Starting phenix.real_space_refine
on Thu Sep 18 07:37:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ynk_39425/09_2025/8ynk_39425.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ynk_39425/09_2025/8ynk_39425.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.62
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ynk_39425/09_2025/8ynk_39425.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ynk_39425/09_2025/8ynk_39425.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ynk_39425/09_2025/8ynk_39425.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ynk_39425/09_2025/8ynk_39425.cif"
  }
  resolution = 3.62
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.041
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4446 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      66      5.16       5
     C    7343      2.51       5
     N    1983      2.21       5
     O    2172      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11564
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 1510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1510
          Classifications: {'peptide': 182}
          Link IDs: {'PTRANS': 3, 'TRANS': 178}
    Chain: "B"
      Number of atoms: 1510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1510
          Classifications: {'peptide': 182}
          Link IDs: {'PTRANS': 3, 'TRANS': 178}
    Chain: "C"
      Number of atoms: 1510
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 182, 1510
          Classifications: {'peptide': 182}
          Link IDs: {'PTRANS': 3, 'TRANS': 178}
    Chain: "H"
      Number of atoms: 1403
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 172, 1403
          Classifications: {'peptide': 172}
          Link IDs: {'PTRANS': 4, 'TRANS': 167}
          Chain breaks: 1
    Chain: "I"
      Number of atoms: 1386
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 170, 1386
          Classifications: {'peptide': 170}
          Link IDs: {'PTRANS': 4, 'TRANS': 165}
          Chain breaks: 1
    Chain: "J"
      Number of atoms: 1397
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 1397
          Classifications: {'peptide': 171}
          Link IDs: {'PTRANS': 4, 'TRANS': 166}
          Chain breaks: 1
    Chain: "K"
      Number of atoms: 1424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1424
          Classifications: {'peptide': 175}
          Link IDs: {'PTRANS': 4, 'TRANS': 170}
    Chain: "G"
      Number of atoms: 1424
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 175, 1424
          Classifications: {'peptide': 175}
          Link IDs: {'PTRANS': 4, 'TRANS': 170}
  Time building chain proxies: 2.92, per 1000 atoms: 0.25
  Number of scatterers: 11564
  At special positions: 0
  Unit cell: (102.48, 101.64, 141.96, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      66     16.00
     O    2172      8.00
     N    1983      7.00
     C    7343      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: 0.99
  Conformation dependent library (CDL) restraints added in 493.7 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2736

  Finding SS restraints...
    Secondary structure from input PDB file:
      96 helices and 0 sheets defined
      76.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 12
    Processing helix  chain 'A' and resid 15 through 26
    Processing helix  chain 'A' and resid 27 through 29
      No H-bonds generated for 'chain 'A' and resid 27 through 29'
    Processing helix  chain 'A' and resid 31 through 36
    Processing helix  chain 'A' and resid 40 through 51
      removed outlier: 3.618A  pdb=" N   LEU A  44 " --> pdb=" O   ASP A  40 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LYS A  51 " --> pdb=" O   ARG A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 69
    Processing helix  chain 'A' and resid 71 through 78
      removed outlier: 3.776A  pdb=" N   LEU A  75 " --> pdb=" O   ARG A  71 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ILE A  76 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 92
      removed outlier: 3.680A  pdb=" N   THR A  92 " --> pdb=" O   ARG A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 111
      removed outlier: 3.523A  pdb=" N   VAL A 103 " --> pdb=" O   SER A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 124
    Processing helix  chain 'A' and resid 130 through 134
      removed outlier: 3.670A  pdb=" N   ASP A 134 " --> pdb=" O   CYS A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 149
    Processing helix  chain 'A' and resid 157 through 168
      removed outlier: 3.907A  pdb=" N   GLN A 166 " --> pdb=" O   ARG A 162 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   ILE A 167 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 169 through 182
    Processing helix  chain 'B' and resid 2 through 12
    Processing helix  chain 'B' and resid 15 through 26
    Processing helix  chain 'B' and resid 31 through 36
    Processing helix  chain 'B' and resid 40 through 51
      removed outlier: 3.763A  pdb=" N   LEU B  44 " --> pdb=" O   ASP B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 59 through 69
      removed outlier: 3.537A  pdb=" N   ILE B  69 " --> pdb=" O   LEU B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 79
      removed outlier: 4.205A  pdb=" N   LEU B  75 " --> pdb=" O   ARG B  71 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
    Processing helix  chain 'B' and resid 99 through 111
    Processing helix  chain 'B' and resid 113 through 125
    Processing helix  chain 'B' and resid 129 through 134
      removed outlier: 3.956A  pdb=" N   ASP B 134 " --> pdb=" O   CYS B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 149
    Processing helix  chain 'B' and resid 157 through 165
    Processing helix  chain 'B' and resid 169 through 182
    Processing helix  chain 'C' and resid 2 through 14
      removed outlier: 3.669A  pdb=" N   GLN C  13 " --> pdb=" O   ASP C   9 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   LEU C  14 " --> pdb=" O   ILE C  10 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 15 through 26
    Processing helix  chain 'C' and resid 31 through 36
    Processing helix  chain 'C' and resid 40 through 51
      removed outlier: 3.717A  pdb=" N   LEU C  44 " --> pdb=" O   ASP C  40 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 69
    Processing helix  chain 'C' and resid 71 through 78
      removed outlier: 3.721A  pdb=" N   LEU C  75 " --> pdb=" O   ARG C  71 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 82 through 92
      removed outlier: 3.511A  pdb=" N   MET C  86 " --> pdb=" O   ARG C  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 111
      removed outlier: 3.519A  pdb=" N   VAL C 103 " --> pdb=" O   SER C  99 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   GLU C 111 " --> pdb=" O   GLN C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 113 through 124
    Processing helix  chain 'C' and resid 130 through 134
    Processing helix  chain 'C' and resid 138 through 149
    Processing helix  chain 'C' and resid 157 through 165
    Processing helix  chain 'C' and resid 169 through 182
    Processing helix  chain 'H' and resid 3 through 12
    Processing helix  chain 'H' and resid 14 through 26
    Processing helix  chain 'H' and resid 36 through 48
    Processing helix  chain 'H' and resid 51 through 62
      removed outlier: 3.638A  pdb=" N   VAL H  62 " --> pdb=" O   LEU H  58 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 64 through 71
    Processing helix  chain 'H' and resid 75 through 86
    Processing helix  chain 'H' and resid 91 through 102
    Processing helix  chain 'H' and resid 105 through 116
    Processing helix  chain 'H' and resid 121 through 126
      removed outlier: 3.735A  pdb=" N   ILE H 125 " --> pdb=" O   GLY H 121 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 130 through 141
      removed outlier: 3.563A  pdb=" N   LEU H 134 " --> pdb=" O   SER H 130 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 149 through 159
    Processing helix  chain 'H' and resid 161 through 175
      removed outlier: 3.946A  pdb=" N   LYS H 165 " --> pdb=" O   ARG H 161 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 2 through 13
    Processing helix  chain 'I' and resid 14 through 25
    Processing helix  chain 'I' and resid 36 through 47
    Processing helix  chain 'I' and resid 51 through 62
    Processing helix  chain 'I' and resid 64 through 71
    Processing helix  chain 'I' and resid 75 through 86
    Processing helix  chain 'I' and resid 91 through 104
      removed outlier: 3.825A  pdb=" N   VAL I  95 " --> pdb=" O   SER I  91 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 105 through 117
    Processing helix  chain 'I' and resid 130 through 141
    Processing helix  chain 'I' and resid 149 through 159
    Processing helix  chain 'I' and resid 161 through 176
      removed outlier: 4.005A  pdb=" N   LYS I 165 " --> pdb=" O   ARG I 161 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 2 through 13
      removed outlier: 3.827A  pdb=" N   ILE J   6 " --> pdb=" O   SER J   2 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 14 through 27
      removed outlier: 4.282A  pdb=" N   ASP J  27 " --> pdb=" O   PHE J  23 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 36 through 47
    Processing helix  chain 'J' and resid 51 through 63
    Processing helix  chain 'J' and resid 64 through 71
      removed outlier: 3.816A  pdb=" N   LEU J  68 " --> pdb=" O   ARG J  64 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 75 through 86
    Processing helix  chain 'J' and resid 91 through 104
      removed outlier: 3.594A  pdb=" N   ASP J 103 " --> pdb=" O   GLU J  99 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LEU J 104 " --> pdb=" O   ILE J 100 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 105 through 117
      removed outlier: 3.862A  pdb=" N   VAL J 109 " --> pdb=" O   ASP J 105 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   SER J 110 " --> pdb=" O   LYS J 106 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 130 through 141
    Processing helix  chain 'J' and resid 149 through 159
    Processing helix  chain 'J' and resid 161 through 175
      removed outlier: 3.902A  pdb=" N   LYS J 165 " --> pdb=" O   ARG J 161 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 2 through 12
      removed outlier: 3.677A  pdb=" N   ILE K   6 " --> pdb=" O   SER K   2 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 14 through 25
      removed outlier: 3.539A  pdb=" N   LYS K  18 " --> pdb=" O   ASP K  14 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   GLU K  19 " --> pdb=" O   THR K  15 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   MET K  20 " --> pdb=" O   ASP K  16 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 36 through 48
    Processing helix  chain 'K' and resid 51 through 62
    Processing helix  chain 'K' and resid 64 through 71
      removed outlier: 3.568A  pdb=" N   LEU K  68 " --> pdb=" O   ARG K  64 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 75 through 85
      removed outlier: 3.512A  pdb=" N   VAL K  79 " --> pdb=" O   ASP K  75 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 91 through 103
    Processing helix  chain 'K' and resid 105 through 116
      removed outlier: 3.897A  pdb=" N   VAL K 109 " --> pdb=" O   ASP K 105 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   SER K 110 " --> pdb=" O   LYS K 106 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   SER K 111 " --> pdb=" O   SER K 107 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 130 through 141
    Processing helix  chain 'K' and resid 149 through 159
    Processing helix  chain 'K' and resid 162 through 175
    Processing helix  chain 'G' and resid 2 through 12
      removed outlier: 3.738A  pdb=" N   ILE G   6 " --> pdb=" O   SER G   2 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 14 through 25
      removed outlier: 3.561A  pdb=" N   LYS G  18 " --> pdb=" O   ASP G  14 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   GLU G  19 " --> pdb=" O   THR G  15 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   MET G  20 " --> pdb=" O   ASP G  16 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 36 through 48
    Processing helix  chain 'G' and resid 51 through 62
      removed outlier: 3.682A  pdb=" N   VAL G  62 " --> pdb=" O   LEU G  58 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 64 through 71
      removed outlier: 3.566A  pdb=" N   LEU G  68 " --> pdb=" O   ARG G  64 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 75 through 85
    Processing helix  chain 'G' and resid 91 through 102
      removed outlier: 3.526A  pdb=" N   VAL G  95 " --> pdb=" O   SER G  91 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 105 through 117
      removed outlier: 3.737A  pdb=" N   SER G 111 " --> pdb=" O   SER G 107 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 130 through 141
    Processing helix  chain 'G' and resid 149 through 159
      removed outlier: 3.716A  pdb=" N   ILE G 159 " --> pdb=" O   CYS G 155 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 162 through 175

