Starting phenix.real_space_refine
on Wed Mar 12 12:58:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6lo8_0935/03_2025/6lo8_0935.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6lo8_0935/03_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_0935/03_2025/6lo8_0935.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6lo8_0935/03_2025/6lo8_0935.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6lo8_0935/03_2025/6lo8_0935.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6lo8_0935/03_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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 5.71, per 1000 atoms: 0.72
  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: 1.74
  Conformation dependent library (CDL) restraints added in 942.8 milliseconds
  

  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: 0.58
  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: 2.11

  Time building geometry restraints manager: 2.14 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:             1.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     21.470
  Find NCS groups from input model:        0.180
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.990
-------------------------------------------------------------------------------
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  : 0.873 
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: 0.2488
  time to fit residues: 106.1429
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  : 1.143 
-------------------------------------------------------------------------------
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 = 0.3517 r_free = 0.3517 target = 0.074083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.059990 restraints weight = 29803.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.061651 restraints weight = 16438.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.062765 restraints weight = 10960.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
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  : 0.891 
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: 0.7745 (tm-30) cc_final: 0.7240 (tm-30)
REVERT: A   56 LEU cc_start: 0.8217 (mp) cc_final: 0.7965 (pp)
REVERT: A  129 PHE cc_start: 0.7948 (m-80) cc_final: 0.7314 (m-80)
REVERT: B   39 MET cc_start: 0.3983 (mtm) cc_final: 0.3518 (tmm)
REVERT: B   67 THR cc_start: 0.8521 (m) cc_final: 0.8131 (p)
REVERT: B   82 LYS cc_start: 0.8192 (mmpt) cc_final: 0.7740 (tptt)
REVERT: C  103 MET cc_start: 0.8310 (mtt) cc_final: 0.8075 (mtt)
REVERT: D   64 MET cc_start: 0.6573 (tmm) cc_final: 0.6207 (tmm)
REVERT: D  111 ASP cc_start: 0.7471 (t0) cc_final: 0.6990 (t0)
REVERT: D  123 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8332 (tm-30)
REVERT: D  144 LYS cc_start: 0.8404 (tttt) cc_final: 0.8098 (pttm)
REVERT: D  155 MET cc_start: 0.7874 (mmp) cc_final: 0.7631 (mmt)
REVERT: D  165 GLU cc_start: 0.8596 (mm-30) cc_final: 0.8354 (mm-30)
REVERT: E   11 GLU cc_start: 0.8268 (mp0) cc_final: 0.8031 (mp0)
REVERT: E   64 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8227 (mm)
REVERT: F   27 ASP cc_start: 0.8839 (m-30) cc_final: 0.8360 (m-30)
REVERT: F   35 ASN cc_start: 0.8914 (t0) cc_final: 0.8704 (t0)
REVERT: F   84 ARG cc_start: 0.8614 (tpp-160) cc_final: 0.8386 (tpp80)
REVERT: G   22 LYS cc_start: 0.8916 (tptp) cc_final: 0.8598 (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: 0.8748 (tp30) cc_final: 0.8458 (tp30)
REVERT: I   35 CYS cc_start: 0.6085 (m) cc_final: 0.5873 (m)
REVERT: J   23 GLU cc_start: 0.8251 (tp30) cc_final: 0.8019 (tp30)
REVERT: J   80 MET cc_start: 0.8151 (mmp) cc_final: 0.7926 (mmp)
  outliers start: 28
  outliers final: 15
  residues processed: 281
  average time/residue: 0.2201
  time to fit residues: 80.3261
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  : 0.893 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 7 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9980
   chunk 9 optimal weight:    9.9990
   chunk 82 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0040
   chunk 26 optimal weight:    6.9990
   overall best weight:    0.6392

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

Flipped N/Q/H residues before XYZ refinement:
A 154 ASN
D 168 ASN
F  94 HIS
G  20 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 = 0.3526 r_free = 0.3526 target = 0.074496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.060784 restraints weight = 29849.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.062391 restraints weight = 16654.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.063489 restraints weight = 11234.778|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.3424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   8117  Z= 0.211
  Angle     :  0.688  15.222  10903  Z= 0.361
