Starting phenix.real_space_refine
on Wed Feb  4 19:08:43 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kq2_62494/02_2026/9kq2_62494.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kq2_62494/02_2026/9kq2_62494.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kq2_62494/02_2026/9kq2_62494.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kq2_62494/02_2026/9kq2_62494.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kq2_62494/02_2026/9kq2_62494.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kq2_62494/02_2026/9kq2_62494.map"
  }
  resolution = 3.9
  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=   0.023 sd=   0.527
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     288      5.49       5
     S      23      5.16       5
     C    6955      2.51       5
     N    2349      2.21       5
     O    2897      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12514
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 802
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 662
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 662
          Classifications: {'peptide': 83}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "C"
      Number of atoms: 786
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 102, 786
          Classifications: {'peptide': 102}
          Link IDs: {'PTRANS': 5, 'TRANS': 96}
    Chain: "D"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "E"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 619
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "G"
      Number of atoms: 777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 777
          Classifications: {'peptide': 101}
          Link IDs: {'PTRANS': 4, 'TRANS': 96}
    Chain: "H"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "I"
      Number of atoms: 2935
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 144, 2935
          Classifications: {'DNA': 144}
          Link IDs: {'rna3p': 143}
    Chain: "J"
      Number of atoms: 2987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2987
          Classifications: {'DNA': 145}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 144}
    Chain: "K"
      Number of atoms: 672
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 672
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 5, 'TRANS': 77}
    Chain: "K"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  11993  SG  CYS K  31      72.905  49.898  81.288  1.00186.06           S
  ATOM  12143  SG  CYS K  51      74.420  46.621  80.056  1.00181.69           S
  ATOM  12167  SG  CYS K  54      71.816  46.577  82.781  1.00184.22           S
  ATOM  11884  SG  CYS K  16      85.402  49.184  74.664  1.00245.85           S
  ATOM  11902  SG  CYS K  19      86.439  47.014  72.389  1.00255.12           S
  ATOM  12032  SG  CYS K  36      85.010  50.023  72.401  1.00225.54           S
  ATOM  12054  SG  CYS K  39      82.711  48.783  71.742  1.00 30.00           S

  Time building chain proxies: 2.27, per 1000 atoms: 0.18
  Number of scatterers: 12514
  At special positions: 0
  Unit cell: (110.21, 116.63, 121.98, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      2     29.99
     S      23     16.00
     P     288     15.00
     O    2897      8.00
     N    2349      7.00
     C    6955      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: 0.72
  Conformation dependent library (CDL) restraints added in 288.9 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 201 "
        pdb="ZN    ZN K 201 " - pdb=" SG  CYS K  54 "
        pdb="ZN    ZN K 201 " - pdb=" SG  CYS K  51 "
        pdb="ZN    ZN K 201 " - pdb=" SG  CYS K  31 "
      pdb="  ZN K 202 "
        pdb="ZN    ZN K 202 " - pdb=" SG  CYS K  36 "
        pdb="ZN    ZN K 202 " - pdb=" SG  CYS K  19 "
        pdb="ZN    ZN K 202 " - pdb=" SG  CYS K  39 "
        pdb="ZN    ZN K 202 " - pdb=" SG  CYS K  16 "
      Number of angles added : 6


  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1560

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 9 sheets defined
      72.3% alpha, 2.4% beta
      133 base pairs and 234 stacking pairs defined.
    Time for finding SS restraints: 1.70
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.819A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.502A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 77
      removed outlier: 4.053A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 17 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.453A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.530A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
    Processing helix  chain 'D' and resid 87 through 99
    Processing helix  chain 'D' and resid 100 through 121
      removed outlier: 3.732A  pdb=" N   ALA D 121 " --> pdb=" O   LYS D 117 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.564A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.541A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
      removed outlier: 3.694A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 77
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 36
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.585A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   LEU G  65 " --> pdb=" O   GLU G  61 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 34 through 46
    Processing helix  chain 'H' and resid 52 through 81
    Processing helix  chain 'H' and resid 87 through 99
    Processing helix  chain 'H' and resid 100 through 121
    Processing helix  chain 'K' and resid 36 through 44
    Processing helix  chain 'K' and resid 58 through 69
    Processing helix  chain 'K' and resid 73 through 84
      removed outlier: 3.517A  pdb=" N   ILE K  79 " --> pdb=" O   GLU K  75 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 84 through 93
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.704A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.278A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.038A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.277A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AA9, first strand: chain 'K' and resid 27 through 28

    442 hydrogen bonds defined for protein.
    1314 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      339 hydrogen bonds
      674 hydrogen bond angles
      0 basepair planarities
      133 basepair parallelities
      234 stacking parallelities
  Total time for adding SS restraints: 1.77

