Starting phenix.real_space_refine
on Thu Aug  6 00:38:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8txv_41706/08_2026/8txv_41706.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8txv_41706/08_2026/8txv_41706.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8txv_41706/08_2026/8txv_41706.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8txv_41706/08_2026/8txv_41706.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8txv_41706/08_2026/8txv_41706.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8txv_41706/08_2026/8txv_41706.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     294      5.49       5
     S      15      5.16       5
     C    7144      2.51       5
     N    2407      2.21       5
     O    2976      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12836
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 661
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "D"
      Number of atoms: 740
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 740
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 653
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 653
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "H"
      Number of atoms: 743
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 731
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 728
    Chain: "I"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 117
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 117
          Classifications: {'peptide': 14}
          Link IDs: {'PTRANS': 1, 'TRANS': 12}
    Chain: "M"
      Number of atoms: 602
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 602
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
    Chain: "C"
      Number of atoms: 827
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 827
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "G"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 836
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   LEU M  73 " occ=0.45
      ... (6 atoms not shown)
      pdb=" CD2 LEU M  73 " occ=0.45
    residue:
      pdb=" N   ARG M  74 " occ=0.45
      ... (9 atoms not shown)
      pdb=" NH2 ARG M  74 " occ=0.45
    residue:
      pdb=" N   GLY M  75 " occ=0.25
      ... (2 atoms not shown)
      pdb=" O   GLY M  75 " occ=0.25
    residue:
      pdb=" N   GLY M  76 " occ=0.25
      ... (3 atoms not shown)
      pdb=" OXT GLY M  76 " occ=0.25
  Time building chain proxies: 3.05, per 1000 atoms: 0.24
  Number of scatterers: 12836
  At special positions: 0
  Unit cell: (94.288, 124.832, 120.848, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      15     16.00
     P     294     15.00
     O    2976      8.00
     N    2407      7.00
     C    7144      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
  Links applied
    TRANS
      " SER C  11 " - " SER D 123 "
      " SER G  11 " - " SER H 123 "
  Time building additional restraints: 1.04
  Conformation dependent library (CDL) restraints added in 426.8 milliseconds
  

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1600

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 10 sheets defined
      66.7% alpha, 4.4% beta
      135 base pairs and 243 stacking pairs defined.
    Time for finding SS restraints: 1.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 55
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.527A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.576A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 4.010A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.596A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   VAL D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.567A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 123
      removed outlier: 3.881A  pdb=" N   SER D 112 " --> pdb=" O   LYS D 108 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 55
      removed outlier: 3.793A  pdb=" N   LEU E  48 " --> pdb=" O   GLY E  44 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ARG E  49 " --> pdb=" O   THR E  45 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.523A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.601A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.014A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
      removed outlier: 3.504A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.629A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.615A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 123
      removed outlier: 3.712A  pdb=" N   SER H 123 " --> pdb=" O   THR H 119 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 22 through 35
    Processing helix  chain 'M' and resid 37 through 39
      No H-bonds generated for 'chain 'M' and resid 37 through 39'
    Processing helix  chain 'M' and resid 56 through 60
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 46 through 73
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.640A  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 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 73
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'G' and resid 112 through 116
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.825A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.603A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
    Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54
      removed outlier: 7.528A  pdb=" N   GLY D  53 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.709A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA8, first strand: chain 'F' and resid 97 through 98
    Processing sheet with id=AA9, first strand: chain 'H' and resid 88 through 89
    Processing sheet with id=AB1, first strand: chain 'M' and resid 12 through 16
      removed outlier: 8.825A  pdb=" N   LEU M  67 " --> pdb=" O   GLN M   2 " (cutoff:3.500A)
      removed outlier: 6.528A  pdb=" N   PHE M   4 " --> pdb=" O   LEU M  67 " (cutoff:3.500A)
      removed outlier: 7.318A  pdb=" N   LEU M  69 " --> pdb=" O   PHE M   4 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   LYS M   6 " --> pdb=" O   LEU M  69 " (cutoff:3.500A)
      removed outlier: 7.810A  pdb=" N   LEU M  71 " --> pdb=" O   LYS M   6 " (cutoff:3.500A)

    420 hydrogen bonds defined for protein.
    1228 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      348 hydrogen bonds
      692 hydrogen bond angles
      0 basepair planarities
      135 basepair parallelities
      243 stacking parallelities
  Total time for adding SS restraints: 2.42

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2529
        1.33 -     1.45: 4339
        1.45 -     1.57: 6179
        1.57 -     1.69: 586
        1.69 -     1.81: 26
  Bond restraints: 13659
  Sorted by residual:
  bond pdb=" C3'  DA J -68 "
       pdb=" C2'  DA J -68 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 8.00e-03 1.56e+04 1.29e+01
  bond pdb=" C3'  DC I  33 "
