Starting phenix.real_space_refine
on Wed Feb 12 12:28:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lo8_0935/02_2025/6lo8_0935.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lo8_0935/02_2025/6lo8_0935.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6lo8_0935/02_2025/6lo8_0935.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lo8_0935/02_2025/6lo8_0935.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lo8_0935/02_2025/6lo8_0935.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lo8_0935/02_2025/6lo8_0935.cif"
  }
  resolution = 3.83
  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: 4
    Type Number    sf(0)   Gaussians
     S      63      5.16       5
     C    5075      2.51       5
     N    1348      2.21       5
     O    1486      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7972
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 938
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 938
          Classifications: {'peptide': 129}
          Link IDs: {'PTRANS': 4, 'TRANS': 124}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1440
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 176, 1440
          Classifications: {'peptide': 176}
          Link IDs: {'PTRANS': 10, 'TRANS': 165}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 859
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 859
          Classifications: {'peptide': 108}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'TRANS': 107}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 13
          Planarities with less than four sites: {'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "D"
      Number of atoms: 984
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 984
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 7, 'TRANS': 111}
    Chain: "E"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 661
          Classifications: {'peptide': 80}
          Link IDs: {'TRANS': 79}
    Chain: "F"
      Number of atoms: 660
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 660
          Classifications: {'peptide': 84}
          Link IDs: {'PTRANS': 3, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 618
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 618
          Classifications: {'peptide': 74}
          Link IDs: {'TRANS': 73}
    Chain: "H"
      Number of atoms: 581
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 581
          Classifications: {'peptide': 74}
          Link IDs: {'TRANS': 73}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "I"
      Number of atoms: 661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 661
          Classifications: {'peptide': 80}
          Link IDs: {'TRANS': 79}
    Chain: "J"
      Number of atoms: 570
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 73, 570
          Classifications: {'peptide': 73}
          Link IDs: {'TRANS': 72}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
  Time building chain proxies: 4.89, per 1000 atoms: 0.61
  Number of scatterers: 7972
  At special positions: 0
  Unit cell: (132.93, 104.445, 106.555, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      63     16.00
     O    1486      8.00
     N    1348      7.00
     C    5075      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=13, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  42 " - pdb=" SG  CYS A 141 " distance=1.79
    Simple disulfide: pdb=" SG  CYS E  35 " - pdb=" SG  CYS E  59 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  39 " - pdb=" SG  CYS E  55 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  40 " - pdb=" SG  CYS F  66 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F  44 " - pdb=" SG  CYS F  62 " distance=2.02
    Simple disulfide: pdb=" SG  CYS G  35 " - pdb=" SG  CYS G  59 " distance=2.04
    Simple disulfide: pdb=" SG  CYS G  39 " - pdb=" SG  CYS G  55 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  40 " - pdb=" SG  CYS H  65 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  44 " - pdb=" SG  CYS H  61 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  35 " - pdb=" SG  CYS I  59 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  39 " - pdb=" SG  CYS I  55 " distance=2.01
    Simple disulfide: pdb=" SG  CYS J  40 " - pdb=" SG  CYS J  65 " distance=2.03
    Simple disulfide: pdb=" SG  CYS J  44 " - pdb=" SG  CYS J  61 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.84
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1860

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 2 sheets defined
      80.3% alpha, 0.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.74
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 41
    Processing helix  chain 'A' and resid 42 through 65
      removed outlier: 3.622A  pdb=" N   SER A  46 " --> pdb=" O   CYS A  42 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   SER A  49 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLY A  50 " --> pdb=" O   SER A  46 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   LEU A  62 " --> pdb=" O   GLY A  58 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   PHE A  63 " --> pdb=" O   VAL A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 146
    Processing helix  chain 'A' and resid 154 through 167
      removed outlier: 3.998A  pdb=" N   PHE A 160 " --> pdb=" O   VAL A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 195
    Processing helix  chain 'B' and resid 37 through 62
    Processing helix  chain 'B' and resid 62 through 71
    Processing helix  chain 'B' and resid 99 through 116
      removed outlier: 4.063A  pdb=" N   TYR B 109 " --> pdb=" O   VAL B 105 " (cutoff:3.500A)
      Proline residue:  B 112  - end of helix
    Processing helix  chain 'B' and resid 117 through 119
      No H-bonds generated for 'chain 'B' and resid 117 through 119'
    Processing helix  chain 'B' and resid 130 through 148
    Processing helix  chain 'B' and resid 244 through 261
      removed outlier: 3.607A  pdb=" N   LEU B 260 " --> pdb=" O   HIS B 256 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 386 through 394
    Processing helix  chain 'B' and resid 395 through 412
    Processing helix  chain 'C' and resid 88 through 120
      removed outlier: 4.060A  pdb=" N   PHE C 114 " --> pdb=" O   PHE C 110 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   SER C 117 " --> pdb=" O   LEU C 113 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLY C 118 " --> pdb=" O   PHE C 114 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   LEU C 119 " --> pdb=" O   GLY C 115 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU C 120 " --> pdb=" O   VAL C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 125 through 137
      removed outlier: 3.555A  pdb=" N   PHE C 137 " --> pdb=" O   TYR C 133 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 167
      removed outlier: 3.959A  pdb=" N   ALA C 154 " --> pdb=" O   ALA C 150 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ILE C 155 " --> pdb=" O   TYR C 151 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   HIS C 156 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 174 through 198
      removed outlier: 3.598A  pdb=" N   ARG C 179 " --> pdb=" O   LYS C 175 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 77 through 93
      Proline residue:  D  91  - end of helix
    Processing helix  chain 'D' and resid 93 through 103
      removed outlier: 3.765A  pdb=" N   PHE D  97 " --> pdb=" O   THR D  93 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   THR D 102 " --> pdb=" O   TYR D  98 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLY D 103 " --> pdb=" O   ALA D  99 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 110 through 134
    Processing helix  chain 'D' and resid 140 through 166
      removed outlier: 3.784A  pdb=" N   LYS D 144 " --> pdb=" O   PRO D 140 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   LEU D 145 " --> pdb=" O   ARG D 141 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 170 through 180
    Processing helix  chain 'E' and resid 8 through 40
      removed outlier: 3.777A  pdb=" N   PHE E  12 " --> pdb=" O   GLU E   8 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   CYS E  39 " --> pdb=" O   CYS E  35 " (cutoff:3.500A)
      removed outlier: 3.796A  pdb=" N   VAL E  40 " --> pdb=" O   PHE E  36 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 49 through 81
      removed outlier: 3.601A  pdb=" N   ALA E  80 " --> pdb=" O   GLU E  76 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 16 through 45
      removed outlier: 3.544A  pdb=" N   THR F  32 " --> pdb=" O   ALA F  28 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   CYS F  44 " --> pdb=" O   CYS F  40 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE F  45 " --> pdb=" O   LEU F  41 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 56 through 84
      removed outlier: 4.038A  pdb=" N   GLN F  82 " --> pdb=" O   GLY F  78 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 87 through 92
    Processing helix  chain 'F' and resid 93 through 98
      removed outlier: 3.719A  pdb=" N   ARG F  97 " --> pdb=" O   HIS F  94 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 39
      removed outlier: 4.212A  pdb=" N   CYS G  39 " --> pdb=" O   CYS G  35 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 49 through 80
      removed outlier: 3.569A  pdb=" N   ALA G  80 " --> pdb=" O   GLU G  76 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 15 through 44
      removed outlier: 3.767A  pdb=" N   LEU H  26 " --> pdb=" O   ALA H  22 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   VAL H  29 " --> pdb=" O   GLU H  25 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.596A  pdb=" N   SER H  60 " --> pdb=" O   LYS H  56 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ASP H  63 " --> pdb=" O   SER H  59 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 8 through 38
    Processing helix  chain 'I' and resid 49 through 81
      removed outlier: 3.941A  pdb=" N   ALA I  80 " --> pdb=" O   GLU I  76 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   LEU I  81 " --> pdb=" O   GLN I  77 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 15 through 44
      removed outlier: 3.758A  pdb=" N   GLU J  25 " --> pdb=" O   ALA J  21 " (cutoff:3.500A)
      removed outlier: 4.304A  pdb=" N   CYS J  44 " --> pdb=" O   CYS J  40 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 57 through 83
      removed outlier: 4.003A  pdb=" N   ASP J  63 " --> pdb=" O   SER J  59 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   GLN J  81 " --> pdb=" O   GLY J  77 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   MET J  83 " --> pdb=" O   ASN J  79 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 88 through 91
    Processing sheet with id=AA2, first strand: chain 'B' and resid 240 through 241
      removed outlier: 6.975A  pdb=" N   VAL B 240 " --> pdb=" O   VAL B 373 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2