    652 hydrogen bonds defined for protein.
    1941 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.73

  Time building geometry restraints manager: 1.30 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3872
        1.34 -     1.46: 2053
        1.46 -     1.58: 5643
        1.58 -     1.69: 0
        1.69 -     1.81: 116
  Bond restraints: 11684
  Sorted by residual:
  bond pdb=" CB  PRO H  87 "
       pdb=" CG  PRO H  87 "
    ideal  model  delta    sigma   weight residual
    1.492  1.531 -0.039 5.00e-02 4.00e+02 6.14e-01
  bond pdb=" CA  ILE B  69 "
       pdb=" C   ILE B  69 "
    ideal  model  delta    sigma   weight residual
    1.530  1.522  0.008 1.12e-02 7.97e+03 5.53e-01
  bond pdb=" CA  ILE K 159 "
       pdb=" C   ILE K 159 "
    ideal  model  delta    sigma   weight residual
    1.523  1.531 -0.008 1.27e-02 6.20e+03 4.11e-01
  bond pdb=" CA  ILE G 159 "
       pdb=" C   ILE G 159 "
    ideal  model  delta    sigma   weight residual
    1.530  1.523  0.007 1.12e-02 7.97e+03 4.11e-01
  bond pdb=" N   GLU H 128 "
       pdb=" CA  GLU H 128 "
    ideal  model  delta    sigma   weight residual
    1.462  1.472 -0.010 1.54e-02 4.22e+03 3.85e-01
  ... (remaining 11679 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.06: 15275
        1.06 -     2.12: 306
        2.12 -     3.19: 55
        3.19 -     4.25: 13
        4.25 -     5.31: 3
  Bond angle restraints: 15652
  Sorted by residual:
  angle pdb=" N   ILE A 151 "
        pdb=" CA  ILE A 151 "
        pdb=" C   ILE A 151 "
      ideal   model   delta    sigma   weight residual
     113.16  108.45    4.71 1.49e+00 4.50e-01 9.99e+00
  angle pdb=" C   ARG B 149 "
        pdb=" N   VAL B 150 "
        pdb=" CA  VAL B 150 "
      ideal   model   delta    sigma   weight residual
     121.97  126.15   -4.18 1.80e+00 3.09e-01 5.40e+00
  angle pdb=" N   ILE B  69 "
        pdb=" CA  ILE B  69 "
        pdb=" C   ILE B  69 "
      ideal   model   delta    sigma   weight residual
     111.91  109.91    2.00 8.90e-01 1.26e+00 5.05e+00
  angle pdb=" C   ARG A 149 "
        pdb=" N   VAL A 150 "
        pdb=" CA  VAL A 150 "
      ideal   model   delta    sigma   weight residual
     121.97  125.96   -3.99 1.80e+00 3.09e-01 4.91e+00
  angle pdb=" N   ILE G 159 "
        pdb=" CA  ILE G 159 "
        pdb=" C   ILE G 159 "
      ideal   model   delta    sigma   weight residual
     111.91  109.97    1.94 8.90e-01 1.26e+00 4.76e+00
  ... (remaining 15647 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 6662
       17.90 -    35.79: 652
       35.79 -    53.69: 82
       53.69 -    71.59: 16
       71.59 -    89.48: 10
  Dihedral angle restraints: 7422
    sinusoidal: 3250
      harmonic: 4172
  Sorted by residual:
  dihedral pdb=" CB  GLU B  12 "
           pdb=" CG  GLU B  12 "
           pdb=" CD  GLU B  12 "
           pdb=" OE1 GLU B  12 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.41   88.41     1      3.00e+01 1.11e-03 1.04e+01
  dihedral pdb=" CB  MET K  97 "
           pdb=" CG  MET K  97 "
           pdb=" SD  MET K  97 "
           pdb=" CE  MET K  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  117.05  -57.05     3      1.50e+01 4.44e-03 9.42e+00
  dihedral pdb=" CG  ARG K  38 "
           pdb=" CD  ARG K  38 "
           pdb=" NE  ARG K  38 "
           pdb=" CZ  ARG K  38 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -131.52   41.52     2      1.50e+01 4.44e-03 9.38e+00
  ... (remaining 7419 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1251
       0.030 -    0.061: 439
       0.061 -    0.091: 94
       0.091 -    0.121: 34
       0.121 -    0.151: 3
  Chirality restraints: 1821
  Sorted by residual:
  chirality pdb=" CB  VAL H  62 "
            pdb=" CA  VAL H  62 "
            pdb=" CG1 VAL H  62 "
            pdb=" CG2 VAL H  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.48   -0.15 2.00e-01 2.50e+01 5.72e-01
  chirality pdb=" CB  VAL A 150 "
            pdb=" CA  VAL A 150 "
            pdb=" CG1 VAL A 150 "
            pdb=" CG2 VAL A 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 4.06e-01
  chirality pdb=" CA  ILE A 128 "
            pdb=" N   ILE A 128 "
            pdb=" C   ILE A 128 "
            pdb=" CB  ILE A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.73e-01
  ... (remaining 1818 not shown)