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2912
        1.34 -     1.46: 4302
        1.46 -     1.58: 5503
        1.58 -     1.70: 575
        1.70 -     1.82: 34
  Bond restraints: 13326
  Sorted by residual:
  bond pdb=" C1'  DG I -70 "
       pdb=" N9   DG I -70 "
    ideal  model  delta    sigma   weight residual
    1.460  1.386  0.074 2.00e-02 2.50e+03 1.38e+01
  bond pdb=" C1'  DA I  72 "
       pdb=" N9   DA I  72 "
    ideal  model  delta    sigma   weight residual
    1.460  1.388  0.072 2.00e-02 2.50e+03 1.28e+01
  bond pdb=" C1'  DA J  72 "
       pdb=" N9   DA J  72 "
    ideal  model  delta    sigma   weight residual
    1.460  1.392  0.068 2.00e-02 2.50e+03 1.17e+01
  bond pdb=" C   GLU K  25 "
       pdb=" O   GLU K  25 "
    ideal  model  delta    sigma   weight residual
    1.234  1.218  0.016 5.00e-03 4.00e+04 1.06e+01
  bond pdb=" C1'  DG J -70 "
       pdb=" N9   DG J -70 "
    ideal  model  delta    sigma   weight residual
    1.460  1.397  0.063 2.00e-02 2.50e+03 9.83e+00
  ... (remaining 13321 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 18931
        2.27 -     4.54: 282
        4.54 -     6.80: 23
        6.80 -     9.07: 7
        9.07 -    11.34: 1
  Bond angle restraints: 19244
  Sorted by residual:
  angle pdb=" N   PRO K  38 "
        pdb=" CA  PRO K  38 "
        pdb=" C   PRO K  38 "
      ideal   model   delta    sigma   weight residual
     113.65  102.31   11.34 1.35e+00 5.49e-01 7.06e+01
  angle pdb=" N   VAL A 117 "
        pdb=" CA  VAL A 117 "
        pdb=" C   VAL A 117 "
      ideal   model   delta    sigma   weight residual
     113.71  108.10    5.61 9.50e-01 1.11e+00 3.48e+01
  angle pdb=" C   CYS K  39 "
        pdb=" CA  CYS K  39 "
        pdb=" CB  CYS K  39 "
      ideal   model   delta    sigma   weight residual
     109.67  117.84   -8.17 2.01e+00 2.48e-01 1.65e+01
  angle pdb=" C   CYS K  19 "
        pdb=" N   MET K  20 "
        pdb=" CA  MET K  20 "
      ideal   model   delta    sigma   weight residual
     121.54  128.88   -7.34 1.91e+00 2.74e-01 1.48e+01
  angle pdb=" CA  CYS K  16 "
        pdb=" CB  CYS K  16 "
        pdb=" SG  CYS K  16 "
      ideal   model   delta    sigma   weight residual
     114.40  122.91   -8.51 2.30e+00 1.89e-01 1.37e+01
  ... (remaining 19239 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.48: 5746
       32.48 -    64.96: 1504
       64.96 -    97.44: 23
       97.44 -   129.92: 3
      129.92 -   162.40: 1
  Dihedral angle restraints: 7277
    sinusoidal: 4865
      harmonic: 2412
  Sorted by residual:
  dihedral pdb=" CA  GLN G 112 "
           pdb=" C   GLN G 112 "
           pdb=" N   SER G 113 "
           pdb=" CA  SER G 113 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.61  -25.39     0      5.00e+00 4.00e-02 2.58e+01
  dihedral pdb=" CA  CYS K  36 "
           pdb=" C   CYS K  36 "
           pdb=" N   LYS K  37 "
           pdb=" CA  LYS K  37 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.68  -23.32     0      5.00e+00 4.00e-02 2.18e+01
  dihedral pdb=" CA  ASP C  90 "
           pdb=" C   ASP C  90 "
           pdb=" N   GLU C  91 "
           pdb=" CA  GLU C  91 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.70  -21.30     0      5.00e+00 4.00e-02 1.82e+01
  ... (remaining 7274 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1618
       0.039 -    0.077: 448
       0.077 -    0.116: 103
       0.116 -    0.154: 19
       0.154 -    0.192: 5
  Chirality restraints: 2193
  Sorted by residual:
  chirality pdb=" C1'  DG I -70 "
            pdb=" O4'  DG I -70 "
            pdb=" C2'  DG I -70 "
            pdb=" N9   DG I -70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.42    2.23    0.19 2.00e-01 2.50e+01 9.26e-01
  chirality pdb=" CA  CYS K  39 "
            pdb=" N   CYS K  39 "
            pdb=" C   CYS K  39 "
            pdb=" CB  CYS K  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.12e-01
  chirality pdb=" CA  ILE B  46 "
            pdb=" N   ILE B  46 "
            pdb=" C   ILE B  46 "
            pdb=" CB  ILE B  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.50e-01
  ... (remaining 2190 not shown)

  Planarity restraints: 1434
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN K  41 "    0.021 2.00e-02 2.50e+03   4.30e-02 1.85e+01
        pdb=" CD  GLN K  41 "   -0.074 2.00e-02 2.50e+03
        pdb=" OE1 GLN K  41 "    0.029 2.00e-02 2.50e+03
        pdb=" NE2 GLN K  41 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C  25 "    0.045 5.00e-02 4.00e+02   6.93e-02 7.69e+00
        pdb=" N   PRO C  26 "   -0.120 5.00e-02 4.00e+02
        pdb=" CA  PRO C  26 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO C  26 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  88 "    0.013 2.00e-02 2.50e+03   1.81e-02 6.55e+00
        pdb=" CG  TYR B  88 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  88 "   -0.001 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  88 "    0.018 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  88 "    0.020 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  88 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  88 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR B  88 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1431 not shown)

