Starting phenix.real_space_refine
on Wed Mar  4 18:22:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pfx_13383/03_2026/7pfx_13383.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pfx_13383/03_2026/7pfx_13383.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pfx_13383/03_2026/7pfx_13383.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pfx_13383/03_2026/7pfx_13383.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pfx_13383/03_2026/7pfx_13383.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pfx_13383/03_2026/7pfx_13383.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     354      5.49       5
     S      10      5.16       5
     C    7612      2.51       5
     N    2606      2.21       5
     O    3298      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13880
  Number of models: 1
  Model: ""
    Number of chains: 11
    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: "I"
      Number of atoms: 3610
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 177, 3610
          Classifications: {'DNA': 177}
          Link IDs: {'rna3p': 176}
    Chain: "J"
      Number of atoms: 3647
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 177, 3647
          Classifications: {'DNA': 177}
          Link IDs: {'rna3p': 176}
    Chain: "S"
      Number of atoms: 535
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 535
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 2, 'TRANS': 72}
  Time building chain proxies: 2.71, per 1000 atoms: 0.20
  Number of scatterers: 13880
  At special positions: 0
  Unit cell: (149.1, 91.35, 122.85, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      10     16.00
     P     354     15.00
     O    3298      8.00
     N    2606      7.00
     C    7612      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  Conformation dependent library (CDL) restraints added in 300.2 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 11 sheets defined
      69.4% alpha, 3.1% beta
      177 base pairs and 311 stacking pairs defined.
    Time for finding SS restraints: 1.91
  Creating SS restraints...
    Processing helix  chain 'K' and resid 44 through 57
    Processing helix  chain 'K' and resid 63 through 77
      removed outlier: 3.593A  pdb=" N   PHE K  67 " --> pdb=" O   ARG K  63 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ASP K  77 " --> pdb=" O   GLU K  73 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 85 through 114
    Processing helix  chain 'K' and resid 120 through 132
      removed outlier: 3.521A  pdb=" N   ILE K 124 " --> pdb=" O   MET K 120 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 30 through 41
    Processing helix  chain 'L' and resid 49 through 76
      removed outlier: 4.039A  pdb=" N   GLU L  53 " --> pdb=" O   LEU L  49 " (cutoff:3.500A)
    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 37
    Processing helix  chain 'M' and resid 45 through 73
      removed outlier: 4.346A  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 'N' and resid 37 through 49
    Processing helix  chain 'N' and resid 55 through 84
    Processing helix  chain 'N' and resid 90 through 102
    Processing helix  chain 'N' and resid 104 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: 3.583A  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: 4.088A  pdb=" N   GLU P  53 " --> pdb=" O   LEU P  49 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   ASP P  68 " --> pdb=" O   ASN P  64 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 82 through 93
      removed outlier: 3.652A  pdb=" N   VAL P  86 " --> pdb=" O   THR P  82 " (cutoff:3.500A)
    Processing helix  chain 'Q' and resid 16 through 22
    Processing helix  chain 'Q' and resid 26 through 37
    Processing helix  chain 'Q' and resid 45 through 73
      removed outlier: 4.207A  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 103 through 124
    Processing helix  chain 'S' and resid 38 through 51
      removed outlier: 4.088A  pdb=" N   LEU S  42 " --> pdb=" O   PRO S  38 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   SER S  50 " --> pdb=" O   ALA S  46 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   LYS S  51 " --> pdb=" O   VAL S  47 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 58 through 69
    Processing helix  chain 'S' and resid 75 through 89
    Processing sheet with id=AA1, first strand: chain 'K' and resid 83 through 84
      removed outlier: 6.889A  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: 7.225A  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 77 through 78
    Processing sheet with id=AA6, first strand: chain 'M' and resid 100 through 101
    Processing sheet with id=AA7, first strand: chain 'O' and resid 83 through 84
      removed outlier: 6.737A  pdb=" N   ARG O  83 " --> pdb=" O   VAL P  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'O' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'Q' and resid 42 through 43
      removed outlier: 7.157A  pdb=" N   ARG Q  42 " --> pdb=" O   ILE R  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'Q' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'S' and resid 56 through 57

    436 hydrogen bonds defined for protein.
    1293 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      456 hydrogen bonds
      912 hydrogen bond angles
      0 basepair planarities
      177 basepair parallelities
      311 stacking parallelities
  Total time for adding SS restraints: 3.28