  Planarity restraints: 1989
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA H 145 "    0.022 5.00e-02 4.00e+02   3.33e-02 1.78e+00
        pdb=" N   PRO H 146 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO H 146 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO H 146 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 150 "   -0.006 2.00e-02 2.50e+03   1.15e-02 1.32e+00
        pdb=" C   VAL C 150 "    0.020 2.00e-02 2.50e+03
        pdb=" O   VAL C 150 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   ILE C 151 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA G 145 "   -0.018 5.00e-02 4.00e+02   2.74e-02 1.20e+00
        pdb=" N   PRO G 146 "    0.047 5.00e-02 4.00e+02
        pdb=" CA  PRO G 146 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO G 146 "   -0.015 5.00e-02 4.00e+02
  ... (remaining 1986 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 2223
        2.77 -     3.30: 11199
        3.30 -     3.84: 17845
        3.84 -     4.37: 19893
        4.37 -     4.90: 34337
  Nonbonded interactions: 85497
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  29 "
            pdb=" O   GLN A  97 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   TYR B 106 "
            pdb=" OG  SER B 109 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" OH  TYR A 106 "
            pdb=" OE2 GLU A 110 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   ASP K 163 "
            pdb=" OG1 THR K 166 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OD1 ASP B  28 "
            pdb=" NH2 ARG B 102 "
     model   vdw
     2.312 3.120
  ... (remaining 85492 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = chain 'C'
}
ncs_group {
  reference = (chain 'G' and (resid 2 through 28 or resid 31 through 121 or resid 128 through  \ 
175))
  selection = (chain 'H' and (resid 2 through 121 or resid 128 through 175))
  selection = (chain 'I' and (resid 2 through 28 or resid 31 through 175))
  selection = (chain 'J' and (resid 2 through 28 or resid 31 through 121 or resid 128 through  \ 
175))
  selection = (chain 'K' and (resid 2 through 28 or resid 31 through 121 or resid 128 through  \ 
175))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.770
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
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      :  0.002   0.039  11684  Z= 0.108
  Angle     :  0.400   5.312  15652  Z= 0.220
  Chirality :  0.034   0.151   1821
  Planarity :  0.002   0.033   1989
  Dihedral  : 13.746  89.483   4686
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  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 aren not related in a simple way.
  whole:  1.98 (0.24), residues: 1387
  helix:  2.01 (0.17), residues: 1032
  sheet:  None (None), residues: 0
  loop : -0.76 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG I  61 
 TYR   0.006   0.001   TYR B 101 
 PHE   0.009   0.001   PHE A  61 
 HIS   0.001   0.000   HIS J  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (11684)
  covalent geometry    : angle       0.40034 (15652)
  hydrogen bonds       : bond        0.15926 (  652)
  hydrogen bonds       : angle       4.34976 ( 1941)

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

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

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  331 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 331
  time to evaluate  : 0.511 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ASN cc_start: 0.8512 (t0) cc_final: 0.8040 (m110)
REVERT: A  101 TYR cc_start: 0.8909 (t80) cc_final: 0.8495 (t80)
REVERT: A  124 LEU cc_start: 0.9147 (mt) cc_final: 0.8756 (tt)
REVERT: C  104 MET cc_start: 0.9507 (ptm) cc_final: 0.9007 (ptm)
REVERT: H    8 GLN cc_start: 0.8910 (mt0) cc_final: 0.8641 (mp10)
REVERT: H   36 ASN cc_start: 0.8654 (m-40) cc_final: 0.8290 (t0)
REVERT: H   40 LEU cc_start: 0.9290 (tp) cc_final: 0.9024 (tp)
REVERT: H   71 ILE cc_start: 0.8843 (mm) cc_final: 0.8587 (mm)
REVERT: H  116 MET cc_start: 0.9138 (mmm) cc_final: 0.8873 (mmm)
REVERT: I   82 HIS cc_start: 0.8883 (t70) cc_final: 0.8620 (t70)
REVERT: J   57 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7912 (tm-30)
REVERT: J   86 ASN cc_start: 0.8878 (t0) cc_final: 0.8576 (m-40)
REVERT: K   39 ASP cc_start: 0.8812 (m-30) cc_final: 0.8605 (m-30)
REVERT: K   70 ARG cc_start: 0.8798 (ttp-170) cc_final: 0.8492 (ptm160)
REVERT: K   86 ASN cc_start: 0.7231 (m110) cc_final: 0.6823 (t0)
REVERT: K  166 THR cc_start: 0.9230 (p) cc_final: 0.8888 (p)
REVERT: G   43 ILE cc_start: 0.9597 (mm) cc_final: 0.9387 (mt)
REVERT: G   60 TYR cc_start: 0.8835 (t80) cc_final: 0.8560 (t80)
REVERT: G   66 ASP cc_start: 0.8700 (p0) cc_final: 0.8405 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 331
  average time/residue: 0.1342
  time to fit residues: 60.1782
Evaluate side-chains
  175 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0670
   chunk 55 optimal weight:    5.9990
   overall best weight:    1.3722