       pdb=" C2'  DC I  33 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 8.00e-03 1.56e+04 1.21e+01
  bond pdb=" C3'  DG I -41 "
       pdb=" C2'  DG I -41 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.09e+01
  bond pdb=" C3'  DT I  15 "
       pdb=" C2'  DT I  15 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.08e+01
  bond pdb=" C3'  DG J  21 "
       pdb=" C2'  DG J  21 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.06e+01
  ... (remaining 13654 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 18374
        1.44 -     2.87: 1242
        2.87 -     4.31: 63
        4.31 -     5.74: 14
        5.74 -     7.18: 5
  Bond angle restraints: 19698
  Sorted by residual:
  angle pdb=" O4'  DG I  26 "
        pdb=" C4'  DG I  26 "
        pdb=" C3'  DG I  26 "
      ideal   model   delta    sigma   weight residual
     106.00  103.07    2.93 6.00e-01 2.78e+00 2.38e+01
  angle pdb=" O4'  DC I -18 "
        pdb=" C4'  DC I -18 "
        pdb=" C3'  DC I -18 "
      ideal   model   delta    sigma   weight residual
     106.00  103.21    2.79 6.00e-01 2.78e+00 2.16e+01
  angle pdb=" N3   DT I -28 "
        pdb=" C4   DT I -28 "
        pdb=" O4   DT I -28 "
      ideal   model   delta    sigma   weight residual
     119.90  122.50   -2.60 6.00e-01 2.78e+00 1.88e+01
  angle pdb=" N3   DT I -59 "
        pdb=" C4   DT I -59 "
        pdb=" O4   DT I -59 "
      ideal   model   delta    sigma   weight residual
     119.90  122.48   -2.58 6.00e-01 2.78e+00 1.85e+01
  angle pdb=" N3   DT I   3 "
        pdb=" C4   DT I   3 "
        pdb=" O4   DT I   3 "
      ideal   model   delta    sigma   weight residual
     119.90  122.47   -2.57 6.00e-01 2.78e+00 1.83e+01
  ... (remaining 19693 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.37: 5861
       29.37 -    58.74: 1527
       58.74 -    88.12: 105
       88.12 -   117.49: 2
      117.49 -   146.86: 2
  Dihedral angle restraints: 7497
    sinusoidal: 5012
      harmonic: 2485
  Sorted by residual:
  dihedral pdb=" C4'  DG J  20 "
           pdb=" C3'  DG J  20 "
           pdb=" O3'  DG J  20 "
           pdb=" P    DG J  21 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   73.14  146.86     1      3.50e+01 8.16e-04 1.44e+01
  dihedral pdb=" C4'  DT J -17 "
           pdb=" C3'  DT J -17 "
           pdb=" O3'  DT J -17 "
           pdb=" P    DT J -16 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   75.89  144.11     1      3.50e+01 8.16e-04 1.42e+01
  dihedral pdb=" CB  GLU C  56 "
           pdb=" CG  GLU C  56 "
           pdb=" CD  GLU C  56 "
           pdb=" OE1 GLU C  56 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.75  -89.75     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 7494 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1158
       0.028 -    0.055: 644
       0.055 -    0.083: 257
       0.083 -    0.110: 158
       0.110 -    0.138: 23
  Chirality restraints: 2240
  Sorted by residual:
  chirality pdb=" CA  ASP B  24 "
            pdb=" N   ASP B  24 "
            pdb=" C   ASP B  24 "
            pdb=" CB  ASP B  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.76e-01
  chirality pdb=" CA  ASP F  24 "
            pdb=" N   ASP F  24 "
            pdb=" C   ASP F  24 "
            pdb=" CB  ASP F  24 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.14 2.00e-01 2.50e+01 4.58e-01
  chirality pdb=" CA  ILE C 111 "
            pdb=" N   ILE C 111 "
            pdb=" C   ILE C 111 "
            pdb=" CB  ILE C 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.98e-01
  ... (remaining 2237 not shown)

  Planarity restraints: 1480
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DA I -35 "    0.021 2.00e-02 2.50e+03   8.92e-03 2.19e+00
        pdb=" N9   DA I -35 "   -0.018 2.00e-02 2.50e+03
        pdb=" C8   DA I -35 "   -0.005 2.00e-02 2.50e+03
        pdb=" N7   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5   DA I -35 "    0.003 2.00e-02 2.50e+03
        pdb=" C6   DA I -35 "   -0.001 2.00e-02 2.50e+03
        pdb=" N6   DA I -35 "    0.008 2.00e-02 2.50e+03
        pdb=" N1   DA I -35 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DA I -35 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3   DA I -35 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4   DA I -35 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  47 "    0.021 2.00e-02 2.50e+03   8.33e-03 2.08e+00
        pdb=" N9   DG I  47 "   -0.017 2.00e-02 2.50e+03
        pdb=" C8   DG I  47 "   -0.006 2.00e-02 2.50e+03
        pdb=" N7   DG I  47 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5   DG I  47 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  47 "    0.003 2.00e-02 2.50e+03
        pdb=" O6   DG I  47 "    0.007 2.00e-02 2.50e+03
        pdb=" N1   DG I  47 "    0.001 2.00e-02 2.50e+03
        pdb=" C2   DG I  47 "   -0.000 2.00e-02 2.50e+03
        pdb=" N2   DG I  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3   DG I  47 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4   DG I  47 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DG I  26 "    0.018 2.00e-02 2.50e+03   7.34e-03 1.61e+00
        pdb=" N9   DG I  26 "   -0.015 2.00e-02 2.50e+03
        pdb=" C8   DG I  26 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7   DG I  26 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5   DG I  26 "    0.001 2.00e-02 2.50e+03
        pdb=" C6   DG I  26 "    0.003 2.00e-02 2.50e+03
        pdb=" O6   DG I  26 "    0.005 2.00e-02 2.50e+03
        pdb=" N1   DG I  26 "    0.003 2.00e-02 2.50e+03
        pdb=" C2   DG I  26 "    0.002 2.00e-02 2.50e+03
        pdb=" N2   DG I  26 "   -0.005 2.00e-02 2.50e+03
        pdb=" N3   DG I  26 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DG I  26 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1477 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 493
        2.70 -     3.25: 11464
        3.25 -     3.80: 23895
        3.80 -     4.35: 28492
        4.35 -     4.90: 41650
  Nonbonded interactions: 105994
  Sorted by model distance:
  nonbonded pdb=" O2   DC I  21 "
            pdb=" N2   DG J -21 "
     model   vdw
     2.151 2.496
  nonbonded pdb=" OG1 THR H  90 "
            pdb=" OE1 GLU H  93 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" NH2 ARG F  35 "
            pdb=" OP2  DC I   8 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" OH  TYR A  99 "
            pdb=" OE1 GLU A 133 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" NH2 ARG D  31 "
            pdb=" OP1  DG J  51 "
     model   vdw
     2.297 3.120
  ... (remaining 105989 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 21 through 102)
  selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ 
e C or name O ))))
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 11 through 118)
}
ncs_group {
  reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
  selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ 
gh 123))
}

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=0.25 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:             1.250
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.190
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8645
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      :  0.005   0.049  13661  Z= 0.493
  Angle     :  0.722   7.178  19704  Z= 0.635
  Chirality :  0.043   0.138   2240
  Planarity :  0.003   0.038   1478
  Dihedral  : 26.649 146.860   5891
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.00 %
    Favored  : 99.86 %
  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:  2.47 (0.30), residues: 839
  helix:  2.61 (0.22), residues: 544
  sheet:  1.56 (1.19), residues: 26
  loop : -0.45 (0.37), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG B  67 
 TYR   0.020   0.001   TYR H  40 
 PHE   0.009   0.001   PHE E  78 
 HIS   0.005   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00537 /  0.49 (13659)
  covalent geometry    : angle       0.72172 /  0.63 (19698)
  hydrogen bonds       : bond        0.10334 /  7.20 (  768)
  hydrogen bonds       : angle       3.99937 /  2.97 ( 1920)
  link_TRANS           : bond        0.00080 /  0.04 (    2)
  link_TRANS           : angle       0.53035 /  0.23 (    6)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 229
  time to evaluate  : 0.224 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.8391 (m-30) cc_final: 0.7873 (t70)
REVERT: B   31 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8769 (ttpp)
REVERT: B   91 LYS cc_start: 0.9420 (ttmm) cc_final: 0.9161 (ttmt)
REVERT: D   35 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7497 (mm-30)
REVERT: D   42 TYR cc_start: 0.8721 (t80) cc_final: 0.8273 (t80)
REVERT: D   46 LYS cc_start: 0.9213 (mmtt) cc_final: 0.8803 (tppt)
REVERT: D   51 ASP cc_start: 0.9279 (p0) cc_final: 0.8707 (p0)
REVERT: D  116 LYS cc_start: 0.9197 (mtmt) cc_final: 0.8989 (ttmt)
REVERT: D  120 LYS cc_start: 0.8988 (ttpt) cc_final: 0.8735 (tttt)
REVERT: E   57 SER cc_start: 0.9388 (p) cc_final: 0.8891 (p)
REVERT: E   59 GLU cc_start: 0.8782 (pm20) cc_final: 0.7940 (pm20)
REVERT: E   82 LEU cc_start: 0.9341 (mt) cc_final: 0.9120 (mm)
REVERT: E   94 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8360 (mm-30)
REVERT: E  110 CYS cc_start: 0.7930 (m) cc_final: 0.7655 (m)
REVERT: E  129 ARG cc_start: 0.8949 (tpt90) cc_final: 0.8743 (tpt-90)
REVERT: F   91 LYS cc_start: 0.9101 (tttp) cc_final: 0.8743 (ttmt)
REVERT: H   59 MET cc_start: 0.8960 (tpt) cc_final: 0.8643 (tpp)
REVERT: H   85 LYS cc_start: 0.9341 (mttm) cc_final: 0.8926 (mttp)
REVERT: C   64 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8416 (tm-30)
REVERT: G   41 GLU cc_start: 0.8633 (tm-30) cc_final: 0.8417 (tm-30)
REVERT: G   64 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8685 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.1248
  time to fit residues: 38.8543
Evaluate side-chains
  179 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    0.6980
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.088559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.056762 restraints weight = 53023.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2733 r_free = 0.2733 target = 0.059112 restraints weight = 22182.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2766 r_free = 0.2766 target = 0.060630 restraints weight = 13649.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.2787 r_free = 0.2787 target = 0.061622 restraints weight = 10438.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.062149 restraints weight = 8979.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.2779
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2778
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2778 r_free = 0.2778    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2776 r_free = 0.2776    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 8 (11 function evaluations)
r_final: 0.2776
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8779
moved from start:          0.1082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13661  Z= 0.158
  Angle     :  0.634   6.536  19704  Z= 0.381
  Chirality :  0.043   0.230   2240
  Planarity :  0.004   0.037   1478
  Dihedral  : 29.847 151.431   4171
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 11.10 %
    Favored  : 87.10 %
  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: 839
  helix:  2.54 (0.22), residues: 554
  sheet:  1.00 (1.14), residues: 26
  loop : -0.57 (0.36), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  33 
 TYR   0.023   0.002   TYR F  88 
 PHE   0.012   0.001   PHE A  78 
 HIS   0.004   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00273 /  0.16 (13659)
  covalent geometry    : angle       0.63408 /  0.38 (19698)
  hydrogen bonds       : bond        0.05237 /  3.48 (  768)
  hydrogen bonds       : angle       3.30857 /  2.48 ( 1920)
  link_TRANS           : bond        0.00044 /  0.02 (    2)
  link_TRANS           : angle       0.50767 /  0.25 (    6)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 188
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.8186 (m-30) cc_final: 0.7946 (t70)
REVERT: B   25 ASN cc_start: 0.8680 (m-40) cc_final: 0.8116 (m110)
REVERT: B   31 LYS cc_start: 0.9170 (ttmt) cc_final: 0.8969 (ttpp)
REVERT: B   88 TYR cc_start: 0.8413 (m-10) cc_final: 0.8092 (m-10)
REVERT: B   91 LYS cc_start: 0.9451 (ttmm) cc_final: 0.9138 (ttmt)
REVERT: D   42 TYR cc_start: 0.9017 (t80) cc_final: 0.8340 (t80)
REVERT: D   46 LYS cc_start: 0.9366 (mmtt) cc_final: 0.8844 (tppt)
REVERT: D   51 ASP cc_start: 0.8996 (p0) cc_final: 0.8328 (p0)
REVERT: D   83 TYR cc_start: 0.8028 (m-10) cc_final: 0.7556 (m-10)
REVERT: D   85 LYS cc_start: 0.9359 (mttm) cc_final: 0.9025 (mmtt)
REVERT: E   57 SER cc_start: 0.9314 (p) cc_final: 0.8791 (p)
REVERT: E   59 GLU cc_start: 0.8760 (pm20) cc_final: 0.7938 (pm20)
REVERT: F   85 ASP cc_start: 0.8709 (m-30) cc_final: 0.8118 (m-30)
REVERT: F   91 LYS cc_start: 0.9284 (tttp) cc_final: 0.9000 (ttmt)
REVERT: H   85 LYS cc_start: 0.9317 (mttm) cc_final: 0.8850 (mtmm)
REVERT: M   44 ILE cc_start: 0.5565 (mm) cc_final: 0.4669 (mp)
REVERT: M   61 ILE cc_start: 0.2463 (tp) cc_final: 0.2205 (mm)
REVERT: C   64 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8442 (tm-30)
REVERT: G   41 GLU cc_start: 0.8419 (tm-30) cc_final: 0.8082 (tm-30)
REVERT: G   64 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8741 (tm-30)
  outliers start: 12
  outliers final: 9
  residues processed: 192
  average time/residue: 0.1260
  time to fit residues: 33.2958
Evaluate side-chains
  182 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 173
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 105 optimal weight:    0.7980