  Time building geometry restraints manager: 1.42 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: 2630
        1.33 -     1.45: 5120
        1.45 -     1.57: 6370
        1.57 -     1.69: 706
        1.69 -     1.82: 20
  Bond restraints: 14846
  Sorted by residual:
  bond pdb=" C3'  DC I 455 "
       pdb=" O3'  DC I 455 "
    ideal  model  delta    sigma   weight residual
    1.422  1.480 -0.058 3.00e-02 1.11e+03 3.77e+00
  bond pdb=" CG  GLU O  97 "
       pdb=" CD  GLU O  97 "
    ideal  model  delta    sigma   weight residual
    1.516  1.472  0.044 2.50e-02 1.60e+03 3.09e+00
  bond pdb=" C3'  DG J 331 "
       pdb=" O3'  DG J 331 "
    ideal  model  delta    sigma   weight residual
    1.422  1.474 -0.052 3.00e-02 1.11e+03 2.96e+00
  bond pdb=" C3'  DG J 253 "
       pdb=" O3'  DG J 253 "
    ideal  model  delta    sigma   weight residual
    1.422  1.472 -0.050 3.00e-02 1.11e+03 2.77e+00
  bond pdb=" CG  GLU P  63 "
       pdb=" CD  GLU P  63 "
    ideal  model  delta    sigma   weight residual
    1.516  1.475  0.041 2.50e-02 1.60e+03 2.65e+00
  ... (remaining 14841 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.09: 21361
        3.09 -     6.18: 175
        6.18 -     9.27: 23
        9.27 -    12.37: 3
       12.37 -    15.46: 1
  Bond angle restraints: 21563
  Sorted by residual:
  angle pdb=" N   GLU L  63 "
        pdb=" CA  GLU L  63 "
        pdb=" CB  GLU L  63 "
      ideal   model   delta    sigma   weight residual
     110.28  118.62   -8.34 1.55e+00 4.16e-01 2.90e+01
  angle pdb=" N   GLU P  63 "
        pdb=" CA  GLU P  63 "
        pdb=" CB  GLU P  63 "
      ideal   model   delta    sigma   weight residual
     110.28  118.19   -7.91 1.55e+00 4.16e-01 2.61e+01
  angle pdb=" N   GLU O  97 "
        pdb=" CA  GLU O  97 "
        pdb=" CB  GLU O  97 "
      ideal   model   delta    sigma   weight residual
     110.40  117.75   -7.35 1.63e+00 3.76e-01 2.03e+01
  angle pdb=" CA  LEU L  62 "
        pdb=" CB  LEU L  62 "
        pdb=" CG  LEU L  62 "
      ideal   model   delta    sigma   weight residual
     116.30  131.76  -15.46 3.50e+00 8.16e-02 1.95e+01
  angle pdb=" N   GLU O  94 "
        pdb=" CA  GLU O  94 "
        pdb=" CB  GLU O  94 "
      ideal   model   delta    sigma   weight residual
     110.22  116.63   -6.41 1.54e+00 4.22e-01 1.73e+01
  ... (remaining 21558 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.87: 6045
       35.87 -    71.74: 1922
       71.74 -   107.60: 34
      107.60 -   143.47: 3
      143.47 -   179.34: 3
  Dihedral angle restraints: 8007
    sinusoidal: 5576
      harmonic: 2431
  Sorted by residual:
  dihedral pdb=" CA  ILE P  50 "
           pdb=" C   ILE P  50 "
           pdb=" N   TYR P  51 "
           pdb=" CA  TYR P  51 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.84  -24.16     0      5.00e+00 4.00e-02 2.34e+01
  dihedral pdb=" CA  PRO R 103 "
           pdb=" C   PRO R 103 "
           pdb=" N   GLY R 104 "
           pdb=" CA  GLY R 104 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.27   23.73     0      5.00e+00 4.00e-02 2.25e+01
  dihedral pdb=" CA  PHE O  84 "
           pdb=" C   PHE O  84 "
           pdb=" N   GLN O  85 "
           pdb=" CA  GLN O  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.41   21.59     0      5.00e+00 4.00e-02 1.87e+01
  ... (remaining 8004 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1884
       0.051 -    0.102: 484
       0.102 -    0.153: 74
       0.153 -    0.205: 11
       0.205 -    0.256: 3
  Chirality restraints: 2456
  Sorted by residual:
  chirality pdb=" CG  LEU Q  23 "
            pdb=" CB  LEU Q  23 "
            pdb=" CD1 LEU Q  23 "
            pdb=" CD2 LEU Q  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.33   -0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CA  PHE O 104 "
            pdb=" N   PHE O 104 "
            pdb=" C   PHE O 104 "
            pdb=" CB  PHE O 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  GLU L  63 "
            pdb=" N   GLU L  63 "
            pdb=" C   GLU L  63 "
            pdb=" CB  GLU L  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 2453 not shown)

  Planarity restraints: 1498
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS L  59 "   -0.014 2.00e-02 2.50e+03   2.73e-02 7.43e+00
        pdb=" C   LYS L  59 "    0.047 2.00e-02 2.50e+03
        pdb=" O   LYS L  59 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   VAL L  60 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE M  79 "   -0.045 5.00e-02 4.00e+02   6.81e-02 7.41e+00
        pdb=" N   PRO M  80 "    0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO M  80 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO M  80 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL L  60 "   -0.012 2.00e-02 2.50e+03   2.38e-02 5.64e+00
        pdb=" C   VAL L  60 "    0.041 2.00e-02 2.50e+03
        pdb=" O   VAL L  60 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   PHE L  61 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1495 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 2510
        2.77 -     3.30: 12738
        3.30 -     3.83: 30793
        3.83 -     4.37: 34366
        4.37 -     4.90: 46793
  Nonbonded interactions: 127200
  Sorted by model distance:
  nonbonded pdb=" O   GLN O  93 "
            pdb=" OG  SER O  96 "
     model   vdw
     2.234 3.040
  nonbonded pdb=" OG  SER M  40 "
            pdb=" O   ARG M  42 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   VAL N 111 "
            pdb=" OG1 THR N 115 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O   THR Q  16 "
            pdb=" OG  SER Q  19 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" NE2 HIS K 113 "
            pdb=" OD1 ASP O 123 "
     model   vdw
     2.302 3.120
  ... (remaining 127195 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.790
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.340
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8604
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      :  0.006   0.058  14846  Z= 0.274
  Angle     :  0.880  15.456  21563  Z= 0.506
  Chirality :  0.047   0.256   2456
  Planarity :  0.006   0.068   1498
  Dihedral  : 30.285 179.340   6441
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.30 (0.27), residues: 825
  helix:  0.59 (0.20), residues: 567
  sheet: -1.82 (1.57), residues: 10
  loop : -0.37 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG L  67 
 TYR   0.022   0.003   TYR N  37 
 PHE   0.040   0.003   PHE O 104 
 HIS   0.007   0.002   HIS K 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00593 (14846)
  covalent geometry    : angle       0.88002 (21563)
  hydrogen bonds       : bond        0.11549 (  892)
  hydrogen bonds       : angle       4.84078 ( 2205)