  Histogram of nonbonded interaction distances:
        2.04 -     2.61: 147
        2.61 -     3.18: 10011
        3.18 -     3.76: 22462
        3.76 -     4.33: 28467
        4.33 -     4.90: 41926
  Nonbonded interactions: 103013
  Sorted by model distance:
  nonbonded pdb=" CB  GLU K  21 "
            pdb=" NH1 ARG K  91 "
     model   vdw
     2.041 3.520
  nonbonded pdb=" OE2 GLU E  73 "
            pdb=" ND2 ASN F  25 "
     model   vdw
     2.106 3.120
  nonbonded pdb=" OG1 THR G  16 "
            pdb=" OG  SER G  19 "
     model   vdw
     2.143 3.040
  nonbonded pdb=" OE1 GLU C  64 "
            pdb=" OG  SER K  60 "
     model   vdw
     2.159 3.040
  nonbonded pdb=" N   GLU D 102 "
            pdb=" OE1 GLU D 102 "
     model   vdw
     2.183 3.120
  ... (remaining 103008 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 39 through 134)
  selection = (chain 'E' and resid 39 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 25 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 16 through 114)
  selection = (chain 'G' and resid 16 through 114)
}
ncs_group {
  reference = (chain 'D' and resid 29 through 121)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             0.970
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.290
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  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:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.725  13333  Z= 0.323
  Angle     :  0.835  35.588  19250  Z= 0.445
  Chirality :  0.038   0.192   2193
  Planarity :  0.006   0.069   1434
  Dihedral  : 27.504 162.403   5717
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 13.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  : 23.86 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.52 (0.28), residues: 811
  helix:  1.80 (0.21), residues: 577
  sheet:  None (None), residues: 0
  loop : -1.02 (0.36), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D  76 
 TYR   0.041   0.002   TYR B  88 
 PHE   0.022   0.002   PHE K  40 
 TRP   0.007   0.002   TRP K  61 
 HIS   0.010   0.002   HIS D  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 (13326)
  covalent geometry    : angle       0.72408 (19244)
  hydrogen bonds       : bond        0.11042 (  781)
  hydrogen bonds       : angle       5.03240 ( 1988)
  metal coordination   : bond        0.28246 (    7)
  metal coordination   : angle      23.53440 (    6)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 168
  time to evaluate  : 0.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   82 LYS cc_start: 0.8551 (mttt) cc_final: 0.8271 (mptt)
REVERT: D  105 LYS cc_start: 0.8717 (tptm) cc_final: 0.8196 (mptt)
REVERT: E   97 GLU cc_start: 0.8183 (tp30) cc_final: 0.7940 (tp30)
REVERT: F   80 THR cc_start: 0.8982 (m) cc_final: 0.8505 (p)
REVERT: G   41 GLU cc_start: 0.7839 (tp30) cc_final: 0.7634 (tp30)
REVERT: G   76 THR cc_start: 0.9036 (m) cc_final: 0.8607 (t)
REVERT: G   90 ASP cc_start: 0.8225 (t0) cc_final: 0.7929 (t0)
REVERT: H  113 LYS cc_start: 0.8871 (ttpt) cc_final: 0.8569 (tttm)
REVERT: H  116 THR cc_start: 0.9082 (m) cc_final: 0.8674 (p)
  outliers start: 4
  outliers final: 3
  residues processed: 171
  average time/residue: 0.1378
  time to fit residues: 31.1528
Evaluate side-chains
  159 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 156
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 ASP
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain D residue   51 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.0030
   chunk 106 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    0.7190

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

Flipped N/Q/H residues before XYZ refinement:
G  38 ASN
G 112 GLN
** K  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.062593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.050629 restraints weight = 51702.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.051889 restraints weight = 26252.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.052666 restraints weight = 17364.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2782 r_free = 0.2782 target = 0.053096 restraints weight = 13593.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 58)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.053378 restraints weight = 11808.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.2784
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2784
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2783 r_free = 0.2783    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2783
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8469
moved from start:          0.1306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13333  Z= 0.176
  Angle     :  0.618  13.215  19250  Z= 0.356
  Chirality :  0.035   0.159   2193
  Planarity :  0.004   0.045   1434
  Dihedral  : 29.730 159.720   4087
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 23.14 %
    Favored  : 74.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.16 (0.29), residues: 811
  helix:  2.27 (0.21), residues: 580
  sheet:  None (None), residues: 0
  loop : -0.79 (0.37), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  76 
 TYR   0.028   0.002   TYR B  88 
 PHE   0.014   0.001   PHE K  40 
 TRP   0.003   0.001   TRP K  61 
 HIS   0.006   0.001   HIS K  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00372 (13326)
  covalent geometry    : angle       0.59573 (19244)
  hydrogen bonds       : bond        0.05185 (  781)
  hydrogen bonds       : angle       3.15448 ( 1988)
  metal coordination   : bond        0.00970 (    7)
  metal coordination   : angle       9.25192 (    6)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   48 ASP cc_start: 0.6764 (p0) cc_final: 0.6563 (p0)
REVERT: D   82 LYS cc_start: 0.8614 (mttt) cc_final: 0.8291 (mptt)
REVERT: D  105 LYS cc_start: 0.8728 (tptm) cc_final: 0.8165 (mptt)
REVERT: F   80 THR cc_start: 0.8998 (OUTLIER) cc_final: 0.8538 (p)
REVERT: G   35 ARG cc_start: 0.8707 (ttm-80) cc_final: 0.8354 (ttm-80)
REVERT: G   76 THR cc_start: 0.8989 (m) cc_final: 0.8615 (t)
REVERT: G   90 ASP cc_start: 0.8096 (t0) cc_final: 0.7760 (t0)
REVERT: H   48 ASP cc_start: 0.8561 (p0) cc_final: 0.8345 (p0)
REVERT: H  113 LYS cc_start: 0.8872 (ttpt) cc_final: 0.8553 (tttm)
REVERT: H  116 THR cc_start: 0.9106 (m) cc_final: 0.8722 (p)
  outliers start: 17
  outliers final: 6
  residues processed: 175
  average time/residue: 0.1430
  time to fit residues: 32.7325
Evaluate side-chains
  166 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 159
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   78 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 72 optimal weight:    4.9990
   chunk 79 optimal weight:    3.9990
   chunk 13 optimal weight:    0.1980
   chunk 2 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 103 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 52 optimal weight:    6.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
D  60 ASN
E  68 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2820 r_free = 0.2820 target = 0.053238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2473 r_free = 0.2473 target = 0.041726 restraints weight = 52888.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2508 r_free = 0.2508 target = 0.042906 restraints weight = 26916.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2529 r_free = 0.2529 target = 0.043634 restraints weight = 17734.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2541 r_free = 0.2541 target = 0.044018 restraints weight = 13742.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.2549 r_free = 0.2549 target = 0.044311 restraints weight = 11958.630|
|-----------------------------------------------------------------------------|
r_work (final): 0.2546
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2546
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2546 r_free = 0.2546    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2546 r_free = 0.2546    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.2546
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8690
moved from start:          0.2847

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  13333  Z= 0.241
  Angle     :  0.681  16.975  19250  Z= 0.387
  Chirality :  0.039   0.166   2193
  Planarity :  0.006   0.095   1434
  Dihedral  : 29.898 160.011   4084
  Min Nonbonded Distance : 2.209

