc_final: 0.9077 (mtp-110)
REVERT: N  102 LEU cc_start: 0.8861 (tp) cc_final: 0.8545 (tp)
REVERT: N  105 GLU cc_start: 0.9584 (mp0) cc_final: 0.9325 (pm20)
REVERT: N  109 HIS cc_start: 0.9790 (m90) cc_final: 0.9440 (m170)
REVERT: O   86 SER cc_start: 0.9796 (t) cc_final: 0.9540 (p)
REVERT: O  104 PHE cc_start: 0.9499 (m-80) cc_final: 0.8939 (m-80)
REVERT: O  106 ASP cc_start: 0.9304 (m-30) cc_final: 0.9025 (t0)
REVERT: R  113 GLU cc_start: 0.9310 (mm-30) cc_final: 0.9050 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1076
  time to fit residues: 19.6468
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  : 0.301 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 101 optimal weight:   20.0000
   chunk 79 optimal weight:   20.0000
   chunk 60 optimal weight:    1.9990
   chunk 16 optimal weight:    7.9990
   chunk 86 optimal weight:   20.0000
   chunk 45 optimal weight:    3.9990
   chunk 41 optimal weight:    0.9990
   chunk 11 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    1.5388

-------------------------------------------------------------------------------
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 = 0.032384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2599 r_free = 0.2599 target = 0.025312 restraints weight = 191177.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.026089 restraints weight = 91293.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2677 r_free = 0.2677 target = 0.026680 restraints weight = 54696.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.027061 restraints weight = 37138.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.027207 restraints weight = 27861.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.3903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  14032  Z= 0.161
  Angle     :  0.738   9.938  20419  Z= 0.418
  Chirality :  0.048   0.288   2320
  Planarity :  0.005   0.056   1398
  Dihedral  : 33.372 177.466   4580
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  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:  0.86 (0.30), residues: 752
  helix:  1.04 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.51 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG M  20 
 TYR   0.015   0.002   TYR P  72 
 PHE   0.025   0.002   PHE M  25 
 HIS   0.008   0.001   HIS O  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00276 /  0.16 (14032)
  covalent geometry    : angle       0.73802 /  0.42 (20419)
  hydrogen bonds       : bond        0.05453 /  3.57 (  829)
  hydrogen bonds       : angle       3.81015 /  2.77 ( 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
  146 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9525 (m-10) cc_final: 0.8995 (m-80)
REVERT: K   85 GLN cc_start: 0.9363 (mt0) cc_final: 0.8883 (mt0)
REVERT: K   90 MET cc_start: 0.9247 (mmp) cc_final: 0.8853 (mmp)
REVERT: K  104 PHE cc_start: 0.9591 (m-10) cc_final: 0.9332 (m-10)
REVERT: K  120 MET cc_start: 0.8837 (mtm) cc_final: 0.8038 (mtt)
REVERT: L   63 GLU cc_start: 0.9371 (mt-10) cc_final: 0.9069 (mt-10)
REVERT: L   75 HIS cc_start: 0.9224 (t70) cc_final: 0.8761 (t70)
REVERT: M   36 LYS cc_start: 0.9469 (mptt) cc_final: 0.9141 (mmtm)
REVERT: M   41 GLU cc_start: 0.8922 (mp0) cc_final: 0.8199 (tp30)
REVERT: M   79 ILE cc_start: 0.9567 (tp) cc_final: 0.9287 (pt)
REVERT: M   90 ASP cc_start: 0.7028 (t0) cc_final: 0.6544 (t0)
REVERT: N   43 LYS cc_start: 0.9406 (mtpp) cc_final: 0.9024 (mtmm)
REVERT: N   71 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8596 (mm-30)
REVERT: N   96 THR cc_start: 0.9716 (m) cc_final: 0.9495 (m)
REVERT: N   99 ARG cc_start: 0.9287 (mtp85) cc_final: 0.9059 (mtp-110)
REVERT: N  102 LEU cc_start: 0.8643 (tp) cc_final: 0.8317 (tp)
REVERT: N  105 GLU cc_start: 0.9605 (mp0) cc_final: 0.9319 (pm20)
REVERT: N  109 HIS cc_start: 0.9796 (m90) cc_final: 0.9464 (m170)
REVERT: O   86 SER cc_start: 0.9826 (t) cc_final: 0.9516 (t)
REVERT: O   90 MET cc_start: 0.9599 (mmp) cc_final: 0.9397 (mmm)
REVERT: O   94 GLU cc_start: 0.9582 (mp0) cc_final: 0.9345 (mp0)
REVERT: O  100 LEU cc_start: 0.9740 (mt) cc_final: 0.9511 (mt)
REVERT: O  104 PHE cc_start: 0.9420 (m-80) cc_final: 0.8934 (m-80)
REVERT: P   72 TYR cc_start: 0.9480 (m-80) cc_final: 0.9111 (m-80)
REVERT: R  113 GLU cc_start: 0.9268 (mm-30) cc_final: 0.8991 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1182
  time to fit residues: 25.4087
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  : 0.334 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 86 optimal weight:   30.0000
   chunk 85 optimal weight:   20.0000
   chunk 97 optimal weight:   30.0000
   chunk 26 optimal weight:    8.9990
   chunk 67 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 98 optimal weight:   30.0000
   chunk 95 optimal weight:   20.0000
   chunk 17 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   overall best weight:    2.5786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  63 ASN ** 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 = 0.2858 r_free = 0.2858 target = 0.028460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2530 r_free = 0.2530 target = 0.020840 restraints weight = 173409.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2569 r_free = 0.2569 target = 0.021598 restraints weight = 85150.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2593 r_free = 0.2593 target = 0.022104 restraints weight = 52921.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2611 r_free = 0.2611 target = 0.022445 restraints weight = 37457.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.022713 restraints weight = 29148.627|