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

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  104 PHE cc_start: 0.9476 (m-80) cc_final: 0.9199 (m-80)
REVERT: K  120 MET cc_start: 0.8002 (tpp) cc_final: 0.7489 (tpp)
REVERT: M   61 GLU cc_start: 0.9314 (pp20) cc_final: 0.9027 (pp20)
REVERT: N   31 ARG cc_start: 0.7836 (mpp80) cc_final: 0.7583 (ttp80)
REVERT: N   37 TYR cc_start: 0.9261 (m-10) cc_final: 0.8909 (m-10)
REVERT: N  102 LEU cc_start: 0.8944 (tp) cc_final: 0.8665 (tp)
REVERT: N  105 GLU cc_start: 0.9568 (tp30) cc_final: 0.9323 (tp30)
REVERT: O   59 GLU cc_start: 0.9536 (tp30) cc_final: 0.9273 (pm20)
REVERT: O   67 PHE cc_start: 0.9295 (t80) cc_final: 0.9070 (t80)
REVERT: O  104 PHE cc_start: 0.9014 (m-80) cc_final: 0.8755 (m-10)
REVERT: O  105 GLU cc_start: 0.9086 (mp0) cc_final: 0.8846 (mp0)
REVERT: P   74 GLU cc_start: 0.9363 (pp20) cc_final: 0.9108 (pp20)
REVERT: Q   56 GLU cc_start: 0.8992 (tt0) cc_final: 0.8476 (mt-10)
REVERT: Q   64 GLU cc_start: 0.9579 (mm-30) cc_final: 0.9360 (mm-30)
REVERT: Q   95 LYS cc_start: 0.9136 (pptt) cc_final: 0.8497 (mmtt)
REVERT: R  102 LEU cc_start: 0.9445 (mm) cc_final: 0.8887 (tp)
REVERT: R  109 HIS cc_start: 0.9717 (m-70) cc_final: 0.9480 (m170)
REVERT: R  113 GLU cc_start: 0.9655 (mm-30) cc_final: 0.9402 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1070
  time to fit residues: 18.9174
Evaluate side-chains
  79 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 108 optimal weight:    8.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    5.9990
   chunk 106 optimal weight:   20.0000
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** N  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  68 ASN
R 109 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.025236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.020361 restraints weight = 242313.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.020976 restraints weight = 113931.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.021453 restraints weight = 68508.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2694 r_free = 0.2694 target = 0.021717 restraints weight = 46296.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.021936 restraints weight = 35354.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8602
moved from start:          0.1516

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.035  14846  Z= 0.280
  Angle     :  0.669   6.285  21563  Z= 0.403
  Chirality :  0.037   0.163   2456
  Planarity :  0.005   0.051   1498
  Dihedral  : 33.736 176.424   4789
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 14.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  4.76 %
    Favored  : 94.95 %
  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:  1.39 (0.28), residues: 825
  helix:  1.45 (0.21), residues: 588
  sheet: -2.47 (1.40), residues: 10
  loop : -0.19 (0.37), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG Q  77 
 TYR   0.014   0.002   TYR N  37 
 PHE   0.021   0.002   PHE P 100 
 HIS   0.010   0.002   HIS R 109 

Details of bonding type rmsd
  covalent geometry    : bond        0.00593 (14846)
  covalent geometry    : angle       0.66936 (21563)
  hydrogen bonds       : bond        0.08268 (  892)
  hydrogen bonds       : angle       3.88897 ( 2205)

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

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 96
  time to evaluate  : 0.316 
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   94 GLU cc_start: 0.9285 (tp30) cc_final: 0.8943 (tp30)
REVERT: K  104 PHE cc_start: 0.9620 (m-80) cc_final: 0.9083 (m-80)
REVERT: K  120 MET cc_start: 0.8402 (tpp) cc_final: 0.8040 (tpp)
REVERT: N   37 TYR cc_start: 0.9320 (m-10) cc_final: 0.8983 (m-10)
REVERT: N   62 MET cc_start: 0.9258 (mmp) cc_final: 0.8930 (mmp)
REVERT: N   71 GLU cc_start: 0.9298 (mm-30) cc_final: 0.8965 (pp20)
REVERT: N  105 GLU cc_start: 0.9531 (tp30) cc_final: 0.9236 (tp30)
REVERT: O   59 GLU cc_start: 0.9422 (tp30) cc_final: 0.9182 (pm20)
REVERT: O   67 PHE cc_start: 0.9220 (t80) cc_final: 0.9016 (t80)
REVERT: O  104 PHE cc_start: 0.9475 (m-80) cc_final: 0.9146 (m-80)
REVERT: O  106 ASP cc_start: 0.9303 (m-30) cc_final: 0.9060 (m-30)
REVERT: O  120 MET cc_start: 0.7321 (mtt) cc_final: 0.7028 (mtt)
REVERT: P   74 GLU cc_start: 0.9370 (pp20) cc_final: 0.9161 (pp20)
REVERT: Q   56 GLU cc_start: 0.9201 (tt0) cc_final: 0.8662 (mt-10)
REVERT: Q   95 LYS cc_start: 0.9223 (pptt) cc_final: 0.8477 (mmtt)
REVERT: R  108 LYS cc_start: 0.9690 (ptpp) cc_final: 0.9440 (pttm)
REVERT: R  109 HIS cc_start: 0.9491 (m90) cc_final: 0.9178 (m90)
REVERT: R  113 GLU cc_start: 0.9596 (mm-30) cc_final: 0.9308 (mm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1084
  time to fit residues: 15.5320
Evaluate side-chains
  70 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 97 optimal weight:    8.9990
   chunk 60 optimal weight:    0.8980
   chunk 104 optimal weight:    7.9990
   chunk 65 optimal weight:    6.9990
   chunk 106 optimal weight:   30.0000
   chunk 38 optimal weight:    8.9990
   chunk 111 optimal weight:    7.9990
   chunk 78 optimal weight:    6.9990
   chunk 82 optimal weight:    7.9990
   chunk 22 optimal weight:    6.9990
   overall best weight:    5.9788

