Starting phenix.real_space_refine
on Sun Jun 15 20:03:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dwi_47249/06_2025/9dwi_47249.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dwi_47249/06_2025/9dwi_47249.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dwi_47249/06_2025/9dwi_47249.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dwi_47249/06_2025/9dwi_47249.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dwi_47249/06_2025/9dwi_47249.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dwi_47249/06_2025/9dwi_47249.cif"
  }
  resolution = 3.3
  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=   0.002 sd=   1.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4192 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     293      5.49       5
     S      19      5.16       5
     C    8313      2.51       5
     N    2722      2.21       5
     O    3314      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14661
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 657
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "C"
      Number of atoms: 846
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 110, 846
          Classifications: {'peptide': 110}
          Link IDs: {'PTRANS': 5, 'TRANS': 104}
    Chain: "D"
      Number of atoms: 733
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 93, 725
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
      Conformer: "B"
        Number of residues, atoms: 93, 725
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
          bond proxies already assigned to first conformer: 727
    Chain: "E"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 818
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 657
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 657
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 1, 'TRANS': 80}
    Chain: "G"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 807
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 743
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
      Conformer: "B"
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          bond proxies already assigned to first conformer: 738
    Chain: "I"
      Number of atoms: 2383
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 2383
          Classifications: {'DNA': 117}
          Link IDs: {'rna3p': 116}
    Chain: "J"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "K"
      Number of atoms: 595
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 595
          Classifications: {'DNA': 29}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 28}
    Chain: "L"
      Number of atoms: 2591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 323, 2591
          Classifications: {'peptide': 323}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 13, 'TRANS': 308}
          Chain breaks: 1
  Time building chain proxies: 17.13, per 1000 atoms: 1.17
  Number of scatterers: 14661
  At special positions: 0
  Unit cell: (98.707, 152.397, 130.921, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      19     16.00
     P     293     15.00
     O    3314      8.00
     N    2722      7.00
     C    8313      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 6.30
  Conformation dependent library (CDL) restraints added in 1.9 seconds
  

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2030

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 11 sheets defined
      68.3% alpha, 4.5% beta
      142 base pairs and 236 stacking pairs defined.
    Time for finding SS restraints: 8.90
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.848A  pdb=" N   ARG A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 76
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.567A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.758A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.531A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.602A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.547A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
    Processing helix  chain 'D' and resid 104 through 124
      removed outlier: 3.538A  pdb=" N   SER D 124 " --> pdb=" O   LYS D 120 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 4.798A  pdb=" N   GLU E  50 " --> pdb=" O   VAL E  46 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   ARG E  53 " --> pdb=" O   ARG E  49 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.551A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.270A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.637A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 72
      removed outlier: 4.511A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   TYR G  50 " --> pdb=" O   GLY G  46 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   ASP G  72 " --> pdb=" O   ASN G  68 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
    Processing helix  chain 'G' and resid 91 through 97
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
    Processing helix  chain 'H' and resid 103 through 124
      removed outlier: 3.628A  pdb=" N   SER H 124 " --> pdb=" O   LYS H 120 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 12 through 29
      removed outlier: 3.995A  pdb=" N   GLU L  21 " --> pdb=" O   ASP L  17 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LEU L  22 " --> pdb=" O   MET L  18 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ASN L  24 " --> pdb=" O   THR L  20 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   PHE L  25 " --> pdb=" O   GLU L  21 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   GLU L  26 " --> pdb=" O   LEU L  22 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 32 through 49
      removed outlier: 4.278A  pdb=" N   ALA L  38 " --> pdb=" O   HIS L  34 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   TYR L  49 " --> pdb=" O   VAL L  45 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 55 through 60
    Processing helix  chain 'L' and resid 66 through 80
    Processing helix  chain 'L' and resid 82 through 91
    Processing helix  chain 'L' and resid 91 through 102
    Processing helix  chain 'L' and resid 107 through 117
    Processing helix  chain 'L' and resid 121 through 128
    Processing helix  chain 'L' and resid 129 through 132
    Processing helix  chain 'L' and resid 133 through 142
    Processing helix  chain 'L' and resid 142 through 147
      removed outlier: 3.541A  pdb=" N   GLU L 147 " --> pdb=" O   PHE L 143 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 152 through 170
    Processing helix  chain 'L' and resid 209 through 221
      removed outlier: 3.663A  pdb=" N   VAL L 214 " --> pdb=" O   LEU L 210 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 261 through 274
      removed outlier: 4.606A  pdb=" N   TYR L 266 " --> pdb=" O   LYS L 262 " (cutoff:3.500A)
      removed outlier: 5.659A  pdb=" N   CYS L 267 " --> pdb=" O   ASP L 263 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLY L 274 " --> pdb=" O   LEU L 270 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 275 through 289
    Processing helix  chain 'L' and resid 315 through 323
      removed outlier: 3.536A  pdb=" N   ILE L 323 " --> pdb=" O   ILE L 319 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 329 through 333
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.153A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.355A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.588A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.210A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.691A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AA9, first strand: chain 'L' and resid 150 through 151
      removed outlier: 3.604A  pdb=" N   ILE L 150 " --> pdb=" O   SER L 188 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   SER L 188 " --> pdb=" O   ILE L 150 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'L' and resid 174 through 177
      removed outlier: 3.733A  pdb=" N   ILE L 174 " --> pdb=" O   THR L 196 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   VAL L 238 " --> pdb=" O   THR L 227 " (cutoff:3.500A)
      removed outlier: 5.591A  pdb=" N   THR L 227 " --> pdb=" O   VAL L 238 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'L' and resid 291 through 293