    611 hydrogen bonds defined for protein.
    1827 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.24

  Time building geometry restraints manager: 2.16 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1324
        1.32 -     1.45: 2170
        1.45 -     1.57: 4530
        1.57 -     1.70: 0
        1.70 -     1.82: 93
  Bond restraints: 8117
  Sorted by residual:
  bond pdb=" N   PRO A  43 "
       pdb=" CD  PRO A  43 "
    ideal  model  delta    sigma   weight residual
    1.473  1.542 -0.069 1.40e-02 5.10e+03 2.43e+01
  bond pdb=" C   CYS I  55 "
       pdb=" O   CYS I  55 "
    ideal  model  delta    sigma   weight residual
    1.237  1.193  0.044 1.17e-02 7.31e+03 1.43e+01
  bond pdb=" CA  ASN G  41 "
       pdb=" C   ASN G  41 "
    ideal  model  delta    sigma   weight residual
    1.522  1.563 -0.042 1.72e-02 3.38e+03 5.85e+00
  bond pdb=" CA  CYS I  55 "
       pdb=" C   CYS I  55 "
    ideal  model  delta    sigma   weight residual
    1.523  1.494  0.029 1.30e-02 5.92e+03 5.05e+00
  bond pdb=" CA  ILE I  56 "
       pdb=" CB  ILE I  56 "
    ideal  model  delta    sigma   weight residual
    1.543  1.506  0.037 1.66e-02 3.63e+03 4.94e+00
  ... (remaining 8112 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.82: 10745
        2.82 -     5.64: 131
        5.64 -     8.46: 21
        8.46 -    11.28: 4
       11.28 -    14.10: 2
  Bond angle restraints: 10903
  Sorted by residual:
  angle pdb=" N   SER A  46 "
        pdb=" CA  SER A  46 "
        pdb=" C   SER A  46 "
      ideal   model   delta    sigma   weight residual
     111.36  119.92   -8.56 1.09e+00 8.42e-01 6.16e+01
  angle pdb=" N   PRO A  43 "
        pdb=" CA  PRO A  43 "
        pdb=" C   PRO A  43 "
      ideal   model   delta    sigma   weight residual
     112.47   98.37   14.10 2.06e+00 2.36e-01 4.69e+01
  angle pdb=" N   CYS I  39 "
        pdb=" CA  CYS I  39 "
        pdb=" C   CYS I  39 "
      ideal   model   delta    sigma   weight residual
     112.94  122.20   -9.26 1.41e+00 5.03e-01 4.32e+01
  angle pdb=" N   ASP I  38 "
        pdb=" CA  ASP I  38 "
        pdb=" C   ASP I  38 "
      ideal   model   delta    sigma   weight residual
     111.36  118.30   -6.94 1.09e+00 8.42e-01 4.06e+01
  angle pdb=" N   CYS A  42 "
        pdb=" CA  CYS A  42 "
        pdb=" C   CYS A  42 "
      ideal   model   delta    sigma   weight residual
     109.81  122.37  -12.56 2.21e+00 2.05e-01 3.23e+01
  ... (remaining 10898 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.54: 4298
       16.54 -    33.09: 497
       33.09 -    49.63: 95
       49.63 -    66.18: 25
       66.18 -    82.72: 13
  Dihedral angle restraints: 4928
    sinusoidal: 2038
      harmonic: 2890
  Sorted by residual:
  dihedral pdb=" CB  CYS I  39 "
           pdb=" SG  CYS I  39 "
           pdb=" SG  CYS I  55 "
           pdb=" CB  CYS I  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   15.45   77.55     1      1.00e+01 1.00e-02 7.53e+01
  dihedral pdb=" CB  CYS H  44 "
           pdb=" SG  CYS H  44 "
           pdb=" SG  CYS H  61 "
           pdb=" CB  CYS H  61 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  168.96  -75.96     1      1.00e+01 1.00e-02 7.27e+01
  dihedral pdb=" CB  CYS J  44 "
           pdb=" SG  CYS J  44 "
           pdb=" SG  CYS J  61 "
           pdb=" CB  CYS J  61 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -147.78   61.78     1      1.00e+01 1.00e-02 5.06e+01
  ... (remaining 4925 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1033
       0.068 -    0.136: 130
       0.136 -    0.204: 17
       0.204 -    0.272: 3
       0.272 -    0.340: 2
  Chirality restraints: 1185
  Sorted by residual:
  chirality pdb=" CA  CYS I  39 "
            pdb=" N   CYS I  39 "
            pdb=" C   CYS I  39 "
            pdb=" CB  CYS I  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.88e+00
  chirality pdb=" CA  ILE I  56 "
            pdb=" N   ILE I  56 "
            pdb=" C   ILE I  56 "
            pdb=" CB  ILE I  56 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.13    0.30 2.00e-01 2.50e+01 2.24e+00
  chirality pdb=" CA  CYS I  35 "
            pdb=" N   CYS I  35 "
            pdb=" C   CYS I  35 "
            pdb=" CB  CYS I  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.54e+00
  ... (remaining 1182 not shown)