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

Flipped N/Q/H residues before XYZ refinement:
M 104 GLN
** N  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  94 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.024069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2571 r_free = 0.2571 target = 0.019371 restraints weight = 254744.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2609 r_free = 0.2609 target = 0.019970 restraints weight = 121712.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2636 r_free = 0.2636 target = 0.020447 restraints weight = 72447.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.020688 restraints weight = 48946.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.020883 restraints weight = 37711.474|
|-----------------------------------------------------------------------------|
r_work (final): 0.2613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.2457

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.042  14846  Z= 0.336
  Angle     :  0.707   7.311  21563  Z= 0.422
  Chirality :  0.038   0.170   2456
  Planarity :  0.006   0.063   1498
  Dihedral  : 34.067 178.186   4789
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 20.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  4.62 %
    Favored  : 95.24 %
  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:  1.58 (0.28), residues: 825
  helix:  1.61 (0.21), residues: 574
  sheet: -3.16 (1.45), residues: 10
  loop :  0.00 (0.37), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG O  40 
 TYR   0.027   0.002   TYR R  42 
 PHE   0.017   0.002   PHE P 100 
 HIS   0.006   0.002   HIS L  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00714 (14846)
  covalent geometry    : angle       0.70698 (21563)
  hydrogen bonds       : bond        0.09786 (  892)
  hydrogen bonds       : angle       4.11328 ( 2205)

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

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 93
  time to evaluate  : 0.348 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   94 GLU cc_start: 0.9187 (tp30) cc_final: 0.8913 (tp30)
REVERT: K  104 PHE cc_start: 0.9652 (m-80) cc_final: 0.9251 (m-80)
REVERT: K  120 MET cc_start: 0.8684 (tpp) cc_final: 0.8331 (tpp)
REVERT: N   37 TYR cc_start: 0.9394 (m-10) cc_final: 0.9044 (m-10)
REVERT: N   62 MET cc_start: 0.9331 (mmp) cc_final: 0.8990 (mmm)
REVERT: N   71 GLU cc_start: 0.9333 (mm-30) cc_final: 0.8928 (pp20)
REVERT: N  105 GLU cc_start: 0.9556 (tp30) cc_final: 0.9247 (tp30)
REVERT: O  106 ASP cc_start: 0.9324 (m-30) cc_final: 0.9101 (m-30)
REVERT: P   74 GLU cc_start: 0.9405 (pp20) cc_final: 0.9202 (pp20)
REVERT: Q   56 GLU cc_start: 0.9365 (tt0) cc_final: 0.8952 (tt0)
REVERT: R  108 LYS cc_start: 0.9688 (ptpp) cc_final: 0.9477 (pttm)
REVERT: R  109 HIS cc_start: 0.9553 (m90) cc_final: 0.9043 (m170)
REVERT: R  113 GLU cc_start: 0.9598 (mm-30) cc_final: 0.9295 (mm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 93
  average time/residue: 0.1136
  time to fit residues: 15.6901
Evaluate side-chains
  66 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 65
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 97 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 100 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 91 optimal weight:    7.9990
   chunk 96 optimal weight:    5.9990
   chunk 105 optimal weight:    7.9990
   chunk 44 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   overall best weight:    2.7988

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

Flipped N/Q/H residues before XYZ refinement:
K  68 GLN
** N  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** N  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.025603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.020739 restraints weight = 240075.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2669 r_free = 0.2669 target = 0.021374 restraints weight = 110822.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.021898 restraints weight = 65617.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.022151 restraints weight = 44312.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.022372 restraints weight = 33813.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.2455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  14846  Z= 0.200
  Angle     :  0.627   6.951  21563  Z= 0.375
  Chirality :  0.035   0.141   2456
  Planarity :  0.004   0.059   1498
  Dihedral  : 33.795 179.987   4789
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 13.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  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:  1.94 (0.29), residues: 825
  helix:  1.86 (0.21), residues: 586
  sheet: -3.25 (1.39), residues: 10
  loop :  0.11 (0.39), residues: 229

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG O  63 
 TYR   0.010   0.001   TYR R 121 
 PHE   0.021   0.002   PHE O 104 
 HIS   0.004   0.001   HIS R  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (14846)
  covalent geometry    : angle       0.62665 (21563)
  hydrogen bonds       : bond        0.05515 (  892)
  hydrogen bonds       : angle       3.56977 ( 2205)

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

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   94 GLU cc_start: 0.9196 (tp30) cc_final: 0.8815 (tp30)
REVERT: K  104 PHE cc_start: 0.9629 (m-80) cc_final: 0.9230 (m-80)
REVERT: K  120 MET cc_start: 0.8689 (tpp) cc_final: 0.8301 (tpp)
REVERT: L   63 GLU cc_start: 0.9564 (pm20) cc_final: 0.9332 (pm20)
REVERT: N   37 TYR cc_start: 0.9348 (m-10) cc_final: 0.8958 (m-10)
REVERT: N   62 MET cc_start: 0.9295 (mmp) cc_final: 0.8948 (mmm)
REVERT: N   71 GLU cc_start: 0.9319 (mm-30) cc_final: 0.8963 (pp20)
REVERT: N   82 HIS cc_start: 0.9591 (t-90) cc_final: 0.9353 (t-90)
REVERT: N  102 LEU cc_start: 0.9034 (tp) cc_final: 0.8650 (tp)
REVERT: N  105 GLU cc_start: 0.9544 (tp30) cc_final: 0.9275 (tp30)
REVERT: O  104 PHE cc_start: 0.9652 (m-80) cc_final: 0.9054 (m-80)
REVERT: O  105 GLU cc_start: 0.9094 (mp0) cc_final: 0.8802 (mm-30)
REVERT: O  106 ASP cc_start: 0.9310 (m-30) cc_final: 0.9095 (m-30)
REVERT: P   74 GLU cc_start: 0.9355 (pp20) cc_final: 0.9109 (pp20)
REVERT: Q   56 GLU cc_start: 0.9319 (tt0) cc_final: 0.8486 (mt-10)
REVERT: R  113 GLU cc_start: 0.9600 (mm-30) cc_final: 0.9287 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 99
  average time/residue: 0.1121
  time to fit residues: 16.6229
Evaluate side-chains
  74 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 93 optimal weight:   10.0000
   chunk 105 optimal weight:   10.0000
   chunk 70 optimal weight:    4.9990
   chunk 7 optimal weight:   10.0000
   chunk 100 optimal weight:    7.9990
   chunk 103 optimal weight:    7.9990
   chunk 27 optimal weight:    9.9990
   chunk 67 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 44 optimal weight:    5.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** N  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O  55 GLN
P  27 GLN
** S  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.024269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2574 r_free = 0.2574 target = 0.019550 restraints weight = 251560.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2613 r_free = 0.2613 target = 0.020148 restraints weight = 119436.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.020596 restraints weight = 71311.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.020882 restraints weight = 49940.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.021068 restraints weight = 37280.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.2618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8644
moved from start:          0.2951