    527 hydrogen bonds defined for protein.
    1553 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      365 hydrogen bonds
      730 hydrogen bond angles
      0 basepair planarities
      142 basepair parallelities
      236 stacking parallelities
  Total time for adding SS restraints: 7.48

  Time building geometry restraints manager: 5.23 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3527
        1.34 -     1.46: 4367
        1.46 -     1.58: 7009
        1.58 -     1.70: 584
        1.70 -     1.82: 35
  Bond restraints: 15522
  Sorted by residual:
  bond pdb=" P    DC K 119 "
       pdb=" OP3  DC K 119 "
    ideal  model  delta    sigma   weight residual
    1.480  1.619 -0.139 2.00e-02 2.50e+03 4.83e+01
  bond pdb=" N   LYS G  36 "
       pdb=" CA  LYS G  36 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.94e+00
  bond pdb=" N   ASN F  25 "
       pdb=" CA  ASN F  25 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.42e-02 4.96e+03 6.11e+00
  bond pdb=" N   ARG L 254 "
       pdb=" CA  ARG L 254 "
    ideal  model  delta    sigma   weight residual
    1.456  1.487 -0.030 1.29e-02 6.01e+03 5.53e+00
  bond pdb=" N   LYS L  84 "
       pdb=" CA  LYS L  84 "
    ideal  model  delta    sigma   weight residual
    1.459  1.485 -0.026 1.19e-02 7.06e+03 4.79e+00
  ... (remaining 15517 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.39: 22135
        3.39 -     6.78: 52
        6.78 -    10.17: 8
       10.17 -    13.56: 1
       13.56 -    16.95: 2
  Bond angle restraints: 22198
  Sorted by residual:
  angle pdb=" C   LYS L  87 "
        pdb=" CA  LYS L  87 "
        pdb=" CB  LYS L  87 "
      ideal   model   delta    sigma   weight residual
     110.88   93.93   16.95 1.57e+00 4.06e-01 1.17e+02
  angle pdb=" CB  LYS L  87 "
        pdb=" CG  LYS L  87 "
        pdb=" CD  LYS L  87 "
      ideal   model   delta    sigma   weight residual
     111.30   94.87   16.43 2.30e+00 1.89e-01 5.10e+01
  angle pdb=" C   ASP G  72 "
        pdb=" N   ASN G  73 "
        pdb=" CA  ASN G  73 "
      ideal   model   delta    sigma   weight residual
     122.83  115.63    7.20 1.54e+00 4.22e-01 2.19e+01
  angle pdb=" N   VAL E  46 "
        pdb=" CA  VAL E  46 "
        pdb=" C   VAL E  46 "
      ideal   model   delta    sigma   weight residual
     112.98  107.48    5.50 1.25e+00 6.40e-01 1.94e+01
  angle pdb=" N   ARG L 253 "
        pdb=" CA  ARG L 253 "
        pdb=" C   ARG L 253 "
      ideal   model   delta    sigma   weight residual
     109.24  102.53    6.71 1.67e+00 3.59e-01 1.62e+01
  ... (remaining 22193 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.34: 6844
       28.34 -    56.68: 1607
       56.68 -    85.02: 167
       85.02 -   113.36: 5
      113.36 -   141.70: 4
  Dihedral angle restraints: 8627
    sinusoidal: 5476
      harmonic: 3151
  Sorted by residual:
  dihedral pdb=" C   LYS L  87 "
           pdb=" N   LYS L  87 "
           pdb=" CA  LYS L  87 "
           pdb=" CB  LYS L  87 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -101.49  -21.11     0      2.50e+00 1.60e-01 7.13e+01
  dihedral pdb=" N   LYS L  87 "
           pdb=" C   LYS L  87 "
           pdb=" CA  LYS L  87 "
           pdb=" CB  LYS L  87 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  111.47   11.33     0      2.50e+00 1.60e-01 2.05e+01
  dihedral pdb=" CA  GLU E  50 "
           pdb=" C   GLU E  50 "
           pdb=" N   ILE E  51 "
           pdb=" CA  ILE E  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.85   22.15     0      5.00e+00 4.00e-02 1.96e+01
  ... (remaining 8624 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.124: 2494
       0.124 -    0.249: 8
       0.249 -    0.373: 1
       0.373 -    0.498: 2
       0.498 -    0.622: 2
  Chirality restraints: 2507
  Sorted by residual:
  chirality pdb=" P    DG J  30 "
            pdb=" OP1  DG J  30 "
            pdb=" OP2  DG J  30 "
            pdb=" O5'  DG J  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.97   -0.62 2.00e-01 2.50e+01 9.67e+00
  chirality pdb=" P    DC K 119 "
            pdb=" OP1  DC K 119 "
            pdb=" OP2  DC K 119 "
            pdb=" O5'  DC K 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35    2.97   -0.62 2.00e-01 2.50e+01 9.65e+00
  chirality pdb=" CA  LYS L  87 "
            pdb=" N   LYS L  87 "
            pdb=" C   LYS L  87 "
            pdb=" CB  LYS L  87 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.97   -0.46 2.00e-01 2.50e+01 5.31e+00
  ... (remaining 2504 not shown)