  Chirality :  0.039   0.175   1185
  Planarity :  0.004   0.068   1392
  Dihedral  :  5.262  44.380   1074
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.83 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 19.13 %
    Favored  : 77.43 %
  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:  0.50 (0.26), residues: 967
  helix:  1.10 (0.18), residues: 761
  sheet:  0.23 (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
  290 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 260
  time to evaluate  : 1.009 
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: 0.8161 (mp) cc_final: 0.7896 (pp)
REVERT: A  129 PHE cc_start: 0.7897 (m-80) cc_final: 0.7220 (m-10)
REVERT: A  194 LYS cc_start: 0.8854 (tppp) cc_final: 0.8574 (mptt)
REVERT: B   39 MET cc_start: 0.4009 (mtm) cc_final: 0.3515 (tmm)
REVERT: B   82 LYS cc_start: 0.8171 (mmpt) cc_final: 0.7738 (tptt)
REVERT: C  163 HIS cc_start: 0.8813 (t70) cc_final: 0.8291 (t70)
REVERT: D   78 GLN cc_start: 0.8335 (tm-30) cc_final: 0.7884 (tm-30)
REVERT: D  111 ASP cc_start: 0.7716 (t0) cc_final: 0.7121 (t0)
REVERT: D  123 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8148 (tm-30)
REVERT: D  144 LYS cc_start: 0.8436 (tttt) cc_final: 0.8180 (pttm)
REVERT: D  165 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8167 (mm-30)
REVERT: E   18 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.8012 (mp10)
REVERT: E   64 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8255 (mm)
REVERT: F   27 ASP cc_start: 0.8757 (m-30) cc_final: 0.8409 (m-30)
REVERT: F   35 ASN cc_start: 0.8929 (t0) cc_final: 0.8691 (t0)
REVERT: G   26 ARG cc_start: 0.8457 (ttp80) cc_final: 0.8203 (ttp80)
REVERT: H   59 SER cc_start: 0.8896 (m) cc_final: 0.8416 (p)
REVERT: I    7 LYS cc_start: 0.9112 (ptmm) cc_final: 0.8475 (tmmt)
REVERT: I   10 GLN cc_start: 0.8843 (mp10) cc_final: 0.7869 (pm20)
REVERT: I   11 GLU cc_start: 0.8024 (mp0) cc_final: 0.7407 (pm20)
REVERT: I   17 GLU cc_start: 0.8691 (tp30) cc_final: 0.8383 (tp30)
REVERT: I   19 LYS cc_start: 0.9458 (mtpp) cc_final: 0.9145 (mtpp)
REVERT: J   80 MET cc_start: 0.7970 (mmp) cc_final: 0.7752 (mmp)
  outliers start: 30
  outliers final: 20
  residues processed: 277
  average time/residue: 0.2187
  time to fit residues: 78.8133
Evaluate side-chains
  260 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 238
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
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   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 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:    4.9990
   chunk 1 optimal weight:   10.0000
   chunk 67 optimal weight:    0.6980
   chunk 28 optimal weight:    0.1980
   chunk 16 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   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:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** E  13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  20 GLN
H  75 GLN
H  79 ASN
** J  39 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 = 0.3526 r_free = 0.3526 target = 0.074604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.061023 restraints weight = 29533.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.062634 restraints weight = 16376.899|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.063716 restraints weight = 10992.659|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.3761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066   8117  Z= 0.211
  Angle     :  0.703  11.302  10903  Z= 0.366
  Chirality :  0.040   0.231   1185
  Planarity :  0.004   0.059   1392
  Dihedral  :  5.211  43.706   1074
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.45 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 20.50 %
    Favored  : 75.72 %
  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:  0.97 (0.26), residues: 967
  helix:  1.44 (0.18), residues: 757
  sheet:  0.18 (1.05), residues: 22
  loop : -2.65 (0.39), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.000   TRP B 106 
 HIS   0.004   0.001   HIS F  94 
 PHE   0.032   0.001   PHE C 107 
 TYR   0.020   0.001   TYR C 151 
 ARG   0.006   0.000   ARG I  26 

*********************** 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
  299 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 266
  time to evaluate  : 1.007 
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: 0.7900 (tm-30) cc_final: 0.7530 (tm-30)
REVERT: A   56 LEU cc_start: 0.8124 (mp) cc_final: 0.7819 (pp)
REVERT: A  140 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7966 (tm-30)
REVERT: A  194 LYS cc_start: 0.8857 (tppp) cc_final: 0.8601 (mptt)
REVERT: B   39 MET cc_start: 0.3995 (mtm) cc_final: 0.3479 (tmm)
REVERT: B   82 LYS cc_start: 0.8157 (mmpt) cc_final: 0.7785 (tptt)
REVERT: C  163 HIS cc_start: 0.8636 (OUTLIER) cc_final: 0.7988 (t70)