  Planarity restraints: 1392
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A  42 "   -0.096 5.00e-02 4.00e+02   1.46e-01 3.41e+01
        pdb=" N   PRO A  43 "    0.252 5.00e-02 4.00e+02
        pdb=" CA  PRO A  43 "   -0.079 5.00e-02 4.00e+02
        pdb=" CD  PRO A  43 "   -0.077 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR I  37 "   -0.024 2.00e-02 2.50e+03   5.06e-02 2.56e+01
        pdb=" C   THR I  37 "    0.087 2.00e-02 2.50e+03
        pdb=" O   THR I  37 "   -0.034 2.00e-02 2.50e+03
        pdb=" N   ASP I  38 "   -0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 107 "    0.016 2.00e-02 2.50e+03   3.22e-02 1.04e+01
        pdb=" C   ARG B 107 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   ARG B 107 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ARG B 108 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1389 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1694
        2.77 -     3.31: 7499
        3.31 -     3.84: 13253
        3.84 -     4.37: 14273
        4.37 -     4.90: 25404
  Nonbonded interactions: 62123
  Sorted by model distance:
  nonbonded pdb=" OG  SER D  71 "
            pdb=" O   SER D 128 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" O   MET A  36 "
            pdb=" OG1 THR A  40 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" O   GLU I  33 "
            pdb=" OG1 THR I  37 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" OH  TYR A 136 "
            pdb=" OG  SER A 186 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" O   ASP E  42 "
            pdb=" NZ  LYS J  68 "
     model   vdw
     2.318 3.120
  ... (remaining 62118 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 'E' and resid 7 through 80)
  selection = chain 'G'
  selection = (chain 'I' and resid 7 through 80)
}
ncs_group {
  reference = (chain 'H' and resid 14 through 86)
  selection = chain 'J'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.840
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  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:0.000
  Internal consistency checks:             0.000
  Total:   26.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073   8117  Z= 0.315
  Angle     :  0.865  14.104  10903  Z= 0.496
  Chirality :  0.049   0.340   1185
  Planarity :  0.007   0.146   1392
  Dihedral  : 14.877  82.722   3029
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 5.11
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  3.72 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  7.10 %
    Favored  : 92.44 %
  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: -3.08 (0.21), residues: 967
  helix: -1.56 (0.14), residues: 753
  sheet: -0.91 (0.97), residues: 22
  loop : -3.38 (0.34), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 106 
 HIS   0.009   0.002   HIS C 156 
 PHE   0.023   0.002   PHE D  65 
 TYR   0.014   0.002   TYR C 133 
 ARG   0.005   0.000   ARG I  73 

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 332
  time to evaluate  : 0.949 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.8288 (mp) cc_final: 0.8030 (pp)
REVERT: A  129 PHE cc_start: 0.7855 (m-80) cc_final: 0.7170 (m-10)
REVERT: A  189 ILE cc_start: 0.9155 (mm) cc_final: 0.8867 (mm)
REVERT: B   39 MET cc_start: 0.4281 (mtm) cc_final: 0.3602 (tmm)
REVERT: B   42 TRP cc_start: 0.7701 (m100) cc_final: 0.7003 (m-10)
REVERT: B   82 LYS cc_start: 0.8166 (mmpt) cc_final: 0.7807 (tptt)
REVERT: C  108 TYR cc_start: 0.8142 (m-80) cc_final: 0.7629 (m-80)
REVERT: C  175 LYS cc_start: 0.8895 (mmmm) cc_final: 0.8646 (tttt)
REVERT: D   82 GLU cc_start: 0.8368 (tp30) cc_final: 0.8101 (tp30)
REVERT: D  123 GLN cc_start: 0.8494 (tm-30) cc_final: 0.8063 (tm-30)
REVERT: D  130 ILE cc_start: 0.9328 (tt) cc_final: 0.9128 (tt)
REVERT: D  165 GLU cc_start: 0.8715 (mm-30) cc_final: 0.8446 (mm-30)
REVERT: G   28 TYR cc_start: 0.8880 (t80) cc_final: 0.8585 (t80)
REVERT: H   19 ILE cc_start: 0.9291 (tt) cc_final: 0.8881 (tp)
REVERT: H   36 LEU cc_start: 0.9542 (tp) cc_final: 0.9313 (tp)
REVERT: H   39 ASN cc_start: 0.8650 (m-40) cc_final: 0.7616 (m110)
REVERT: I   17 GLU cc_start: 0.8570 (tp30) cc_final: 0.8214 (tp30)
REVERT: I   19 LYS cc_start: 0.9305 (mmtt) cc_final: 0.8708 (mtpp)
  outliers start: 4
  outliers final: 2
  residues processed: 336
  average time/residue: 0.2549
  time to fit residues: 108.3922
Evaluate side-chains
  232 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 230
  time to evaluate  : 0.948 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain I residue   35 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 80 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 39 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 74 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9980
   chunk 86 optimal weight:    0.8980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 150 ASN
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 135 ASN
C 156 HIS
F  34 ASN
F  90 ASN
F  91 GLN
G  20 GLN
G  30 ASN
G  53 GLN
G  77 GLN
** H  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
I  30 ASN
J  20 GLN
J  34 ASN
** J  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  75 GLN
J  85 GLN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.074110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.060064 restraints weight = 29567.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.061716 restraints weight = 16334.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.062834 restraints weight = 10914.868|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.102   8117  Z= 0.253
  Angle     :  0.716  13.752  10903  Z= 0.381
  Chirality :  0.040   0.170   1185
  Planarity :  0.005   0.090   1392
  Dihedral  :  5.568  51.923   1075
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.72 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  3.21 %
    Allowed  : 16.38 %
    Favored  : 80.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    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: -0.51 (0.25), residues: 967
  helix:  0.35 (0.17), residues: 762
  sheet:  0.06 (1.07), residues: 22
  loop : -3.07 (0.37), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 106 
 HIS   0.004   0.001   HIS B  65 
 PHE   0.011   0.001   PHE A 182 
 TYR   0.019   0.001   TYR H  49 
 ARG   0.004   0.001   ARG E  69 

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  293 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 265
  time to evaluate  : 1.010 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7240 (tm-30)
REVERT: A   56 LEU cc_start: 0.8232 (mp) cc_final: 0.7975 (pp)
REVERT: A  129 PHE cc_start: 0.7942 (m-80) cc_final: 0.7310 (m-80)
REVERT: B   39 MET cc_start: 0.3961 (mtm) cc_final: 0.3507 (tmm)
REVERT: B   67 THR cc_start: 0.8521 (m) cc_final: 0.8132 (p)
REVERT: B   82 LYS cc_start: 0.8201 (mmpt) cc_final: 0.7742 (tptt)
REVERT: C  103 MET cc_start: 0.8302 (mtt) cc_final: 0.8072 (mtt)
REVERT: D   64 MET cc_start: 0.6572 (tmm) cc_final: 0.6206 (tmm)
REVERT: D  111 ASP cc_start: 0.7475 (t0) cc_final: 0.6997 (t0)
REVERT: D  123 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8327 (tm-30)
REVERT: D  144 LYS cc_start: 0.8404 (tttt) cc_final: 0.8100 (pttm)
REVERT: D  155 MET cc_start: 0.7868 (mmp) cc_final: 0.7625 (mmt)
REVERT: D  165 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8351 (mm-30)
REVERT: E   11 GLU cc_start: 0.8261 (mp0) cc_final: 0.8020 (mp0)
REVERT: E   64 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8227 (mm)
REVERT: F   27 ASP cc_start: 0.8833 (m-30) cc_final: 0.8354 (m-30)
REVERT: F   35 ASN cc_start: 0.8916 (t0) cc_final: 0.8707 (t0)
REVERT: F   84 ARG cc_start: 0.8613 (tpp-160) cc_final: 0.8387 (tpp80)
REVERT: G   22 LYS cc_start: 0.8916 (tptp) cc_final: 0.8599 (tptt)
REVERT: G   28 TYR cc_start: 0.8849 (t80) cc_final: 0.8614 (t80)
REVERT: H   62 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8694 (mm)
REVERT: I   17 GLU cc_start: 0.8736 (tp30) cc_final: 0.8448 (tp30)
REVERT: I   35 CYS cc_start: 0.6086 (m) cc_final: 0.5869 (m)
REVERT: J   23 GLU cc_start: 0.8240 (tp30) cc_final: 0.8010 (tp30)
REVERT: J   80 MET cc_start: 0.8152 (mmp) cc_final: 0.7927 (mmp)
  outliers start: 28
  outliers final: 15
  residues processed: 281
  average time/residue: 0.2294
  time to fit residues: 83.3762
Evaluate side-chains
  245 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 228
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain B residue  401 ASP
Chi-restraints excluded: chain D residue  105 VAL
Chi-restraints excluded: chain D residue  129 CYS
Chi-restraints excluded: chain D residue  149 CYS
Chi-restraints excluded: chain E residue   56 ILE
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain G residue   20 GLN
Chi-restraints excluded: chain G residue   51 LYS
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain H residue   47 THR
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain I residue   41 ASN
Chi-restraints excluded: chain J residue   32 MET
Chi-restraints excluded: chain J residue   44 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 7 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 9 optimal weight:    9.9990
   chunk 82 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 26 optimal weight:    5.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 168 ASN
F  94 HIS
G  20 GLN
G  72 GLN
** H  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** J  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.074212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.060440 restraints weight = 29818.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.062094 restraints weight = 16470.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.063094 restraints weight = 10998.439|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.3414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   8117  Z= 0.226
  Angle     :  0.690  15.359  10903  Z= 0.363
  Chirality :  0.039   0.175   1185
  Planarity :  0.004   0.068   1392
  Dihedral  :  5.266  43.828   1074
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.93 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 18.67 %
    Favored  : 77.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    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:  0.49 (0.26), residues: 967
  helix:  1.09 (0.18), residues: 761
  sheet:  0.19 (1.04), residues: 22
  loop : -2.87 (0.39), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 106 
 HIS   0.005   0.001   HIS E  66 
 PHE   0.020   0.001   PHE C 187 
 TYR   0.016   0.001   TYR E  28 
 ARG   0.004   0.000   ARG I  26 

