Starting phenix.real_space_refine
on Wed Jul 30 16:54:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8txv_41706/07_2025/8txv_41706.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8txv_41706/07_2025/8txv_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_41706/07_2025/8txv_41706.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8txv_41706/07_2025/8txv_41706.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8txv_41706/07_2025/8txv_41706.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8txv_41706/07_2025/8txv_41706.cif"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.50, per 1000 atoms: 0.66
  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: 3.27
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 5.71
  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: 4.87

  Time building geometry restraints manager: 3.87 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=" CG1 ILE A 112 "
       pdb=" CD1 ILE A 112 "
    ideal  model  delta    sigma   weight residual
    1.513  1.464  0.049 3.90e-02 6.57e+02 1.59e+00
  bond pdb=" CG  LEU A 126 "
       pdb=" CD1 LEU A 126 "
    ideal  model  delta    sigma   weight residual
    1.521  1.486  0.035 3.30e-02 9.18e+02 1.13e+00
  bond pdb=" CB  CYS E  96 "
       pdb=" SG  CYS E  96 "
    ideal  model  delta    sigma   weight residual
    1.808  1.774  0.034 3.30e-02 9.18e+02 1.06e+00
  bond pdb=" CB  ASP C  72 "
       pdb=" CG  ASP C  72 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 2.50e-02 1.60e+03 1.01e+00
  bond pdb=" CB  ASP E  81 "
       pdb=" CG  ASP E  81 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 2.50e-02 1.60e+03 9.98e-01
  ... (remaining 13654 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.44: 19072
        1.44 -     2.87: 566
        2.87 -     4.31: 41
        4.31 -     5.74: 14
        5.74 -     7.18: 5
  Bond angle restraints: 19698
  Sorted by residual:
  angle pdb=" C   ARG B  23 "
        pdb=" N   ASP B  24 "
        pdb=" CA  ASP B  24 "
      ideal   model   delta    sigma   weight residual
     121.54  128.48   -6.94 1.91e+00 2.74e-01 1.32e+01
  angle pdb=" C   ARG F  23 "
        pdb=" N   ASP F  24 "
        pdb=" CA  ASP F  24 "
      ideal   model   delta    sigma   weight residual
     121.54  127.71   -6.17 1.91e+00 2.74e-01 1.04e+01
  angle pdb=" CB  ARG B  67 "
        pdb=" CG  ARG B  67 "
        pdb=" CD  ARG B  67 "
      ideal   model   delta    sigma   weight residual
     111.30  118.48   -7.18 2.30e+00 1.89e-01 9.74e+00
  angle pdb=" CA  ARG B  67 "
        pdb=" CB  ARG B  67 "
        pdb=" CG  ARG B  67 "
      ideal   model   delta    sigma   weight residual
     114.10  119.28   -5.18 2.00e+00 2.50e-01 6.72e+00
  angle pdb=" N   GLN A 125 "
        pdb=" CA  GLN A 125 "
        pdb=" CB  GLN A 125 "
      ideal   model   delta    sigma   weight residual
     110.28  113.84   -3.56 1.55e+00 4.16e-01 5.28e+00
  ... (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: 1558
       0.028 -    0.055: 471
       0.055 -    0.083: 135
       0.083 -    0.110: 62
       0.110 -    0.138: 14
  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:             8.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     36.150
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.010
  Internal consistency checks:             0.000
  Total:   48.350
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8503
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      :  0.003   0.049  13661  Z= 0.151
  Angle     :  0.557   7.178  19704  Z= 0.330
  Chirality :  0.033   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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 HIS   0.005   0.001   HIS A 113 
 PHE   0.009   0.001   PHE E  78 
 TYR   0.020   0.001   TYR H  40 
 ARG   0.013   0.000   ARG B  67 

Details of bonding type rmsd
  link_TRANS           : bond        0.00080 (    2)
  link_TRANS           : angle       0.53035 (    6)
  hydrogen bonds       : bond        0.10334 (  768)
  hydrogen bonds       : angle       3.99937 ( 1920)
  covalent geometry    : bond        0.00321 (13659)
  covalent geometry    : angle       0.55738 (19698)

*********************** 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  : 0.906 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.8392 (m-30) cc_final: 0.7864 (t70)
REVERT: B   31 LYS cc_start: 0.9018 (ttmt) cc_final: 0.8770 (ttpp)
REVERT: B   91 LYS cc_start: 0.9420 (ttmm) cc_final: 0.9160 (ttmt)
REVERT: D   51 ASP cc_start: 0.9279 (p0) cc_final: 0.8711 (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: 0.8894 (p)
REVERT: E   59 GLU cc_start: 0.8782 (pm20) cc_final: 0.7941 (pm20)
REVERT: E   82 LEU cc_start: 0.9341 (mt) cc_final: 0.9119 (mm)
REVERT: E   94 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8359 (mm-30)
REVERT: E  110 CYS cc_start: 0.7931 (m) cc_final: 0.7656 (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: 0.8923 (mttp)
REVERT: M   44 ILE cc_start: 0.5531 (mm) cc_final: 0.4842 (mp)
REVERT: C   64 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8415 (tm-30)
REVERT: G   41 GLU cc_start: 0.8634 (tm-30) cc_final: 0.8178 (tm-30)
REVERT: G   64 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8684 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 229
  average time/residue: 0.3021
  time to fit residues: 92.3665
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  : 0.910 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 91 optimal weight:    0.8980
   chunk 81 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 32 optimal weight:    0.5980
   chunk 51 optimal weight:    0.6980
   chunk 63 optimal weight:    4.9990
   chunk 98 optimal weight:    8.9990
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.086555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.054945 restraints weight = 48981.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.057163 restraints weight = 21574.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.058597 restraints weight = 13648.682|
|-----------------------------------------------------------------------------|
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2695
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2695 r_free = 0.2695    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.25   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 = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2693
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.1216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  13661  Z= 0.219
  Angle     :  0.603   7.407  19704  Z= 0.352
  Chirality :  0.036   0.149   2240
  Planarity :  0.004   0.043   1478
  Dihedral  : 29.676 148.629   4171
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 11.51 %
    Favored  : 86.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.29), residues: 839
  helix:  2.58 (0.22), residues: 555
  sheet:  2.08 (1.30), residues: 18
  loop : -0.51 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS A 113 
 PHE   0.013   0.001   PHE A  78 
 TYR   0.013   0.002   TYR B  88 
 ARG   0.013   0.000   ARG M  42 