REVERT: D   64 MET cc_start: 0.6276 (tmm) cc_final: 0.6020 (tmm)
REVERT: D   78 GLN cc_start: 0.8415 (tm-30) cc_final: 0.7811 (tm-30)
REVERT: D  111 ASP cc_start: 0.7847 (t0) cc_final: 0.7450 (t0)
REVERT: D  118 PHE cc_start: 0.8750 (t80) cc_final: 0.8519 (t80)
REVERT: D  123 GLN cc_start: 0.8540 (tm-30) cc_final: 0.8096 (tm-30)
REVERT: D  155 MET cc_start: 0.7636 (mmt) cc_final: 0.7415 (mmp)
REVERT: D  165 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8171 (mm-30)
REVERT: E   64 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8306 (mm)
REVERT: F   27 ASP cc_start: 0.8754 (m-30) cc_final: 0.8345 (m-30)
REVERT: F   60 GLN cc_start: 0.8382 (mt0) cc_final: 0.7779 (mp10)
REVERT: F   84 ARG cc_start: 0.8636 (tpp80) cc_final: 0.8261 (tpp80)
REVERT: H   59 SER cc_start: 0.8903 (m) cc_final: 0.8462 (p)
REVERT: I    7 LYS cc_start: 0.9011 (ptmm) cc_final: 0.8418 (tmmt)
REVERT: I   10 GLN cc_start: 0.8728 (mp10) cc_final: 0.8143 (pm20)
REVERT: I   17 GLU cc_start: 0.8712 (tp30) cc_final: 0.8400 (tp30)
REVERT: I   19 LYS cc_start: 0.9365 (mtpp) cc_final: 0.9159 (mtpp)
REVERT: J   23 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8152 (mm-30)
  outliers start: 33
  outliers final: 18
  residues processed: 284
  average time/residue: 0.2185
  time to fit residues: 80.9139
Evaluate side-chains
  253 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 233
  time to evaluate  : 0.938 
-------------------------------------------------------------------------------
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   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 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   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:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 91 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   chunk 19 optimal weight:    0.5980
   chunk 52 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 94 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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**
G  72 GLN
H  75 GLN
** J  39 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 = 0.3521 r_free = 0.3521 target = 0.074153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.061433 restraints weight = 29922.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.062569 restraints weight = 16381.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.063078 restraints weight = 12102.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.4003

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     :  0.709  11.867  10903  Z= 0.371
  Chirality :  0.040   0.234   1185
  Planarity :  0.004   0.057   1392
  Dihedral  :  5.150  43.128   1074
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.76 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 22.57 %
    Favored  : 73.65 %
  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:  1.11 (0.26), residues: 967
  helix:  1.52 (0.18), residues: 759
  sheet:  0.07 (1.06), residues: 22
  loop : -2.53 (0.40), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 106 
 HIS   0.005   0.001   HIS F  47 
 PHE   0.032   0.001   PHE C 107 
 TYR   0.023   0.001   TYR C 151 
 ARG   0.004   0.000   ARG F  84 

*********************** 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
  282 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 249
  time to evaluate  : 0.886 
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: 0.7935 (tm-30) cc_final: 0.7508 (tm-30)
REVERT: A  140 GLU cc_start: 0.8309 (tm-30) cc_final: 0.7912 (tm-30)
REVERT: A  194 LYS cc_start: 0.8886 (tppp) cc_final: 0.8602 (mptt)
REVERT: B   39 MET cc_start: 0.4138 (mtm) cc_final: 0.3558 (tmm)
REVERT: B   67 THR cc_start: 0.8546 (m) cc_final: 0.8280 (p)
REVERT: B   82 LYS cc_start: 0.8289 (mmpt) cc_final: 0.7973 (tptt)
REVERT: C  163 HIS cc_start: 0.8572 (OUTLIER) cc_final: 0.7957 (t70)
REVERT: D   78 GLN cc_start: 0.8471 (tm-30) cc_final: 0.7869 (tm-30)
REVERT: D  111 ASP cc_start: 0.7972 (t0) cc_final: 0.7311 (t0)
REVERT: D  118 PHE cc_start: 0.8741 (t80) cc_final: 0.8445 (t80)
REVERT: D  123 GLN cc_start: 0.8568 (tm-30) cc_final: 0.8154 (tm-30)
REVERT: D  155 MET cc_start: 0.7631 (mmt) cc_final: 0.7413 (mmp)
REVERT: D  165 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8079 (mm-30)
REVERT: E   64 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8405 (mm)
REVERT: F   27 ASP cc_start: 0.8709 (m-30) cc_final: 0.8383 (m-30)
REVERT: F   60 GLN cc_start: 0.8294 (mt0) cc_final: 0.7907 (mt0)
REVERT: F   84 ARG cc_start: 0.8587 (tpp80) cc_final: 0.8177 (tpp80)
REVERT: G   42 ASP cc_start: 0.7594 (t0) cc_final: 0.7163 (t0)
REVERT: H   59 SER cc_start: 0.8984 (m) cc_final: 0.8512 (p)
REVERT: I    7 LYS cc_start: 0.9127 (ptmm) cc_final: 0.8661 (tmmt)
REVERT: I   10 GLN cc_start: 0.8840 (mp10) cc_final: 0.8381 (pm20)