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 23.00 %
    Favored  : 73.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.01 (0.28), residues: 811
  helix:  2.20 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop : -0.92 (0.37), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D  76 
 TYR   0.027   0.002   TYR H  37 
 PHE   0.022   0.003   PHE K  40 
 TRP   0.004   0.001   TRP K  77 
 HIS   0.007   0.002   HIS K  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00529 (13326)
  covalent geometry    : angle       0.65115 (19244)
  hydrogen bonds       : bond        0.06727 (  781)
  hydrogen bonds       : angle       3.21863 ( 1988)
  metal coordination   : bond        0.01477 (    7)
  metal coordination   : angle      11.28963 (    6)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 160
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 THR cc_start: 0.8804 (m) cc_final: 0.8314 (p)
REVERT: B   67 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8376 (mtp180)
REVERT: B   92 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.6038 (ttm-80)
REVERT: D   82 LYS cc_start: 0.8577 (mttt) cc_final: 0.8325 (mmtt)
REVERT: D  105 LYS cc_start: 0.8935 (tptm) cc_final: 0.8272 (mptt)
REVERT: E   63 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8182 (mmp80)
REVERT: G   36 LYS cc_start: 0.8980 (mtpp) cc_final: 0.8439 (ttmm)
REVERT: G   76 THR cc_start: 0.9032 (m) cc_final: 0.8651 (t)
REVERT: G   90 ASP cc_start: 0.8223 (t0) cc_final: 0.7805 (t70)
REVERT: H   48 ASP cc_start: 0.8592 (p0) cc_final: 0.8352 (p0)
REVERT: H  113 LYS cc_start: 0.8898 (ttpt) cc_final: 0.8582 (tttm)
REVERT: H  116 THR cc_start: 0.9117 (m) cc_final: 0.8733 (p)
REVERT: K   41 GLN cc_start: 0.8981 (pp30) cc_final: 0.8777 (pp30)
  outliers start: 28
  outliers final: 13
  residues processed: 178
  average time/residue: 0.1456
  time to fit residues: 33.7105
Evaluate side-chains
  169 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 153
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   67 ARG
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain E residue   63 ARG
Chi-restraints excluded: chain F residue   49 LEU
Chi-restraints excluded: chain K residue   46 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 53 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0980
   chunk 57 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
D  60 ASN
** K  33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.054739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2528 r_free = 0.2528 target = 0.043341 restraints weight = 52378.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2562 r_free = 0.2562 target = 0.044517 restraints weight = 26620.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.2583 r_free = 0.2583 target = 0.045238 restraints weight = 17596.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.2595 r_free = 0.2595 target = 0.045679 restraints weight = 13714.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.045907 restraints weight = 11854.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.2598
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2598
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2598 r_free = 0.2598    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2598 r_free = 0.2598    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.2598
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8646
moved from start:          0.3110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13333  Z= 0.161
  Angle     :  0.585  15.806  19250  Z= 0.340
  Chirality :  0.034   0.168   2193
  Planarity :  0.004   0.043   1434
  Dihedral  : 29.731 160.832   4084
  Min Nonbonded Distance : 2.212