Details of bonding type rmsd
  link_TRANS           : bond        0.00034 (    2)
  link_TRANS           : angle       0.43106 (    6)
  hydrogen bonds       : bond        0.04957 (  768)
  hydrogen bonds       : angle       3.35835 ( 1920)
  covalent geometry    : bond        0.00499 (13659)
  covalent geometry    : angle       0.60314 (19698)

*********************** 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
  201 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 185
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.8173 (m-30) cc_final: 0.7915 (t70)
REVERT: B   25 ASN cc_start: 0.8675 (m-40) cc_final: 0.8046 (m110)
REVERT: B   31 LYS cc_start: 0.9232 (ttmt) cc_final: 0.9007 (ttpp)
REVERT: B   91 LYS cc_start: 0.9478 (ttmm) cc_final: 0.9177 (ttmt)
REVERT: D   51 ASP cc_start: 0.9083 (p0) cc_final: 0.8412 (p0)
REVERT: D   85 LYS cc_start: 0.9384 (mttm) cc_final: 0.9119 (mmtt)
REVERT: E   57 SER cc_start: 0.9389 (p) cc_final: 0.8896 (p)
REVERT: E   59 GLU cc_start: 0.8824 (pm20) cc_final: 0.7987 (pm20)
REVERT: E   82 LEU cc_start: 0.9513 (mt) cc_final: 0.9275 (mm)
REVERT: E  105 GLU cc_start: 0.8552 (tp30) cc_final: 0.8236 (tp30)
REVERT: F   85 ASP cc_start: 0.8805 (m-30) cc_final: 0.8329 (m-30)
REVERT: F   88 TYR cc_start: 0.8459 (m-10) cc_final: 0.8064 (m-10)
REVERT: F   91 LYS cc_start: 0.9349 (tttp) cc_final: 0.8990 (ttmt)
REVERT: H   83 TYR cc_start: 0.8824 (m-10) cc_final: 0.8501 (m-80)
REVERT: H   85 LYS cc_start: 0.9332 (mttm) cc_final: 0.8956 (mttp)
REVERT: H  105 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6823 (pm20)
REVERT: C   64 GLU cc_start: 0.9139 (tm-30) cc_final: 0.8483 (tm-30)
REVERT: G   41 GLU cc_start: 0.8369 (tm-30) cc_final: 0.8074 (tm-30)
  outliers start: 16
  outliers final: 13
  residues processed: 191
  average time/residue: 0.3439
  time to fit residues: 89.4734
Evaluate side-chains
  186 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 172
  time to evaluate  : 1.115 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 D residue  122 THR
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 H residue  105 GLU
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=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 102 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 19 optimal weight:    3.9990
   chunk 84 optimal weight:    8.9990
   chunk 95 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 99 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   overall best weight:    1.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.084329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2593 r_free = 0.2593 target = 0.053133 restraints weight = 40192.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2639 r_free = 0.2639 target = 0.055120 restraints weight = 19716.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2668 r_free = 0.2668 target = 0.056377 restraints weight = 13222.779|
|-----------------------------------------------------------------------------|
r_work (final): 0.2646
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2646
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2646 r_free = 0.2646    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2646 r_free = 0.2646    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2646
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8740
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040  13661  Z= 0.270
  Angle     :  0.646   8.269  19704  Z= 0.372
  Chirality :  0.038   0.161   2240
  Planarity :  0.005   0.050   1478
  Dihedral  : 29.840 149.640   4171
  Min Nonbonded Distance : 2.110

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 14.56 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.25 (0.29), residues: 839
  helix:  2.47 (0.22), residues: 554
  sheet:  2.13 (1.29), residues: 18
  loop : -0.70 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H  49 
 PHE   0.021   0.002   PHE A  78 
 TYR   0.028   0.002   TYR B  88 
 ARG   0.006   0.000   ARG H  33 

Details of bonding type rmsd
  link_TRANS           : bond        0.00156 (    2)
  link_TRANS           : angle       0.38583 (    6)
  hydrogen bonds       : bond        0.05461 (  768)
  hydrogen bonds       : angle       3.43014 ( 1920)
  covalent geometry    : bond        0.00622 (13659)
  covalent geometry    : angle       0.64591 (19698)

