Starting phenix.real_space_refine
on Sat Oct 24 03:42:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/10gl_75154/10_2026/10gl_75154.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/10gl_75154/10_2026/10gl_75154.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/10gl_75154/10_2026/10gl_75154.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/10gl_75154/10_2026/10gl_75154.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/10gl_75154/10_2026/10gl_75154.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/10gl_75154/10_2026/10gl_75154.cif"
  }
  resolution = 2.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     294      5.49       5
     S      10      5.16       5
     C    6680      2.51       5
     N    2275      2.21       5
     O    2830      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12089
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 805
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 805
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 668
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 668
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 841
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 841
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 789
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 789
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 672
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
    Chain: "G"
      Number of atoms: 823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 823
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 725
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 2997
      Number of conformers: 1
      Conformer: "B"
        Number of residues, atoms: 147, 2997
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
    Chain: "J"
      Number of atoms: 3033
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3033
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" P  B8OG I  44 " occ=0.96
      ... (21 atoms not shown)
      pdb=" O8 B8OG I  44 " occ=0.96
  Time building chain proxies: 2.57, per 1000 atoms: 0.21
  Number of scatterers: 12089
  At special positions: 0
  Unit cell: (73.678, 123.322, 115.048, 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     294     15.00
     O    2830      8.00
     N    2275      7.00
     C    6680      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.96
  Conformation dependent library (CDL) restraints added in 357.8 milliseconds
  

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1426

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 9 sheets defined
      72.1% alpha, 2.6% beta
      146 base pairs and 260 stacking pairs defined.
    Time for finding SS restraints: 2.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 49
    Processing helix  chain 'A' and resid 50 through 57
      removed outlier: 3.870A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 4.117A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.552A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.542A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.351A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 124
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 76
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.674A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.540A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
      removed outlier: 3.521A  pdb=" N   ARG G  20 " --> pdb=" O   THR G  16 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.385A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 124
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.110A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.688A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.267A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.180A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.021A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78

    401 hydrogen bonds defined for protein.
    1185 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      373 hydrogen bonds
      746 hydrogen bond angles
      0 basepair planarities
      146 basepair parallelities
      260 stacking parallelities
  Total time for adding SS restraints: 2.35

  Time building geometry restraints manager: 1.31 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2128
        1.33 -     1.45: 4308
        1.45 -     1.57: 5862
        1.57 -     1.69: 585
        1.69 -     1.80: 20
  Bond restraints: 12903
  Sorted by residual:
  bond pdb=" P  B8OG I  44 "
       pdb=" O5'B8OG I  44 "
    ideal  model  delta    sigma   weight residual
    1.708  1.559  0.149 2.00e-02 2.50e+03 5.52e+01
  bond pdb=" C   ARG E  83 "
       pdb=" N   PHE E  84 "
    ideal  model  delta    sigma   weight residual
    1.330  1.268  0.061 1.32e-02 5.74e+03 2.16e+01
  bond pdb=" C   LEU A  48 "
       pdb=" N   ARG A  49 "
    ideal  model  delta    sigma   weight residual
    1.330  1.393 -0.063 1.38e-02 5.25e+03 2.10e+01
  bond pdb=" CA  SER H  64 "
       pdb=" CB  SER H  64 "
    ideal  model  delta    sigma   weight residual
    1.529  1.472  0.057 1.62e-02 3.81e+03 1.23e+01
  bond pdb=" C3'  DC J  81 "
       pdb=" O3'  DC J  81 "
    ideal  model  delta    sigma   weight residual
    1.435  1.392  0.043 1.30e-02 5.92e+03 1.10e+01
  ... (remaining 12898 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.04: 17423
        2.04 -     4.07: 1134
        4.07 -     6.11: 92
        6.11 -     8.15: 29
        8.15 -    10.18: 4
  Bond angle restraints: 18682
  Sorted by residual:
  angle pdb=" O4'  DT I  27 "
        pdb=" C4'  DT I  27 "
        pdb=" C3'  DT I  27 "
      ideal   model   delta    sigma   weight residual