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.041  14846  Z= 0.309
  Angle     :  0.680   6.497  21563  Z= 0.405
  Chirality :  0.037   0.165   2456
  Planarity :  0.005   0.063   1498
  Dihedral  : 33.919 178.994   4789
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 19.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  2.60 %
    Favored  : 97.11 %
  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:  1.84 (0.28), residues: 825
  helix:  1.86 (0.21), residues: 572
  sheet: -3.48 (1.42), residues: 10
  loop : -0.02 (0.39), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG O  40 
 TYR   0.014   0.002   TYR N  37 
 PHE   0.015   0.002   PHE O 104 
 HIS   0.008   0.002   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00657 (14846)
  covalent geometry    : angle       0.67978 (21563)
  hydrogen bonds       : bond        0.08872 (  892)
  hydrogen bonds       : angle       3.91992 ( 2205)

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

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 95
  time to evaluate  : 0.552 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   94 GLU cc_start: 0.9184 (tp30) cc_final: 0.8924 (tp30)
REVERT: K  104 PHE cc_start: 0.9646 (m-80) cc_final: 0.9296 (m-80)
REVERT: K  105 GLU cc_start: 0.9468 (mm-30) cc_final: 0.9187 (mm-30)
REVERT: K  120 MET cc_start: 0.8707 (tpp) cc_final: 0.8336 (tpp)
REVERT: N   62 MET cc_start: 0.9345 (mmp) cc_final: 0.8980 (mmm)
REVERT: N   71 GLU cc_start: 0.9373 (mm-30) cc_final: 0.9008 (pp20)
REVERT: N   82 HIS cc_start: 0.9594 (t-90) cc_final: 0.9374 (t-90)
REVERT: N  105 GLU cc_start: 0.9559 (tp30) cc_final: 0.9284 (tp30)
REVERT: O   90 MET cc_start: 0.9600 (mmp) cc_final: 0.9362 (mmm)
REVERT: O  104 PHE cc_start: 0.9685 (m-80) cc_final: 0.9175 (m-80)
REVERT: P   74 GLU cc_start: 0.9431 (pp20) cc_final: 0.9213 (pp20)
REVERT: Q   56 GLU cc_start: 0.9324 (tt0) cc_final: 0.8396 (mt-10)
REVERT: R  108 LYS cc_start: 0.9695 (ptpp) cc_final: 0.9488 (pttm)
REVERT: R  109 HIS cc_start: 0.9562 (m90) cc_final: 0.9118 (m170)
REVERT: R  113 GLU cc_start: 0.9600 (mm-30) cc_final: 0.9328 (mm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 96
  average time/residue: 0.1109
  time to fit residues: 16.1866
Evaluate side-chains
  74 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 96 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   chunk 68 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 36 optimal weight:   20.0000
   chunk 75 optimal weight:    6.9990
   chunk 59 optimal weight:    0.8980
   chunk 38 optimal weight:    9.9990
   chunk 106 optimal weight:   20.0000
   chunk 46 optimal weight:    5.9990
   overall best weight:    2.2984

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

Flipped N/Q/H residues before XYZ refinement:
** N  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
Q  84 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2881 r_free = 0.2881 target = 0.025911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.021023 restraints weight = 234956.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2684 r_free = 0.2684 target = 0.021682 restraints weight = 108619.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.022213 restraints weight = 63808.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.022515 restraints weight = 42368.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2734 r_free = 0.2734 target = 0.022712 restraints weight = 32127.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.2685
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8564
moved from start:          0.2957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14846  Z= 0.186
  Angle     :  0.620   6.388  21563  Z= 0.370
  Chirality :  0.035   0.158   2456
  Planarity :  0.004   0.063   1498
  Dihedral  : 33.640 179.624   4789
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.73 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.11 (0.29), residues: 825
  helix:  2.10 (0.21), residues: 572
  sheet: -3.35 (1.41), residues: 10
  loop : -0.02 (0.39), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Q  42 
 TYR   0.010   0.001   TYR R 121 
 PHE   0.013   0.002   PHE O 104 
 HIS   0.004   0.001   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 (14846)
  covalent geometry    : angle       0.61982 (21563)
  hydrogen bonds       : bond        0.04907 (  892)
  hydrogen bonds       : angle       3.47503 ( 2205)