   chunk 53 optimal weight:   20.0000
   chunk 67 optimal weight:   10.0000
   chunk 97 optimal weight:    0.6980
   chunk 104 optimal weight:    1.9990
   chunk 54 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 83 optimal weight:    8.9990
   overall best weight:    1.4986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.086510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.054232 restraints weight = 61536.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.056596 restraints weight = 24539.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.058116 restraints weight = 14794.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.2730 r_free = 0.2730 target = 0.059088 restraints weight = 11200.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.059612 restraints weight = 9618.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.2724
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2724
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2724 r_free = 0.2724    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2723 r_free = 0.2723    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2723
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8822
moved from start:          0.1397

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13661  Z= 0.200
  Angle     :  0.650   8.222  19704  Z= 0.378
  Chirality :  0.043   0.223   2240
  Planarity :  0.004   0.065   1478
  Dihedral  : 30.011 153.203   4171
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 12.62 %
    Favored  : 84.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.37 (0.29), residues: 839
  helix:  2.58 (0.22), residues: 554
  sheet:  0.73 (1.10), residues: 26
  loop : -0.65 (0.36), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG H  33 
 TYR   0.014   0.002   TYR F  88 
 PHE   0.016   0.001   PHE A  78 
 HIS   0.004   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00399 /  0.20 (13659)
  covalent geometry    : angle       0.65023 /  0.38 (19698)
  hydrogen bonds       : bond        0.05334 /  3.58 (  768)
  hydrogen bonds       : angle       3.33988 /  2.50 ( 1920)
  link_TRANS           : bond        0.00120 /  0.06 (    2)
  link_TRANS           : angle       0.31540 /  0.15 (    6)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 181
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.8143 (m-30) cc_final: 0.7891 (t70)
REVERT: B   25 ASN cc_start: 0.8630 (m-40) cc_final: 0.8009 (m110)
REVERT: B   88 TYR cc_start: 0.8727 (m-10) cc_final: 0.7861 (m-10)
REVERT: B   91 LYS cc_start: 0.9468 (ttmm) cc_final: 0.9163 (ttmt)
REVERT: D   42 TYR cc_start: 0.9166 (t80) cc_final: 0.8421 (t80)
REVERT: D   46 LYS cc_start: 0.9416 (mmtt) cc_final: 0.8870 (tppt)
REVERT: D   51 ASP cc_start: 0.9037 (p0) cc_final: 0.8482 (p0)
REVERT: D   59 MET cc_start: 0.9309 (tpp) cc_final: 0.9061 (tpp)
REVERT: D   83 TYR cc_start: 0.8255 (m-10) cc_final: 0.7366 (m-10)
REVERT: D   85 LYS cc_start: 0.9388 (mttm) cc_final: 0.9120 (mmtt)
REVERT: E   57 SER cc_start: 0.9374 (p) cc_final: 0.8818 (p)
REVERT: E   59 GLU cc_start: 0.8810 (pm20) cc_final: 0.8100 (pm20)
REVERT: E  105 GLU cc_start: 0.8544 (tp30) cc_final: 0.8229 (tp30)
REVERT: F   91 LYS cc_start: 0.9339 (tttp) cc_final: 0.8975 (ttmt)
REVERT: H   85 LYS cc_start: 0.9326 (mttm) cc_final: 0.8869 (mtmm)
REVERT: C   64 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8477 (tm-30)
REVERT: G   41 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8041 (tm-30)
  outliers start: 21
  outliers final: 19
  residues processed: 188
  average time/residue: 0.1271
  time to fit residues: 32.9523
Evaluate side-chains
  191 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 172
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain E residue  126 LEU
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 71 optimal weight:    9.9990
   chunk 21 optimal weight:    0.5980
   chunk 74 optimal weight:   10.0000
   chunk 80 optimal weight:    8.9990
   chunk 76 optimal weight:    9.9990
   chunk 65 optimal weight:    9.9990
   chunk 62 optimal weight:   10.0000
   chunk 107 optimal weight:    0.9990
   chunk 73 optimal weight:   10.0000
   chunk 93 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   overall best weight:    2.8786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 475 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.083848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2564 r_free = 0.2564 target = 0.052038 restraints weight = 52582.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2614 r_free = 0.2614 target = 0.054196 restraints weight = 23203.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2646 r_free = 0.2646 target = 0.055582 restraints weight = 14725.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2666 r_free = 0.2666 target = 0.056445 restraints weight = 11458.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.056953 restraints weight = 9972.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.2659
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2659
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2659 r_free = 0.2659    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2659 r_free = 0.2659    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2659
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8876
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.046  13661  Z= 0.305
  Angle     :  0.754   8.211  19704  Z= 0.420
  Chirality :  0.047   0.241   2240
  Planarity :  0.005   0.060   1478
  Dihedral  : 30.250 155.087   4171
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 14.98 %
    Favored  : 80.72 %
  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:  1.97 (0.29), residues: 839
  helix:  2.27 (0.22), residues: 554
  sheet:  0.78 (1.15), residues: 26
  loop : -0.81 (0.36), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  33 
 TYR   0.020   0.002   TYR A  99 
 PHE   0.010   0.002   PHE B  61 
 HIS   0.008   0.002   HIS H 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00665 /  0.31 (13659)
  covalent geometry    : angle       0.75423 /  0.42 (19698)
  hydrogen bonds       : bond        0.06223 /  4.16 (  768)
  hydrogen bonds       : angle       3.68106 /  2.74 ( 1920)
  link_TRANS           : bond        0.00339 /  0.16 (    2)
  link_TRANS           : angle       0.41113 /  0.18 (    6)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 174
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   25 ASN cc_start: 0.8691 (m-40) cc_final: 0.8068 (m110)
REVERT: B   88 TYR cc_start: 0.8769 (m-10) cc_final: 0.8400 (m-10)
REVERT: B   91 LYS cc_start: 0.9490 (ttmm) cc_final: 0.9182 (ttmt)
REVERT: D   42 TYR cc_start: 0.9169 (t80) cc_final: 0.8763 (t80)
REVERT: D   46 LYS cc_start: 0.9425 (mmtt) cc_final: 0.9088 (tppt)
REVERT: D   51 ASP cc_start: 0.9095 (p0) cc_final: 0.8586 (p0)