REVERT: I   11 GLU cc_start: 0.8387 (mp0) cc_final: 0.8042 (pm20)
REVERT: I   17 GLU cc_start: 0.8763 (tp30) cc_final: 0.8409 (tp30)
REVERT: I   52 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7189 (mt-10)
  outliers start: 33
  outliers final: 26
  residues processed: 264
  average time/residue: 0.2053
  time to fit residues: 71.3020
Evaluate side-chains
  255 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 227
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
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  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   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   45 THR
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 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
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:    0.5980
   chunk 51 optimal weight:    0.9980
   chunk 3 optimal weight:    7.9990
   chunk 76 optimal weight:    0.0010
   chunk 67 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0270
   chunk 25 optimal weight:    1.9990
   overall best weight:    0.5244

-------------------------------------------------------------------------------
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
I  66 HIS
J  39 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.074813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.062415 restraints weight = 29509.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.063485 restraints weight = 15388.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.064222 restraints weight = 11536.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.4166

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8117  Z= 0.210
  Angle     :  0.710  12.011  10903  Z= 0.367
  Chirality :  0.040   0.226   1185
  Planarity :  0.004   0.055   1392
  Dihedral  :  5.143  43.397   1074
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.55 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  3.89 %
    Allowed  : 23.60 %
    Favored  : 72.51 %
  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:  0.22 (1.08), residues: 22
  loop : -2.49 (0.40), residues: 188

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.000   TRP B 106 
 HIS   0.006   0.001   HIS F  94 
 PHE   0.033   0.001   PHE C 107 
 TYR   0.027   0.001   TYR C 151 
 ARG   0.004   0.000   ARG E  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
  286 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 252
  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: A   33 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7445 (tm-30)
REVERT: A  140 GLU cc_start: 0.8262 (tm-30) cc_final: 0.7878 (tm-30)
REVERT: A  194 LYS cc_start: 0.8871 (tppp) cc_final: 0.8609 (mptt)
REVERT: B   39 MET cc_start: 0.4128 (mtm) cc_final: 0.3555 (tmm)
REVERT: B   67 THR cc_start: 0.8455 (m) cc_final: 0.8196 (p)
REVERT: B   82 LYS cc_start: 0.8194 (mmpt) cc_final: 0.7920 (tptt)
REVERT: C  163 HIS cc_start: 0.8459 (OUTLIER) cc_final: 0.8090 (t70)
REVERT: D   64 MET cc_start: 0.6126 (OUTLIER) cc_final: 0.5368 (tmm)
REVERT: D   78 GLN cc_start: 0.8452 (tm-30) cc_final: 0.7863 (tm-30)
REVERT: D  111 ASP cc_start: 0.7951 (t0) cc_final: 0.7351 (t0)
REVERT: D  118 PHE cc_start: 0.8640 (t80) cc_final: 0.8362 (t80)
REVERT: D  123 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8153 (tm-30)
REVERT: D  155 MET cc_start: 0.7689 (mmt) cc_final: 0.7482 (mmp)
REVERT: D  165 GLU cc_start: 0.8506 (mm-30) cc_final: 0.7976 (mm-30)
REVERT: E   52 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7951 (mp0)
REVERT: E   64 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8417 (mm)
REVERT: F   27 ASP cc_start: 0.8691 (m-30) cc_final: 0.8356 (m-30)
REVERT: F   60 GLN cc_start: 0.8296 (mt0) cc_final: 0.7899 (mt0)
REVERT: G   42 ASP cc_start: 0.7660 (t0) cc_final: 0.7276 (t0)
REVERT: H   59 SER cc_start: 0.8987 (m) cc_final: 0.8524 (p)
REVERT: I    7 LYS cc_start: 0.9040 (ptmm) cc_final: 0.8558 (tmmt)
REVERT: I   10 GLN cc_start: 0.8633 (mp10) cc_final: 0.8092 (pm20)
REVERT: I   11 GLU cc_start: 0.8108 (mp0) cc_final: 0.7771 (mp0)
REVERT: I   17 GLU cc_start: 0.8690 (tp30) cc_final: 0.8382 (tp30)
REVERT: I   19 LYS cc_start: 0.9426 (mtpp) cc_final: 0.9146 (mtpp)
REVERT: I   52 GLU cc_start: 0.7591 (mt-10) cc_final: 0.7181 (mt-10)
REVERT: J   23 GLU cc_start: 0.8686 (tp30) cc_final: 0.8369 (tp30)
  outliers start: 34
  outliers final: 22
  residues processed: 267
  average time/residue: 0.2103
  time to fit residues: 74.2282
Evaluate side-chains
  256 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 230
  time to evaluate  : 0.913 
-------------------------------------------------------------------------------
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  157 THR
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   64 MET