  Planarity restraints: 1802
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G  71 "   -0.647 9.50e-02 1.11e+02   2.90e-01 5.14e+01
        pdb=" NE  ARG G  71 "    0.038 2.00e-02 2.50e+03
        pdb=" CZ  ARG G  71 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG G  71 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG G  71 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN G  68 "   -0.021 2.00e-02 2.50e+03   4.28e-02 1.83e+01
        pdb=" C   ASN G  68 "    0.074 2.00e-02 2.50e+03
        pdb=" O   ASN G  68 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   ALA G  69 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  83 "    0.018 2.00e-02 2.50e+03   1.69e-02 5.70e+00
        pdb=" CG  TYR D  83 "   -0.042 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  83 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  83 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  83 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  83 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  83 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR D  83 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1799 not shown)

  Histogram of nonbonded interaction distances:
        2.29 -     2.81: 3218
        2.81 -     3.33: 13195
        3.33 -     3.85: 28520
        3.85 -     4.38: 31766
        4.38 -     4.90: 46425
  Nonbonded interactions: 123124
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  99 "
            pdb=" OE1 GLU A 133 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" OE2 GLU C  41 "
            pdb=" OG  SER D  87 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   ASP L  17 "
            pdb=" OG1 THR L  20 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" OH  TYR C  39 "
            pdb=" OE1 GLU D  71 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" OG  SER C  18 "
            pdb=" O   LEU C  23 "
     model   vdw
     2.317 3.040
  ... (remaining 123119 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'E' and resid 38 through 134)
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 14 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and (resid 32 or resid 34 through 81 or resid 83 through 124))
  selection = (chain 'H' and (resid 32 or resid 34 through 81 or resid 83 through 124))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:                  0.010
  Normalize map: mean=0, sd=1:             1505.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.140
  Construct map_model_manager:             0.020
  Extract box with map and model:          100.690
  Check model and map are aligned:         0.130
  Set scattering table:                    0.160
  Process input model:                     54.510
  Find NCS groups from input model:        0.620
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:4.700
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total: 1666.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8440
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      :  0.004   0.139  15522  Z= 0.177
  Angle     :  0.634  16.954  22198  Z= 0.366
  Chirality :  0.043   0.622   2507
  Planarity :  0.008   0.290   1802
  Dihedral  : 25.838 141.698   6597
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.98 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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:  1.79 (0.26), residues: 1067
  helix:  1.89 (0.20), residues: 702
  sheet:  1.41 (0.88), residues: 29
  loop : -0.28 (0.35), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP L 325 
 HIS   0.010   0.001   HIS L 135 
 PHE   0.009   0.001   PHE D  65 
 TYR   0.042   0.002   TYR D  83 
 ARG   0.008   0.000   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11620 (  892)
  hydrogen bonds       : angle       4.01131 ( 2283)
  covalent geometry    : bond        0.00352 (15522)
  covalent geometry    : angle       0.63436 (22198)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 155
  time to evaluate  : 1.237 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8036 (mt-10)
REVERT: A  120 MET cc_start: 0.7920 (mtm) cc_final: 0.7309 (mtp)
REVERT: C   36 LYS cc_start: 0.8876 (mtpt) cc_final: 0.8590 (ttmt)
REVERT: C   61 GLU cc_start: 0.8133 (tp30) cc_final: 0.7861 (tp30)
REVERT: G  110 ASN cc_start: 0.8874 (t0) cc_final: 0.8649 (t0)
REVERT: L   72 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8330 (mptt)
REVERT: L  135 HIS cc_start: 0.8523 (t70) cc_final: 0.8303 (t-170)
REVERT: L  282 MET cc_start: -0.1462 (mmp) cc_final: -0.1741 (mmp)
REVERT: L  325 TRP cc_start: 0.7697 (t-100) cc_final: 0.7371 (t-100)
  outliers start: 1
  outliers final: 0
  residues processed: 156
  average time/residue: 0.3600
  time to fit residues: 78.1560
Evaluate side-chains
  127 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 1.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   72 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    6.9990
   chunk 100 optimal weight:    9.9990