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

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.345 
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   94 GLU cc_start: 0.9176 (tp30) cc_final: 0.8807 (tp30)
REVERT: K  104 PHE cc_start: 0.9613 (m-80) cc_final: 0.9244 (m-80)
REVERT: K  105 GLU cc_start: 0.9487 (mm-30) cc_final: 0.9189 (mm-30)
REVERT: K  120 MET cc_start: 0.8699 (tpp) cc_final: 0.8363 (tpp)
REVERT: N   37 TYR cc_start: 0.9351 (m-10) cc_final: 0.8937 (m-10)
REVERT: N   62 MET cc_start: 0.9329 (mmp) cc_final: 0.9096 (mmm)
REVERT: N   71 GLU cc_start: 0.9329 (mm-30) cc_final: 0.8938 (pp20)
REVERT: N   82 HIS cc_start: 0.9568 (t-90) cc_final: 0.9299 (t70)
REVERT: N  102 LEU cc_start: 0.8995 (tp) cc_final: 0.8628 (tp)
REVERT: N  105 GLU cc_start: 0.9563 (tp30) cc_final: 0.9310 (tp30)
REVERT: O  104 PHE cc_start: 0.9600 (m-80) cc_final: 0.9098 (m-80)
REVERT: O  106 ASP cc_start: 0.9346 (m-30) cc_final: 0.9102 (m-30)
REVERT: P   74 GLU cc_start: 0.9378 (pp20) cc_final: 0.9135 (pp20)
REVERT: Q   56 GLU cc_start: 0.9197 (tt0) cc_final: 0.8789 (tt0)
REVERT: R  102 LEU cc_start: 0.9450 (mm) cc_final: 0.9087 (mp)
REVERT: R  113 GLU cc_start: 0.9606 (mm-30) cc_final: 0.9336 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1024
  time to fit residues: 16.2308
Evaluate side-chains
  77 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 111 optimal weight:    5.9990
   chunk 50 optimal weight:   10.0000
   chunk 94 optimal weight:    8.9990
   chunk 25 optimal weight:    2.9990
   chunk 88 optimal weight:   10.0000
   chunk 87 optimal weight:    8.9990
   chunk 49 optimal weight:    0.9990
   chunk 81 optimal weight:   10.0000
   chunk 100 optimal weight:    7.9990
   chunk 1 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
** N  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  93 GLN
** S  75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.024874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.020103 restraints weight = 244611.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2639 r_free = 0.2639 target = 0.020714 restraints weight = 115507.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.021196 restraints weight = 68918.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.021508 restraints weight = 46691.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2691 r_free = 0.2691 target = 0.021683 restraints weight = 35578.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.2644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
moved from start:          0.3268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046  14846  Z= 0.264
  Angle     :  0.655   6.584  21563  Z= 0.390
  Chirality :  0.036   0.183   2456
  Planarity :  0.005   0.066   1498
  Dihedral  : 33.694 178.825   4789
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 17.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.98 (0.29), residues: 825
  helix:  1.98 (0.21), residues: 572
  sheet: -3.55 (1.43), residues: 10
  loop :  0.01 (0.40), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG N  31 
 TYR   0.015   0.001   TYR R 121 
 PHE   0.012   0.002   PHE R  65 
 HIS   0.004   0.001   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 (14846)
  covalent geometry    : angle       0.65525 (21563)
  hydrogen bonds       : bond        0.07430 (  892)
  hydrogen bonds       : angle       3.76231 ( 2205)

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

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.343 
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: K   94 GLU cc_start: 0.9149 (tp30) cc_final: 0.8796 (tp30)
REVERT: K  104 PHE cc_start: 0.9635 (m-80) cc_final: 0.9253 (m-80)
REVERT: K  105 GLU cc_start: 0.9473 (mm-30) cc_final: 0.9198 (mm-30)
REVERT: K  120 MET cc_start: 0.8722 (tpp) cc_final: 0.8479 (tpp)
REVERT: L   63 GLU cc_start: 0.9546 (pm20) cc_final: 0.9295 (pm20)
REVERT: L   74 GLU cc_start: 0.9323 (mt-10) cc_final: 0.9014 (pt0)
REVERT: N   62 MET cc_start: 0.9384 (mmp) cc_final: 0.9131 (mmm)
REVERT: N   71 GLU cc_start: 0.9360 (mm-30) cc_final: 0.8970 (pp20)
REVERT: N   82 HIS cc_start: 0.9586 (t-90) cc_final: 0.9321 (t-90)
REVERT: N  102 LEU cc_start: 0.9101 (tp) cc_final: 0.8738 (tp)
REVERT: N  105 GLU cc_start: 0.9553 (tp30) cc_final: 0.9293 (tp30)
REVERT: O   59 GLU cc_start: 0.9474 (tp30) cc_final: 0.9220 (pm20)
REVERT: O  104 PHE cc_start: 0.9613 (m-80) cc_final: 0.9102 (m-80)
REVERT: O  105 GLU cc_start: 0.9069 (mp0) cc_final: 0.8778 (mp0)
REVERT: O  106 ASP cc_start: 0.9347 (m-30) cc_final: 0.9105 (m-30)
REVERT: P   74 GLU cc_start: 0.9404 (pp20) cc_final: 0.9140 (pp20)
REVERT: Q   95 LYS cc_start: 0.9075 (pptt) cc_final: 0.8134 (tptt)
REVERT: R   95 GLN cc_start: 0.9662 (pt0) cc_final: 0.9384 (pp30)
REVERT: R  102 LEU cc_start: 0.9463 (mm) cc_final: 0.9209 (mp)
REVERT: R  109 HIS cc_start: 0.9581 (m90) cc_final: 0.9242 (m90)
REVERT: R  113 GLU cc_start: 0.9610 (mm-30) cc_final: 0.9346 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1018
  time to fit residues: 14.7177
Evaluate side-chains
  75 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 17 optimal weight:   20.0000
   chunk 73 optimal weight:   10.0000
   chunk 74 optimal weight:    7.9990
   chunk 51 optimal weight:    3.9990
   chunk 85 optimal weight:   10.0000
   chunk 47 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 63 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.2865 r_free = 0.2865 target = 0.025447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.020632 restraints weight = 238814.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.021268 restraints weight = 112608.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2695 r_free = 0.2695 target = 0.021774 restraints weight = 67033.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.2708 r_free = 0.2708 target = 0.022070 restraints weight = 45287.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.022283 restraints weight = 33840.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.2670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.3392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  14846  Z= 0.213
  Angle     :  0.627   6.447  21563  Z= 0.374
  Chirality :  0.035   0.170   2456
  Planarity :  0.004   0.063   1498
  Dihedral  : 33.561 178.967   4789
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 14.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.29), residues: 825
  helix:  2.06 (0.21), residues: 572
  sheet: -3.26 (1.52), residues: 10
  loop : -0.04 (0.40), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG O  69 
 TYR   0.010   0.001   TYR R  37 
 PHE   0.011   0.002   PHE O 104 
 HIS   0.005   0.001   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 (14846)
  covalent geometry    : angle       0.62714 (21563)
  hydrogen bonds       : bond        0.05848 (  892)
  hydrogen bonds       : angle       3.60500 ( 2205)