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   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   41 LEU
Chi-restraints excluded: chain G residue   18 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 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:    3.9990
   chunk 92 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 26 optimal weight:    0.4980
   chunk 10 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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  46 ASN
** I  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.074733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.062164 restraints weight = 30040.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.063426 restraints weight = 15176.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.063888 restraints weight = 10715.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.4329

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= 0.225
  Angle     :  0.731  11.911  10903  Z= 0.377
  Chirality :  0.041   0.276   1185
  Planarity :  0.004   0.055   1392
  Dihedral  :  5.105  43.010   1074
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.96 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 24.63 %
    Favored  : 71.36 %
  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:  1.30 (0.26), residues: 967
  helix:  1.67 (0.18), residues: 759
  sheet:  0.19 (1.07), residues: 22
  loop : -2.52 (0.39), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.000   TRP B 106 
 HIS   0.005   0.001   HIS F  94 
 PHE   0.035   0.001   PHE C 107 
 TYR   0.030   0.001   TYR C 151 
 ARG   0.007   0.000   ARG I  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
  281 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 246
  time to evaluate  : 0.888 
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: 0.7655 (tm-30) cc_final: 0.7227 (tm-30)
REVERT: A   45 LYS cc_start: 0.8651 (mmtt) cc_final: 0.8379 (mmtm)
REVERT: A  140 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7924 (tm-30)
REVERT: A  194 LYS cc_start: 0.8922 (tppp) cc_final: 0.8630 (mptt)
REVERT: B   39 MET cc_start: 0.4104 (mtm) cc_final: 0.3519 (tmm)
REVERT: B   67 THR cc_start: 0.8478 (m) cc_final: 0.8221 (p)
REVERT: B   82 LYS cc_start: 0.8329 (mmpt) cc_final: 0.7966 (tptt)
REVERT: C  163 HIS cc_start: 0.8660 (OUTLIER) cc_final: 0.8057 (t70)
REVERT: D   64 MET cc_start: 0.6143 (OUTLIER) cc_final: 0.5496 (tmm)
REVERT: D   78 GLN cc_start: 0.8465 (tm-30) cc_final: 0.7883 (tm-30)
REVERT: D  111 ASP cc_start: 0.7998 (t0) cc_final: 0.7371 (t0)
REVERT: D  118 PHE cc_start: 0.8627 (t80) cc_final: 0.8378 (t80)
REVERT: D  123 GLN cc_start: 0.8598 (tm-30) cc_final: 0.8179 (tm-30)
REVERT: D  155 MET cc_start: 0.7704 (mmt) cc_final: 0.7501 (mmp)
REVERT: D  165 GLU cc_start: 0.8505 (mm-30) cc_final: 0.7994 (mm-30)
REVERT: E   52 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8021 (mp0)
REVERT: E   64 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8329 (mm)
REVERT: F   27 ASP cc_start: 0.8713 (m-30) cc_final: 0.8374 (m-30)
REVERT: F   60 GLN cc_start: 0.8270 (mt0) cc_final: 0.7812 (mt0)
REVERT: G   42 ASP cc_start: 0.7614 (t0) cc_final: 0.7205 (t0)
REVERT: H   39 ASN cc_start: 0.7645 (m110) cc_final: 0.6373 (m110)
REVERT: H   59 SER cc_start: 0.8923 (m) cc_final: 0.8508 (p)
REVERT: I    7 LYS cc_start: 0.9004 (ptmm) cc_final: 0.8517 (tmmt)
REVERT: I   10 GLN cc_start: 0.8644 (mp10) cc_final: 0.8120 (pm20)
REVERT: I   11 GLU cc_start: 0.8086 (mp0) cc_final: 0.7674 (mp0)
REVERT: I   17 GLU cc_start: 0.8739 (tp30) cc_final: 0.8421 (tp30)
REVERT: I   19 LYS cc_start: 0.9416 (mtpp) cc_final: 0.9142 (mtpp)
REVERT: I   33 GLU cc_start: 0.8082 (tm-30) cc_final: 0.7777 (tp30)
REVERT: I   51 LYS cc_start: 0.8267 (ttpp) cc_final: 0.7638 (pptt)
REVERT: I   52 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7509 (mm-30)
REVERT: J   23 GLU cc_start: 0.8750 (tp30) cc_final: 0.8465 (tp30)
  outliers start: 35
  outliers final: 22
  residues processed: 264
  average time/residue: 0.2073
  time to fit residues: 72.3403
Evaluate side-chains
  258 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 232
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
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  157 THR
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  165 ILE
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue   64 MET
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   31 LEU
Chi-restraints excluded: chain E residue   52 GLU
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 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=2.00
-------------------------------------------------------------------------------
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:    0.9980
   chunk 50 optimal weight:    6.9990