REVERT: D   59 MET cc_start: 0.9370 (tpp) cc_final: 0.8859 (tpt)
REVERT: D   85 LYS cc_start: 0.9385 (mttm) cc_final: 0.9153 (mmtt)
REVERT: E   57 SER cc_start: 0.9348 (p) cc_final: 0.8956 (p)
REVERT: E   59 GLU cc_start: 0.8789 (pm20) cc_final: 0.8120 (pm20)
REVERT: E  105 GLU cc_start: 0.8649 (tp30) cc_final: 0.8359 (tp30)
REVERT: F   91 LYS cc_start: 0.9403 (tttp) cc_final: 0.9030 (ttmt)
REVERT: H   85 LYS cc_start: 0.9312 (mttm) cc_final: 0.8938 (mttp)
REVERT: M   62 GLN cc_start: 0.7421 (pm20) cc_final: 0.7122 (pm20)
REVERT: C   64 GLU cc_start: 0.9174 (tm-30) cc_final: 0.8494 (tm-30)
REVERT: G   41 GLU cc_start: 0.8478 (tm-30) cc_final: 0.8000 (tm-30)
  outliers start: 30
  outliers final: 26
  residues processed: 188
  average time/residue: 0.1254
  time to fit residues: 32.8247
Evaluate side-chains
  192 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 166
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue   69 ILE
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   60 LEU
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   47 SER
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain M residue   25 ASN
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 76 optimal weight:   10.0000
   chunk 87 optimal weight:    0.5980
   chunk 53 optimal weight:   20.0000
   chunk 63 optimal weight:   10.0000
   chunk 82 optimal weight:   20.0000
   chunk 55 optimal weight:    9.9990
   chunk 23 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 40 optimal weight:    0.8980
   chunk 84 optimal weight:    4.9990
   chunk 98 optimal weight:    5.9990
   overall best weight:    1.6582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.084916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2605 r_free = 0.2605 target = 0.053793 restraints weight = 43335.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2653 r_free = 0.2653 target = 0.055875 restraints weight = 20296.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2682 r_free = 0.2682 target = 0.057160 restraints weight = 13286.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.058066 restraints weight = 10542.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.058479 restraints weight = 9226.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2693
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2693 r_free = 0.2693    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2693 r_free = 0.2693    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2693
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8843
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  13661  Z= 0.207
  Angle     :  0.674   8.800  19704  Z= 0.388
  Chirality :  0.044   0.235   2240
  Planarity :  0.004   0.036   1478
  Dihedral  : 30.181 154.406   4171
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 17.06 %
    Favored  : 79.89 %
  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: 839
  helix:  2.44 (0.22), residues: 553
  sheet:  0.78 (1.18), residues: 26
  loop : -0.79 (0.37), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG M  72 
 TYR   0.019   0.002   TYR H  83 
 PHE   0.010   0.001   PHE E  78 
 HIS   0.003   0.001   HIS H  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00425 /  0.21 (13659)
  covalent geometry    : angle       0.67430 /  0.39 (19698)
  hydrogen bonds       : bond        0.05499 /  3.67 (  768)
  hydrogen bonds       : angle       3.36117 /  2.50 ( 1920)
  link_TRANS           : bond        0.00174 /  0.08 (    2)
  link_TRANS           : angle       0.35323 /  0.19 (    6)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 177
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLN cc_start: 0.8180 (mt0) cc_final: 0.7418 (mt0)
REVERT: B   25 ASN cc_start: 0.8657 (m-40) cc_final: 0.8028 (m110)
REVERT: B   88 TYR cc_start: 0.8746 (m-10) cc_final: 0.8357 (m-10)
REVERT: B   91 LYS cc_start: 0.9484 (ttmm) cc_final: 0.9171 (ttmt)
REVERT: D   42 TYR cc_start: 0.9135 (t80) cc_final: 0.8242 (t80)
REVERT: D   46 LYS cc_start: 0.9398 (mmtt) cc_final: 0.8850 (tppt)
REVERT: D   51 ASP cc_start: 0.9053 (p0) cc_final: 0.8566 (p0)
REVERT: D   85 LYS cc_start: 0.9389 (mttm) cc_final: 0.9183 (mmtt)
REVERT: E   57 SER cc_start: 0.9353 (p) cc_final: 0.8919 (p)
REVERT: E   59 GLU cc_start: 0.8765 (pm20) cc_final: 0.8087 (pm20)
REVERT: E  105 GLU cc_start: 0.8606 (tp30) cc_final: 0.8298 (tp30)
REVERT: F   91 LYS cc_start: 0.9363 (tttp) cc_final: 0.8992 (ttmt)
REVERT: H   85 LYS cc_start: 0.9320 (mttm) cc_final: 0.8908 (mttp)
REVERT: C   64 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8437 (tm-30)
REVERT: G   41 GLU cc_start: 0.8496 (tm-30) cc_final: 0.8008 (tm-30)
  outliers start: 21
  outliers final: 18
  residues processed: 185
  average time/residue: 0.1091
  time to fit residues: 28.2553
Evaluate side-chains
  189 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 171
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 107 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 86 optimal weight:    7.9990
   chunk 78 optimal weight:   10.0000
   chunk 63 optimal weight:   10.0000
   chunk 4 optimal weight:    2.9990
   chunk 93 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 72 optimal weight:   10.0000
   overall best weight:    1.0384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.085804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2622 r_free = 0.2622 target = 0.054402 restraints weight = 45966.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.056559 restraints weight = 20819.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.057951 restraints weight = 13418.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.058828 restraints weight = 10493.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.059239 restraints weight = 9203.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2711
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2711 r_free = 0.2711    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2711 r_free = 0.2711    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2711
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8827
moved from start:          0.1865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  13661  Z= 0.169
  Angle     :  0.649   8.711  19704  Z= 0.377
  Chirality :  0.042   0.230   2240
  Planarity :  0.004   0.037   1478
  Dihedral  : 30.120 154.425   4171
  Min Nonbonded Distance : 2.139

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 16.92 %
    Favored  : 78.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.29 (0.30), residues: 839
  helix:  2.55 (0.22), residues: 555
  sheet:  1.26 (1.33), residues: 20
  loop : -0.80 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG M  42 
 TYR   0.012   0.001   TYR C  57 
 PHE   0.011   0.001   PHE E  78 
 HIS   0.004   0.001   HIS H  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.17 (13659)