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 260
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   56 LEU cc_start: 0.8115 (mp) cc_final: 0.7846 (pp)
REVERT: A  129 PHE cc_start: 0.7928 (m-80) cc_final: 0.7222 (m-10)
REVERT: A  194 LYS cc_start: 0.8872 (tppp) cc_final: 0.8588 (mptt)
REVERT: B   39 MET cc_start: 0.3930 (mtm) cc_final: 0.3487 (tmm)
REVERT: B   82 LYS cc_start: 0.8212 (mmpt) cc_final: 0.7776 (tptt)
REVERT: C  163 HIS cc_start: 0.8838 (OUTLIER) cc_final: 0.8316 (t70)
REVERT: D   78 GLN cc_start: 0.8354 (tm-30) cc_final: 0.7917 (tm-30)
REVERT: D  111 ASP cc_start: 0.7756 (t0) cc_final: 0.7174 (t0)
REVERT: D  123 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8162 (tm-30)
REVERT: D  165 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8153 (mm-30)
REVERT: E   18 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.8021 (mp10)
REVERT: E   64 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8285 (mm)
REVERT: F   27 ASP cc_start: 0.8761 (m-30) cc_final: 0.8414 (m-30)
REVERT: F   29 MET cc_start: 0.8012 (mtp) cc_final: 0.7808 (mtt)
REVERT: F   35 ASN cc_start: 0.8944 (t0) cc_final: 0.8724 (t0)
REVERT: G   26 ARG cc_start: 0.8473 (ttp80) cc_final: 0.8227 (ttp80)
REVERT: H   59 SER cc_start: 0.8919 (m) cc_final: 0.8389 (p)
REVERT: H   62 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8747 (mm)
REVERT: I    7 LYS cc_start: 0.9137 (ptmm) cc_final: 0.8560 (tmmt)
REVERT: I   10 GLN cc_start: 0.8863 (mp10) cc_final: 0.8349 (pm20)
REVERT: I   11 GLU cc_start: 0.8013 (mp0) cc_final: 0.7297 (pm20)
REVERT: I   17 GLU cc_start: 0.8700 (tp30) cc_final: 0.8415 (tp30)
REVERT: I   19 LYS cc_start: 0.9449 (mtpp) cc_final: 0.9136 (mtpp)
REVERT: J   80 MET cc_start: 0.7977 (mmp) cc_final: 0.7756 (mmp)
  outliers start: 32
  outliers final: 21
  residues processed: 278
  average time/residue: 0.2393
  time to fit residues: 86.7543
Evaluate side-chains
  257 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 232
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain A residue  162 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  401 ASP
Chi-restraints excluded: chain C residue  163 HIS
Chi-restraints excluded: chain D residue   84 ILE
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  105 VAL
Chi-restraints excluded: chain D residue  129 CYS
Chi-restraints excluded: chain D residue  149 CYS
Chi-restraints excluded: chain E residue   18 GLN
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain F residue   31 SER
Chi-restraints excluded: chain F residue   41 LEU
Chi-restraints excluded: chain G residue   20 GLN
Chi-restraints excluded: chain G residue   41 ASN
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   62 LEU
Chi-restraints excluded: chain I residue    4 LEU
Chi-restraints excluded: chain I residue   41 ASN
Chi-restraints excluded: chain J residue   32 MET
Chi-restraints excluded: chain J residue   44 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 1 optimal weight:   10.0000
   chunk 67 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 16 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   chunk 37 optimal weight:    6.9990
   chunk 81 optimal weight:    0.6980
   chunk 44 optimal weight:    4.9990
   overall best weight:    1.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
** E  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  20 GLN
G  72 GLN
H  75 GLN
H  79 ASN
I  30 ASN
** J  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.073760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.060086 restraints weight = 29610.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.061670 restraints weight = 16568.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.062733 restraints weight = 11180.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.3719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   8117  Z= 0.245
  Angle     :  0.710  11.355  10903  Z= 0.372
  Chirality :  0.041   0.244   1185
  Planarity :  0.004   0.059   1392
  Dihedral  :  5.251  43.480   1074
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.86 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 20.05 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    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:  0.87 (0.26), residues: 967
  helix:  1.35 (0.18), residues: 762
  sheet:  0.05 (1.04), residues: 22
  loop : -2.68 (0.40), residues: 183

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 106 
 HIS   0.005   0.001   HIS F  47 
 PHE   0.032   0.001   PHE C 107 
 TYR   0.019   0.001   TYR C 151 
 ARG   0.005   0.001   ARG F  84 