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

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.347 
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   94 GLU cc_start: 0.9158 (tp30) cc_final: 0.8788 (tp30)
REVERT: K  104 PHE cc_start: 0.9627 (m-80) cc_final: 0.9242 (m-80)
REVERT: K  105 GLU cc_start: 0.9478 (mm-30) cc_final: 0.9201 (mm-30)
REVERT: K  120 MET cc_start: 0.8784 (tpp) cc_final: 0.8552 (tpp)
REVERT: L   63 GLU cc_start: 0.9516 (pm20) cc_final: 0.9276 (pm20)
REVERT: L   74 GLU cc_start: 0.9282 (mt-10) cc_final: 0.8961 (pt0)
REVERT: N   62 MET cc_start: 0.9377 (mmp) cc_final: 0.9118 (mmm)
REVERT: N   71 GLU cc_start: 0.9334 (mm-30) cc_final: 0.8947 (pp20)
REVERT: N   82 HIS cc_start: 0.9567 (t-90) cc_final: 0.9306 (t-90)
REVERT: N  102 LEU cc_start: 0.9052 (tp) cc_final: 0.8656 (tp)
REVERT: N  105 GLU cc_start: 0.9562 (tp30) cc_final: 0.9320 (tp30)
REVERT: O  104 PHE cc_start: 0.9577 (m-80) cc_final: 0.9015 (m-10)
REVERT: O  105 GLU cc_start: 0.9067 (mp0) cc_final: 0.8759 (mp0)
REVERT: O  106 ASP cc_start: 0.9327 (m-30) cc_final: 0.9086 (m-30)
REVERT: P   74 GLU cc_start: 0.9366 (pp20) cc_final: 0.9133 (pp20)
REVERT: Q   95 LYS cc_start: 0.9091 (pptt) cc_final: 0.8204 (tptt)
REVERT: R  102 LEU cc_start: 0.9447 (mm) cc_final: 0.9095 (mp)
REVERT: R  105 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8586 (tm-30)
REVERT: R  109 HIS cc_start: 0.9572 (m90) cc_final: 0.9174 (m90)
REVERT: R  113 GLU cc_start: 0.9620 (mm-30) cc_final: 0.9351 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1070
  time to fit residues: 16.1064
Evaluate side-chains
  75 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 55 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 90 optimal weight:   10.0000
   chunk 103 optimal weight:    7.9990
   chunk 62 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 41 optimal weight:    0.6980
   chunk 98 optimal weight:   10.0000
   chunk 76 optimal weight:   10.0000
   overall best weight:    2.1384

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

Flipped N/Q/H residues before XYZ refinement:
** N  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2889 r_free = 0.2889 target = 0.026001 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.021168 restraints weight = 236343.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.021836 restraints weight = 110162.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.022356 restraints weight = 65356.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2740 r_free = 0.2740 target = 0.022652 restraints weight = 43411.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.022836 restraints weight = 33593.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8555
moved from start:          0.3529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14846  Z= 0.181
  Angle     :  0.619   7.742  21563  Z= 0.368
  Chirality :  0.035   0.178   2456
  Planarity :  0.004   0.068   1498
  Dihedral  : 33.356 178.258   4789
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.16 (0.29), residues: 825
  helix:  2.14 (0.21), residues: 572
  sheet: -3.28 (1.42), residues: 10
  loop : -0.02 (0.40), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG Q  77 
 TYR   0.016   0.001   TYR R 121 
 PHE   0.022   0.002   PHE Q  25 
 HIS   0.004   0.001   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (14846)
  covalent geometry    : angle       0.61923 (21563)
  hydrogen bonds       : bond        0.04784 (  892)
  hydrogen bonds       : angle       3.49373 ( 2205)

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

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: K   94 GLU cc_start: 0.9201 (tp30) cc_final: 0.8833 (tp30)
REVERT: K  104 PHE cc_start: 0.9588 (m-80) cc_final: 0.9160 (m-80)
REVERT: K  105 GLU cc_start: 0.9480 (mm-30) cc_final: 0.9190 (mm-30)
REVERT: L   74 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8945 (pt0)
REVERT: N   62 MET cc_start: 0.9451 (mmp) cc_final: 0.9134 (mmm)
REVERT: N   71 GLU cc_start: 0.9336 (mm-30) cc_final: 0.8961 (pp20)
REVERT: N   82 HIS cc_start: 0.9562 (t-90) cc_final: 0.9300 (t70)
REVERT: N  105 GLU cc_start: 0.9551 (tp30) cc_final: 0.9310 (tp30)
REVERT: O   90 MET cc_start: 0.9614 (mmp) cc_final: 0.9396 (mmm)
REVERT: O  104 PHE cc_start: 0.9491 (m-80) cc_final: 0.9066 (m-80)
REVERT: O  106 ASP cc_start: 0.9333 (m-30) cc_final: 0.9119 (m-30)
REVERT: P   74 GLU cc_start: 0.9333 (pp20) cc_final: 0.9061 (pp20)
REVERT: Q   61 GLU cc_start: 0.9318 (pp20) cc_final: 0.8955 (pp20)
REVERT: Q   79 ILE cc_start: 0.9774 (tp) cc_final: 0.9477 (tp)
REVERT: Q   95 LYS cc_start: 0.9073 (pptt) cc_final: 0.8178 (tptt)
REVERT: R   59 MET cc_start: 0.9038 (tmm) cc_final: 0.8822 (tpp)
REVERT: R   95 GLN cc_start: 0.9643 (pt0) cc_final: 0.9374 (pp30)
REVERT: R  102 LEU cc_start: 0.9427 (mm) cc_final: 0.9085 (mp)
REVERT: R  105 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8529 (tm-30)
REVERT: R  109 HIS cc_start: 0.9571 (m90) cc_final: 0.9235 (m170)
REVERT: R  113 GLU cc_start: 0.9621 (mm-30) cc_final: 0.9346 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.0953
  time to fit residues: 15.1300
Evaluate side-chains
  75 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 82 optimal weight:    8.9990
   chunk 111 optimal weight:    8.9990
   chunk 48 optimal weight:    5.9990
   chunk 107 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   chunk 38 optimal weight:    9.9990
   chunk 11 optimal weight:    0.3980
   chunk 29 optimal weight:    7.9990
   chunk 98 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 72 optimal weight:   10.0000
   overall best weight:    5.0788