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

Flipped N/Q/H residues before XYZ refinement:
H 173 GLN
K 169 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.097590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.075262 restraints weight = 34867.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.078059 restraints weight = 18031.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.079871 restraints weight = 11957.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.081017 restraints weight = 9178.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.081645 restraints weight = 7763.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11684  Z= 0.137
  Angle     :  0.557   7.032  15652  Z= 0.288
  Chirality :  0.038   0.160   1821
  Planarity :  0.003   0.036   1989
  Dihedral  :  3.502  12.931   1542
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 6.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  :  9.93 %
    Favored  : 88.32 %
  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 aren not related in a simple way.
  whole:  1.70 (0.24), residues: 1387
  helix:  1.70 (0.17), residues: 1089
  sheet:  None (None), residues: 0
  loop : -0.94 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H 122 
 TYR   0.012   0.001   TYR A 101 
 PHE   0.015   0.001   PHE C  24 
 HIS   0.002   0.001   HIS I 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (11684)
  covalent geometry    : angle       0.55664 (15652)
  hydrogen bonds       : bond        0.03716 (  652)
  hydrogen bonds       : angle       3.86718 ( 1941)

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

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

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 189
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ASN cc_start: 0.8619 (t0) cc_final: 0.8260 (m110)
REVERT: B   92 THR cc_start: 0.8773 (m) cc_final: 0.8305 (p)
REVERT: B  110 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7557 (pp20)
REVERT: C  104 MET cc_start: 0.9365 (ptm) cc_final: 0.9044 (ptm)
REVERT: C  124 LEU cc_start: 0.8757 (tp) cc_final: 0.8406 (tt)
REVERT: C  176 ASN cc_start: 0.9044 (m110) cc_final: 0.8783 (p0)
REVERT: H    8 GLN cc_start: 0.8953 (mt0) cc_final: 0.8671 (mt0)
REVERT: H   66 ASP cc_start: 0.7692 (p0) cc_final: 0.7424 (p0)
REVERT: H  133 ASP cc_start: 0.8249 (m-30) cc_final: 0.7933 (m-30)
REVERT: K   93 TYR cc_start: 0.8225 (t80) cc_final: 0.7954 (t80)
REVERT: K  116 MET cc_start: 0.8635 (mtm) cc_final: 0.8139 (mmm)
REVERT: K  131 PHE cc_start: 0.8968 (t80) cc_final: 0.8766 (t80)
REVERT: G    6 ILE cc_start: 0.9080 (mt) cc_final: 0.8748 (mt)
REVERT: G   60 TYR cc_start: 0.9018 (t80) cc_final: 0.8638 (t80)
REVERT: G   66 ASP cc_start: 0.8685 (p0) cc_final: 0.8401 (p0)
  outliers start: 23
  outliers final: 12
  residues processed: 204
  average time/residue: 0.0967
  time to fit residues: 29.2855
Evaluate side-chains
  157 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 144
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue  110 GLU
Chi-restraints excluded: chain C residue    6 ASN
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain H residue  130 SER
Chi-restraints excluded: chain I residue   20 MET
Chi-restraints excluded: chain I residue   91 SER
Chi-restraints excluded: chain J residue   77 LYS
Chi-restraints excluded: chain K residue   79 VAL
Chi-restraints excluded: chain K residue  111 SER
Chi-restraints excluded: chain G residue   15 THR
Chi-restraints excluded: chain G residue   30 ILE
Chi-restraints excluded: chain G residue  125 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 115 optimal weight:    4.9990
   chunk 103 optimal weight:    0.7980
   chunk 113 optimal weight:   10.0000
   chunk 130 optimal weight:    0.0570
   chunk 117 optimal weight:    0.0980
   chunk 81 optimal weight:    0.9990
   chunk 133 optimal weight:    6.9990
   chunk 112 optimal weight:    3.9990
   chunk 123 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 69 optimal weight:    4.9990
   overall best weight:    0.5700

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

Flipped N/Q/H residues before XYZ refinement:
I  88 HIS
J  86 ASN
K   8 GLN
G 158 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.100438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.078498 restraints weight = 35515.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.081450 restraints weight = 17585.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.083349 restraints weight = 11445.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.084543 restraints weight = 8718.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.085281 restraints weight = 7347.820|
|-----------------------------------------------------------------------------|
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.3038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  11684  Z= 0.102
  Angle     :  0.509   7.174  15652  Z= 0.263
  Chirality :  0.036   0.145   1821
  Planarity :  0.003   0.032   1989
  Dihedral  :  3.440  13.344   1542
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.68 %
    Favored  : 86.66 %
  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 aren not related in a simple way.
  whole:  1.64 (0.24), residues: 1387
  helix:  1.69 (0.17), residues: 1087
  sheet:  None (None), residues: 0
  loop : -1.09 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  45 
 TYR   0.013   0.001   TYR A 101 
 PHE   0.014   0.001   PHE H  65 
 HIS   0.002   0.000   HIS G   7 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 (11684)
  covalent geometry    : angle       0.50884 (15652)
  hydrogen bonds       : bond        0.02924 (  652)
  hydrogen bonds       : angle       3.59757 ( 1941)