*********************** 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
  210 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 185
  time to evaluate  : 1.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.8280 (pm20)
REVERT: A   81 ASP cc_start: 0.7973 (m-30) cc_final: 0.7762 (t70)
REVERT: A  123 ASP cc_start: 0.9347 (m-30) cc_final: 0.9117 (m-30)
REVERT: B   25 ASN cc_start: 0.8691 (m-40) cc_final: 0.8006 (m110)
REVERT: B   91 LYS cc_start: 0.9477 (ttmm) cc_final: 0.9170 (ttmt)
REVERT: D   33 ARG cc_start: 0.8388 (ttm-80) cc_final: 0.7978 (ttm-80)
REVERT: D   42 TYR cc_start: 0.8851 (t80) cc_final: 0.8360 (t80)
REVERT: D   46 LYS cc_start: 0.9453 (tppt) cc_final: 0.9201 (tppt)
REVERT: D   51 ASP cc_start: 0.9077 (p0) cc_final: 0.8593 (p0)
REVERT: D   85 LYS cc_start: 0.9388 (mttm) cc_final: 0.9187 (mmtt)
REVERT: E   57 SER cc_start: 0.9378 (p) cc_final: 0.8644 (p)
REVERT: E   59 GLU cc_start: 0.8841 (pm20) cc_final: 0.8077 (pm20)
REVERT: F   88 TYR cc_start: 0.8817 (m-10) cc_final: 0.8160 (m-10)
REVERT: F   91 LYS cc_start: 0.9422 (tttp) cc_final: 0.9169 (ttmt)
REVERT: H   83 TYR cc_start: 0.8940 (m-10) cc_final: 0.8314 (m-10)
REVERT: H   85 LYS cc_start: 0.9328 (mttm) cc_final: 0.8851 (mtmm)
REVERT: C   64 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8465 (tm-30)
REVERT: G   41 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8057 (tm-30)
  outliers start: 25
  outliers final: 20
  residues processed: 196
  average time/residue: 0.3611
  time to fit residues: 98.7010
Evaluate side-chains
  195 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 174
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
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 D residue   52 THR
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  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 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 41 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 46 optimal weight:    0.5980
   chunk 73 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 47 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 71 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
** M  40 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 = 0.3279 r_free = 0.3279 target = 0.086991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2657 r_free = 0.2657 target = 0.055994 restraints weight = 38488.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.058023 restraints weight = 18906.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.059285 restraints weight = 12718.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2708
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2708 r_free = 0.2708    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2708
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  13661  Z= 0.167
  Angle     :  0.585   8.438  19704  Z= 0.341
  Chirality :  0.034   0.150   2240
  Planarity :  0.004   0.036   1478
  Dihedral  : 29.636 148.389   4171
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 16.78 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.29), residues: 839
  helix:  2.69 (0.22), residues: 554
  sheet:  1.89 (1.22), residues: 18
  loop : -0.68 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS H 109 
 PHE   0.016   0.001   PHE A  78 
 TYR   0.024   0.001   TYR B  88 
 ARG   0.009   0.000   ARG M  42 

Details of bonding type rmsd
  link_TRANS           : bond        0.00029 (    2)
  link_TRANS           : angle       0.39116 (    6)
  hydrogen bonds       : bond        0.04366 (  768)
  hydrogen bonds       : angle       3.00199 ( 1920)
  covalent geometry    : bond        0.00368 (13659)
  covalent geometry    : angle       0.58501 (19698)

*********************** 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
  210 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 190
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8441 (OUTLIER) cc_final: 0.8192 (pm20)
REVERT: A  125 GLN cc_start: 0.8230 (mt0) cc_final: 0.7351 (mp10)
REVERT: B   25 ASN cc_start: 0.8620 (m-40) cc_final: 0.7898 (m110)
REVERT: B   88 TYR cc_start: 0.8498 (m-10) cc_final: 0.8059 (m-10)
REVERT: B   91 LYS cc_start: 0.9453 (ttmm) cc_final: 0.9154 (ttmt)
REVERT: D   33 ARG cc_start: 0.8310 (ttm-80) cc_final: 0.7900 (ttm-80)
REVERT: D   42 TYR cc_start: 0.8681 (t80) cc_final: 0.8341 (t80)
REVERT: D   46 LYS cc_start: 0.9457 (tppt) cc_final: 0.9256 (tppt)
REVERT: D   51 ASP cc_start: 0.8993 (p0) cc_final: 0.8499 (p0)
REVERT: D   83 TYR cc_start: 0.8101 (m-10) cc_final: 0.7787 (m-10)
REVERT: D  120 LYS cc_start: 0.9064 (ttmt) cc_final: 0.8821 (tttt)
REVERT: E   57 SER cc_start: 0.9341 (p) cc_final: 0.8529 (p)
REVERT: E   59 GLU cc_start: 0.8761 (pm20) cc_final: 0.8052 (pm20)
REVERT: F   85 ASP cc_start: 0.8907 (m-30) cc_final: 0.8419 (m-30)
REVERT: F   88 TYR cc_start: 0.8833 (m-10) cc_final: 0.8280 (m-10)
REVERT: F   91 LYS cc_start: 0.9379 (tttp) cc_final: 0.9159 (ttmt)
REVERT: H   83 TYR cc_start: 0.8722 (m-10) cc_final: 0.8358 (m-80)
REVERT: H   85 LYS cc_start: 0.9345 (mttm) cc_final: 0.8886 (mtmm)
REVERT: C   64 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8634 (tm-30)
REVERT: C   74 LYS cc_start: 0.9368 (mtmt) cc_final: 0.9124 (tppt)
REVERT: G   41 GLU cc_start: 0.8455 (tm-30) cc_final: 0.8031 (tm-30)
  outliers start: 20
  outliers final: 16
  residues processed: 198
  average time/residue: 0.4259
  time to fit residues: 116.6867
Evaluate side-chains
  191 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 174
  time to evaluate  : 3.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain D residue  118 VAL
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   81 VAL
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   79 ILE
Chi-restraints excluded: chain C residue  116 LEU
Chi-restraints excluded: chain G residue   16 THR
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 78 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   chunk 92 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0030
   chunk 0 optimal weight:    4.9990
   chunk 20 optimal weight:    0.5980
   chunk 96 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 70 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   overall best weight:    1.5194