   chunk 78 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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**
** I  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.073928 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.061382 restraints weight = 30430.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.062532 restraints weight = 15475.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.063304 restraints weight = 10957.906|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.4414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   8117  Z= 0.260
  Angle     :  0.752  12.583  10903  Z= 0.389
  Chirality :  0.042   0.240   1185
  Planarity :  0.004   0.052   1392
  Dihedral  :  5.116  43.445   1074
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.17 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 24.28 %
    Favored  : 71.59 %
  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:  1.36 (0.26), residues: 967
  helix:  1.75 (0.18), residues: 759
  sheet:  0.10 (1.06), residues: 22
  loop : -2.64 (0.38), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 106 
 HIS   0.006   0.002   HIS I  66 
 PHE   0.037   0.002   PHE C 107 
 TYR   0.033   0.001   TYR C 151 
 ARG   0.006   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
  278 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 242
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7535 (tm-30) cc_final: 0.7055 (tm-30)
REVERT: A   45 LYS cc_start: 0.8802 (mmtt) cc_final: 0.8540 (mmtm)
REVERT: A  140 GLU cc_start: 0.8308 (tm-30) cc_final: 0.7937 (tm-30)
REVERT: A  194 LYS cc_start: 0.8920 (tppp) cc_final: 0.8631 (mptt)
REVERT: B   39 MET cc_start: 0.4198 (mtm) cc_final: 0.3607 (tmm)
REVERT: B   82 LYS cc_start: 0.8427 (mmpt) cc_final: 0.8044 (tptt)
REVERT: C  151 TYR cc_start: 0.8223 (m-80) cc_final: 0.7959 (m-80)
REVERT: C  163 HIS cc_start: 0.8655 (OUTLIER) cc_final: 0.8090 (t70)
REVERT: D   78 GLN cc_start: 0.8469 (tm-30) cc_final: 0.7894 (tm-30)
REVERT: D  111 ASP cc_start: 0.8080 (t0) cc_final: 0.7446 (t0)
REVERT: D  118 PHE cc_start: 0.8625 (t80) cc_final: 0.8386 (t80)
REVERT: D  123 GLN cc_start: 0.8617 (tm-30) cc_final: 0.8202 (tm-30)
REVERT: D  155 MET cc_start: 0.7700 (mmt) cc_final: 0.7491 (mmp)
REVERT: D  165 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8029 (mm-30)
REVERT: E   52 GLU cc_start: 0.8686 (OUTLIER) cc_final: 0.7989 (mp0)
REVERT: E   64 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8364 (mm)
REVERT: F   27 ASP cc_start: 0.8735 (m-30) cc_final: 0.8404 (m-30)
REVERT: F   60 GLN cc_start: 0.8280 (mt0) cc_final: 0.7936 (mt0)
REVERT: G   42 ASP cc_start: 0.7599 (t0) cc_final: 0.7244 (t0)
REVERT: H   39 ASN cc_start: 0.7794 (m110) cc_final: 0.6438 (m110)
REVERT: H   59 SER cc_start: 0.8988 (m) cc_final: 0.8550 (p)
REVERT: I    7 LYS cc_start: 0.9021 (ptmm) cc_final: 0.8560 (tmmt)
REVERT: I   10 GLN cc_start: 0.8625 (mp10) cc_final: 0.7864 (pm20)
REVERT: I   11 GLU cc_start: 0.8062 (mp0) cc_final: 0.7549 (mp0)
REVERT: I   17 GLU cc_start: 0.8757 (tp30) cc_final: 0.8441 (tp30)
REVERT: I   19 LYS cc_start: 0.9447 (mtpp) cc_final: 0.9122 (mtpp)
REVERT: I   33 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7727 (tp30)
REVERT: J   23 GLU cc_start: 0.8769 (tp30) cc_final: 0.8470 (tp30)
  outliers start: 36
  outliers final: 26
  residues processed: 258
  average time/residue: 0.2033
  time to fit residues: 69.4250
Evaluate side-chains
  261 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 232
  time to evaluate  : 0.886 
-------------------------------------------------------------------------------
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 A residue  157 THR
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  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   31 LEU
Chi-restraints excluded: chain E residue   45 THR
Chi-restraints excluded: chain E residue   52 GLU
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 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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 94 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0050
   chunk 4 optimal weight:    9.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    0.7398

-------------------------------------------------------------------------------
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  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 = 0.3528 r_free = 0.3528 target = 0.074521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.061838 restraints weight = 30467.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.063254 restraints weight = 16720.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.063645 restraints weight = 12793.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.4494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   8117  Z= 0.232