     106.00  103.07    2.93 6.00e-01 2.78e+00 2.38e+01
  angle pdb=" C   GLU A 133 "
        pdb=" CA  GLU A 133 "
        pdb=" CB  GLU A 133 "
      ideal   model   delta    sigma   weight residual
     110.92  103.47    7.45 1.59e+00 3.96e-01 2.19e+01
  angle pdb=" N   GLU E  97 "
        pdb=" CA  GLU E  97 "
        pdb=" C   GLU E  97 "
      ideal   model   delta    sigma   weight residual
     111.36  106.36    5.00 1.09e+00 8.42e-01 2.10e+01
  angle pdb=" N3   DT I  32 "
        pdb=" C4   DT I  32 "
        pdb=" O4   DT I  32 "
      ideal   model   delta    sigma   weight residual
     119.90  122.62   -2.72 6.00e-01 2.78e+00 2.05e+01
  angle pdb=" N   GLU H  35 "
        pdb=" CA  GLU H  35 "
        pdb=" CB  GLU H  35 "
      ideal   model   delta    sigma   weight residual
     110.56  103.51    7.05 1.56e+00 4.11e-01 2.04e+01
  ... (remaining 18677 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.17: 5186
       29.17 -    58.33: 1721
       58.33 -    87.50: 115
       87.50 -   116.66: 1
      116.66 -   145.83: 3
  Dihedral angle restraints: 7026
    sinusoidal: 4814
      harmonic: 2212
  Sorted by residual:
  dihedral pdb=" CD  ARG A 134 "
           pdb=" NE  ARG A 134 "
           pdb=" CZ  ARG A 134 "
           pdb=" NH1 ARG A 134 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   85.86  -85.86     1      1.00e+01 1.00e-02 8.91e+01
  dihedral pdb=" CD  ARG B  19 "
           pdb=" NE  ARG B  19 "
           pdb=" CZ  ARG B  19 "
           pdb=" NH1 ARG B  19 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -63.18   63.18     1      1.00e+01 1.00e-02 5.27e+01
  dihedral pdb=" CD  ARG F  19 "
           pdb=" NE  ARG F  19 "
           pdb=" CZ  ARG F  19 "
           pdb=" NH1 ARG F  19 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -40.70   40.70     1      1.00e+01 1.00e-02 2.32e+01
  ... (remaining 7023 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.125: 2047
       0.125 -    0.251: 64
       0.251 -    0.376: 3
       0.376 -    0.502: 1
       0.502 -    0.627: 9
  Chirality restraints: 2124
  Sorted by residual:
  chirality pdb=" P    DT I  89 "
            pdb=" OP1  DT I  89 "
            pdb=" OP2  DT I  89 "
            pdb=" O5'  DT I  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.96   -0.63 2.00e-01 2.50e+01 9.84e+00
  chirality pdb=" P    DT J  87 "
            pdb=" OP1  DT J  87 "
            pdb=" OP2  DT J  87 "
            pdb=" O5'  DT J  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.93   -0.60 2.00e-01 2.50e+01 8.91e+00
  chirality pdb=" P    DG J   5 "
            pdb=" OP1  DG J   5 "
            pdb=" OP2  DG J   5 "
            pdb=" O5'  DG J   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.92   -0.58 2.00e-01 2.50e+01 8.52e+00
  ... (remaining 2121 not shown)

  Planarity restraints: 1342
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 134 "    1.115 9.50e-02 1.11e+02   5.00e-01 1.51e+02
        pdb=" NE  ARG A 134 "   -0.066 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 134 "   -0.014 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 134 "    0.014 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 134 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  19 "    0.987 9.50e-02 1.11e+02   4.42e-01 1.18e+02
        pdb=" NE  ARG B  19 "   -0.059 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  19 "   -0.012 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  19 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  19 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG F  19 "    0.709 9.50e-02 1.11e+02   3.18e-01 6.15e+01
        pdb=" NE  ARG F  19 "   -0.043 2.00e-02 2.50e+03
        pdb=" CZ  ARG F  19 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG F  19 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG F  19 "    0.022 2.00e-02 2.50e+03
  ... (remaining 1339 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 1576
        2.75 -     3.29: 10277
        3.29 -     3.83: 24583
        3.83 -     4.36: 29374
        4.36 -     4.90: 40946
  Nonbonded interactions: 106756
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  98 "
            pdb=" OD2 ASP H  68 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" N   GLU E  59 "
            pdb=" OE1 GLU E  59 "
     model   vdw
     2.278 3.120
  nonbonded pdb=" NE  ARG C  11 "
            pdb=" O4'  DT I  32 "
     model   vdw
     2.301 3.120
  nonbonded pdb=" O   TYR G  39 "
            pdb=" OG  SER H  78 "
     model   vdw
     2.335 3.040
  nonbonded pdb=" NH1 ARG C  32 "
            pdb=" OP1  DA I  30 "
     model   vdw
     2.361 3.120
  ... (remaining 106751 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 38 through 133)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 19 through 101)
}
ncs_group {
  reference = (chain 'C' and resid 11 through 117)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 32 through 124)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.96 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             19.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.390
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.130
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8887
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.149  12903  Z= 0.654
  Angle     :  1.015  10.184  18682  Z= 0.803
  Chirality :  0.069   0.627   2124
  Planarity :  0.022   0.500   1342
  Dihedral  : 28.361 145.826   5600
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 14.04 %
    Favored  : 85.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.29), residues: 748
  helix:  1.05 (0.22), residues: 531
  sheet:  None (None), residues: 0