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
F  25 ASN
** M  40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
M  62 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.085421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2611 r_free = 0.2611 target = 0.053991 restraints weight = 43066.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.056049 restraints weight = 20384.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.057368 restraints weight = 13446.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2667
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2667 r_free = 0.2667    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2668 r_free = 0.2668    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2668
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8723
moved from start:          0.1983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  13661  Z= 0.223
  Angle     :  0.622  13.720  19704  Z= 0.356
  Chirality :  0.036   0.155   2240
  Planarity :  0.004   0.036   1478
  Dihedral  : 29.763 149.892   4171
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 17.75 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.40 (0.29), residues: 839
  helix:  2.62 (0.22), residues: 555
  sheet:  1.71 (1.22), residues: 18
  loop : -0.73 (0.37), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS H 109 
 PHE   0.015   0.001   PHE A  78 
 TYR   0.024   0.002   TYR B  88 
 ARG   0.008   0.000   ARG M  42 

Details of bonding type rmsd
  link_TRANS           : bond        0.00118 (    2)
  link_TRANS           : angle       0.29370 (    6)
  hydrogen bonds       : bond        0.04935 (  768)
  hydrogen bonds       : angle       3.18828 ( 1920)
  covalent geometry    : bond        0.00511 (13659)
  covalent geometry    : angle       0.62171 (19698)

*********************** 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
  206 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 178
  time to evaluate  : 0.936 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8178 (pm20)
REVERT: A  123 ASP cc_start: 0.9310 (m-30) cc_final: 0.9045 (m-30)
REVERT: A  125 GLN cc_start: 0.8276 (mt0) cc_final: 0.7536 (mt0)
REVERT: B   25 ASN cc_start: 0.8681 (m-40) cc_final: 0.7973 (m110)
REVERT: B   88 TYR cc_start: 0.8512 (m-10) cc_final: 0.7938 (m-10)
REVERT: B   91 LYS cc_start: 0.9465 (ttmm) cc_final: 0.9184 (ttmt)
REVERT: D   33 ARG cc_start: 0.8377 (ttm-80) cc_final: 0.8015 (ttm-80)
REVERT: D   42 TYR cc_start: 0.8771 (t80) cc_final: 0.8259 (t80)
REVERT: D   46 LYS cc_start: 0.9438 (tppt) cc_final: 0.8974 (tppt)
REVERT: D   51 ASP cc_start: 0.9059 (p0) cc_final: 0.8530 (p0)
REVERT: D   83 TYR cc_start: 0.8146 (m-10) cc_final: 0.7559 (m-10)
REVERT: E   57 SER cc_start: 0.9365 (p) cc_final: 0.8467 (p)
REVERT: E   59 GLU cc_start: 0.8772 (pm20) cc_final: 0.8069 (pm20)
REVERT: F   88 TYR cc_start: 0.8848 (m-10) cc_final: 0.8232 (m-10)
REVERT: F   91 LYS cc_start: 0.9399 (tttp) cc_final: 0.9190 (ttmt)
REVERT: H   83 TYR cc_start: 0.8805 (m-10) cc_final: 0.8333 (m-10)
REVERT: H   85 LYS cc_start: 0.9336 (mttm) cc_final: 0.8868 (mtmm)
REVERT: C   64 GLU cc_start: 0.9146 (tm-30) cc_final: 0.8446 (tm-30)
REVERT: G   41 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8028 (tm-30)
  outliers start: 28
  outliers final: 21
  residues processed: 189
  average time/residue: 0.2754
  time to fit residues: 72.4750
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  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
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 D residue  118 VAL
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 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  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  116 LEU
Chi-restraints excluded: chain G residue   16 THR
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 25 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 103 optimal weight:    0.7980
   chunk 76 optimal weight:    4.9990
   chunk 95 optimal weight:    0.9980
   chunk 107 optimal weight:    0.0970
   chunk 80 optimal weight:    0.0470
   chunk 8 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 54 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.5076

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
** M  40 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 = 0.3296 r_free = 0.3296 target = 0.087961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.056943 restraints weight = 39094.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.059021 restraints weight = 19030.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2754 r_free = 0.2754 target = 0.060333 restraints weight = 12701.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.2731
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2731
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2731 r_free = 0.2731    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 = 0.2731 r_free = 0.2731    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2731
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.1977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13661  Z= 0.152
  Angle     :  0.577   8.975  19704  Z= 0.335
  Chirality :  0.034   0.151   2240
  Planarity :  0.004   0.036   1478
  Dihedral  : 29.581 148.300   4171
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 18.72 %
    Favored  : 78.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.62 (0.29), residues: 839
  helix:  2.81 (0.22), residues: 553
  sheet:  1.62 (1.21), residues: 18
  loop : -0.66 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.005   0.001   HIS H 109 
 PHE   0.010   0.001   PHE E  78 
 TYR   0.014   0.001   TYR B  88 
 ARG   0.009   0.000   ARG H  33 