  Angle     :  0.775  12.861  10903  Z= 0.396
  Chirality :  0.041   0.221   1185
  Planarity :  0.004   0.054   1392
  Dihedral  :  5.050  42.871   1074
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.76 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 25.32 %
    Favored  : 70.68 %
  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:  1.39 (0.26), residues: 967
  helix:  1.78 (0.18), residues: 758
  sheet:  0.15 (1.07), residues: 22
  loop : -2.66 (0.38), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 106 
 HIS   0.008   0.002   HIS I  66 
 PHE   0.033   0.001   PHE C 107 
 TYR   0.031   0.001   TYR C 151 
 ARG   0.008   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
  276 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 241
  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: A   33 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7176 (tm-30)
REVERT: A   45 LYS cc_start: 0.8656 (mmtt) cc_final: 0.8388 (mmtm)
REVERT: A  140 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7915 (tm-30)
REVERT: A  194 LYS cc_start: 0.8971 (tppp) cc_final: 0.8658 (mptt)
REVERT: B   39 MET cc_start: 0.4087 (mtm) cc_final: 0.3555 (tmm)
REVERT: B   82 LYS cc_start: 0.8450 (mmpt) cc_final: 0.8048 (tptt)
REVERT: C  151 TYR cc_start: 0.8268 (m-80) cc_final: 0.8004 (m-80)
REVERT: C  163 HIS cc_start: 0.8594 (OUTLIER) cc_final: 0.8053 (t70)
REVERT: D   64 MET cc_start: 0.6075 (OUTLIER) cc_final: 0.5567 (tmm)
REVERT: D   78 GLN cc_start: 0.8480 (tm-30) cc_final: 0.7920 (tm-30)
REVERT: D  111 ASP cc_start: 0.8090 (t0) cc_final: 0.7447 (t0)
REVERT: D  118 PHE cc_start: 0.8614 (t80) cc_final: 0.8387 (t80)
REVERT: D  123 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8200 (tm-30)
REVERT: D  155 MET cc_start: 0.7711 (mmt) cc_final: 0.7507 (mmp)
REVERT: D  165 GLU cc_start: 0.8493 (mm-30) cc_final: 0.7955 (mm-30)
REVERT: E   52 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.7965 (mp0)
REVERT: E   64 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.8283 (mm)
REVERT: F   27 ASP cc_start: 0.8792 (m-30) cc_final: 0.8399 (m-30)
REVERT: F   60 GLN cc_start: 0.8250 (mt0) cc_final: 0.7924 (mt0)
REVERT: G   42 ASP cc_start: 0.7631 (t0) cc_final: 0.7274 (t0)
REVERT: H   39 ASN cc_start: 0.7785 (m110) cc_final: 0.6868 (m110)
REVERT: H   59 SER cc_start: 0.8999 (m) cc_final: 0.8583 (p)
REVERT: I    7 LYS cc_start: 0.8977 (ptmm) cc_final: 0.8530 (tmmt)
REVERT: I   10 GLN cc_start: 0.8584 (mp10) cc_final: 0.7749 (pm20)
REVERT: I   11 GLU cc_start: 0.8012 (mp0) cc_final: 0.7504 (mp0)
REVERT: I   19 LYS cc_start: 0.9428 (mtpp) cc_final: 0.9105 (mtpp)
REVERT: I   33 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7808 (tp30)
REVERT: J   23 GLU cc_start: 0.8729 (tp30) cc_final: 0.8507 (tp30)
  outliers start: 35
  outliers final: 27
  residues processed: 258
  average time/residue: 0.2053
  time to fit residues: 70.0123
Evaluate side-chains
  265 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 234
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
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 A residue  157 THR
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  165 ILE
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain D residue   64 MET
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   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   41 LEU
Chi-restraints excluded: chain F residue   83 THR
Chi-restraints excluded: chain G residue   20 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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0010
   chunk 35 optimal weight:    5.9990
   chunk 84 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   chunk 91 optimal weight:    0.4980
   chunk 12 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 89 optimal weight:    0.6980
   chunk 54 optimal weight:    0.0470
   overall best weight:    0.4084

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

Flipped N/Q/H residues before XYZ refinement:
F  16 GLN
G  20 GLN
** G  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.075433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.062620 restraints weight = 30082.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.063941 restraints weight = 14682.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.064761 restraints weight = 10385.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.4654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8117  Z= 0.219
  Angle     :  0.800  15.412  10903  Z= 0.403
  Chirality :  0.042   0.346   1185
  Planarity :  0.004   0.053   1392
  Dihedral  :  4.980  43.152   1074
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.86 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 26.46 %
    Favored  : 70.56 %