  loop : -0.96 (0.37), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG G  71 
 TYR   0.010   0.002   TYR A  54 
 PHE   0.012   0.002   PHE E  67 
 HIS   0.004   0.001   HIS H  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00839 /  0.65 (12903)
  covalent geometry    : angle       1.01485 /  0.80 (18682)
  hydrogen bonds       : bond        0.11687 /  7.96 (  774)
  hydrogen bonds       : angle       4.34934 /  3.04 ( 1931)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A   42 ARG cc_start: 0.8081 (mtp-110) cc_final: 0.7716 (ttm-80)
REVERT: A  133 GLU cc_start: 0.7621 (mm-30) cc_final: 0.7369 (mt-10)
REVERT: B   74 GLU cc_start: 0.9051 (mt-10) cc_final: 0.8803 (mt-10)
REVERT: C   95 LYS cc_start: 0.9126 (tptp) cc_final: 0.8800 (ttmt)
REVERT: D   63 ASN cc_start: 0.8386 (t0) cc_final: 0.8182 (m-40)
REVERT: D   68 ASP cc_start: 0.9179 (t0) cc_final: 0.8956 (t0)
REVERT: E   79 LYS cc_start: 0.8748 (tttp) cc_final: 0.8533 (tttp)
REVERT: E  120 MET cc_start: 0.8530 (mtp) cc_final: 0.8286 (mtt)
REVERT: E  123 ASP cc_start: 0.9380 (m-30) cc_final: 0.9171 (m-30)
REVERT: G   73 ASN cc_start: 0.8721 (t0) cc_final: 0.8412 (m110)
REVERT: G   95 LYS cc_start: 0.9122 (tptt) cc_final: 0.8915 (tppp)
  outliers start: 0
  outliers final: 0
  residues processed: 193
  average time/residue: 0.7983
  time to fit residues: 163.0027
Evaluate side-chains
  173 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks: [49, 97, 53, 5, 33, 65, 62, 51, 38, 61, 45]
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:   10.0000
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  55 GLN
C 104 GLN
D  84 ASN
E  68 GLN
H  63 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.090902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2938 r_free = 0.2938 target = 0.061200 restraints weight = 21729.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.2836 rms_B_bonded: 1.66
r_work: 0.2617 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work: 0.2463 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2463
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2517
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2517 r_free = 0.2517    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.96   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2517 r_free = 0.2517    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2517
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8822
moved from start:          0.0875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  12903  Z= 0.157
  Angle     :  0.651   7.406  18682  Z= 0.380
  Chirality :  0.044   0.230   2124
  Planarity :  0.006   0.136   1342
  Dihedral  : 30.883 143.896   4084
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 14.83 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.00 (0.30), residues: 748
  helix:  2.03 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.68 (0.39), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 134 
 TYR   0.011   0.001   TYR B  51 
 PHE   0.009   0.001   PHE E  67 
 HIS   0.005   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.16 (12903)
  covalent geometry    : angle       0.65123 /  0.38 (18682)
  hydrogen bonds       : bond        0.04495 /  3.01 (  774)
  hydrogen bonds       : angle       3.22724 /  2.18 ( 1931)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 177
  time to evaluate  : 0.278 
Fit side-chains
REVERT: A  133 GLU cc_start: 0.7833 (mm-30) cc_final: 0.7492 (mt-10)
REVERT: B   93 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7231 (mp10)
REVERT: C   95 LYS cc_start: 0.9116 (tptp) cc_final: 0.8773 (ttmt)
REVERT: D   71 GLU cc_start: 0.8531 (tp30) cc_final: 0.8221 (tp30)
REVERT: D  116 LYS cc_start: 0.9004 (ttmm) cc_final: 0.8803 (ttmt)
REVERT: E   79 LYS cc_start: 0.8711 (tttp) cc_final: 0.8503 (tttp)
REVERT: F   91 LYS cc_start: 0.9007 (ttpp) cc_final: 0.8754 (ttmt)
REVERT: G   15 LYS cc_start: 0.7582 (ttmm) cc_final: 0.7264 (ttpp)
REVERT: G   73 ASN cc_start: 0.8502 (t0) cc_final: 0.8236 (m110)
REVERT: G   92 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.8415 (mt-10)
REVERT: G   95 LYS cc_start: 0.9094 (tptt) cc_final: 0.8889 (tppp)
REVERT: H   71 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8243 (mt-10)
  outliers start: 17
  outliers final: 4
  residues processed: 181
  average time/residue: 0.7902
  time to fit residues: 151.4305
Evaluate side-chains
  179 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 172
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   71 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks: [34, 75, 2, 50, 37, 90, 47, 51, 23, 46, 48]
   chunk 34 optimal weight:    0.9980
   chunk 75 optimal weight:   10.0000
   chunk 2 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 90 optimal weight:   20.0000
   chunk 47 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    1.5988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  63 ASN
E  68 GLN
H  63 ASN
** H  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.090246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.060421 restraints weight = 21855.740|
|-----------------------------------------------------------------------------|
r_work (start): 0.2869 rms_B_bonded: 1.68
r_work: 0.2648 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2491 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2491
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2436
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2436 r_free = 0.2436    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2436 r_free = 0.2436    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2436
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8866