Details of bonding type rmsd
  link_TRANS           : bond        0.00040 (    2)
  link_TRANS           : angle       0.41954 (    6)
  hydrogen bonds       : bond        0.04121 (  768)
  hydrogen bonds       : angle       2.85936 ( 1920)
  covalent geometry    : bond        0.00327 (13659)
  covalent geometry    : angle       0.57748 (19698)

*********************** 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
  212 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 192
  time to evaluate  : 0.952 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8090 (pm20)
REVERT: A  123 ASP cc_start: 0.9227 (m-30) cc_final: 0.8918 (m-30)
REVERT: A  125 GLN cc_start: 0.8233 (mt0) cc_final: 0.7412 (mt0)
REVERT: B   25 ASN cc_start: 0.8599 (m-40) cc_final: 0.7757 (m110)
REVERT: B   88 TYR cc_start: 0.8530 (m-10) cc_final: 0.7942 (m-10)
REVERT: B   91 LYS cc_start: 0.9451 (ttmm) cc_final: 0.9203 (ttmt)
REVERT: D   33 ARG cc_start: 0.8389 (ttm-80) cc_final: 0.8093 (ttm-80)
REVERT: D   42 TYR cc_start: 0.8648 (t80) cc_final: 0.8191 (t80)
REVERT: D   46 LYS cc_start: 0.9448 (tppt) cc_final: 0.9126 (tppt)
REVERT: D   51 ASP cc_start: 0.8970 (p0) cc_final: 0.8469 (p0)
REVERT: D   83 TYR cc_start: 0.8121 (m-10) cc_final: 0.7603 (m-10)
REVERT: D  120 LYS cc_start: 0.8998 (ttmt) cc_final: 0.8781 (tttt)
REVERT: E   57 SER cc_start: 0.9324 (p) cc_final: 0.8890 (p)
REVERT: E   59 GLU cc_start: 0.8727 (pm20) cc_final: 0.8084 (pm20)
REVERT: F   85 ASP cc_start: 0.8814 (m-30) cc_final: 0.8343 (m-30)
REVERT: F   88 TYR cc_start: 0.8819 (m-10) cc_final: 0.8281 (m-10)
REVERT: H   83 TYR cc_start: 0.8767 (m-10) cc_final: 0.8357 (m-10)
REVERT: H   85 LYS cc_start: 0.9339 (mttm) cc_final: 0.8882 (mtmm)
REVERT: C   64 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8636 (tm-30)
REVERT: G   41 GLU cc_start: 0.8291 (tm-30) cc_final: 0.7943 (tm-30)
  outliers start: 20
  outliers final: 15
  residues processed: 199
  average time/residue: 0.2943
  time to fit residues: 80.5017
Evaluate side-chains
  197 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 181
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
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 E residue  110 CYS
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  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   16 THR
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 100 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 0 optimal weight:    4.9990
   chunk 77 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 83 optimal weight:    6.9990
   chunk 63 optimal weight:    4.9990
   chunk 41 optimal weight:    0.1980
   chunk 104 optimal weight:    2.9990
   chunk 56 optimal weight:    4.9990
   chunk 64 optimal weight:    4.9990
   overall best weight:    1.4388

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
** M  40 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 = 0.3260 r_free = 0.3260 target = 0.085967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.054765 restraints weight = 40206.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2674 r_free = 0.2674 target = 0.056801 restraints weight = 19521.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.058051 restraints weight = 13079.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.2682
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2682
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2682 r_free = 0.2682    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2682 r_free = 0.2682    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2682
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8712
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  13661  Z= 0.214
  Angle     :  0.612  11.764  19704  Z= 0.351
  Chirality :  0.035   0.157   2240
  Planarity :  0.004   0.036   1478
  Dihedral  : 29.722 149.640   4171
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 18.86 %
    Favored  : 77.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.52 (0.29), residues: 839
  helix:  2.73 (0.22), residues: 554
  sheet:  1.62 (1.21), residues: 18
  loop : -0.70 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.004   0.001   HIS H 109 
 PHE   0.009   0.001   PHE E  78 
 TYR   0.019   0.002   TYR B  88 
 ARG   0.009   0.000   ARG H  33 

Details of bonding type rmsd
  link_TRANS           : bond        0.00108 (    2)
  link_TRANS           : angle       0.32476 (    6)
  hydrogen bonds       : bond        0.04726 (  768)
  hydrogen bonds       : angle       3.08997 ( 1920)
  covalent geometry    : bond        0.00489 (13659)
  covalent geometry    : angle       0.61193 (19698)