  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:  1.49 (0.26), residues: 967
  helix:  1.80 (0.18), residues: 759
  sheet:  0.31 (1.09), residues: 22
  loop : -2.49 (0.39), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 106 
 HIS   0.007   0.001   HIS I  66 
 PHE   0.031   0.001   PHE C 107 
 TYR   0.029   0.001   TYR C 151 
 ARG   0.008   0.001   ARG I  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
  271 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 245
  time to evaluate  : 0.893 
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: 0.7609 (tm-30) cc_final: 0.7181 (tm-30)
REVERT: A   45 LYS cc_start: 0.8694 (mmtt) cc_final: 0.8428 (mmtm)
REVERT: A  140 GLU cc_start: 0.8147 (tm-30) cc_final: 0.7780 (tm-30)
REVERT: A  194 LYS cc_start: 0.8940 (tppp) cc_final: 0.8638 (mptt)
REVERT: B   39 MET cc_start: 0.4257 (mtm) cc_final: 0.3663 (tmm)
REVERT: B   82 LYS cc_start: 0.8326 (mmpt) cc_final: 0.8058 (tptt)
REVERT: C  108 TYR cc_start: 0.8088 (m-80) cc_final: 0.7655 (m-80)
REVERT: C  151 TYR cc_start: 0.8327 (m-80) cc_final: 0.7987 (m-80)
REVERT: C  163 HIS cc_start: 0.8638 (OUTLIER) cc_final: 0.8133 (t70)
REVERT: D   64 MET cc_start: 0.5974 (OUTLIER) cc_final: 0.5468 (tmm)
REVERT: D   78 GLN cc_start: 0.8449 (tm-30) cc_final: 0.7866 (tm-30)
REVERT: D  118 PHE cc_start: 0.8597 (t80) cc_final: 0.8359 (t80)
REVERT: D  123 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8194 (tm-30)
REVERT: D  155 MET cc_start: 0.7709 (mmt) cc_final: 0.7481 (mmp)
REVERT: E   52 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7886 (mp0)
REVERT: E   64 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8278 (mm)
REVERT: F   27 ASP cc_start: 0.8798 (m-30) cc_final: 0.8448 (m-30)
REVERT: F   60 GLN cc_start: 0.8223 (mt0) cc_final: 0.7862 (mt0)
REVERT: G   42 ASP cc_start: 0.7567 (t0) cc_final: 0.7174 (t0)
REVERT: H   39 ASN cc_start: 0.7595 (m110) cc_final: 0.6606 (m110)
REVERT: H   59 SER cc_start: 0.8960 (m) cc_final: 0.8525 (p)
REVERT: I    7 LYS cc_start: 0.8987 (ptmm) cc_final: 0.8542 (tmmt)
REVERT: I   10 GLN cc_start: 0.8482 (mp10) cc_final: 0.7652 (pm20)
REVERT: I   11 GLU cc_start: 0.8077 (mp0) cc_final: 0.7511 (mp0)
REVERT: I   19 LYS cc_start: 0.9464 (mtpp) cc_final: 0.9160 (mtpp)
  outliers start: 26
  outliers final: 21
  residues processed: 258
  average time/residue: 0.2043
  time to fit residues: 69.6782
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  : 0.885 
-------------------------------------------------------------------------------
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  103 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   64 MET
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   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   16 GLN
Chi-restraints excluded: chain F residue   41 LEU
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 95
   random chunks:
   chunk 84 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9990
   chunk 80 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 81 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0970
   chunk 27 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 76 optimal weight:    0.6980
   chunk 36 optimal weight:    1.9990
   chunk 21 optimal weight:    0.2980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
** G  20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  34 ASN
** H  79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** I  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 = 0.3551 r_free = 0.3551 target = 0.075692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.061787 restraints weight = 29972.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.063461 restraints weight = 16327.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.064664 restraints weight = 10945.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.4670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.243   8117  Z= 0.427
  Angle     :  1.102  58.965  10903  Z= 0.611
  Chirality :  0.043   0.336   1185
  Planarity :  0.004   0.052   1392
  Dihedral  :  4.868  43.093   1073
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 14.70
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.96 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 27.49 %
    Favored  : 69.42 %
  Cbeta Deviations :  0.11 %
  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:  1.46 (0.26), residues: 967
  helix:  1.78 (0.18), residues: 759
  sheet:  0.32 (1.09), residues: 22
  loop : -2.48 (0.39), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.000   TRP B 106 
 HIS   0.007   0.001   HIS I  66 
 PHE   0.029   0.001   PHE C 107 
 TYR   0.027   0.001   TYR C 151 
 ARG   0.007   0.000   ARG I  26 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2877.13 seconds
wall clock time: 50 minutes 41.05 seconds (3041.05 seconds total)