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

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

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 172
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ASN cc_start: 0.8639 (t0) cc_final: 0.8335 (m110)
REVERT: A  148 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8636 (mtmm)
REVERT: B  110 GLU cc_start: 0.7839 (OUTLIER) cc_final: 0.7272 (pp20)
REVERT: C   42 LEU cc_start: 0.8492 (mt) cc_final: 0.8271 (mt)
REVERT: C  104 MET cc_start: 0.9340 (ptm) cc_final: 0.9066 (ptm)
REVERT: H   66 ASP cc_start: 0.7611 (p0) cc_final: 0.7322 (p0)
REVERT: H   97 MET cc_start: 0.8491 (mmm) cc_final: 0.7826 (mmm)
REVERT: H  133 ASP cc_start: 0.8174 (m-30) cc_final: 0.7924 (m-30)
REVERT: I  176 GLN cc_start: 0.7318 (mp10) cc_final: 0.7012 (mp10)
REVERT: K  116 MET cc_start: 0.8518 (mtm) cc_final: 0.8191 (mmm)
REVERT: G   60 TYR cc_start: 0.8972 (t80) cc_final: 0.8538 (t80)
REVERT: G   66 ASP cc_start: 0.8608 (p0) cc_final: 0.8345 (p0)
REVERT: G  102 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7729 (tp30)
  outliers start: 22
  outliers final: 10
  residues processed: 189
  average time/residue: 0.0892
  time to fit residues: 25.9481
Evaluate side-chains
  159 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 147
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain B residue   86 MET
Chi-restraints excluded: chain B residue  109 SER
Chi-restraints excluded: chain B residue  110 GLU
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain I residue   20 MET
Chi-restraints excluded: chain K residue   79 VAL
Chi-restraints excluded: chain K residue  111 SER
Chi-restraints excluded: chain G residue   15 THR
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue  125 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 86 optimal weight:    0.0980
   chunk 17 optimal weight:    0.7980
   chunk 51 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 84 optimal weight:    0.0000
   chunk 13 optimal weight:   10.0000
   chunk 90 optimal weight:    3.9990
   chunk 111 optimal weight:    4.9990
   chunk 82 optimal weight:    0.9980
   chunk 125 optimal weight:    4.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
A  46 GLN
B  46 GLN
C 176 ASN
H 173 GLN
K   8 GLN
K  86 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.101957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.081113 restraints weight = 31893.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.083794 restraints weight = 16130.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.085550 restraints weight = 10523.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.086666 restraints weight = 8022.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.087267 restraints weight = 6741.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.3579
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.3314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  11684  Z= 0.107
  Angle     :  0.496   6.203  15652  Z= 0.256
  Chirality :  0.036   0.145   1821
  Planarity :  0.003   0.031   1989
  Dihedral  :  3.468  13.944   1542
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.42 %
    Favored  : 84.46 %
  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 aren not related in a simple way.
  whole:  1.79 (0.24), residues: 1387
  helix:  1.85 (0.17), residues: 1055
  sheet:  None (None), residues: 0
  loop : -0.95 (0.32), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG I 161 
 TYR   0.016   0.001   TYR A 101 
 PHE   0.021   0.001   PHE B 181 
 HIS   0.003   0.000   HIS I  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (11684)
  covalent geometry    : angle       0.49591 (15652)
  hydrogen bonds       : bond        0.02862 (  652)
  hydrogen bonds       : angle       3.58037 ( 1941)

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

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

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 160
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ASN cc_start: 0.8702 (t0) cc_final: 0.8436 (m110)
REVERT: A  101 TYR cc_start: 0.8827 (t80) cc_final: 0.8602 (t80)
REVERT: A  148 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8660 (mtmm)
REVERT: B  110 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7382 (pp20)
REVERT: C   42 LEU cc_start: 0.8403 (mt) cc_final: 0.8177 (mt)
REVERT: C  104 MET cc_start: 0.9297 (ptm) cc_final: 0.8954 (ptm)
REVERT: C  176 ASN cc_start: 0.8909 (m110) cc_final: 0.8678 (p0)
REVERT: H   66 ASP cc_start: 0.7659 (p0) cc_final: 0.7363 (p0)
REVERT: H  133 ASP cc_start: 0.8104 (m-30) cc_final: 0.7888 (m-30)
REVERT: G   60 TYR cc_start: 0.9041 (t80) cc_final: 0.8625 (t80)
REVERT: G   66 ASP cc_start: 0.8536 (p0) cc_final: 0.8289 (p0)
REVERT: G  102 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7776 (tp30)
  outliers start: 28
  outliers final: 20
  residues processed: 177
  average time/residue: 0.0880
  time to fit residues: 24.1144
Evaluate side-chains
  170 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 148
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain B residue   46 GLN
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   86 MET
Chi-restraints excluded: chain B residue  110 GLU
Chi-restraints excluded: chain C residue    6 ASN
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain H residue  130 SER
Chi-restraints excluded: chain H residue  159 ILE
Chi-restraints excluded: chain H residue  173 GLN
Chi-restraints excluded: chain I residue   20 MET
Chi-restraints excluded: chain I residue   91 SER
Chi-restraints excluded: chain K residue   15 THR
Chi-restraints excluded: chain K residue   44 LEU
Chi-restraints excluded: chain K residue   79 VAL
Chi-restraints excluded: chain K residue  111 SER
Chi-restraints excluded: chain G residue   15 THR
Chi-restraints excluded: chain G residue   52 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 106 optimal weight:    0.0060
   chunk 52 optimal weight:    1.9990
   chunk 42 optimal weight:    0.8980
   chunk 93 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 132 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 109 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.9598

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.096816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.073941 restraints weight = 34981.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.076735 restraints weight = 18024.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.078533 restraints weight = 11961.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.079661 restraints weight = 9233.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.080420 restraints weight = 7841.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.3461

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  11684  Z= 0.105
  Angle     :  0.499   7.229  15652  Z= 0.256
  Chirality :  0.036   0.186   1821
  Planarity :  0.003   0.031   1989
  Dihedral  :  3.497  17.635   1542
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 14.78 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.24), residues: 1387
  helix:  1.85 (0.17), residues: 1064
  sheet:  None (None), residues: 0
  loop : -0.92 (0.33), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 161 
 TYR   0.011   0.001   TYR K  93 
 PHE   0.009   0.001   PHE C 120 
 HIS   0.002   0.000   HIS I  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 (11684)
  covalent geometry    : angle       0.49881 (15652)
  hydrogen bonds       : bond        0.02778 (  652)
  hydrogen bonds       : angle       3.50412 ( 1941)

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

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

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 154
  time to evaluate  : 0.562 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ASN cc_start: 0.8722 (t0) cc_final: 0.8401 (m110)
REVERT: A  101 TYR cc_start: 0.8855 (t80) cc_final: 0.8612 (t80)
REVERT: B   92 THR cc_start: 0.8833 (m) cc_final: 0.8386 (p)
REVERT: B  110 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7436 (pp20)
REVERT: C   42 LEU cc_start: 0.8356 (mt) cc_final: 0.8075 (mt)
REVERT: C  104 MET cc_start: 0.9346 (ptm) cc_final: 0.9114 (ptm)
REVERT: C  110 GLU cc_start: 0.8695 (tp30) cc_final: 0.8101 (tp30)
REVERT: C  176 ASN cc_start: 0.9011 (m110) cc_final: 0.8747 (p0)
REVERT: H   66 ASP cc_start: 0.7661 (p0) cc_final: 0.7349 (p0)
REVERT: H   97 MET cc_start: 0.8432 (mmm) cc_final: 0.7858 (mmm)
REVERT: H  133 ASP cc_start: 0.8188 (m-30) cc_final: 0.7945 (m-30)
REVERT: K   88 HIS cc_start: 0.8308 (m-70) cc_final: 0.7882 (m-70)
REVERT: G   60 TYR cc_start: 0.9018 (t80) cc_final: 0.8779 (t80)
REVERT: G   66 ASP cc_start: 0.8609 (p0) cc_final: 0.8355 (p0)
REVERT: G  102 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7725 (tp30)
  outliers start: 28
  outliers final: 19
  residues processed: 175
  average time/residue: 0.0914
  time to fit residues: 24.7579
Evaluate side-chains
  165 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 145
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   86 MET
Chi-restraints excluded: chain B residue  110 GLU
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain H residue  130 SER
Chi-restraints excluded: chain H residue  159 ILE
Chi-restraints excluded: chain I residue   20 MET
Chi-restraints excluded: chain I residue   58 LEU
Chi-restraints excluded: chain I residue  113 ILE
Chi-restraints excluded: chain K residue   15 THR
Chi-restraints excluded: chain K residue   44 LEU
Chi-restraints excluded: chain K residue   79 VAL
Chi-restraints excluded: chain K residue   83 LEU
Chi-restraints excluded: chain K residue  111 SER
Chi-restraints excluded: chain G residue   15 THR
Chi-restraints excluded: chain G residue   52 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 124 optimal weight:    0.1980
   chunk 38 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 5 optimal weight:    0.5980
   chunk 120 optimal weight:    6.9990
   chunk 32 optimal weight:    0.9980
   chunk 65 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 117 optimal weight:    0.9980
   chunk 80 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
H 173 GLN
** K   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 173 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.099930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.078528 restraints weight = 34111.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.081196 restraints weight = 17791.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.082924 restraints weight = 11876.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.084047 restraints weight = 9191.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.084631 restraints weight = 7809.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.3617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  11684  Z= 0.098
  Angle     :  0.506  10.619  15652  Z= 0.256
  Chirality :  0.036   0.161   1821
  Planarity :  0.002   0.031   1989
  Dihedral  :  3.488  17.728   1542
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 14.94 %
    Favored  : 82.87 %
  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 aren not related in a simple way.
  whole:  1.75 (0.24), residues: 1387
  helix:  1.77 (0.17), residues: 1082
  sheet:  None (None), residues: 0
  loop : -1.02 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 162 
 TYR   0.010   0.001   TYR C 101 
 PHE   0.024   0.001   PHE B 181 
 HIS   0.001   0.000   HIS H  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00223 (11684)
  covalent geometry    : angle       0.50579 (15652)
  hydrogen bonds       : bond        0.02612 (  652)
  hydrogen bonds       : angle       3.43377 ( 1941)