  covalent geometry    : angle       0.64888 /  0.38 (19698)
  hydrogen bonds       : bond        0.05147 /  3.43 (  768)
  hydrogen bonds       : angle       3.18955 /  2.36 ( 1920)
  link_TRANS           : bond        0.00072 /  0.03 (    2)
  link_TRANS           : angle       0.36056 /  0.20 (    6)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 178
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 GLN cc_start: 0.8164 (mt0) cc_final: 0.7381 (mt0)
REVERT: B   25 ASN cc_start: 0.8608 (m-40) cc_final: 0.7915 (m110)
REVERT: B   88 TYR cc_start: 0.8727 (m-10) cc_final: 0.8352 (m-10)
REVERT: B   91 LYS cc_start: 0.9470 (ttmm) cc_final: 0.9104 (ttmt)
REVERT: D   42 TYR cc_start: 0.9116 (t80) cc_final: 0.8212 (t80)
REVERT: D   46 LYS cc_start: 0.9395 (mmtt) cc_final: 0.8881 (tppt)
REVERT: D   51 ASP cc_start: 0.9022 (p0) cc_final: 0.8545 (p0)
REVERT: E   57 SER cc_start: 0.9328 (p) cc_final: 0.8781 (p)
REVERT: E   59 GLU cc_start: 0.8737 (pm20) cc_final: 0.7998 (pm20)
REVERT: F   91 LYS cc_start: 0.9347 (tttp) cc_final: 0.8997 (ttmt)
REVERT: H   85 LYS cc_start: 0.9301 (mttm) cc_final: 0.8896 (mttp)
REVERT: C   64 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8438 (tm-30)
REVERT: G   41 GLU cc_start: 0.8482 (tm-30) cc_final: 0.8001 (tm-30)
  outliers start: 29
  outliers final: 22
  residues processed: 192
  average time/residue: 0.1075
  time to fit residues: 28.9090
Evaluate side-chains
  191 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 169
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  122 THR
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   47 SER
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain M residue   25 ASN
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 75 optimal weight:    9.9990
   chunk 15 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 49 optimal weight:    0.0670
   chunk 40 optimal weight:    0.9980
   chunk 76 optimal weight:    9.9990
   chunk 71 optimal weight:   10.0000
   chunk 82 optimal weight:    8.9990
   chunk 85 optimal weight:    7.9990
   chunk 7 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   overall best weight:    0.9322

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  93 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.086346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.054694 restraints weight = 48349.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2677 r_free = 0.2677 target = 0.056910 restraints weight = 21573.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.058347 restraints weight = 13777.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.059187 restraints weight = 10734.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.059734 restraints weight = 9378.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2721
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2721 r_free = 0.2721    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2721 r_free = 0.2721    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2721
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8820
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13661  Z= 0.162
  Angle     :  0.638   9.036  19704  Z= 0.372
  Chirality :  0.042   0.225   2240
  Planarity :  0.004   0.037   1478
  Dihedral  : 30.092 154.818   4171
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 18.45 %
    Favored  : 77.81 %
  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:  2.38 (0.29), residues: 839
  helix:  2.62 (0.22), residues: 555
  sheet:  1.04 (1.25), residues: 20
  loop : -0.75 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG H  33 
 TYR   0.028   0.002   TYR F  88 
 PHE   0.011   0.001   PHE E  78 
 HIS   0.003   0.001   HIS H  82 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.16 (13659)
  covalent geometry    : angle       0.63783 /  0.37 (19698)
  hydrogen bonds       : bond        0.04968 /  3.30 (  768)
  hydrogen bonds       : angle       3.12084 /  2.32 ( 1920)
  link_TRANS           : bond        0.00052 /  0.02 (    2)
  link_TRANS           : angle       0.34688 /  0.19 (    6)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 174
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 ASP cc_start: 0.9164 (m-30) cc_final: 0.8860 (m-30)
REVERT: A  125 GLN cc_start: 0.8149 (mt0) cc_final: 0.7449 (mt0)
REVERT: B   25 ASN cc_start: 0.8606 (m-40) cc_final: 0.7853 (m110)
REVERT: B   88 TYR cc_start: 0.8671 (m-10) cc_final: 0.7792 (m-10)
REVERT: B   91 LYS cc_start: 0.9460 (ttmm) cc_final: 0.9100 (ttmt)
REVERT: D   42 TYR cc_start: 0.9086 (t80) cc_final: 0.8186 (t80)
REVERT: D   46 LYS cc_start: 0.9378 (mmtt) cc_final: 0.8852 (tppt)
REVERT: D   51 ASP cc_start: 0.8998 (p0) cc_final: 0.8499 (p0)
REVERT: D   83 TYR cc_start: 0.8377 (m-10) cc_final: 0.7558 (m-10)
REVERT: E   57 SER cc_start: 0.9319 (p) cc_final: 0.8759 (p)
REVERT: E   59 GLU cc_start: 0.8703 (pm20) cc_final: 0.8051 (pm20)
REVERT: E   61 LEU cc_start: 0.9128 (mp) cc_final: 0.8927 (mp)
REVERT: F   88 TYR cc_start: 0.8078 (m-10) cc_final: 0.7523 (m-10)
REVERT: F   91 LYS cc_start: 0.9387 (tttp) cc_final: 0.9148 (ttmt)
REVERT: H   83 TYR cc_start: 0.8118 (m-10) cc_final: 0.7840 (m-80)
REVERT: H   85 LYS cc_start: 0.9288 (mttm) cc_final: 0.8891 (mttp)
REVERT: C   64 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8448 (tm-30)
REVERT: G   41 GLU cc_start: 0.8471 (tm-30) cc_final: 0.8000 (tm-30)
  outliers start: 26
  outliers final: 22
  residues processed: 185
  average time/residue: 0.1332
  time to fit residues: 34.3791
Evaluate side-chains
  190 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 168
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue   90 MET
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain E residue  120 MET
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue   91 GLU
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 57 optimal weight:   10.0000
   chunk 75 optimal weight:    9.9990
   chunk 91 optimal weight:    0.6980
   chunk 84 optimal weight:    0.4980
   chunk 18 optimal weight:    0.6980
   chunk 28 optimal weight:    1.9990
   chunk 79 optimal weight:    9.9990
   chunk 105 optimal weight:    0.9980
   chunk 77 optimal weight:    9.9990
   chunk 44 optimal weight:    0.5980
   chunk 55 optimal weight:    9.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  25 ASN
** M  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.087112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.054986 restraints weight = 60959.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.057403 restraints weight = 24144.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2723 r_free = 0.2723 target = 0.058960 restraints weight = 14522.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.059934 restraints weight = 10983.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.2757 r_free = 0.2757 target = 0.060501 restraints weight = 9396.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.2739
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2739