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 246
  time to evaluate  : 0.916 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7496 (tm-30)
REVERT: A   56 LEU cc_start: 0.8225 (mp) cc_final: 0.7963 (pp)
REVERT: A  194 LYS cc_start: 0.8846 (tppp) cc_final: 0.8594 (mptt)
REVERT: B   39 MET cc_start: 0.4045 (mtm) cc_final: 0.3492 (tmm)
REVERT: B   82 LYS cc_start: 0.8244 (mmpt) cc_final: 0.7818 (tptt)
REVERT: D   64 MET cc_start: 0.6290 (tmm) cc_final: 0.5898 (tmm)
REVERT: D   78 GLN cc_start: 0.8430 (tm-30) cc_final: 0.7918 (tm-30)
REVERT: D  111 ASP cc_start: 0.7893 (t0) cc_final: 0.7359 (t0)
REVERT: D  123 GLN cc_start: 0.8582 (tm-30) cc_final: 0.8147 (tm-30)
REVERT: D  155 MET cc_start: 0.7622 (mmt) cc_final: 0.7407 (mmp)
REVERT: D  165 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8025 (mm-30)
REVERT: E   64 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8311 (mm)
REVERT: F   27 ASP cc_start: 0.8743 (m-30) cc_final: 0.8361 (m-30)
REVERT: F   60 GLN cc_start: 0.8421 (mt0) cc_final: 0.7864 (mp10)
REVERT: G   42 ASP cc_start: 0.7535 (t0) cc_final: 0.7154 (t0)
REVERT: H   59 SER cc_start: 0.8897 (m) cc_final: 0.8428 (p)
REVERT: I    7 LYS cc_start: 0.9026 (ptmm) cc_final: 0.8436 (tmmt)
REVERT: I   10 GLN cc_start: 0.8710 (mp10) cc_final: 0.8144 (pm20)
REVERT: I   17 GLU cc_start: 0.8676 (tp30) cc_final: 0.8368 (tp30)
REVERT: J   23 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8236 (tp30)
  outliers start: 41
  outliers final: 25
  residues processed: 268
  average time/residue: 0.2171
  time to fit residues: 76.1732
Evaluate side-chains
  255 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 229
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  401 ASP
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue   84 ILE
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  105 VAL
Chi-restraints excluded: chain D residue  129 CYS
Chi-restraints excluded: chain D residue  149 CYS
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain F residue   31 SER
Chi-restraints excluded: chain F residue   41 LEU
Chi-restraints excluded: chain G residue   20 GLN
Chi-restraints excluded: chain G residue   53 GLN
Chi-restraints excluded: chain G residue   66 HIS
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain I residue    4 LEU
Chi-restraints excluded: chain I residue    8 GLU
Chi-restraints excluded: chain I residue   41 ASN
Chi-restraints excluded: chain J residue   32 MET
Chi-restraints excluded: chain J residue   44 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 91 optimal weight:    0.2980
   chunk 65 optimal weight:    2.9990
   chunk 12 optimal weight:    7.9990
   chunk 19 optimal weight:    0.9990
   chunk 52 optimal weight:    0.6980
   chunk 61 optimal weight:    0.3980
   chunk 94 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
G  20 GLN
H  75 GLN
** I  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
J  39 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.074587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.060921 restraints weight = 29769.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.062517 restraints weight = 16373.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.063638 restraints weight = 11044.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.3925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8117  Z= 0.206
  Angle     :  0.694  11.767  10903  Z= 0.362
  Chirality :  0.040   0.257   1185
  Planarity :  0.004   0.058   1392
  Dihedral  :  5.175  43.156   1074
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.03 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 22.57 %
    Favored  : 74.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    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:  1.08 (0.26), residues: 967
  helix:  1.50 (0.18), residues: 758
  sheet:  0.20 (1.05), residues: 22
  loop : -2.49 (0.40), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.000   TRP B 106 
 HIS   0.008   0.002   HIS C 163 
 PHE   0.033   0.001   PHE C 107 
 TYR   0.023   0.001   TYR C 151 
 ARG   0.005   0.000   ARG E  26 

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 258
  time to evaluate  : 0.911 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7920 (tm-30) cc_final: 0.7490 (tm-30)
REVERT: A  194 LYS cc_start: 0.8864 (tppp) cc_final: 0.8603 (mptt)
REVERT: B   39 MET cc_start: 0.4083 (mtm) cc_final: 0.3532 (tmm)
REVERT: B   82 LYS cc_start: 0.8284 (mmpt) cc_final: 0.8012 (tptt)
REVERT: C  163 HIS cc_start: 0.8752 (OUTLIER) cc_final: 0.8369 (t70)
REVERT: D   78 GLN cc_start: 0.8433 (tm-30) cc_final: 0.7814 (tm-30)
REVERT: D  111 ASP cc_start: 0.7922 (t0) cc_final: 0.7319 (t0)
REVERT: D  123 GLN cc_start: 0.8528 (tm-30) cc_final: 0.8111 (tm-30)
REVERT: D  155 MET cc_start: 0.7611 (mmt) cc_final: 0.7391 (mmp)
REVERT: D  165 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8003 (mm-30)
REVERT: E   18 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8153 (mp10)
REVERT: E   64 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8418 (mm)
REVERT: E   73 ARG cc_start: 0.7908 (tpp-160) cc_final: 0.7641 (ttm-80)
REVERT: F   27 ASP cc_start: 0.8707 (m-30) cc_final: 0.8382 (m-30)
REVERT: F   60 GLN cc_start: 0.8422 (mt0) cc_final: 0.7824 (mp10)
REVERT: F   84 ARG cc_start: 0.8515 (tpp80) cc_final: 0.8132 (tpp80)
REVERT: G   42 ASP cc_start: 0.7632 (t0) cc_final: 0.7282 (t0)
REVERT: H   59 SER cc_start: 0.8907 (m) cc_final: 0.8457 (p)
REVERT: I    7 LYS cc_start: 0.9028 (ptmm) cc_final: 0.8538 (tmmt)
REVERT: I   10 GLN cc_start: 0.8766 (mp10) cc_final: 0.8510 (pm20)
REVERT: I   17 GLU cc_start: 0.8718 (tp30) cc_final: 0.8409 (tp30)
REVERT: I   19 LYS cc_start: 0.9368 (mtpp) cc_final: 0.9068 (mtpp)
REVERT: I   52 GLU cc_start: 0.7485 (mt-10) cc_final: 0.7107 (mt-10)
REVERT: J   23 GLU cc_start: 0.8575 (mm-30) cc_final: 0.8050 (tp30)
  outliers start: 29
  outliers final: 22
  residues processed: 271
  average time/residue: 0.2285
  time to fit residues: 81.2049
Evaluate side-chains
  255 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 230
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  401 ASP
Chi-restraints excluded: chain C residue  163 HIS
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  105 VAL
Chi-restraints excluded: chain D residue  129 CYS
Chi-restraints excluded: chain D residue  149 CYS
Chi-restraints excluded: chain E residue   18 GLN
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain F residue   41 LEU
Chi-restraints excluded: chain F residue   83 THR
Chi-restraints excluded: chain G residue   20 GLN
Chi-restraints excluded: chain G residue   41 ASN
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   47 THR
Chi-restraints excluded: chain I residue    4 LEU
Chi-restraints excluded: chain I residue   35 CYS
Chi-restraints excluded: chain J residue   32 MET
Chi-restraints excluded: chain J residue   44 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 3 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0020
   chunk 67 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.1394

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

Flipped N/Q/H residues before XYZ refinement:
G  20 GLN
** G  66 HIS ** 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 = 0.3508 r_free = 0.3508 target = 0.073740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.061314 restraints weight = 30072.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.062155 restraints weight = 16373.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.062587 restraints weight = 14956.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.4121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   8117  Z= 0.246
  Angle     :  0.717  11.834  10903  Z= 0.374
  Chirality :  0.041   0.226   1185
  Planarity :  0.004   0.054   1392
  Dihedral  :  5.147  43.490   1074
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.96 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 23.37 %
    Favored  : 72.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    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:  1.14 (0.26), residues: 967
  helix:  1.56 (0.18), residues: 758
  sheet:  0.02 (1.06), residues: 22
  loop : -2.52 (0.40), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 106 
 HIS   0.007   0.002   HIS C 163 
 PHE   0.035   0.002   PHE C 107 
 TYR   0.026   0.001   TYR C 151 
 ARG   0.009   0.000   ARG I  26 