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 24.29 %
    Favored  : 73.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.45 (0.29), residues: 811
  helix:  2.53 (0.21), residues: 579
  sheet:  None (None), residues: 0
  loop : -0.82 (0.38), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C  99 
 TYR   0.016   0.001   TYR H  37 
 PHE   0.009   0.001   PHE E  78 
 TRP   0.005   0.001   TRP K  61 
 HIS   0.004   0.001   HIS K  33 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (13326)
  covalent geometry    : angle       0.56919 (19244)
  hydrogen bonds       : bond        0.04867 (  781)
  hydrogen bonds       : angle       2.95692 ( 1988)
  metal coordination   : bond        0.01172 (    7)
  metal coordination   : angle       7.77132 (    6)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 167
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 HIS cc_start: 0.8131 (t70) cc_final: 0.7375 (t70)
REVERT: A   41 TYR cc_start: 0.8319 (m-80) cc_final: 0.8048 (m-10)
REVERT: B   92 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.5934 (ttm-80)
REVERT: C   99 ARG cc_start: 0.7996 (ttp-170) cc_final: 0.7748 (mtp180)
REVERT: D   73 GLU cc_start: 0.7683 (tp30) cc_final: 0.7017 (tp30)
REVERT: D   82 LYS cc_start: 0.8523 (mttt) cc_final: 0.8039 (mmtt)
REVERT: D  105 LYS cc_start: 0.8817 (tptm) cc_final: 0.8221 (mptt)
REVERT: E   63 ARG cc_start: 0.8802 (OUTLIER) cc_final: 0.8035 (mmp80)
REVERT: F   80 THR cc_start: 0.9011 (m) cc_final: 0.8591 (p)
REVERT: G   36 LYS cc_start: 0.8986 (mtpp) cc_final: 0.8484 (ttmm)
REVERT: G   76 THR cc_start: 0.8971 (m) cc_final: 0.8628 (t)
REVERT: G   90 ASP cc_start: 0.8080 (t0) cc_final: 0.7688 (t0)
REVERT: H   48 ASP cc_start: 0.8515 (p0) cc_final: 0.8242 (p0)
REVERT: H  113 LYS cc_start: 0.8911 (ttpt) cc_final: 0.8634 (tttm)
REVERT: H  116 THR cc_start: 0.9126 (m) cc_final: 0.8797 (p)
REVERT: K   41 GLN cc_start: 0.8877 (pp30) cc_final: 0.8522 (pp30)
REVERT: K   46 LYS cc_start: 0.8617 (pttm) cc_final: 0.7930 (ptmm)
  outliers start: 16
  outliers final: 9
  residues processed: 177
  average time/residue: 0.1455
  time to fit residues: 33.8836
Evaluate side-chains
  166 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 155
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain E residue   63 ARG
Chi-restraints excluded: chain H residue   31 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 81 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 85 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9990
   chunk 86 optimal weight:    3.9990
   chunk 80 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
G  38 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.050880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.2420 r_free = 0.2420 target = 0.039672 restraints weight = 53006.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.2454 r_free = 0.2454 target = 0.040819 restraints weight = 27154.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.2475 r_free = 0.2475 target = 0.041505 restraints weight = 18019.186|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2487 r_free = 0.2487 target = 0.041862 restraints weight = 14076.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.2495 r_free = 0.2495 target = 0.042159 restraints weight = 12296.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.2490
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2490
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2490 r_free = 0.2490    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2490 r_free = 0.2490    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2490
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8736
moved from start:          0.3693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  13333  Z= 0.205
  Angle     :  0.619  12.020  19250  Z= 0.359
  Chirality :  0.036   0.181   2193
  Planarity :  0.005   0.045   1434
  Dihedral  : 29.630 162.491   4084
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 22.43 %
    Favored  : 74.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.39 (0.29), residues: 811
  helix:  2.49 (0.21), residues: 578
  sheet:  None (None), residues: 0
  loop : -0.85 (0.38), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A  40 
 TYR   0.021   0.002   TYR K  64 
 PHE   0.014   0.002   PHE E  78 
 TRP   0.004   0.001   TRP K  77 
 HIS   0.005   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 (13326)
  covalent geometry    : angle       0.60668 (19244)
  hydrogen bonds       : bond        0.05799 (  781)
  hydrogen bonds       : angle       3.03632 ( 1988)
  metal coordination   : bond        0.00887 (    7)
  metal coordination   : angle       7.00714 (    6)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 165
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 HIS cc_start: 0.8025 (t70) cc_final: 0.7320 (t70)
REVERT: A   41 TYR cc_start: 0.8309 (m-80) cc_final: 0.7955 (m-80)
REVERT: A  118 THR cc_start: 0.8820 (m) cc_final: 0.8270 (p)
REVERT: B   67 ARG cc_start: 0.8718 (OUTLIER) cc_final: 0.8351 (mtp180)
REVERT: B   92 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.6053 (ttm-80)
REVERT: C   99 ARG cc_start: 0.8045 (ttp-170) cc_final: 0.7724 (mtp180)
REVERT: D   73 GLU cc_start: 0.7624 (tp30) cc_final: 0.7278 (tp30)
REVERT: D   82 LYS cc_start: 0.8587 (mttt) cc_final: 0.8019 (mmtt)
REVERT: D   90 GLU cc_start: 0.8414 (mp0) cc_final: 0.8204 (mp0)
REVERT: D   91 ILE cc_start: 0.8810 (mt) cc_final: 0.8597 (mm)
REVERT: D  105 LYS cc_start: 0.8812 (tptm) cc_final: 0.8198 (mptt)
REVERT: F   80 THR cc_start: 0.9033 (m) cc_final: 0.8610 (p)
REVERT: G   36 LYS cc_start: 0.9114 (mtpp) cc_final: 0.8647 (ttmm)
REVERT: G   76 THR cc_start: 0.9014 (m) cc_final: 0.8693 (t)
REVERT: G   90 ASP cc_start: 0.8142 (t0) cc_final: 0.7823 (t70)
REVERT: H   48 ASP cc_start: 0.8514 (p0) cc_final: 0.8250 (p0)
REVERT: H   56 MET cc_start: 0.8742 (tpp) cc_final: 0.8488 (tpp)
REVERT: H  113 LYS cc_start: 0.8887 (ttpt) cc_final: 0.8596 (tttm)
REVERT: H  116 THR cc_start: 0.9168 (m) cc_final: 0.8807 (p)
  outliers start: 22
  outliers final: 17
  residues processed: 178
  average time/residue: 0.1303
  time to fit residues: 30.7955
Evaluate side-chains
  178 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 159
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   67 ARG
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain E residue  105 GLU
Chi-restraints excluded: chain F residue   29 ILE
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain K residue   20 MET
Chi-restraints excluded: chain K residue   39 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 52 optimal weight:    4.9990
   chunk 104 optimal weight:    6.9990
   chunk 70 optimal weight:    0.5980
   chunk 87 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   chunk 68 optimal weight:    0.8980
   chunk 63 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 96 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    1.6984

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
B  75 HIS
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.048486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2359 r_free = 0.2359 target = 0.037543 restraints weight = 53167.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.2393 r_free = 0.2393 target = 0.038653 restraints weight = 27209.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.2413 r_free = 0.2413 target = 0.039318 restraints weight = 18065.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.2426 r_free = 0.2426 target = 0.039700 restraints weight = 14129.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.2433 r_free = 0.2433 target = 0.039917 restraints weight = 12288.106|
|-----------------------------------------------------------------------------|
r_work (final): 0.2428
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2428
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2428 r_free = 0.2428    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2428 r_free = 0.2428    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2428
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8792
moved from start:          0.4248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  13333  Z= 0.224
  Angle     :  0.625   9.447  19250  Z= 0.365
  Chirality :  0.037   0.164   2193
  Planarity :  0.004   0.046   1434
  Dihedral  : 29.682 160.714   4084
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 23.57 %
    Favored  : 72.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.31 (0.29), residues: 811
  helix:  2.49 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop : -1.00 (0.38), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  35 
 TYR   0.029   0.002   TYR B  88 
 PHE   0.017   0.002   PHE K  40 
 TRP   0.005   0.001   TRP K  61 
 HIS   0.004   0.001   HIS D  79 