moved from start:          0.1147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12903  Z= 0.170
  Angle     :  0.622   6.615  18682  Z= 0.365
  Chirality :  0.043   0.248   2124
  Planarity :  0.004   0.041   1342
  Dihedral  : 31.014 142.976   4084
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 15.62 %
    Favored  : 81.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.46 (0.30), residues: 748
  helix:  2.38 (0.22), residues: 549
  sheet:  None (None), residues: 0
  loop : -0.53 (0.39), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  86 
 TYR   0.011   0.001   TYR A  54 
 PHE   0.012   0.002   PHE E  67 
 HIS   0.004   0.001   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.17 (12903)
  covalent geometry    : angle       0.62158 /  0.36 (18682)
  hydrogen bonds       : bond        0.04124 /  2.78 (  774)
  hydrogen bonds       : angle       2.96696 /  2.02 ( 1931)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 173
  time to evaluate  : 0.419 
Fit side-chains
REVERT: A  133 GLU cc_start: 0.7973 (mm-30) cc_final: 0.7719 (mt-10)
REVERT: B   93 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.7266 (mp10)
REVERT: C   95 LYS cc_start: 0.9140 (tptp) cc_final: 0.8799 (ttmt)
REVERT: D  116 LYS cc_start: 0.9064 (ttmm) cc_final: 0.8852 (ttmt)
REVERT: E   79 LYS cc_start: 0.8808 (tttp) cc_final: 0.8608 (tttp)
REVERT: E  120 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7541 (mtt)
REVERT: E  123 ASP cc_start: 0.9332 (m-30) cc_final: 0.9055 (m-30)
REVERT: F   91 LYS cc_start: 0.9067 (ttpp) cc_final: 0.8816 (ttmt)
REVERT: G   73 ASN cc_start: 0.8558 (t0) cc_final: 0.8349 (m-40)
REVERT: G   92 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8434 (mt-10)
REVERT: H   71 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8262 (mt-10)
  outliers start: 20
  outliers final: 7
  residues processed: 179
  average time/residue: 0.7901
  time to fit residues: 149.7902
Evaluate side-chains
  178 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 167
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   71 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks: [60, 0, 67, 95, 75, 21, 79, 53, 89, 78, 40]
   chunk 60 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   chunk 67 optimal weight:    0.9980
   chunk 95 optimal weight:   10.0000
   chunk 75 optimal weight:   10.0000
   chunk 21 optimal weight:    2.9990
   chunk 79 optimal weight:   10.0000
   chunk 53 optimal weight:    9.9990
   chunk 89 optimal weight:    9.9990
   chunk 78 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   overall best weight:    3.1586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 104 GLN
D  63 ASN
F  75 HIS
G 104 GLN
H  63 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.087761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.057964 restraints weight = 21761.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.2831 rms_B_bonded: 1.61
r_work: 0.2605 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work: 0.2447 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.2447
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2394
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2394 r_free = 0.2394    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2394 r_free = 0.2394    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2394
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8934
moved from start:          0.1470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  12903  Z= 0.251
  Angle     :  0.685   7.011  18682  Z= 0.382
  Chirality :  0.047   0.258   2124
  Planarity :  0.005   0.046   1342
  Dihedral  : 31.415 144.273   4084
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 16.56 %
    Favored  : 80.13 %
  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:  2.57 (0.30), residues: 748
  helix:  2.40 (0.22), residues: 551
  sheet:  None (None), residues: 0
  loop : -0.35 (0.40), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG F  40 
 TYR   0.019   0.002   TYR A  54 
 PHE   0.016   0.002   PHE E  67 
 HIS   0.005   0.001   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00534 /  0.25 (12903)
  covalent geometry    : angle       0.68493 /  0.38 (18682)
  hydrogen bonds       : bond        0.04812 /  3.25 (  774)
  hydrogen bonds       : angle       2.95326 /  2.01 ( 1931)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 164
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8697 (ptpp)
REVERT: A  129 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8134 (ttp-170)
REVERT: A  133 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7979 (mt-10)
REVERT: B   93 GLN cc_start: 0.8507 (OUTLIER) cc_final: 0.7215 (mp10)
REVERT: C   95 LYS cc_start: 0.9141 (tptp) cc_final: 0.8806 (ttmt)
REVERT: D  116 LYS cc_start: 0.9078 (ttmm) cc_final: 0.8850 (ttmt)
REVERT: F   91 LYS cc_start: 0.9121 (ttpp) cc_final: 0.8903 (ttmt)
REVERT: G   73 ASN cc_start: 0.8675 (t0) cc_final: 0.8380 (m110)
REVERT: G   92 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8464 (mt-10)
REVERT: H   71 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8302 (mt-10)
  outliers start: 21
  outliers final: 11
  residues processed: 174
  average time/residue: 0.8159
  time to fit residues: 150.0090
Evaluate side-chains
  176 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 160
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   71 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks: [13, 44, 8, 66, 80, 34, 79, 24, 94, 81, 89]
   chunk 13 optimal weight:    0.0980
   chunk 44 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9980
   chunk 80 optimal weight:   10.0000
   chunk 34 optimal weight:    0.9990
   chunk 79 optimal weight:   10.0000
   chunk 24 optimal weight:    0.8980