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

Flipped N/Q/H residues before XYZ refinement:
** N  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
P  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.024326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2582 r_free = 0.2582 target = 0.019721 restraints weight = 251431.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.020328 restraints weight = 117842.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.020810 restraints weight = 71323.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.021091 restraints weight = 48033.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.021252 restraints weight = 36088.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.2625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.3780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  14846  Z= 0.290
  Angle     :  0.677   6.886  21563  Z= 0.402
  Chirality :  0.037   0.176   2456
  Planarity :  0.005   0.060   1498
  Dihedral  : 33.673 178.452   4789
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 19.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.83 (0.29), residues: 825
  helix:  1.87 (0.21), residues: 572
  sheet: -3.46 (1.43), residues: 10
  loop : -0.06 (0.40), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  31 
 TYR   0.012   0.002   TYR R  40 
 PHE   0.013   0.002   PHE O  67 
 HIS   0.010   0.002   HIS Q  82 

Details of bonding type rmsd
  covalent geometry    : bond        0.00617 (14846)
  covalent geometry    : angle       0.67662 (21563)
  hydrogen bonds       : bond        0.08188 (  892)
  hydrogen bonds       : angle       3.93721 ( 2205)

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

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

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

  1650 Ramachandran restraints generated.
    825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.367 
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: K   94 GLU cc_start: 0.9154 (tp30) cc_final: 0.8858 (tp30)
REVERT: K  105 GLU cc_start: 0.9464 (mm-30) cc_final: 0.9209 (mm-30)
REVERT: K  120 MET cc_start: 0.9406 (tpt) cc_final: 0.9014 (tpp)
REVERT: L   74 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8999 (pt0)
REVERT: N   62 MET cc_start: 0.9453 (mmp) cc_final: 0.9178 (mmm)
REVERT: N   71 GLU cc_start: 0.9394 (mm-30) cc_final: 0.9033 (pp20)
REVERT: N   82 HIS cc_start: 0.9586 (t-90) cc_final: 0.9325 (t-90)
REVERT: N  102 LEU cc_start: 0.9101 (tp) cc_final: 0.8728 (tp)
REVERT: N  105 GLU cc_start: 0.9557 (tp30) cc_final: 0.9327 (tp30)
REVERT: O  104 PHE cc_start: 0.9611 (m-80) cc_final: 0.9162 (m-80)
REVERT: O  106 ASP cc_start: 0.9350 (m-30) cc_final: 0.9136 (m-30)
REVERT: P   66 ILE cc_start: 0.9838 (tp) cc_final: 0.9612 (pt)
REVERT: P   74 GLU cc_start: 0.9409 (pp20) cc_final: 0.9137 (pp20)
REVERT: R   59 MET cc_start: 0.8853 (tmm) cc_final: 0.8633 (tpt)
REVERT: R   95 GLN cc_start: 0.9651 (pt0) cc_final: 0.9360 (pp30)
REVERT: R  105 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8476 (tm-30)
REVERT: R  109 HIS cc_start: 0.9580 (m90) cc_final: 0.9110 (m170)
REVERT: R  113 GLU cc_start: 0.9624 (mm-30) cc_final: 0.9382 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.1051
  time to fit residues: 15.5124
Evaluate side-chains
  71 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 113
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 106 optimal weight:    0.9990
   chunk 81 optimal weight:   10.0000
   chunk 103 optimal weight:    6.9990
   chunk 48 optimal weight:    7.9990
   chunk 22 optimal weight:    6.9990
   chunk 100 optimal weight:    6.9990
   chunk 89 optimal weight:   10.0000
   chunk 94 optimal weight:    8.9990
   chunk 46 optimal weight:    2.9990
   chunk 79 optimal weight:    6.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
** 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 = 0.2840 r_free = 0.2840 target = 0.024831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2600 r_free = 0.2600 target = 0.020167 restraints weight = 247012.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2643 r_free = 0.2643 target = 0.020837 restraints weight = 115876.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.021268 restraints weight = 67732.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.021582 restraints weight = 46693.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.021760 restraints weight = 34681.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.2645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.3857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  14846  Z= 0.238
  Angle     :  0.653   8.692  21563  Z= 0.387
  Chirality :  0.036   0.170   2456
  Planarity :  0.004   0.064   1498
  Dihedral  : 33.648 179.205   4789
  Min Nonbonded Distance : 2.328

Molprobity Statistics.
  All-atom Clashscore : 15.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.88 (0.29), residues: 825
  helix:  1.93 (0.21), residues: 572
  sheet: -3.37 (1.49), residues: 10
  loop : -0.12 (0.40), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  31 
 TYR   0.018   0.001   TYR R 121 
 PHE   0.013   0.002   PHE Q  25 
 HIS   0.004   0.001   HIS N  49 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 (14846)
  covalent geometry    : angle       0.65283 (21563)
  hydrogen bonds       : bond        0.06641 (  892)
  hydrogen bonds       : angle       3.78887 ( 2205)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1698.26 seconds
wall clock time: 30 minutes 24.12 seconds (1824.12 seconds total)