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 242
  time to evaluate  : 0.987 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7928 (tm-30) cc_final: 0.7459 (tm-30)
REVERT: A  194 LYS cc_start: 0.8901 (tppp) cc_final: 0.8623 (mptt)
REVERT: B   39 MET cc_start: 0.4175 (mtm) cc_final: 0.3603 (tmm)
REVERT: B   82 LYS cc_start: 0.8406 (mmpt) cc_final: 0.7972 (tptt)
REVERT: C  163 HIS cc_start: 0.8651 (OUTLIER) cc_final: 0.8439 (t70)
REVERT: D   64 MET cc_start: 0.6205 (OUTLIER) cc_final: 0.5552 (tmm)
REVERT: D   78 GLN cc_start: 0.8488 (tm-30) cc_final: 0.7899 (tm-30)
REVERT: D  111 ASP cc_start: 0.8066 (t0) cc_final: 0.7471 (t0)
REVERT: D  123 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8110 (tm-30)
REVERT: D  155 MET cc_start: 0.7649 (mmt) cc_final: 0.7428 (mmp)
REVERT: D  165 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8048 (mm-30)
REVERT: E   18 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8164 (mp10)
REVERT: E   52 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8087 (mp0)
REVERT: E   64 LEU cc_start: 0.8624 (OUTLIER) cc_final: 0.8353 (mm)
REVERT: F   27 ASP cc_start: 0.8654 (m-30) cc_final: 0.8343 (m-30)
REVERT: F   60 GLN cc_start: 0.8458 (mt0) cc_final: 0.8096 (mt0)
REVERT: G   42 ASP cc_start: 0.7535 (t0) cc_final: 0.7166 (t0)
REVERT: H   59 SER cc_start: 0.8972 (m) cc_final: 0.8513 (p)
REVERT: I    7 LYS cc_start: 0.9091 (ptmm) cc_final: 0.8629 (tmmt)
REVERT: I   17 GLU cc_start: 0.8753 (tp30) cc_final: 0.8429 (tp30)
REVERT: I   52 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7446 (mt-10)
REVERT: J   23 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8313 (tp30)
  outliers start: 37
  outliers final: 24
  residues processed: 257
  average time/residue: 0.2119
  time to fit residues: 71.8455
Evaluate side-chains
  254 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 225
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   67 THR
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  401 ASP
Chi-restraints excluded: chain C residue  163 HIS
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue   64 MET
Chi-restraints excluded: chain D residue   84 ILE
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  105 VAL
Chi-restraints excluded: chain D residue  149 CYS
Chi-restraints excluded: chain E residue   18 GLN
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   52 GLU
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain F residue   31 SER
Chi-restraints excluded: chain F residue   41 LEU
Chi-restraints excluded: chain F residue   83 THR
Chi-restraints excluded: chain G residue   20 GLN
Chi-restraints excluded: chain G residue   41 ASN
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   47 THR
Chi-restraints excluded: chain I residue    4 LEU
Chi-restraints excluded: chain I residue    8 GLU
Chi-restraints excluded: chain I residue   35 CYS
Chi-restraints excluded: chain J residue   32 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 60 optimal weight:    0.9990
   chunk 91 optimal weight:    0.4980
   chunk 17 optimal weight:    0.8980
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
G  20 GLN
** G  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
I  30 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.074532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.062237 restraints weight = 30094.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.062688 restraints weight = 16426.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.063579 restraints weight = 12514.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.4210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   8117  Z= 0.223
  Angle     :  0.721  11.923  10903  Z= 0.376
  Chirality :  0.041   0.226   1185
  Planarity :  0.004   0.056   1392
  Dihedral  :  5.121  43.037   1074
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.24 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 25.09 %
    Favored  : 70.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    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:  1.23 (0.26), residues: 967
  helix:  1.61 (0.18), residues: 757
  sheet:  0.16 (1.07), residues: 22
  loop : -2.47 (0.40), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 106 
 HIS   0.008   0.002   HIS C 163 
 PHE   0.040   0.001   PHE C 107 
 TYR   0.031   0.001   TYR C 151 
 ARG   0.006   0.000   ARG E  26 

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 242
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7509 (tm-30)
REVERT: A  140 GLU cc_start: 0.8284 (tm-30) cc_final: 0.8068 (tm-30)
REVERT: A  194 LYS cc_start: 0.8909 (tppp) cc_final: 0.8631 (mptt)
REVERT: B   39 MET cc_start: 0.4174 (mtm) cc_final: 0.3597 (tmm)
REVERT: B   82 LYS cc_start: 0.8420 (mmpt) cc_final: 0.8034 (tptt)
REVERT: D   78 GLN cc_start: 0.8466 (tm-30) cc_final: 0.7864 (tm-30)
REVERT: D  111 ASP cc_start: 0.8022 (t0) cc_final: 0.7384 (t0)
REVERT: D  123 GLN cc_start: 0.8496 (tm-30) cc_final: 0.8103 (tm-30)
REVERT: D  155 MET cc_start: 0.7698 (mmt) cc_final: 0.7482 (mmp)
REVERT: D  165 GLU cc_start: 0.8487 (mm-30) cc_final: 0.7981 (mm-30)
REVERT: E   18 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8162 (mp10)
REVERT: E   52 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.8073 (mp0)
REVERT: E   64 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8382 (mm)
REVERT: F   27 ASP cc_start: 0.8693 (m-30) cc_final: 0.8359 (m-30)
REVERT: F   60 GLN cc_start: 0.8472 (mt0) cc_final: 0.8051 (mt0)
REVERT: G   42 ASP cc_start: 0.7552 (t0) cc_final: 0.7199 (t0)
REVERT: H   39 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.6515 (m110)
REVERT: H   59 SER cc_start: 0.9009 (m) cc_final: 0.8541 (p)
REVERT: I    7 LYS cc_start: 0.9129 (ptmm) cc_final: 0.8647 (tmmt)
REVERT: I   17 GLU cc_start: 0.8756 (tp30) cc_final: 0.8450 (tp30)
REVERT: I   33 GLU cc_start: 0.8101 (tm-30) cc_final: 0.7896 (tp30)
REVERT: J   23 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8340 (tp30)
  outliers start: 35
  outliers final: 23
  residues processed: 257
  average time/residue: 0.2147
  time to fit residues: 72.8239
Evaluate side-chains
  257 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 230
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue  129 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  401 ASP
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  105 VAL
Chi-restraints excluded: chain D residue  149 CYS
Chi-restraints excluded: chain E residue   18 GLN
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   52 GLU
Chi-restraints excluded: chain E residue   55 CYS
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain F residue   31 SER
Chi-restraints excluded: chain F residue   41 LEU
Chi-restraints excluded: chain F residue   83 THR
Chi-restraints excluded: chain G residue   31 LEU
Chi-restraints excluded: chain G residue   41 ASN
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   39 ASN
Chi-restraints excluded: chain I residue    4 LEU
Chi-restraints excluded: chain I residue    8 GLU
Chi-restraints excluded: chain I residue   35 CYS
Chi-restraints excluded: chain J residue   32 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 59 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   chunk 65 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
D 168 ASN
G  20 GLN
** G  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  79 ASN
** I  30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.074371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.060820 restraints weight = 29772.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.062456 restraints weight = 16519.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.063553 restraints weight = 11048.770|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.4373

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   8117  Z= 0.238
  Angle     :  0.743  12.027  10903  Z= 0.385
  Chirality :  0.041   0.252   1185
  Planarity :  0.004   0.053   1392
  Dihedral  :  5.135  43.463   1074
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.65 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 24.86 %
    Favored  : 70.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.10 %