   chunk 94 optimal weight:   10.0000
   chunk 81 optimal weight:   10.0000
   chunk 89 optimal weight:   10.0000
   overall best weight:    0.7984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 108 ASN
D  63 ASN
H  47 GLN
H  63 ASN
** H  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.088830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.058467 restraints weight = 21757.067|
|-----------------------------------------------------------------------------|
r_work (start): 0.2774 rms_B_bonded: 1.70
r_work: 0.2551 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.2396 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2396
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2450
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2450 r_free = 0.2450    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2450 r_free = 0.2450    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.2450
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8876
moved from start:          0.1520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12903  Z= 0.144
  Angle     :  0.654   7.042  18682  Z= 0.369
  Chirality :  0.045   0.261   2124
  Planarity :  0.004   0.044   1342
  Dihedral  : 31.417 145.301   4084
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 18.61 %
    Favored  : 78.08 %
  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:  2.68 (0.30), residues: 748
  helix:  2.47 (0.22), residues: 551
  sheet:  None (None), residues: 0
  loop : -0.25 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  86 
 TYR   0.012   0.001   TYR D  40 
 PHE   0.011   0.002   PHE E  67 
 HIS   0.004   0.001   HIS B  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00259 /  0.14 (12903)
  covalent geometry    : angle       0.65362 /  0.37 (18682)
  hydrogen bonds       : bond        0.04089 /  2.76 (  774)
  hydrogen bonds       : angle       2.91366 /  1.98 ( 1931)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 167
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A   56 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8686 (ptpp)
REVERT: A  133 GLU cc_start: 0.8169 (mt-10) cc_final: 0.7861 (mt-10)
REVERT: B   93 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.7160 (mp10)
REVERT: C   95 LYS cc_start: 0.9123 (tptp) cc_final: 0.8782 (ttmt)
REVERT: D   85 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8701 (mttp)
REVERT: D  116 LYS cc_start: 0.9081 (ttmm) cc_final: 0.8865 (ttmt)
REVERT: F   91 LYS cc_start: 0.9084 (ttpp) cc_final: 0.8872 (ttmt)
REVERT: G   73 ASN cc_start: 0.8641 (t0) cc_final: 0.8349 (m110)
REVERT: G   92 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8445 (mt-10)
REVERT: H   71 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8281 (mt-10)
  outliers start: 21
  outliers final: 11
  residues processed: 175
  average time/residue: 0.8014
  time to fit residues: 148.4087
Evaluate side-chains
  180 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 164
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   56 LYS
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   71 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks: [73, 57, 32, 70, 84, 43, 82, 45, 8, 50, 15]
   chunk 73 optimal weight:   20.0000
   chunk 57 optimal weight:    4.9990
   chunk 32 optimal weight:    5.9990
   chunk 70 optimal weight:    0.0670
   chunk 84 optimal weight:   20.0000
   chunk 43 optimal weight:    5.9990
   chunk 82 optimal weight:    9.9990
   chunk 45 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 50 optimal weight:    0.3980
   chunk 15 optimal weight:    3.9990
   overall best weight:    2.0922

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  63 ASN
H  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.088846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.059235 restraints weight = 21918.287|
|-----------------------------------------------------------------------------|
r_work (start): 0.2765 rms_B_bonded: 1.68
r_work: 0.2544 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2390 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2390
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2382
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2382 r_free = 0.2382    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2382 r_free = 0.2382    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2382
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8871
moved from start:          0.1589

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12903  Z= 0.193
  Angle     :  0.645   7.024  18682  Z= 0.366
  Chirality :  0.044   0.266   2124
  Planarity :  0.004   0.045   1342
  Dihedral  : 31.374 143.603   4084
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 18.45 %
    Favored  : 77.92 %
  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:  2.80 (0.31), residues: 748
  helix:  2.56 (0.22), residues: 551
  sheet:  None (None), residues: 0
  loop : -0.23 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  86 
 TYR   0.011   0.001   TYR D  40 
 PHE   0.013   0.002   PHE A  67 
 HIS   0.004   0.001   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00389 /  0.19 (12903)
  covalent geometry    : angle       0.64533 /  0.37 (18682)
  hydrogen bonds       : bond        0.03993 /  2.69 (  774)
  hydrogen bonds       : angle       2.86411 /  1.95 ( 1931)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 163
  time to evaluate  : 0.338 
Fit side-chains
REVERT: A  129 ARG cc_start: 0.8767 (OUTLIER) cc_final: 0.8142 (ttp-170)
REVERT: A  133 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7973 (mt-10)
REVERT: B   93 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7179 (mp10)