Details of bonding type rmsd
  covalent geometry    : bond        0.00500 (13326)
  covalent geometry    : angle       0.61660 (19244)
  hydrogen bonds       : bond        0.05788 (  781)
  hydrogen bonds       : angle       3.05010 ( 1988)
  metal coordination   : bond        0.00934 (    7)
  metal coordination   : angle       5.80663 (    6)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 160
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 THR cc_start: 0.8826 (m) cc_final: 0.8329 (p)
REVERT: B   67 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8356 (mtp180)
REVERT: B   92 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.6420 (ttm-80)
REVERT: C   71 ARG cc_start: 0.8942 (mmm-85) cc_final: 0.8410 (ttp-170)
REVERT: C   99 ARG cc_start: 0.8003 (ttp-170) cc_final: 0.7580 (mtp180)
REVERT: D   45 VAL cc_start: 0.8800 (t) cc_final: 0.8556 (p)
REVERT: D   82 LYS cc_start: 0.8588 (mttt) cc_final: 0.8005 (mmtt)
REVERT: D  105 LYS cc_start: 0.8766 (tptm) cc_final: 0.8179 (mptt)
REVERT: E   63 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8084 (mmp80)
REVERT: F   80 THR cc_start: 0.9048 (m) cc_final: 0.8595 (p)
REVERT: G   36 LYS cc_start: 0.9113 (mtpp) cc_final: 0.8682 (ttmm)
REVERT: G   76 THR cc_start: 0.9025 (m) cc_final: 0.8738 (t)
REVERT: G   90 ASP cc_start: 0.8179 (t0) cc_final: 0.7868 (t70)
REVERT: H   48 ASP cc_start: 0.8527 (p0) cc_final: 0.8295 (p0)
REVERT: H  113 LYS cc_start: 0.8915 (ttpt) cc_final: 0.8644 (tttm)
REVERT: H  116 THR cc_start: 0.9160 (m) cc_final: 0.8813 (p)
  outliers start: 26
  outliers final: 19
  residues processed: 175
  average time/residue: 0.1338
  time to fit residues: 31.1494
Evaluate side-chains
  178 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 156
  time to evaluate  : 0.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue   82 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   67 ARG
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain E residue   63 ARG
Chi-restraints excluded: chain F residue   29 ILE
Chi-restraints excluded: chain F residue   86 VAL
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain K residue   39 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 67 optimal weight:    6.9990
   chunk 72 optimal weight:    3.9990
   chunk 97 optimal weight:    3.9990
   chunk 71 optimal weight:    5.9990
   chunk 59 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0970
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
B  75 HIS
E 108 ASN
** K  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.050036 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2414 r_free = 0.2414 target = 0.039205 restraints weight = 52320.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.2448 r_free = 0.2448 target = 0.040337 restraints weight = 26732.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.2468 r_free = 0.2468 target = 0.041006 restraints weight = 17610.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 52)----------------|
| r_work = 0.2481 r_free = 0.2481 target = 0.041424 restraints weight = 13722.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2488 r_free = 0.2488 target = 0.041646 restraints weight = 11827.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.2483
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2483
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2483 r_free = 0.2483    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2483 r_free = 0.2483    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
r_final: 0.2483
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8747
moved from start:          0.4439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  13333  Z= 0.162
  Angle     :  0.581   8.749  19250  Z= 0.342
  Chirality :  0.034   0.174   2193
  Planarity :  0.004   0.055   1434
  Dihedral  : 29.543 162.971   4084
  Min Nonbonded Distance : 2.138

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  3.57 %
    Allowed  : 23.43 %
    Favored  : 73.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.60 (0.29), residues: 811
  helix:  2.67 (0.21), residues: 580
  sheet:  None (None), residues: 0
  loop : -0.86 (0.39), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG G  35 
 TYR   0.018   0.001   TYR K  64 
 PHE   0.008   0.001   PHE E  78 
 TRP   0.006   0.001   TRP K  61 
 HIS   0.004   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (13326)
  covalent geometry    : angle       0.57341 (19244)
  hydrogen bonds       : bond        0.04736 (  781)
  hydrogen bonds       : angle       2.90371 ( 1988)
  metal coordination   : bond        0.00821 (    7)
  metal coordination   : angle       5.41367 (    6)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 168
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 THR cc_start: 0.8727 (m) cc_final: 0.8310 (p)
REVERT: B   67 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8324 (mtp180)
REVERT: B   92 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7089 (ttm-80)
REVERT: C   71 ARG cc_start: 0.8821 (mmm-85) cc_final: 0.8252 (ttp-170)
REVERT: C   74 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8619 (tppt)
REVERT: C   99 ARG cc_start: 0.7966 (ttp-170) cc_final: 0.7753 (mtp180)
REVERT: D   82 LYS cc_start: 0.8451 (mttt) cc_final: 0.7943 (mmtt)
REVERT: D  105 LYS cc_start: 0.8659 (tptm) cc_final: 0.8122 (mptt)
REVERT: F   80 THR cc_start: 0.8989 (m) cc_final: 0.8591 (p)
REVERT: G   36 LYS cc_start: 0.9113 (mtpp) cc_final: 0.8685 (ttmm)
REVERT: G   76 THR cc_start: 0.8985 (m) cc_final: 0.8661 (t)
REVERT: G   90 ASP cc_start: 0.8141 (t0) cc_final: 0.7815 (t70)
REVERT: H   48 ASP cc_start: 0.8475 (p0) cc_final: 0.8266 (p0)
REVERT: H  113 LYS cc_start: 0.8912 (ttpt) cc_final: 0.8637 (tttm)
REVERT: H  116 THR cc_start: 0.9182 (m) cc_final: 0.8808 (p)
  outliers start: 25
  outliers final: 16
  residues processed: 182
  average time/residue: 0.1298
  time to fit residues: 31.3095
Evaluate side-chains
  180 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 161
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   67 ARG
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   92 ARG
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   50 TYR
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue   98 LEU
Chi-restraints excluded: chain K residue   39 CYS
Chi-restraints excluded: chain K residue   46 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 95 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 19 optimal weight:    5.9990
   chunk 47 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 9 optimal weight:    2.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2620 r_free = 0.2620 target = 0.045301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2278 r_free = 0.2278 target = 0.034867 restraints weight = 54013.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2313 r_free = 0.2313 target = 0.035951 restraints weight = 27325.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.2335 r_free = 0.2335 target = 0.036602 restraints weight = 17925.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2346 r_free = 0.2346 target = 0.036939 restraints weight = 13965.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.2355 r_free = 0.2355 target = 0.037210 restraints weight = 12144.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.2352
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2352
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2352 r_free = 0.2352    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2352 r_free = 0.2352    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.2352
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8845
moved from start:          0.4849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036  13333  Z= 0.256
  Angle     :  0.667  10.131  19250  Z= 0.385
  Chirality :  0.039   0.176   2193
  Planarity :  0.005   0.043   1434
  Dihedral  : 29.660 160.479   4084
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.07 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 23.57 %
    Favored  : 72.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.25 (0.29), residues: 811
  helix:  2.45 (0.21), residues: 577
  sheet:  None (None), residues: 0
  loop : -1.05 (0.38), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG G  35 
 TYR   0.042   0.002   TYR B  88 
 PHE   0.015   0.002   PHE K  53 
 TRP   0.004   0.001   TRP K  61 
 HIS   0.006   0.001   HIS A  39 