*********************** 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
  196 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 171
  time to evaluate  : 0.954 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8097 (pm20)
REVERT: A  123 ASP cc_start: 0.9321 (m-30) cc_final: 0.9026 (m-30)
REVERT: A  125 GLN cc_start: 0.8285 (mt0) cc_final: 0.7526 (mt0)
REVERT: B   25 ASN cc_start: 0.8661 (m-40) cc_final: 0.7904 (m110)
REVERT: B   88 TYR cc_start: 0.8586 (m-10) cc_final: 0.7923 (m-10)
REVERT: B   91 LYS cc_start: 0.9471 (ttmm) cc_final: 0.9229 (ttmt)
REVERT: D   33 ARG cc_start: 0.8431 (ttm-80) cc_final: 0.8078 (ttm-80)
REVERT: D   42 TYR cc_start: 0.8860 (t80) cc_final: 0.8196 (t80)
REVERT: D   46 LYS cc_start: 0.9455 (tppt) cc_final: 0.8920 (tppt)
REVERT: D   51 ASP cc_start: 0.9024 (p0) cc_final: 0.8565 (p0)
REVERT: D   83 TYR cc_start: 0.8252 (m-10) cc_final: 0.7712 (m-10)
REVERT: E   57 SER cc_start: 0.9297 (p) cc_final: 0.8845 (p)
REVERT: E   59 GLU cc_start: 0.8748 (pm20) cc_final: 0.8156 (pm20)
REVERT: F   85 ASP cc_start: 0.8897 (m-30) cc_final: 0.8484 (m-30)
REVERT: F   88 TYR cc_start: 0.8873 (m-10) cc_final: 0.8300 (m-10)
REVERT: H   83 TYR cc_start: 0.8741 (m-10) cc_final: 0.8324 (m-10)
REVERT: H   85 LYS cc_start: 0.9329 (mttm) cc_final: 0.8861 (mtmm)
REVERT: C   64 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8476 (tm-30)
REVERT: G   41 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8006 (tm-30)
  outliers start: 25
  outliers final: 21
  residues processed: 182
  average time/residue: 0.2722
  time to fit residues: 68.8075
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  : 0.954 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   92 LEU
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  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   16 THR
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 105 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 34 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 53 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   chunk 89 optimal weight:    0.5980
   chunk 69 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
** M  40 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 = 0.3279 r_free = 0.3279 target = 0.086979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.055376 restraints weight = 51820.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.057645 restraints weight = 21886.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2728 r_free = 0.2728 target = 0.059119 restraints weight = 13632.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2706
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2706 r_free = 0.2706    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 = 0.2706 r_free = 0.2706    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2706
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8684
moved from start:          0.2121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13661  Z= 0.169
  Angle     :  0.586   8.488  19704  Z= 0.339
  Chirality :  0.034   0.158   2240
  Planarity :  0.004   0.036   1478
  Dihedral  : 29.637 148.635   4171
  Min Nonbonded Distance : 2.133

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 19.28 %
    Favored  : 77.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.62 (0.29), residues: 839
  helix:  2.80 (0.22), residues: 554
  sheet:  1.56 (1.20), residues: 18
  loop : -0.63 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H 109 
 PHE   0.010   0.001   PHE E  78 
 TYR   0.013   0.001   TYR B  88 
 ARG   0.008   0.000   ARG M  42 

Details of bonding type rmsd
  link_TRANS           : bond        0.00030 (    2)
  link_TRANS           : angle       0.38652 (    6)
  hydrogen bonds       : bond        0.04280 (  768)
  hydrogen bonds       : angle       2.91362 ( 1920)
  covalent geometry    : bond        0.00374 (13659)
  covalent geometry    : angle       0.58615 (19698)

*********************** 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
  201 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 180
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.8050 (pm20)
REVERT: A  123 ASP cc_start: 0.9258 (m-30) cc_final: 0.8954 (m-30)
REVERT: A  125 GLN cc_start: 0.8251 (mt0) cc_final: 0.7448 (mt0)
REVERT: B   25 ASN cc_start: 0.8622 (m-40) cc_final: 0.7757 (m110)
REVERT: B   88 TYR cc_start: 0.8553 (m-10) cc_final: 0.7913 (m-10)
REVERT: B   91 LYS cc_start: 0.9467 (ttmm) cc_final: 0.9205 (ttmt)
REVERT: D   33 ARG cc_start: 0.8404 (ttm-80) cc_final: 0.8084 (ttm-80)
REVERT: D   42 TYR cc_start: 0.8802 (t80) cc_final: 0.8093 (t80)
REVERT: D   46 LYS cc_start: 0.9459 (tppt) cc_final: 0.9071 (tppt)
REVERT: D   51 ASP cc_start: 0.8992 (p0) cc_final: 0.8458 (p0)
REVERT: D   83 TYR cc_start: 0.8187 (m-10) cc_final: 0.7568 (m-10)
REVERT: D  100 LEU cc_start: 0.9483 (mt) cc_final: 0.9240 (mt)
REVERT: E   57 SER cc_start: 0.9265 (p) cc_final: 0.8814 (p)
REVERT: E   59 GLU cc_start: 0.8729 (pm20) cc_final: 0.8159 (pm20)
REVERT: F   85 ASP cc_start: 0.8879 (m-30) cc_final: 0.8392 (m-30)
REVERT: F   88 TYR cc_start: 0.8852 (m-10) cc_final: 0.8392 (m-10)
REVERT: H   83 TYR cc_start: 0.8779 (m-10) cc_final: 0.8418 (m-10)
REVERT: H   85 LYS cc_start: 0.9319 (mttm) cc_final: 0.8860 (mtmm)
REVERT: M   42 ARG cc_start: 0.5800 (ttp-110) cc_final: 0.5342 (ttp-110)
REVERT: C   64 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8621 (tm-30)
REVERT: G   41 GLU cc_start: 0.8322 (tm-30) cc_final: 0.7973 (tm-30)
  outliers start: 21
  outliers final: 17
  residues processed: 188
  average time/residue: 0.2726
  time to fit residues: 71.0463
Evaluate side-chains
  195 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 177
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue   93 GLN
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  101 LEU
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   16 THR
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 80 optimal weight:    0.2980
   chunk 61 optimal weight:    4.9990
   chunk 64 optimal weight:    4.9990
   chunk 81 optimal weight:   10.0000
   chunk 20 optimal weight:    0.5980
   chunk 52 optimal weight:    5.9990
   chunk 42 optimal weight:    0.5980
   chunk 71 optimal weight:    3.9990
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** M  40 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 = 0.3282 r_free = 0.3282 target = 0.087176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.055665 restraints weight = 51152.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.057921 restraints weight = 21775.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.059379 restraints weight = 13587.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2709
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2709 r_free = 0.2709    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2709 r_free = 0.2709    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2709
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.2138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13661  Z= 0.170
  Angle     :  0.590   8.499  19704  Z= 0.341
  Chirality :  0.034   0.161   2240
  Planarity :  0.004   0.039   1478
  Dihedral  : 29.628 148.796   4171
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.65 (0.29), residues: 839
  helix:  2.81 (0.22), residues: 554
  sheet:  1.55 (1.08), residues: 26
  loop : -0.65 (0.36), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H 109 
 PHE   0.009   0.001   PHE E  78 
 TYR   0.013   0.001   TYR B  88 
 ARG   0.011   0.000   ARG M  42 