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2739 r_free = 0.2739    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2739
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8803
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13661  Z= 0.150
  Angle     :  0.626   8.769  19704  Z= 0.366
  Chirality :  0.041   0.218   2240
  Planarity :  0.004   0.039   1478
  Dihedral  : 30.050 155.114   4171
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 18.86 %
    Favored  : 77.81 %
  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:  2.52 (0.30), residues: 839
  helix:  2.73 (0.22), residues: 555
  sheet:  0.80 (1.11), residues: 26
  loop : -0.70 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG H  33 
 TYR   0.026   0.001   TYR F  88 
 PHE   0.012   0.001   PHE A  78 
 HIS   0.004   0.001   HIS H 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.15 (13659)
  covalent geometry    : angle       0.62637 /  0.37 (19698)
  hydrogen bonds       : bond        0.04707 /  3.13 (  768)
  hydrogen bonds       : angle       3.01380 /  2.25 ( 1920)
  link_TRANS           : bond        0.00038 /  0.02 (    2)
  link_TRANS           : angle       0.37330 /  0.20 (    6)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 176
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 ASP cc_start: 0.9162 (m-30) cc_final: 0.8843 (m-30)
REVERT: A  125 GLN cc_start: 0.8137 (mt0) cc_final: 0.7412 (mt0)
REVERT: B   25 ASN cc_start: 0.8596 (m-40) cc_final: 0.7818 (m110)
REVERT: B   88 TYR cc_start: 0.8646 (m-10) cc_final: 0.8332 (m-80)
REVERT: B   91 LYS cc_start: 0.9451 (ttmm) cc_final: 0.9107 (ttmt)
REVERT: D   42 TYR cc_start: 0.9063 (t80) cc_final: 0.8173 (t80)
REVERT: D   46 LYS cc_start: 0.9376 (mmtt) cc_final: 0.8848 (tppt)
REVERT: D   51 ASP cc_start: 0.8989 (p0) cc_final: 0.8482 (p0)
REVERT: E   57 SER cc_start: 0.9334 (p) cc_final: 0.8773 (p)
REVERT: E   59 GLU cc_start: 0.8690 (pm20) cc_final: 0.8028 (pm20)
REVERT: F   88 TYR cc_start: 0.8139 (m-10) cc_final: 0.7544 (m-10)
REVERT: F   91 LYS cc_start: 0.9335 (tttp) cc_final: 0.9069 (ttmt)
REVERT: H   83 TYR cc_start: 0.8211 (m-10) cc_final: 0.7867 (m-80)
REVERT: H   85 LYS cc_start: 0.9316 (mttm) cc_final: 0.8934 (mttp)
REVERT: C   64 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8574 (tm-30)
REVERT: G   41 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8029 (tm-30)
  outliers start: 23
  outliers final: 18
  residues processed: 187
  average time/residue: 0.1297
  time to fit residues: 34.0564
Evaluate side-chains
  189 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 171
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain A residue   93 GLN
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 105 optimal weight:    0.9990
   chunk 59 optimal weight:   10.0000
   chunk 32 optimal weight:    0.5980
   chunk 84 optimal weight:    0.5980
   chunk 9 optimal weight:    0.9990
   chunk 81 optimal weight:    9.9990
   chunk 47 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 101 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  93 GLN
** M  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  62 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.087364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.056446 restraints weight = 39477.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2714 r_free = 0.2714 target = 0.058554 restraints weight = 18921.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.059859 restraints weight = 12516.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.060672 restraints weight = 9969.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.061087 restraints weight = 8828.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2750
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2750 r_free = 0.2750    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2750 r_free = 0.2750    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2750
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8791
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13661  Z= 0.148
  Angle     :  0.626  13.250  19704  Z= 0.363
  Chirality :  0.040   0.219   2240
  Planarity :  0.004   0.037   1478
  Dihedral  : 30.052 155.599   4171
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 19.28 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.57 (0.29), residues: 839
  helix:  2.74 (0.22), residues: 556
  sheet:  0.89 (1.09), residues: 26
  loop : -0.63 (0.37), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG H  33 
 TYR   0.020   0.001   TYR F  88 
 PHE   0.010   0.001   PHE A  78 
 HIS   0.004   0.001   HIS H 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.15 (13659)
  covalent geometry    : angle       0.62580 /  0.36 (19698)
  hydrogen bonds       : bond        0.04661 /  3.09 (  768)
  hydrogen bonds       : angle       2.99166 /  2.23 ( 1920)
  link_TRANS           : bond        0.00041 /  0.02 (    2)
  link_TRANS           : angle       0.37493 /  0.20 (    6)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 174
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 ASP cc_start: 0.9150 (m-30) cc_final: 0.8826 (m-30)
REVERT: A  125 GLN cc_start: 0.8142 (mt0) cc_final: 0.7408 (mt0)
REVERT: B   25 ASN cc_start: 0.8597 (m-40) cc_final: 0.7819 (m110)
REVERT: B   88 TYR cc_start: 0.8620 (m-10) cc_final: 0.8316 (m-80)
REVERT: B   91 LYS cc_start: 0.9463 (ttmm) cc_final: 0.9156 (ttmt)
REVERT: D   42 TYR cc_start: 0.9058 (t80) cc_final: 0.8167 (t80)
REVERT: D   46 LYS cc_start: 0.9379 (mmtt) cc_final: 0.8861 (tppt)
REVERT: D   51 ASP cc_start: 0.8990 (p0) cc_final: 0.8420 (p0)
REVERT: E   57 SER cc_start: 0.9320 (p) cc_final: 0.8746 (p)
REVERT: E   59 GLU cc_start: 0.8698 (pm20) cc_final: 0.8047 (pm20)
REVERT: F   88 TYR cc_start: 0.8121 (m-10) cc_final: 0.7587 (m-10)
REVERT: F   91 LYS cc_start: 0.9340 (tttp) cc_final: 0.9074 (ttmt)
REVERT: H   83 TYR cc_start: 0.8271 (m-10) cc_final: 0.7944 (m-80)
REVERT: H   85 LYS cc_start: 0.9314 (mttm) cc_final: 0.8931 (mttp)
REVERT: C   64 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8568 (tm-30)
REVERT: G   41 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8032 (tm-30)
  outliers start: 23
  outliers final: 20
  residues processed: 187
  average time/residue: 0.1265
  time to fit residues: 33.2914
Evaluate side-chains
  188 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 168
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain B residue   93 GLN
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain M residue   62 GLN
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 101 optimal weight:    0.7980
   chunk 63 optimal weight:   10.0000
   chunk 76 optimal weight:    9.9990
   chunk 13 optimal weight:    0.6980