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:  1.25 (0.26), residues: 967
  helix:  1.63 (0.18), residues: 758
  sheet:  0.20 (1.07), residues: 22
  loop : -2.48 (0.40), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 106 
 HIS   0.009   0.002   HIS C 163 
 PHE   0.041   0.001   PHE C 107 
 TYR   0.036   0.001   TYR C 151 
 ARG   0.005   0.000   ARG I  26 

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 245
  time to evaluate  : 0.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7580 (tm-30) cc_final: 0.7158 (tm-30)
REVERT: A   45 LYS cc_start: 0.8803 (mmtt) cc_final: 0.8499 (mmtm)
REVERT: A  194 LYS cc_start: 0.8908 (tppp) cc_final: 0.8644 (mptt)
REVERT: B   39 MET cc_start: 0.4118 (mtm) cc_final: 0.3596 (tmm)
REVERT: B   82 LYS cc_start: 0.8317 (mmpt) cc_final: 0.7988 (tptt)
REVERT: C  151 TYR cc_start: 0.8132 (m-80) cc_final: 0.7857 (m-80)
REVERT: C  163 HIS cc_start: 0.8590 (OUTLIER) cc_final: 0.8005 (t70)
REVERT: D   78 GLN cc_start: 0.8467 (tm-30) cc_final: 0.7899 (tm-30)
REVERT: D  111 ASP cc_start: 0.8091 (t0) cc_final: 0.7430 (t0)
REVERT: D  123 GLN cc_start: 0.8509 (tm-30) cc_final: 0.8102 (tm-30)
REVERT: D  155 MET cc_start: 0.7704 (mmt) cc_final: 0.7496 (mmp)
REVERT: D  165 GLU cc_start: 0.8460 (mm-30) cc_final: 0.7958 (mm-30)
REVERT: E   18 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.8104 (mp10)
REVERT: E   52 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8019 (mp0)
REVERT: E   64 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8307 (mm)
REVERT: F   27 ASP cc_start: 0.8700 (m-30) cc_final: 0.8425 (m-30)
REVERT: F   60 GLN cc_start: 0.8469 (mt0) cc_final: 0.8064 (mt0)
REVERT: G   42 ASP cc_start: 0.7626 (t0) cc_final: 0.7289 (t0)
REVERT: H   59 SER cc_start: 0.8905 (m) cc_final: 0.8489 (p)
REVERT: I    7 LYS cc_start: 0.8956 (ptmm) cc_final: 0.8424 (tmmt)
REVERT: I   17 GLU cc_start: 0.8675 (tp30) cc_final: 0.8364 (tp30)
REVERT: J   23 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8286 (tp30)
  outliers start: 37
  outliers final: 29
  residues processed: 261
  average time/residue: 0.2112
  time to fit residues: 72.4374
Evaluate side-chains
  255 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 222
  time to evaluate  : 0.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue  129 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue  103 LEU
Chi-restraints excluded: chain B residue  401 ASP
Chi-restraints excluded: chain C residue  163 HIS
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  105 VAL
Chi-restraints excluded: chain D residue  149 CYS
Chi-restraints excluded: chain E residue   18 GLN
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   52 GLU
Chi-restraints excluded: chain E residue   55 CYS
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain F residue   31 SER
Chi-restraints excluded: chain F residue   41 LEU
Chi-restraints excluded: chain F residue   83 THR
Chi-restraints excluded: chain G residue   20 GLN
Chi-restraints excluded: chain G residue   31 LEU
Chi-restraints excluded: chain G residue   41 ASN
Chi-restraints excluded: chain G residue   53 GLN
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain H residue   47 THR
Chi-restraints excluded: chain I residue    4 LEU
Chi-restraints excluded: chain I residue    8 GLU
Chi-restraints excluded: chain I residue   35 CYS
Chi-restraints excluded: chain I residue   41 ASN
Chi-restraints excluded: chain J residue   32 MET
Chi-restraints excluded: chain J residue   72 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 50 optimal weight:    0.0980
   chunk 90 optimal weight:    0.7980
   chunk 86 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 94 optimal weight:    0.5980
   chunk 29 optimal weight:    4.9990
   chunk 58 optimal weight:    2.9990
   chunk 4 optimal weight:    8.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
G  20 GLN
** G  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  46 ASN
H  79 ASN
I  66 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.074680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.061722 restraints weight = 30987.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.063135 restraints weight = 15569.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.063964 restraints weight = 10895.534|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.4508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8117  Z= 0.227
  Angle     :  0.780  12.562  10903  Z= 0.397
  Chirality :  0.041   0.234   1185
  Planarity :  0.004   0.055   1392
  Dihedral  :  5.026  42.772   1074
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.24 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 26.58 %
    Favored  : 69.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.10 %

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:  1.37 (0.26), residues: 967
  helix:  1.71 (0.18), residues: 760
  sheet:  0.27 (1.08), residues: 22
  loop : -2.46 (0.40), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 106 
 HIS   0.009   0.002   HIS C 163 
 PHE   0.035   0.001   PHE C 107 
 TYR   0.032   0.001   TYR C 151 
 ARG   0.010   0.000   ARG I  26 

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  273 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 236
  time to evaluate  : 1.004 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7174 (tm-30)
REVERT: A   45 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8454 (mmtm)
REVERT: A  194 LYS cc_start: 0.8944 (tppp) cc_final: 0.8629 (mptt)
REVERT: B   39 MET cc_start: 0.4303 (mtm) cc_final: 0.3685 (tmm)
REVERT: B   82 LYS cc_start: 0.8443 (mmpt) cc_final: 0.8012 (tptt)
REVERT: C  151 TYR cc_start: 0.8323 (m-80) cc_final: 0.8007 (m-80)
REVERT: C  163 HIS cc_start: 0.8686 (OUTLIER) cc_final: 0.8180 (t70)
REVERT: D   78 GLN cc_start: 0.8468 (tm-30) cc_final: 0.7869 (tm-30)
REVERT: D  111 ASP cc_start: 0.8027 (t0) cc_final: 0.7361 (t0)
REVERT: D  123 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8099 (tm-30)
REVERT: D  155 MET cc_start: 0.7707 (mmt) cc_final: 0.7488 (mmp)
REVERT: D  165 GLU cc_start: 0.8508 (mm-30) cc_final: 0.7949 (mm-30)
REVERT: E   18 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8176 (mp10)
REVERT: E   52 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8014 (mp0)
REVERT: E   64 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8253 (mm)
REVERT: F   20 ASP cc_start: 0.9580 (p0) cc_final: 0.9319 (p0)
REVERT: F   27 ASP cc_start: 0.8820 (m-30) cc_final: 0.8537 (m-30)
REVERT: F   60 GLN cc_start: 0.8321 (mt0) cc_final: 0.7967 (mt0)
REVERT: G   42 ASP cc_start: 0.7664 (t0) cc_final: 0.7291 (t0)
REVERT: H   59 SER cc_start: 0.8968 (m) cc_final: 0.8537 (p)
REVERT: I    7 LYS cc_start: 0.9060 (ptmm) cc_final: 0.8611 (tmmt)
REVERT: I   17 GLU cc_start: 0.8848 (tp30) cc_final: 0.8509 (tp30)
REVERT: J   23 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8426 (tp30)
REVERT: J   26 LEU cc_start: 0.9496 (mt) cc_final: 0.9281 (mt)
  outliers start: 37
  outliers final: 26
  residues processed: 255
  average time/residue: 0.2099
  time to fit residues: 71.1574
Evaluate side-chains
  254 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 224
  time to evaluate  : 0.895 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 CYS
Chi-restraints excluded: chain A residue  129 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue  401 ASP
Chi-restraints excluded: chain C residue  163 HIS
Chi-restraints excluded: chain C residue  165 ILE
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  105 VAL
Chi-restraints excluded: chain D residue  149 CYS
Chi-restraints excluded: chain E residue   18 GLN
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   52 GLU
Chi-restraints excluded: chain E residue   55 CYS
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain F residue   31 SER
Chi-restraints excluded: chain F residue   41 LEU
Chi-restraints excluded: chain G residue   31 LEU
Chi-restraints excluded: chain G residue   41 ASN
Chi-restraints excluded: chain G residue   53 GLN
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain I residue    4 LEU
Chi-restraints excluded: chain I residue    8 GLU
Chi-restraints excluded: chain I residue   35 CYS
Chi-restraints excluded: chain I residue   41 ASN
Chi-restraints excluded: chain J residue   72 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0020
   chunk 35 optimal weight:    4.9990
   chunk 84 optimal weight:    7.9990
   chunk 75 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9980
   chunk 54 optimal weight:    0.3980
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
G  20 GLN
** G  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  79 ASN
I  30 ASN
** I  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.074938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.062313 restraints weight = 29988.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.063744 restraints weight = 16480.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.064125 restraints weight = 12712.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3283
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.4526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8117  Z= 0.227
  Angle     :  0.789  13.311  10903  Z= 0.401
  Chirality :  0.042   0.332   1185
  Planarity :  0.004   0.052   1392
  Dihedral  :  5.012  43.289   1074
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.45 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.67 %
    Allowed  : 27.15 %
    Favored  : 69.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.10 %