REVERT: C   95 LYS cc_start: 0.9121 (tptp) cc_final: 0.8788 (ttmt)
REVERT: D   46 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8607 (mptm)
REVERT: D   85 LYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8704 (mttp)
REVERT: D  116 LYS cc_start: 0.9080 (ttmm) cc_final: 0.8866 (ttmt)
REVERT: E   59 GLU cc_start: 0.7923 (pm20) cc_final: 0.7611 (pm20)
REVERT: F   91 LYS cc_start: 0.9079 (ttpp) cc_final: 0.8868 (ttmt)
REVERT: G   73 ASN cc_start: 0.8642 (t0) cc_final: 0.8349 (m110)
REVERT: G   92 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8460 (mt-10)
REVERT: H   71 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8007 (mp0)
  outliers start: 23
  outliers final: 12
  residues processed: 172
  average time/residue: 0.8213
  time to fit residues: 149.3181
Evaluate side-chains
  180 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 162
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   46 LYS
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain G residue   76 THR
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   71 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks: [6, 64, 23, 56, 95, 31, 60, 15, 25, 59, 10]
   chunk 6 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 95 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0010
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.9588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  63 ASN
H  63 ASN
H  95 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.088931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.059111 restraints weight = 21600.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.2846 rms_B_bonded: 1.67
r_work: 0.2623 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2466 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2466
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2409
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2409 r_free = 0.2409    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2409 r_free = 0.2409    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2409
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8888
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12903  Z= 0.143
  Angle     :  0.629   7.060  18682  Z= 0.360
  Chirality :  0.044   0.270   2124
  Planarity :  0.004   0.044   1342
  Dihedral  : 31.345 143.983   4084
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 18.93 %
    Favored  : 77.60 %
  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:  2.83 (0.30), residues: 748
  helix:  2.57 (0.22), residues: 551
  sheet:  None (None), residues: 0
  loop : -0.19 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D  86 
 TYR   0.011   0.001   TYR D  40 
 PHE   0.012   0.001   PHE A  67 
 HIS   0.004   0.001   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.14 (12903)
  covalent geometry    : angle       0.62913 /  0.36 (18682)
  hydrogen bonds       : bond        0.03789 /  2.55 (  774)
  hydrogen bonds       : angle       2.83655 /  1.93 ( 1931)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 165
  time to evaluate  : 0.256 
Fit side-chains
REVERT: A  129 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.8153 (ttp-170)
REVERT: A  133 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7931 (mt-10)
REVERT: B   93 GLN cc_start: 0.8481 (OUTLIER) cc_final: 0.7205 (mp10)
REVERT: C   95 LYS cc_start: 0.9139 (tptp) cc_final: 0.8809 (ttmt)
REVERT: D   85 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.8728 (mttp)
REVERT: D  116 LYS cc_start: 0.9087 (ttmm) cc_final: 0.8877 (ttmt)
REVERT: E   59 GLU cc_start: 0.7888 (pm20) cc_final: 0.7601 (pm20)
REVERT: F   91 LYS cc_start: 0.9105 (ttpp) cc_final: 0.8889 (ttmt)
REVERT: G   73 ASN cc_start: 0.8645 (t0) cc_final: 0.8353 (m110)
REVERT: G   92 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8461 (mt-10)
REVERT: H   71 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8262 (mt-10)
  outliers start: 22
  outliers final: 10
  residues processed: 174
  average time/residue: 0.8015
  time to fit residues: 147.4452
Evaluate side-chains
  181 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 166
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   71 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks: [7, 98, 19, 41, 10, 28, 34, 94, 5, 68, 21]
   chunk 7 optimal weight:    3.9990
   chunk 98 optimal weight:   20.0000
   chunk 19 optimal weight:    2.9990
   chunk 41 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 94 optimal weight:   10.0000
   chunk 5 optimal weight:    0.6980
   chunk 68 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.9184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  63 ASN
H  63 ASN
H  95 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.089109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.059193 restraints weight = 21725.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.2797 rms_B_bonded: 1.68
r_work: 0.2577 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2421 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2421
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2414
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2414 r_free = 0.2414    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2414 r_free = 0.2414    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2414
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8851
moved from start:          0.1625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  12903  Z= 0.140
  Angle     :  0.625   7.106  18682  Z= 0.358
  Chirality :  0.043   0.273   2124
  Planarity :  0.004   0.043   1342
  Dihedral  : 31.324 143.781   4084
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 18.93 %
    Favored  : 78.39 %