|-----------------------------------------------------------------------------|
r_work (final): 0.2611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8474
moved from start:          0.4034

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= 0.181
  Angle     :  0.732  13.991  20419  Z= 0.414
  Chirality :  0.046   0.281   2320
  Planarity :  0.005   0.058   1398
  Dihedral  : 33.150 177.417   4580
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 16.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  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:  0.95 (0.30), residues: 752
  helix:  1.09 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.41 (0.41), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.001   ARG L  95 
 TYR   0.020   0.002   TYR R  37 
 PHE   0.021   0.002   PHE M  25 
 HIS   0.006   0.001   HIS O  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.18 (14032)
  covalent geometry    : angle       0.73173 /  0.41 (20419)
  hydrogen bonds       : bond        0.06490 /  4.22 (  829)
  hydrogen bonds       : angle       3.85341 /  2.83 ( 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  : 0.350 
Fit side-chains
   revert: symmetry clash
REVERT: K   54 TYR cc_start: 0.9582 (m-10) cc_final: 0.9056 (m-80)
REVERT: K   85 GLN cc_start: 0.9423 (mt0) cc_final: 0.8899 (mt0)
REVERT: K   90 MET cc_start: 0.9125 (mmp) cc_final: 0.8801 (mmp)
REVERT: K   94 GLU cc_start: 0.8932 (mp0) cc_final: 0.8631 (pm20)
REVERT: K  104 PHE cc_start: 0.9611 (m-10) cc_final: 0.9359 (m-10)
REVERT: K  120 MET cc_start: 0.8881 (mtm) cc_final: 0.8067 (mtt)
REVERT: K  123 ASP cc_start: 0.9650 (m-30) cc_final: 0.9444 (m-30)
REVERT: L   63 GLU cc_start: 0.9371 (mt-10) cc_final: 0.9018 (mt-10)
REVERT: L   75 HIS cc_start: 0.9198 (t70) cc_final: 0.8777 (t70)
REVERT: L   97 LEU cc_start: 0.9514 (tp) cc_final: 0.9095 (tp)
REVERT: M   36 LYS cc_start: 0.9520 (mptt) cc_final: 0.9240 (mmtm)
REVERT: M   41 GLU cc_start: 0.8929 (mp0) cc_final: 0.8193 (tp30)
REVERT: M   79 ILE cc_start: 0.9588 (tp) cc_final: 0.9327 (pt)
REVERT: M   90 ASP cc_start: 0.7110 (t0) cc_final: 0.6604 (t0)
REVERT: N   71 GLU cc_start: 0.9042 (mm-30) cc_final: 0.8603 (mm-30)
REVERT: N   99 ARG cc_start: 0.9281 (mtp85) cc_final: 0.9048 (mtp-110)
REVERT: N  102 LEU cc_start: 0.8735 (tp) cc_final: 0.8418 (tp)
REVERT: N  105 GLU cc_start: 0.9590 (mp0) cc_final: 0.9308 (pm20)
REVERT: N  109 HIS cc_start: 0.9794 (m90) cc_final: 0.9468 (m170)
REVERT: O   86 SER cc_start: 0.9812 (t) cc_final: 0.9494 (t)
REVERT: O   90 MET cc_start: 0.9545 (mmp) cc_final: 0.9323 (mmm)
REVERT: O   94 GLU cc_start: 0.9559 (mp0) cc_final: 0.9285 (mp0)
REVERT: O  100 LEU cc_start: 0.9737 (mt) cc_final: 0.9489 (mt)
REVERT: O  104 PHE cc_start: 0.9450 (m-80) cc_final: 0.8961 (m-80)
REVERT: P   72 TYR cc_start: 0.9515 (m-80) cc_final: 0.9139 (m-80)
REVERT: R  113 GLU cc_start: 0.9208 (mm-30) cc_final: 0.8937 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 135
  average time/residue: 0.1129
  time to fit residues: 22.6615
Evaluate side-chains
  106 residues out of total 636 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
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:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 53 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9980
   chunk 96 optimal weight:   20.0000
   chunk 61 optimal weight:    0.2980
   chunk 11 optimal weight:    4.9990
   chunk 12 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 86 optimal weight:   30.0000
   overall best weight:    1.2384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** M  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  63 ASN ** 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 = 0.2893 r_free = 0.2893 target = 0.029385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2561 r_free = 0.2561 target = 0.021546 restraints weight = 168624.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.2603 r_free = 0.2603 target = 0.022350 restraints weight = 82349.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.022881 restraints weight = 50650.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2644 r_free = 0.2644 target = 0.023221 restraints weight = 35686.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.023501 restraints weight = 27754.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.4079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  14032  Z= 0.150
  Angle     :  0.703  11.899  20419  Z= 0.402
  Chirality :  0.045   0.272   2320
  Planarity :  0.005   0.059   1398
  Dihedral  : 33.026 177.693   4580
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 13.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  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:  1.10 (0.30), residues: 752
  helix:  1.19 (0.22), residues: 542
  sheet:  None (None), residues: 0
  loop : -0.31 (0.41), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG L  95 
 TYR   0.019   0.002   TYR R  83 
 PHE   0.024   0.002   PHE M  25 
 HIS   0.007   0.001   HIS O  39 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.15 (14032)
  covalent geometry    : angle       0.70335 /  0.40 (20419)
  hydrogen bonds       : bond        0.04753 /  3.16 (  829)
  hydrogen bonds       : angle       3.74424 /  2.75 ( 2037)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1826.42 seconds
wall clock time: 32 minutes 34.96 seconds (1954.96 seconds total)