Details of bonding type rmsd
  link_TRANS           : bond        0.00034 (    2)
  link_TRANS           : angle       0.38646 (    6)
  hydrogen bonds       : bond        0.04281 (  768)
  hydrogen bonds       : angle       2.91339 ( 1920)
  covalent geometry    : bond        0.00377 (13659)
  covalent geometry    : angle       0.58960 (19698)

*********************** 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
  203 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 180
  time to evaluate  : 0.955 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.8016 (pm20)
REVERT: A  123 ASP cc_start: 0.9254 (m-30) cc_final: 0.8945 (m-30)
REVERT: A  125 GLN cc_start: 0.8264 (mt0) cc_final: 0.7416 (mt0)
REVERT: B   25 ASN cc_start: 0.8616 (m-40) cc_final: 0.7771 (m110)
REVERT: B   88 TYR cc_start: 0.8569 (m-10) cc_final: 0.7883 (m-10)
REVERT: B   91 LYS cc_start: 0.9463 (ttmm) cc_final: 0.9211 (ttmt)
REVERT: D   33 ARG cc_start: 0.8346 (ttm-80) cc_final: 0.8031 (ttm-80)
REVERT: D   42 TYR cc_start: 0.8797 (t80) cc_final: 0.8151 (t80)
REVERT: D   46 LYS cc_start: 0.9461 (tppt) cc_final: 0.8927 (tppt)
REVERT: D   51 ASP cc_start: 0.8974 (p0) cc_final: 0.8465 (p0)
REVERT: D   59 MET cc_start: 0.9362 (tpp) cc_final: 0.9051 (mmm)
REVERT: D   83 TYR cc_start: 0.8201 (m-10) cc_final: 0.7539 (m-10)
REVERT: E   57 SER cc_start: 0.9249 (p) cc_final: 0.8800 (p)
REVERT: E   59 GLU cc_start: 0.8726 (pm20) cc_final: 0.8141 (pm20)
REVERT: F   85 ASP cc_start: 0.8880 (m-30) cc_final: 0.8392 (m-30)
REVERT: F   88 TYR cc_start: 0.8860 (m-10) cc_final: 0.8383 (m-10)
REVERT: H   83 TYR cc_start: 0.8783 (m-10) cc_final: 0.8411 (m-10)
REVERT: H   85 LYS cc_start: 0.9319 (mttm) cc_final: 0.8859 (mtmm)
REVERT: M   42 ARG cc_start: 0.5984 (ttp-110) cc_final: 0.5756 (ttp-110)
REVERT: C   64 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8621 (tm-30)
REVERT: G   41 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7971 (tm-30)
  outliers start: 23
  outliers final: 20
  residues processed: 189
  average time/residue: 0.2821
  time to fit residues: 74.2276
Evaluate side-chains
  195 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 174
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   92 LEU
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 H residue  122 THR
Chi-restraints excluded: chain M residue   56 LEU
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 22 optimal weight:    0.0470
   chunk 28 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0370
   chunk 76 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 36 optimal weight:    0.8980
   chunk 73 optimal weight:    4.9990
   chunk 82 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.4556

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
** M  40 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 = 0.3318 r_free = 0.3318 target = 0.089021 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2685 r_free = 0.2685 target = 0.057419 restraints weight = 54308.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.059818 restraints weight = 22073.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.061388 restraints weight = 13391.188|
|-----------------------------------------------------------------------------|
r_work (final): 0.2751
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2751
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2751 r_free = 0.2751    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2751
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13661  Z= 0.150
  Angle     :  0.584   8.475  19704  Z= 0.337
  Chirality :  0.033   0.160   2240
  Planarity :  0.004   0.036   1478
  Dihedral  : 29.500 148.037   4171
  Min Nonbonded Distance : 2.142