  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:  2.88 (0.31), residues: 748
  helix:  2.61 (0.22), residues: 551
  sheet:  None (None), residues: 0
  loop : -0.17 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  86 
 TYR   0.011   0.001   TYR D  40 
 PHE   0.012   0.001   PHE A  67 
 HIS   0.003   0.001   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.14 (12903)
  covalent geometry    : angle       0.62484 /  0.36 (18682)
  hydrogen bonds       : bond        0.03713 /  2.50 (  774)
  hydrogen bonds       : angle       2.81769 /  1.91 ( 1931)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 165
  time to evaluate  : 0.345 
Fit side-chains
REVERT: A  129 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8142 (ttp-170)
REVERT: A  133 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7965 (mt-10)
REVERT: B   93 GLN cc_start: 0.8446 (OUTLIER) cc_final: 0.7178 (mp10)
REVERT: C   95 LYS cc_start: 0.9121 (tptp) cc_final: 0.8788 (ttmt)
REVERT: D   85 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8700 (mttp)
REVERT: D  116 LYS cc_start: 0.9081 (ttmm) cc_final: 0.8876 (ttmt)
REVERT: E   59 GLU cc_start: 0.7808 (pm20) cc_final: 0.7516 (pm20)
REVERT: F   91 LYS cc_start: 0.9085 (ttpp) cc_final: 0.8875 (ttmt)
REVERT: G   73 ASN cc_start: 0.8623 (t0) cc_final: 0.8329 (m110)
REVERT: G   92 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8444 (mt-10)
REVERT: H   71 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8236 (mt-10)
  outliers start: 17
  outliers final: 9
  residues processed: 173
  average time/residue: 0.8226
  time to fit residues: 150.2215
Evaluate side-chains
  179 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 165
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   71 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks: [29, 89, 65, 19, 28, 99, 74, 53, 1, 30, 26]
   chunk 29 optimal weight:    0.4980
   chunk 89 optimal weight:   10.0000
   chunk 65 optimal weight:    0.4980
   chunk 19 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 99 optimal weight:   20.0000
   chunk 74 optimal weight:    9.9990
   chunk 53 optimal weight:   10.0000
   chunk 1 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  63 ASN
H  63 ASN
** H  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.089328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.059418 restraints weight = 21652.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.2803 rms_B_bonded: 1.68
r_work: 0.2584 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work: 0.2429 rms_B_bonded: 4.85 restraints_weight: 0.2500
r_work (final): 0.2429
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2421
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2421 r_free = 0.2421    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2421 r_free = 0.2421    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2421
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8847
moved from start:          0.1646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12903  Z= 0.132
  Angle     :  0.623   7.051  18682  Z= 0.357
  Chirality :  0.043   0.274   2124
  Planarity :  0.004   0.042   1342
  Dihedral  : 31.306 143.603   4084
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 18.93 %
    Favored  : 78.08 %
  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:  2.91 (0.31), residues: 748
  helix:  2.64 (0.22), residues: 551
  sheet:  None (None), residues: 0
  loop : -0.17 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  86 
 TYR   0.011   0.001   TYR D  40 
 PHE   0.012   0.001   PHE A  67 
 HIS   0.003   0.001   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00221 /  0.13 (12903)
  covalent geometry    : angle       0.62263 /  0.36 (18682)
  hydrogen bonds       : bond        0.03656 /  2.45 (  774)
  hydrogen bonds       : angle       2.80494 /  1.90 ( 1931)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 168
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A  129 ARG cc_start: 0.8769 (OUTLIER) cc_final: 0.8146 (ttp-170)
REVERT: A  133 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7971 (mt-10)
REVERT: B   93 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.7180 (mp10)
REVERT: C   95 LYS cc_start: 0.9119 (tptp) cc_final: 0.8785 (ttmt)
REVERT: D   85 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8700 (mttp)
REVERT: D  116 LYS cc_start: 0.9081 (ttmm) cc_final: 0.8877 (ttmt)
REVERT: E   59 GLU cc_start: 0.7785 (pm20) cc_final: 0.7477 (pm20)
REVERT: F   91 LYS cc_start: 0.9085 (ttpp) cc_final: 0.8874 (ttmt)
REVERT: G   73 ASN cc_start: 0.8617 (t0) cc_final: 0.8322 (m110)
REVERT: G   92 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8441 (mt-10)
REVERT: H   71 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8230 (mt-10)
  outliers start: 19
  outliers final: 10
  residues processed: 176
  average time/residue: 0.8069
  time to fit residues: 150.1487
Evaluate side-chains
  182 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 167
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain H residue   71 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks: [51, 33, 34, 37, 19, 15, 27, 55, 12, 81, 28]
   chunk 51 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 34 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 19 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 27 optimal weight:    8.9990
   chunk 55 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 81 optimal weight:   20.0000
   chunk 28 optimal weight:    0.5980
   overall best weight:    1.0786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  63 ASN