Details of bonding type rmsd
  covalent geometry    : bond        0.00578 (13326)
  covalent geometry    : angle       0.65811 (19244)
  hydrogen bonds       : bond        0.06583 (  781)
  hydrogen bonds       : angle       3.17952 ( 1988)
  metal coordination   : bond        0.00958 (    7)
  metal coordination   : angle       6.09624 (    6)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 164
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 THR cc_start: 0.8821 (OUTLIER) cc_final: 0.8289 (p)
REVERT: B   67 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8375 (mtp180)
REVERT: D   82 LYS cc_start: 0.8608 (mttt) cc_final: 0.8010 (mmtt)
REVERT: D  105 LYS cc_start: 0.8817 (tptm) cc_final: 0.8227 (mptt)
REVERT: E   63 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8131 (mmp80)
REVERT: F   80 THR cc_start: 0.9038 (m) cc_final: 0.8588 (p)
REVERT: F   88 TYR cc_start: 0.8321 (OUTLIER) cc_final: 0.7843 (m-80)
REVERT: G   36 LYS cc_start: 0.9096 (mtpp) cc_final: 0.8825 (ttpp)
REVERT: G   76 THR cc_start: 0.9080 (m) cc_final: 0.8812 (t)
REVERT: G   90 ASP cc_start: 0.8256 (t0) cc_final: 0.7954 (t70)
REVERT: H   48 ASP cc_start: 0.8533 (p0) cc_final: 0.8315 (p0)
REVERT: H   56 MET cc_start: 0.8719 (tpp) cc_final: 0.8499 (tpp)
REVERT: H   80 TYR cc_start: 0.8594 (t80) cc_final: 0.8357 (t80)
  outliers start: 28
  outliers final: 19
  residues processed: 179
  average time/residue: 0.1410
  time to fit residues: 33.0681
Evaluate side-chains
  183 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 160
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   67 ARG
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue   74 LYS
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   77 LEU
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain E residue   63 ARG
Chi-restraints excluded: chain E residue  105 GLU
Chi-restraints excluded: chain F residue   88 TYR
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain G residue  111 ILE
Chi-restraints excluded: chain H residue  120 SER
Chi-restraints excluded: chain K residue   39 CYS
Chi-restraints excluded: chain K residue   46 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 36 optimal weight:    0.7980
   chunk 53 optimal weight:    0.4980
   chunk 29 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 32 optimal weight:    3.9990
   chunk 95 optimal weight:    3.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.2692 r_free = 0.2692 target = 0.047839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2365 r_free = 0.2365 target = 0.037499 restraints weight = 53718.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2400 r_free = 0.2400 target = 0.038613 restraints weight = 26604.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.2421 r_free = 0.2421 target = 0.039290 restraints weight = 17213.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2434 r_free = 0.2434 target = 0.039663 restraints weight = 13286.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.2442 r_free = 0.2442 target = 0.039921 restraints weight = 11455.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.2437
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2437
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2437 r_free = 0.2437    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2437 r_free = 0.2437    target_work(ls_wunit_k1) = 0.040         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2437
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8780
moved from start:          0.4965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13333  Z= 0.167
  Angle     :  0.607   8.796  19250  Z= 0.353
  Chirality :  0.034   0.175   2193
  Planarity :  0.004   0.044   1434
  Dihedral  : 29.590 160.208   4084
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 25.86 %
    Favored  : 71.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.54 (0.29), residues: 811
  helix:  2.65 (0.21), residues: 580
  sheet:  None (None), residues: 0
  loop : -0.95 (0.38), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  35 
 TYR   0.025   0.002   TYR B  88 
 PHE   0.008   0.001   PHE E  78 
 TRP   0.005   0.001   TRP K  61 
 HIS   0.005   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (13326)
  covalent geometry    : angle       0.59984 (19244)
  hydrogen bonds       : bond        0.04877 (  781)
  hydrogen bonds       : angle       2.94885 ( 1988)
  metal coordination   : bond        0.00835 (    7)
  metal coordination   : angle       5.42334 (    6)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 165
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 THR cc_start: 0.8724 (m) cc_final: 0.8256 (p)
REVERT: B   67 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8351 (mtp180)
REVERT: D   33 SER cc_start: 0.9265 (t) cc_final: 0.8919 (m)
REVERT: D   45 VAL cc_start: 0.8692 (t) cc_final: 0.8471 (p)
REVERT: D   82 LYS cc_start: 0.8565 (mttt) cc_final: 0.7977 (mmtt)
REVERT: D  105 LYS cc_start: 0.8661 (tptm) cc_final: 0.8137 (mptt)
REVERT: E   42 ARG cc_start: 0.8124 (mmm-85) cc_final: 0.7715 (mmm-85)
REVERT: E   90 MET cc_start: 0.8237 (mmm) cc_final: 0.7977 (mmm)
REVERT: F   80 THR cc_start: 0.8993 (m) cc_final: 0.8586 (p)
REVERT: F   88 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.7856 (m-80)
REVERT: G   76 THR cc_start: 0.9015 (m) cc_final: 0.8738 (t)
REVERT: G   90 ASP cc_start: 0.8177 (t0) cc_final: 0.7870 (t70)
REVERT: H   56 MET cc_start: 0.8605 (tpp) cc_final: 0.8376 (tpp)
REVERT: H   80 TYR cc_start: 0.8536 (t80) cc_final: 0.8301 (t80)
  outliers start: 16
  outliers final: 11
  residues processed: 173
  average time/residue: 0.1351
  time to fit residues: 30.7197
Evaluate side-chains
  174 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 161
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   67 ARG
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain F residue   88 TYR
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain K residue   39 CYS
Chi-restraints excluded: chain K residue   46 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 89 optimal weight:    3.9990
   chunk 78 optimal weight:    3.9990
   chunk 43 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 72 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    2.1388