   chunk 90 optimal weight:    0.8980
   chunk 92 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 97 optimal weight:    0.2980
   chunk 67 optimal weight:   10.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B  93 GLN
** M  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  62 GLN
** G  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.087618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.056396 restraints weight = 45356.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.058612 restraints weight = 20375.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.060016 restraints weight = 13040.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.060914 restraints weight = 10193.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.061418 restraints weight = 8898.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2758
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2758 r_free = 0.2758    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2758 r_free = 0.2758    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2758
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8783
moved from start:          0.2025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13661  Z= 0.146
  Angle     :  0.627  13.362  19704  Z= 0.362
  Chirality :  0.040   0.221   2240
  Planarity :  0.004   0.037   1478
  Dihedral  : 30.039 155.723   4171
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 20.25 %
    Favored  : 76.56 %
  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:  2.56 (0.29), residues: 839
  helix:  2.74 (0.22), residues: 556
  sheet:  0.90 (1.10), residues: 26
  loop : -0.65 (0.37), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG H  33 
 TYR   0.019   0.001   TYR F  88 
 PHE   0.009   0.001   PHE E  78 
 HIS   0.004   0.001   HIS H 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00255 /  0.15 (13659)
  covalent geometry    : angle       0.62708 /  0.36 (19698)
  hydrogen bonds       : bond        0.04611 /  3.06 (  768)
  hydrogen bonds       : angle       2.97014 /  2.22 ( 1920)
  link_TRANS           : bond        0.00031 /  0.02 (    2)
  link_TRANS           : angle       0.38435 /  0.21 (    6)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 176
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  123 ASP cc_start: 0.9147 (m-30) cc_final: 0.8825 (m-30)
REVERT: A  125 GLN cc_start: 0.8138 (mt0) cc_final: 0.7403 (mt0)
REVERT: B   25 ASN cc_start: 0.8596 (m-40) cc_final: 0.7763 (m110)
REVERT: B   88 TYR cc_start: 0.8594 (m-10) cc_final: 0.8297 (m-80)
REVERT: B   91 LYS cc_start: 0.9444 (ttmm) cc_final: 0.9110 (ttmt)
REVERT: D   42 TYR cc_start: 0.9066 (t80) cc_final: 0.8204 (t80)
REVERT: D   46 LYS cc_start: 0.9381 (mmtt) cc_final: 0.8867 (tppt)
REVERT: D   51 ASP cc_start: 0.8997 (p0) cc_final: 0.8408 (p0)
REVERT: D  100 LEU cc_start: 0.9504 (mt) cc_final: 0.9288 (mt)
REVERT: E   57 SER cc_start: 0.9313 (p) cc_final: 0.8735 (p)
REVERT: E   59 GLU cc_start: 0.8696 (pm20) cc_final: 0.8102 (pm20)
REVERT: F   88 TYR cc_start: 0.8135 (m-10) cc_final: 0.7556 (m-10)
REVERT: F   91 LYS cc_start: 0.9338 (tttp) cc_final: 0.9077 (ttmt)
REVERT: H   83 TYR cc_start: 0.8289 (m-10) cc_final: 0.7820 (m-80)
REVERT: H   85 LYS cc_start: 0.9313 (mttm) cc_final: 0.8932 (mttp)
REVERT: C   64 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8565 (tm-30)
REVERT: G   41 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8034 (tm-30)
  outliers start: 22
  outliers final: 19
  residues processed: 185
  average time/residue: 0.1198
  time to fit residues: 31.3599
Evaluate side-chains
  191 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 172
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   80 THR
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain E residue  115 LYS
Chi-restraints excluded: chain F residue   30 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   80 THR
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  101 LEU
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain C residue   23 LEU
Chi-restraints excluded: chain C residue   40 SER
Chi-restraints excluded: chain C residue   79 ILE
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   62 ILE
Chi-restraints excluded: chain G residue   79 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 75 optimal weight:   10.0000
   chunk 58 optimal weight:   10.0000
   chunk 88 optimal weight:    4.9990
   chunk 56 optimal weight:    9.9990
   chunk 13 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 61 optimal weight:    9.9990
   chunk 37 optimal weight:    0.0470
   overall best weight:    0.9880

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** M  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  62 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.087207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.056277 restraints weight = 39976.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.058386 restraints weight = 19039.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2740 r_free = 0.2740 target = 0.059694 restraints weight = 12554.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.060424 restraints weight = 10012.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.060966 restraints weight = 8902.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.2749
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2750
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2750 r_free = 0.2750    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2750 r_free = 0.2750    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.21   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2750
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8790
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13661  Z= 0.163
  Angle     :  0.633  12.787  19704  Z= 0.364
  Chirality :  0.040   0.223   2240
  Planarity :  0.004   0.037   1478
  Dihedral  : 30.050 155.937   4171
  Min Nonbonded Distance : 2.144

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 20.39 %
    Favored  : 76.70 %
  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:  2.55 (0.29), residues: 839
  helix:  2.73 (0.22), residues: 556
  sheet:  0.87 (1.11), residues: 26
  loop : -0.66 (0.37), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG H  33 
 TYR   0.019   0.001   TYR F  88 
 PHE   0.008   0.001   PHE E  78 
 HIS   0.005   0.001   HIS H 109 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.16 (13659)
  covalent geometry    : angle       0.63278 /  0.36 (19698)
  hydrogen bonds       : bond        0.04659 /  3.09 (  768)
  hydrogen bonds       : angle       3.01216 /  2.25 ( 1920)
  link_TRANS           : bond        0.00074 /  0.04 (    2)
  link_TRANS           : angle       0.35162 /  0.19 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2097.98 seconds
wall clock time: 36 minutes 42.81 seconds (2202.81 seconds total)