H  63 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.089501 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.059636 restraints weight = 21684.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.2810 rms_B_bonded: 1.69
r_work: 0.2589 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.2433 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2433
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2485
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2485 r_free = 0.2485    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 1.00   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2485 r_free = 0.2485    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.2485
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8831
moved from start:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12903  Z= 0.146
  Angle     :  0.618   7.815  18682  Z= 0.355
  Chirality :  0.043   0.280   2124
  Planarity :  0.004   0.042   1342
  Dihedral  : 31.233 142.506   4084
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 19.09 %
    Favored  : 78.08 %
  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:  2.99 (0.31), residues: 748
  helix:  2.70 (0.22), residues: 551
  sheet:  None (None), residues: 0
  loop : -0.15 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG D  86 
 TYR   0.011   0.001   TYR F  88 
 PHE   0.014   0.002   PHE A  78 
 HIS   0.003   0.001   HIS C  31 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00267 /  0.15 (12903)
  covalent geometry    : angle       0.61774 /  0.36 (18682)
  hydrogen bonds       : bond        0.03611 /  2.42 (  774)
  hydrogen bonds       : angle       2.76089 /  1.87 ( 1931)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 168
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A  129 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8148 (ttp-170)
REVERT: A  133 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7997 (mt-10)
REVERT: B   93 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7174 (mp10)
REVERT: C   95 LYS cc_start: 0.9118 (tptp) cc_final: 0.8780 (ttmt)
REVERT: D   85 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8705 (mttp)
REVERT: D  116 LYS cc_start: 0.9073 (ttmm) cc_final: 0.8873 (ttmt)
REVERT: E   59 GLU cc_start: 0.7733 (pm20) cc_final: 0.7388 (pm20)
REVERT: F   91 LYS cc_start: 0.9078 (ttpp) cc_final: 0.8872 (ttmt)
REVERT: G   73 ASN cc_start: 0.8603 (t0) cc_final: 0.8298 (m110)
REVERT: G   92 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.8449 (mt-10)
REVERT: H   71 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8232 (mt-10)
  outliers start: 18
  outliers final: 11
  residues processed: 174
  average time/residue: 0.8123
  time to fit residues: 149.4987
Evaluate side-chains
  182 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 166
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 LEU
Chi-restraints excluded: chain A residue   87 SER
Chi-restraints excluded: chain A residue  115 LYS
Chi-restraints excluded: chain A residue  129 ARG
Chi-restraints excluded: chain B residue   44 LYS
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain D residue   85 LYS
Chi-restraints excluded: chain E residue   61 LEU
Chi-restraints excluded: chain E residue   87 SER
Chi-restraints excluded: chain E residue   94 GLU
Chi-restraints excluded: chain G residue   19 SER
Chi-restraints excluded: chain G residue   92 GLU
Chi-restraints excluded: chain G residue  114 VAL
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain H residue   71 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks: [34, 71, 94, 30, 3, 60, 52, 54, 38, 43, 57]
   chunk 34 optimal weight:    0.6980
   chunk 71 optimal weight:    0.9990
   chunk 94 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.8986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D  63 ASN
H  63 ASN
** H  95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.089674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.059838 restraints weight = 21734.958|
|-----------------------------------------------------------------------------|
r_work (start): 0.2809 rms_B_bonded: 1.69
r_work: 0.2590 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.2436 rms_B_bonded: 4.87 restraints_weight: 0.2500
r_work (final): 0.2436
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2493
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2493 r_free = 0.2493    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.95   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2493 r_free = 0.2493    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.94   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.2493
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8815
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.051  12903  Z= 0.139
  Angle     :  0.613   7.578  18682  Z= 0.354
  Chirality :  0.043   0.282   2124
  Planarity :  0.004   0.042   1342
  Dihedral  : 31.206 142.466   4084
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 6.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 19.09 %
    Favored  : 78.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.97 (0.31), residues: 748
  helix:  2.68 (0.22), residues: 551
  sheet:  None (None), residues: 0
  loop : -0.14 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  86 
 TYR   0.011   0.001   TYR D  40 
 PHE   0.012   0.001   PHE A  67 
 HIS   0.003   0.001   HIS F  75 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00246 /  0.14 (12903)
  covalent geometry    : angle       0.61316 /  0.35 (18682)
  hydrogen bonds       : bond        0.03583 /  2.40 (  774)
  hydrogen bonds       : angle       2.75934 /  1.87 ( 1931)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6015.08 seconds
wall clock time: 102 minutes 35.60 seconds (6155.60 seconds total)