-------------------------------------------------------------------------------
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 = 0.2604 r_free = 0.2604 target = 0.044632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2263 r_free = 0.2263 target = 0.034295 restraints weight = 55629.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.2298 r_free = 0.2298 target = 0.035403 restraints weight = 27730.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2320 r_free = 0.2320 target = 0.036071 restraints weight = 18072.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 60)----------------|
| r_work = 0.2333 r_free = 0.2333 target = 0.036467 restraints weight = 13980.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2340 r_free = 0.2340 target = 0.036664 restraints weight = 12025.085|
|-----------------------------------------------------------------------------|
r_work (final): 0.2337
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2337
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2337 r_free = 0.2337    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2337 r_free = 0.2337    target_work(ls_wunit_k1) = 0.037         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
r_final: 0.2337
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8865
moved from start:          0.5195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039  13333  Z= 0.267
  Angle     :  0.675  10.468  19250  Z= 0.388
  Chirality :  0.040   0.178   2193
  Planarity :  0.006   0.066   1434
  Dihedral  : 29.634 157.860   4084
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 8.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 25.14 %
    Favored  : 72.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.37 (0.29), residues: 811
  helix:  2.52 (0.21), residues: 576
  sheet:  None (None), residues: 0
  loop : -0.94 (0.40), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG G  35 
 TYR   0.039   0.002   TYR B  88 
 PHE   0.014   0.002   PHE E  78 
 TRP   0.004   0.001   TRP K  61 
 HIS   0.007   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00605 (13326)
  covalent geometry    : angle       0.66612 (19244)
  hydrogen bonds       : bond        0.06377 (  781)
  hydrogen bonds       : angle       3.16957 ( 1988)
  metal coordination   : bond        0.00883 (    7)
  metal coordination   : angle       6.22113 (    6)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 159
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 THR cc_start: 0.8849 (OUTLIER) cc_final: 0.8332 (p)
REVERT: B   67 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8305 (mtp180)
REVERT: C   61 GLU cc_start: 0.7328 (tp30) cc_final: 0.7105 (tp30)
REVERT: C   71 ARG cc_start: 0.9088 (mmm-85) cc_final: 0.8453 (ttp-170)
REVERT: D   33 SER cc_start: 0.9283 (t) cc_final: 0.9000 (m)
REVERT: D   82 LYS cc_start: 0.8641 (mttt) cc_final: 0.8023 (mmtt)
REVERT: D  105 LYS cc_start: 0.8773 (tptm) cc_final: 0.8146 (mptt)
REVERT: F   80 THR cc_start: 0.9105 (m) cc_final: 0.8656 (p)
REVERT: F   88 TYR cc_start: 0.8341 (OUTLIER) cc_final: 0.7821 (m-80)
REVERT: G   76 THR cc_start: 0.9120 (m) cc_final: 0.8874 (t)
REVERT: G   90 ASP cc_start: 0.8265 (t0) cc_final: 0.7949 (t70)
REVERT: H   56 MET cc_start: 0.8630 (tpp) cc_final: 0.8356 (tpp)
  outliers start: 18
  outliers final: 15
  residues processed: 169
  average time/residue: 0.1300
  time to fit residues: 29.2615
Evaluate side-chains
  175 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 157
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain A residue  131 ARG
Chi-restraints excluded: chain B residue   67 ARG
Chi-restraints excluded: chain B residue   82 THR
Chi-restraints excluded: chain B residue   97 LEU
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain D residue   36 ILE
Chi-restraints excluded: chain D residue   51 ILE
Chi-restraints excluded: chain D residue   86 ILE
Chi-restraints excluded: chain E residue   92 LEU
Chi-restraints excluded: chain F residue   88 TYR
Chi-restraints excluded: chain F residue   93 GLN
Chi-restraints excluded: chain G residue   65 LEU
Chi-restraints excluded: chain G residue  108 LEU
Chi-restraints excluded: chain K residue   39 CYS
Chi-restraints excluded: chain K residue   46 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 107
   random chunks:
   chunk 26 optimal weight:    8.9990
   chunk 38 optimal weight:    1.9990
   chunk 103 optimal weight:    0.0970
   chunk 24 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 93 optimal weight:    3.9990
   chunk 19 optimal weight:    6.9990
   chunk 25 optimal weight:    0.8980
   chunk 75 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9980
   chunk 87 optimal weight:    3.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2648 r_free = 0.2648 target = 0.046086 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2318 r_free = 0.2318 target = 0.035866 restraints weight = 55117.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2353 r_free = 0.2353 target = 0.036981 restraints weight = 27081.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2374 r_free = 0.2374 target = 0.037655 restraints weight = 17515.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.2387 r_free = 0.2387 target = 0.038048 restraints weight = 13469.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2394 r_free = 0.2394 target = 0.038272 restraints weight = 11568.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.2392
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2392
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2392 r_free = 0.2392    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2392 r_free = 0.2392    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
r_final: 0.2392
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8820
moved from start:          0.5296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  13333  Z= 0.189
  Angle     :  0.624   9.270  19250  Z= 0.362
  Chirality :  0.035   0.176   2193
  Planarity :  0.005   0.046   1434
  Dihedral  : 29.642 157.921   4084
  Min Nonbonded Distance : 2.121

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 25.71 %
    Favored  : 72.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.51 (0.29), residues: 811
  helix:  2.63 (0.21), residues: 577
  sheet:  None (None), residues: 0
  loop : -0.92 (0.39), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G  35 
 TYR   0.031   0.002   TYR D  37 
 PHE   0.010   0.001   PHE E  78 
 TRP   0.005   0.001   TRP K  61 
 HIS   0.007   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00415 (13326)
  covalent geometry    : angle       0.61645 (19244)
  hydrogen bonds       : bond        0.05237 (  781)
  hydrogen bonds       : angle       3.01804 ( 1988)
  metal coordination   : bond        0.00889 (    7)
  metal coordination   : angle       5.61692 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1782.61 seconds
wall clock time: 31 minutes 22.98 seconds (1882.98 seconds total)