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:  1.47 (0.26), residues: 967
  helix:  1.78 (0.18), residues: 759
  sheet:  0.28 (1.08), residues: 22
  loop : -2.43 (0.40), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 106 
 HIS   0.009   0.001   HIS C 163 
 PHE   0.036   0.001   PHE C 107 
 TYR   0.031   0.001   TYR C 151 
 ARG   0.004   0.000   ARG E  26 

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

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

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1934 Ramachandran restraints generated.
    967 Oldfield, 0 Emsley, 967 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 230
  time to evaluate  : 0.972 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7605 (tm-30) cc_final: 0.7169 (tm-30)
REVERT: A   45 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8542 (mmtm)
REVERT: A  194 LYS cc_start: 0.8972 (tppp) cc_final: 0.8654 (mptt)
REVERT: B   39 MET cc_start: 0.4188 (mtm) cc_final: 0.3624 (tmm)
REVERT: B   82 LYS cc_start: 0.8451 (mmpt) cc_final: 0.8059 (tptt)
REVERT: C  151 TYR cc_start: 0.8264 (m-80) cc_final: 0.8002 (m-80)
REVERT: C  163 HIS cc_start: 0.8563 (OUTLIER) cc_final: 0.8030 (t70)
REVERT: D   78 GLN cc_start: 0.8502 (tm-30) cc_final: 0.7906 (tm-30)
REVERT: D  111 ASP cc_start: 0.8066 (t0) cc_final: 0.7459 (t0)
REVERT: D  123 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8079 (tm-30)
REVERT: D  155 MET cc_start: 0.7714 (mmt) cc_final: 0.7503 (mmp)
REVERT: D  165 GLU cc_start: 0.8431 (mm-30) cc_final: 0.8051 (mm-30)
REVERT: E   18 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8113 (mp10)
REVERT: E   52 GLU cc_start: 0.8676 (OUTLIER) cc_final: 0.7918 (mp0)
REVERT: E   64 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8233 (mm)
REVERT: F   27 ASP cc_start: 0.8767 (m-30) cc_final: 0.8520 (m-30)
REVERT: F   60 GLN cc_start: 0.8256 (mt0) cc_final: 0.7916 (mt0)
REVERT: G   42 ASP cc_start: 0.7727 (t0) cc_final: 0.7348 (t0)
REVERT: H   59 SER cc_start: 0.8990 (m) cc_final: 0.8556 (p)
REVERT: I    7 LYS cc_start: 0.8994 (ptmm) cc_final: 0.8553 (tmmt)
REVERT: I   57 MET cc_start: 0.8079 (mmp) cc_final: 0.7844 (mmm)
REVERT: J   23 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8280 (tp30)
REVERT: J   26 LEU cc_start: 0.9409 (mt) cc_final: 0.9175 (mt)
  outliers start: 32
  outliers final: 27
  residues processed: 244
  average time/residue: 0.2118
  time to fit residues: 68.4481
Evaluate side-chains
  256 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 225
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 PHE
Chi-restraints excluded: chain A residue  152 ILE
Chi-restraints excluded: chain B residue   73 LEU
Chi-restraints excluded: chain B residue  401 ASP
Chi-restraints excluded: chain C residue  163 HIS
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue   93 THR
Chi-restraints excluded: chain D residue  105 VAL
Chi-restraints excluded: chain D residue  149 CYS
Chi-restraints excluded: chain E residue   18 GLN
Chi-restraints excluded: chain E residue   31 LEU
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   52 GLU
Chi-restraints excluded: chain E residue   55 CYS
Chi-restraints excluded: chain E residue   64 LEU
Chi-restraints excluded: chain F residue   31 SER
Chi-restraints excluded: chain F residue   41 LEU
Chi-restraints excluded: chain G residue   18 GLN
Chi-restraints excluded: chain G residue   20 GLN
Chi-restraints excluded: chain G residue   31 LEU
Chi-restraints excluded: chain G residue   41 ASN
Chi-restraints excluded: chain G residue   53 GLN
Chi-restraints excluded: chain H residue   26 LEU
Chi-restraints excluded: chain H residue   28 LEU
Chi-restraints excluded: chain H residue   29 VAL
Chi-restraints excluded: chain I residue    4 LEU
Chi-restraints excluded: chain I residue    8 GLU
Chi-restraints excluded: chain I residue   30 ASN
Chi-restraints excluded: chain I residue   35 CYS
Chi-restraints excluded: chain J residue   32 MET
Chi-restraints excluded: chain J residue   72 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 80 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 27 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 21 optimal weight:    0.1980
   overall best weight:    0.7984

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

Flipped N/Q/H residues before XYZ refinement:
G  20 GLN
** G  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  79 ASN
I  30 ASN
** I  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.074737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.062232 restraints weight = 30324.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.063516 restraints weight = 17370.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.063931 restraints weight = 13922.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.4625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   8117  Z= 0.243
  Angle     :  0.799  13.212  10903  Z= 0.408
  Chirality :  0.042   0.302   1185
  Planarity :  0.004   0.047   1392
  Dihedral  :  4.910  43.582   1073
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.34 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 28.41 %
    Favored  : 68.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.17 %
    Twisted General : 0.10 %

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:  1.47 (0.26), residues: 967
  helix:  1.77 (0.18), residues: 764
  sheet:  0.29 (1.08), residues: 22
  loop : -2.51 (0.41), residues: 181

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 106 
 HIS   0.009   0.002   HIS C 163 
 PHE   0.037   0.001   PHE C 107 
 TYR   0.029   0.001   TYR C 151 
 ARG   0.008   0.000   ARG I  26 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2821.41 seconds
wall clock time: 51 minutes 21.59 seconds (3081.59 seconds total)