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

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

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 162
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ASN cc_start: 0.8677 (t0) cc_final: 0.8427 (m110)
REVERT: A  148 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8649 (mtmm)
REVERT: B   92 THR cc_start: 0.8806 (m) cc_final: 0.8392 (p)
REVERT: C   42 LEU cc_start: 0.8268 (mt) cc_final: 0.7971 (mt)
REVERT: C  104 MET cc_start: 0.9276 (ptm) cc_final: 0.9041 (ptm)
REVERT: C  110 GLU cc_start: 0.8571 (tp30) cc_final: 0.8020 (tp30)
REVERT: H   66 ASP cc_start: 0.7753 (p0) cc_final: 0.7442 (p0)
REVERT: H   97 MET cc_start: 0.8374 (mmm) cc_final: 0.7748 (mmm)
REVERT: K   88 HIS cc_start: 0.8256 (m-70) cc_final: 0.7970 (m-70)
REVERT: G   60 TYR cc_start: 0.9051 (t80) cc_final: 0.8809 (t80)
REVERT: G   66 ASP cc_start: 0.8524 (p0) cc_final: 0.8278 (p0)
REVERT: G  102 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7765 (tp30)
  outliers start: 29
  outliers final: 18
  residues processed: 182
  average time/residue: 0.0833
  time to fit residues: 23.5138
Evaluate side-chains
  169 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 150
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   86 MET
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain H residue  130 SER
Chi-restraints excluded: chain H residue  159 ILE
Chi-restraints excluded: chain H residue  164 LEU
Chi-restraints excluded: chain I residue   20 MET
Chi-restraints excluded: chain I residue   58 LEU
Chi-restraints excluded: chain J residue   33 VAL
Chi-restraints excluded: chain K residue   15 THR
Chi-restraints excluded: chain K residue   79 VAL
Chi-restraints excluded: chain K residue  111 SER
Chi-restraints excluded: chain G residue   15 THR
Chi-restraints excluded: chain G residue   52 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 11 optimal weight:    8.9990
   chunk 99 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 47 optimal weight:   10.0000
   chunk 6 optimal weight:    1.9990
   chunk 50 optimal weight:    4.9990
   chunk 70 optimal weight:    4.9990
   chunk 89 optimal weight:    1.9990
   chunk 124 optimal weight:    0.5980
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
** K   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.100352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.079355 restraints weight = 31623.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.081882 restraints weight = 16617.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.083538 restraints weight = 11120.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.084593 restraints weight = 8620.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.085236 restraints weight = 7327.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.3710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11684  Z= 0.144
  Angle     :  0.563  16.390  15652  Z= 0.283
  Chirality :  0.037   0.148   1821
  Planarity :  0.003   0.046   1989
  Dihedral  :  3.616  17.144   1542
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 15.09 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.70 (0.24), residues: 1387
  helix:  1.75 (0.17), residues: 1079
  sheet:  None (None), residues: 0
  loop : -1.09 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 161 
 TYR   0.038   0.001   TYR A 101 
 PHE   0.020   0.001   PHE I 114 
 HIS   0.002   0.001   HIS I 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (11684)
  covalent geometry    : angle       0.56349 (15652)
  hydrogen bonds       : bond        0.03183 (  652)
  hydrogen bonds       : angle       3.70793 ( 1941)

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

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

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 149
  time to evaluate  : 0.354 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ASN cc_start: 0.8729 (t0) cc_final: 0.8476 (m110)
REVERT: B   92 THR cc_start: 0.8790 (m) cc_final: 0.8382 (p)
REVERT: C   42 LEU cc_start: 0.8433 (mt) cc_final: 0.8196 (mt)
REVERT: C   78 TYR cc_start: 0.8942 (m-80) cc_final: 0.8551 (m-10)
REVERT: C  104 MET cc_start: 0.9250 (ptm) cc_final: 0.9023 (ptm)
REVERT: C  110 GLU cc_start: 0.8445 (tp30) cc_final: 0.7917 (tp30)
REVERT: H   66 ASP cc_start: 0.7811 (p0) cc_final: 0.7500 (p0)
REVERT: H   97 MET cc_start: 0.8429 (mmm) cc_final: 0.7783 (mmm)
REVERT: K   88 HIS cc_start: 0.8131 (m-70) cc_final: 0.7837 (m-70)
REVERT: G   66 ASP cc_start: 0.8527 (p0) cc_final: 0.8227 (p0)
REVERT: G  102 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7821 (tp30)
REVERT: G  120 MET cc_start: 0.8220 (ppp) cc_final: 0.7929 (ppp)
REVERT: G  125 ILE cc_start: 0.4331 (OUTLIER) cc_final: 0.3958 (mt)
  outliers start: 37
  outliers final: 25
  residues processed: 172
  average time/residue: 0.0903
  time to fit residues: 23.7942
Evaluate side-chains
  169 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 143
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   86 MET
Chi-restraints excluded: chain C residue    6 ASN
Chi-restraints excluded: chain C residue   97 GLN
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain H residue   44 LEU
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain H residue  130 SER
Chi-restraints excluded: chain H residue  159 ILE
Chi-restraints excluded: chain H residue  164 LEU
Chi-restraints excluded: chain I residue   20 MET
Chi-restraints excluded: chain I residue   58 LEU
Chi-restraints excluded: chain J residue   33 VAL
Chi-restraints excluded: chain J residue  175 VAL
Chi-restraints excluded: chain K residue   15 THR
Chi-restraints excluded: chain K residue   44 LEU
Chi-restraints excluded: chain K residue   79 VAL
Chi-restraints excluded: chain K residue  111 SER
Chi-restraints excluded: chain K residue  164 LEU
Chi-restraints excluded: chain G residue    6 ILE
Chi-restraints excluded: chain G residue   15 THR
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue  125 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 111 optimal weight:    9.9990
   chunk 117 optimal weight:    0.1980
   chunk 101 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 127 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 128 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 75 optimal weight:   10.0000
   chunk 113 optimal weight:    6.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** K   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 169 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.101458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.080306 restraints weight = 31680.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.082964 restraints weight = 16142.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.084704 restraints weight = 10607.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.085811 restraints weight = 8130.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.086502 restraints weight = 6865.499|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.3818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11684  Z= 0.112
  Angle     :  0.537  16.412  15652  Z= 0.271
  Chirality :  0.036   0.153   1821
  Planarity :  0.003   0.034   1989
  Dihedral  :  3.584  17.121   1542
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 15.39 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.71 (0.24), residues: 1387
  helix:  1.74 (0.17), residues: 1080
  sheet:  None (None), residues: 0
  loop : -1.03 (0.34), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 161 
 TYR   0.032   0.001   TYR A 101 
 PHE   0.020   0.001   PHE C 181 
 HIS   0.002   0.000   HIS H  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (11684)
  covalent geometry    : angle       0.53662 (15652)
  hydrogen bonds       : bond        0.02846 (  652)
  hydrogen bonds       : angle       3.58356 ( 1941)