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  : 20.67 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.77 (0.29), residues: 839
  helix:  2.89 (0.22), residues: 554
  sheet:  1.48 (1.08), residues: 26
  loop : -0.57 (0.36), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H 109 
 PHE   0.009   0.001   PHE E  78 
 TYR   0.011   0.001   TYR B  88 
 ARG   0.020   0.000   ARG M  42 

Details of bonding type rmsd
  link_TRANS           : bond        0.00014 (    2)
  link_TRANS           : angle       0.45183 (    6)
  hydrogen bonds       : bond        0.03906 (  768)
  hydrogen bonds       : angle       2.77469 ( 1920)
  covalent geometry    : bond        0.00321 (13659)
  covalent geometry    : angle       0.58362 (19698)

********************** 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
  194 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 181
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.8034 (pm20)
REVERT: A  123 ASP cc_start: 0.9214 (m-30) cc_final: 0.8893 (m-30)
REVERT: A  125 GLN cc_start: 0.8232 (mt0) cc_final: 0.7290 (mt0)
REVERT: B   25 ASN cc_start: 0.8592 (m-40) cc_final: 0.7645 (m110)
REVERT: B   88 TYR cc_start: 0.8444 (m-10) cc_final: 0.7861 (m-10)
REVERT: B   91 LYS cc_start: 0.9463 (ttmm) cc_final: 0.9220 (ttmt)
REVERT: D   33 ARG cc_start: 0.8243 (ttm-80) cc_final: 0.7972 (ttm-80)
REVERT: D   42 TYR cc_start: 0.8513 (t80) cc_final: 0.7973 (t80)
REVERT: D   46 LYS cc_start: 0.9432 (tppt) cc_final: 0.9067 (tppt)
REVERT: D   51 ASP cc_start: 0.8987 (p0) cc_final: 0.8456 (p0)
REVERT: D   59 MET cc_start: 0.9310 (tpp) cc_final: 0.8973 (mmm)
REVERT: D   83 TYR cc_start: 0.8097 (m-10) cc_final: 0.7519 (m-10)
REVERT: D   92 ARG cc_start: 0.8853 (ttt-90) cc_final: 0.8645 (ttm170)
REVERT: E   57 SER cc_start: 0.9186 (p) cc_final: 0.8679 (p)
REVERT: E   59 GLU cc_start: 0.8692 (pm20) cc_final: 0.8141 (pm20)
REVERT: F   85 ASP cc_start: 0.8809 (m-30) cc_final: 0.8330 (m-30)
REVERT: F   88 TYR cc_start: 0.8851 (m-10) cc_final: 0.8369 (m-10)
REVERT: H   83 TYR cc_start: 0.8774 (m-10) cc_final: 0.8427 (m-10)
REVERT: H   85 LYS cc_start: 0.9333 (mttm) cc_final: 0.8887 (mtmm)
REVERT: M   40 GLN cc_start: 0.5274 (tt0) cc_final: 0.4876 (pt0)
REVERT: C   64 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8581 (tm-30)
REVERT: G   41 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7955 (tm-30)
  outliers start: 13
  outliers final: 10
  residues processed: 185
  average time/residue: 0.2757
  time to fit residues: 70.4664
Evaluate side-chains
  188 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 177
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 GLU
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  110 CYS
Chi-restraints excluded: chain E residue   80 THR
Chi-restraints excluded: chain E residue  110 CYS
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain F residue   81 VAL
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 28 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   chunk 82 optimal weight:    8.9990
   chunk 38 optimal weight:    0.9990
   chunk 105 optimal weight:    0.8980
   chunk 78 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 42 optimal weight:    3.9990
   chunk 90 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
** M  40 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 = 0.3305 r_free = 0.3305 target = 0.088354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2667 r_free = 0.2667 target = 0.056631 restraints weight = 56536.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.2720 r_free = 0.2720 target = 0.059020 restraints weight = 22860.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.060620 restraints weight = 13814.616|
|-----------------------------------------------------------------------------|
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2733
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.24   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2733 r_free = 0.2733    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2733
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  13661  Z= 0.172
  Angle     :  0.595   8.493  19704  Z= 0.342
  Chirality :  0.034   0.164   2240
  Planarity :  0.004   0.037   1478
  Dihedral  : 29.530 148.533   4171
  Min Nonbonded Distance : 2.136

Molprobity Statistics.
  All-atom Clashscore : 8.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 20.94 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.74 (0.29), residues: 839
  helix:  2.87 (0.22), residues: 554
  sheet:  1.49 (1.07), residues: 26
  loop : -0.57 (0.36), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 HIS   0.003   0.001   HIS H 109 
 PHE   0.007   0.001   PHE E  78 
 TYR   0.015   0.001   TYR C  57 
 ARG   0.012   0.000   ARG M  42 

Details of bonding type rmsd
  link_TRANS           : bond        0.00062 (    2)
  link_TRANS           : angle       0.37416 (    6)
  hydrogen bonds       : bond        0.04053 (  768)
  hydrogen bonds       : angle       2.82177 ( 1920)
  covalent geometry    : bond        0.00384 (13659)
  covalent geometry    : angle       0.59468 (19698)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4558.82 seconds
wall clock time: 83 minutes 20.47 seconds (5000.47 seconds total)