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

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

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 154
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ASN cc_start: 0.8706 (t0) cc_final: 0.8453 (m110)
REVERT: B   43 MET cc_start: 0.7361 (mtt) cc_final: 0.7150 (mpp)
REVERT: B   92 THR cc_start: 0.8800 (m) cc_final: 0.8378 (p)
REVERT: C   42 LEU cc_start: 0.8341 (mt) cc_final: 0.8121 (mt)
REVERT: C   78 TYR cc_start: 0.8950 (m-80) cc_final: 0.8545 (m-10)
REVERT: C  104 MET cc_start: 0.9253 (ptm) cc_final: 0.9024 (ptm)
REVERT: C  110 GLU cc_start: 0.8510 (tp30) cc_final: 0.8035 (tp30)
REVERT: H   66 ASP cc_start: 0.7799 (p0) cc_final: 0.7454 (p0)
REVERT: H   97 MET cc_start: 0.8440 (mmm) cc_final: 0.7776 (mmm)
REVERT: K    1 MET cc_start: 0.6257 (mmp) cc_final: 0.6035 (mmp)
REVERT: K   88 HIS cc_start: 0.8134 (m-70) cc_final: 0.7847 (m-70)
REVERT: G   66 ASP cc_start: 0.8523 (p0) cc_final: 0.8296 (p0)
REVERT: G  102 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7804 (tp30)
REVERT: G  120 MET cc_start: 0.8272 (ppp) cc_final: 0.7958 (ppp)
REVERT: G  125 ILE cc_start: 0.4405 (OUTLIER) cc_final: 0.3988 (mt)
  outliers start: 33
  outliers final: 24
  residues processed: 175
  average time/residue: 0.0818
  time to fit residues: 22.2753
Evaluate side-chains
  170 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 145
  time to evaluate  : 0.521 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   86 MET
Chi-restraints excluded: chain C residue    6 ASN
Chi-restraints excluded: chain C residue   97 GLN
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain H residue   44 LEU
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain H residue  130 SER
Chi-restraints excluded: chain H residue  159 ILE
Chi-restraints excluded: chain I residue   20 MET
Chi-restraints excluded: chain I residue   58 LEU
Chi-restraints excluded: chain I residue   91 SER
Chi-restraints excluded: chain J residue   33 VAL
Chi-restraints excluded: chain J residue  175 VAL
Chi-restraints excluded: chain K residue   15 THR
Chi-restraints excluded: chain K residue   79 VAL
Chi-restraints excluded: chain K residue  111 SER
Chi-restraints excluded: chain K residue  164 LEU
Chi-restraints excluded: chain G residue    6 ILE
Chi-restraints excluded: chain G residue   15 THR
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue  125 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 12 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 120 optimal weight:    2.9990
   chunk 98 optimal weight:    0.7980
   chunk 135 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 112 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 138 optimal weight:    5.9990
   chunk 118 optimal weight:    0.7980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** K   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G   7 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.101050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.079927 restraints weight = 31585.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.082560 restraints weight = 16195.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.084310 restraints weight = 10671.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.085394 restraints weight = 8178.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.085977 restraints weight = 6919.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.3928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11684  Z= 0.114
  Angle     :  0.556  16.775  15652  Z= 0.278
  Chirality :  0.037   0.163   1821
  Planarity :  0.003   0.028   1989
  Dihedral  :  3.574  16.210   1542
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 16.38 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.24), residues: 1387
  helix:  1.72 (0.17), residues: 1081
  sheet:  None (None), residues: 0
  loop : -1.02 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 161 
 TYR   0.036   0.001   TYR A 101 
 PHE   0.019   0.001   PHE C  24 
 HIS   0.002   0.000   HIS H  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (11684)
  covalent geometry    : angle       0.55616 (15652)
  hydrogen bonds       : bond        0.02891 (  652)
  hydrogen bonds       : angle       3.57680 ( 1941)

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

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

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 146
  time to evaluate  : 0.623 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ASN cc_start: 0.8713 (t0) cc_final: 0.8453 (m110)
REVERT: B   92 THR cc_start: 0.8827 (m) cc_final: 0.8411 (p)
REVERT: C   42 LEU cc_start: 0.8332 (mt) cc_final: 0.8060 (mt)
REVERT: C   78 TYR cc_start: 0.8949 (m-80) cc_final: 0.8546 (m-10)
REVERT: C  104 MET cc_start: 0.9263 (ptm) cc_final: 0.9033 (ptm)
REVERT: C  110 GLU cc_start: 0.8516 (tp30) cc_final: 0.8062 (tp30)
REVERT: C  146 MET cc_start: 0.8854 (tpp) cc_final: 0.8491 (tmm)
REVERT: H   66 ASP cc_start: 0.7792 (p0) cc_final: 0.7452 (p0)
REVERT: H  116 MET cc_start: 0.8948 (mmm) cc_final: 0.8633 (mmt)
REVERT: K   88 HIS cc_start: 0.8106 (m-70) cc_final: 0.7779 (m-70)
REVERT: G   66 ASP cc_start: 0.8510 (p0) cc_final: 0.8286 (p0)
REVERT: G  102 GLU cc_start: 0.8114 (mm-30) cc_final: 0.7774 (tp30)
REVERT: G  120 MET cc_start: 0.8281 (ppp) cc_final: 0.7948 (ppp)
REVERT: G  125 ILE cc_start: 0.4444 (OUTLIER) cc_final: 0.4007 (mt)
  outliers start: 24
  outliers final: 23
  residues processed: 162
  average time/residue: 0.0927
  time to fit residues: 23.1543
Evaluate side-chains
  166 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 142
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   86 MET
Chi-restraints excluded: chain C residue    6 ASN
Chi-restraints excluded: chain C residue   97 GLN
Chi-restraints excluded: chain C residue  167 ILE
Chi-restraints excluded: chain H residue   44 LEU
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain H residue  130 SER
Chi-restraints excluded: chain H residue  159 ILE
Chi-restraints excluded: chain H residue  164 LEU
Chi-restraints excluded: chain I residue   20 MET
Chi-restraints excluded: chain I residue   58 LEU
Chi-restraints excluded: chain J residue   33 VAL
Chi-restraints excluded: chain J residue  175 VAL
Chi-restraints excluded: chain K residue   15 THR
Chi-restraints excluded: chain K residue   79 VAL
Chi-restraints excluded: chain K residue  111 SER
Chi-restraints excluded: chain K residue  164 LEU
Chi-restraints excluded: chain G residue   15 THR
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue  125 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 75 optimal weight:    7.9990
   chunk 56 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 24 optimal weight:    0.8980
   chunk 112 optimal weight:   10.0000
   chunk 82 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
** K   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.100565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.079408 restraints weight = 31743.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.082044 restraints weight = 16264.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.083767 restraints weight = 10700.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.084827 restraints weight = 8203.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.085403 restraints weight = 6943.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3526
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.3978

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  11684  Z= 0.127
  Angle     :  0.577  16.577  15652  Z= 0.286
  Chirality :  0.037   0.160   1821
  Planarity :  0.003   0.028   1989
  Dihedral  :  3.609  18.708   1542
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 16.00 %
    Favored  : 81.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.70 (0.24), residues: 1387
  helix:  1.73 (0.17), residues: 1083
  sheet:  None (None), residues: 0
  loop : -1.05 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 161 
 TYR   0.036   0.001   TYR K  93 
 PHE   0.015   0.001   PHE I 114 
 HIS   0.002   0.000   HIS H  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (11684)
  covalent geometry    : angle       0.57740 (15652)
  hydrogen bonds       : bond        0.02993 (  652)
  hydrogen bonds       : angle       3.62221 ( 1941)

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

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

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2774 Ramachandran restraints generated.
    1387 Oldfield, 0 Emsley, 1387 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 143
  time to evaluate  : 0.502 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 ASN cc_start: 0.8726 (t0) cc_final: 0.8463 (m110)
REVERT: B   92 THR cc_start: 0.8831 (m) cc_final: 0.8416 (p)
REVERT: C   42 LEU cc_start: 0.8377 (mt) cc_final: 0.8128 (mt)
REVERT: C   78 TYR cc_start: 0.8959 (m-80) cc_final: 0.8560 (m-10)
REVERT: C  104 MET cc_start: 0.9269 (ptm) cc_final: 0.9044 (ptm)
REVERT: C  110 GLU cc_start: 0.8524 (tp30) cc_final: 0.8060 (tp30)
REVERT: C  146 MET cc_start: 0.8804 (tpp) cc_final: 0.8547 (tmm)
REVERT: H   66 ASP cc_start: 0.7801 (p0) cc_final: 0.7468 (p0)
REVERT: H   97 MET cc_start: 0.8271 (mmm) cc_final: 0.7734 (mmm)
REVERT: I  116 MET cc_start: 0.8711 (mmm) cc_final: 0.8402 (mmt)
REVERT: K   88 HIS cc_start: 0.8107 (m-70) cc_final: 0.7779 (m-70)
REVERT: G   66 ASP cc_start: 0.8514 (p0) cc_final: 0.8208 (p0)
REVERT: G  102 GLU cc_start: 0.8117 (mm-30) cc_final: 0.7779 (tp30)
REVERT: G  120 MET cc_start: 0.8301 (ppp) cc_final: 0.7942 (ppp)
REVERT: G  125 ILE cc_start: 0.4468 (OUTLIER) cc_final: 0.4031 (mt)
  outliers start: 29
  outliers final: 23
  residues processed: 164
  average time/residue: 0.0876
  time to fit residues: 22.3540
Evaluate side-chains
  166 residues out of total 1319 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 142
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  181 PHE
Chi-restraints excluded: chain B residue   66 LEU
Chi-restraints excluded: chain B residue   81 THR
Chi-restraints excluded: chain B residue   86 MET
Chi-restraints excluded: chain C residue    6 ASN
Chi-restraints excluded: chain C residue   97 GLN
Chi-restraints excluded: chain H residue   59 LEU
Chi-restraints excluded: chain H residue  130 SER
Chi-restraints excluded: chain H residue  159 ILE
Chi-restraints excluded: chain H residue  164 LEU
Chi-restraints excluded: chain I residue   20 MET
Chi-restraints excluded: chain I residue   58 LEU
Chi-restraints excluded: chain I residue   91 SER
Chi-restraints excluded: chain J residue   33 VAL
Chi-restraints excluded: chain J residue  175 VAL
Chi-restraints excluded: chain K residue   15 THR
Chi-restraints excluded: chain K residue   79 VAL
Chi-restraints excluded: chain K residue   83 LEU
Chi-restraints excluded: chain K residue  111 SER
Chi-restraints excluded: chain K residue  164 LEU
Chi-restraints excluded: chain G residue   15 THR
Chi-restraints excluded: chain G residue   52 VAL
Chi-restraints excluded: chain G residue  125 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 30 optimal weight:    0.6980
   chunk 126 optimal weight:    0.3980
   chunk 67 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 49 optimal weight:    0.4980
   chunk 94 optimal weight:    0.8980
   chunk 138 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 71 optimal weight:    0.1980
   chunk 113 optimal weight:    0.6980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
C  80 ASN
** K   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.097928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.076060 restraints weight = 35626.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.078681 restraints weight = 18706.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.080428 restraints weight = 12563.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.081502 restraints weight = 9739.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.082242 restraints weight = 8304.878|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.4098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  11684  Z= 0.101
  Angle     :  0.569  16.790  15652  Z= 0.282
  Chirality :  0.036   0.160   1821
  Planarity :  0.003   0.035   1989
  Dihedral  :  3.512  19.504   1542
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 16.30 %
    Favored  : 81.96 %
  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 aren not related in a simple way.
  whole:  1.79 (0.24), residues: 1387
  helix:  1.80 (0.17), residues: 1081
  sheet:  None (None), residues: 0
  loop : -1.00 (0.34), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  61 
 TYR   0.032   0.001   TYR A 101 
 PHE   0.022   0.001   PHE C  24 
 HIS   0.002   0.000   HIS H  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (11684)
  covalent geometry    : angle       0.56915 (15652)
  hydrogen bonds       : bond        0.02600 (  652)
  hydrogen bonds       : angle       3.43107 ( 1941)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2023.07 seconds
wall clock time: 35 minutes 43.92 seconds (2143.92 seconds total)