   chunk 55 optimal weight:    0.0970
   chunk 34 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 103 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 77 optimal weight:    7.9990
   chunk 119 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
E  39 HIS
F  25 ASN
L  34 HIS
L 157 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.095853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.057517 restraints weight = 84481.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.2991 rms_B_bonded: 3.11
r_work: 0.2803 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.2803
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2792
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2792 r_free = 0.2792    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2792 r_free = 0.2792    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2792
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8713
moved from start:          0.1033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  15522  Z= 0.136
  Angle     :  0.531   8.019  22198  Z= 0.311
  Chirality :  0.033   0.137   2507
  Planarity :  0.004   0.052   1802
  Dihedral  : 28.747 143.886   4410
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  6.96 %
    Favored  : 92.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.35 (0.26), residues: 1067
  helix:  2.32 (0.19), residues: 726
  sheet:  1.34 (0.77), residues: 29
  loop : -0.24 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP L 325 
 HIS   0.005   0.001   HIS L 135 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.029   0.001   TYR H  83 
 ARG   0.005   0.000   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03392 (  892)
  hydrogen bonds       : angle       3.04982 ( 2283)
  covalent geometry    : bond        0.00288 (15522)
  covalent geometry    : angle       0.53086 (22198)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 128
  time to evaluate  : 1.443 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8705 (mt-10)
REVERT: A  120 MET cc_start: 0.8564 (mtm) cc_final: 0.8241 (mtp)
REVERT: C   36 LYS cc_start: 0.9123 (mtpt) cc_final: 0.8866 (ttmt)
REVERT: C   61 GLU cc_start: 0.8886 (tp30) cc_final: 0.8563 (tp30)
REVERT: E   59 GLU cc_start: 0.8202 (pm20) cc_final: 0.7897 (pm20)
REVERT: G  110 ASN cc_start: 0.8970 (t0) cc_final: 0.8633 (t0)
REVERT: H   83 TYR cc_start: 0.8500 (m-80) cc_final: 0.8107 (m-80)
REVERT: L  282 MET cc_start: -0.1105 (mmp) cc_final: -0.1352 (mmp)
REVERT: L  325 TRP cc_start: 0.7822 (t-100) cc_final: 0.7514 (t-100)
  outliers start: 6
  outliers final: 5
  residues processed: 132
  average time/residue: 0.4631
  time to fit residues: 85.5852
Evaluate side-chains
  127 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 122
  time to evaluate  : 1.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   34 LYS
Chi-restraints excluded: chain L residue  255 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 124 optimal weight:    6.9990
   chunk 100 optimal weight:    3.9990
   chunk 27 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   chunk 95 optimal weight:    6.9990
   chunk 102 optimal weight:    5.9990
   chunk 63 optimal weight:    5.9990
   overall best weight:    1.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
E  39 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.094452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.056332 restraints weight = 58587.306|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 2.54
r_work: 0.2787 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2777
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2777 r_free = 0.2777    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2777 r_free = 0.2777    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2777
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8735
moved from start:          0.1317

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  15522  Z= 0.165
  Angle     :  0.526   6.678  22198  Z= 0.309
  Chirality :  0.034   0.138   2507
  Planarity :  0.004   0.049   1802
  Dihedral  : 28.934 146.064   4406
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.72 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  8.04 %
    Favored  : 91.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.26), residues: 1067
  helix:  2.43 (0.20), residues: 729
  sheet:  1.57 (0.75), residues: 29
  loop : -0.30 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP L 325 
 HIS   0.005   0.001   HIS L 135 
 PHE   0.011   0.001   PHE L 181 
 TYR   0.033   0.002   TYR H  83 
 ARG   0.005   0.000   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03512 (  892)
  hydrogen bonds       : angle       2.94946 ( 2283)
  covalent geometry    : bond        0.00368 (15522)
  covalent geometry    : angle       0.52597 (22198)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 124
  time to evaluate  : 3.335 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8704 (mt-10)
REVERT: A  120 MET cc_start: 0.8603 (mtm) cc_final: 0.8313 (mtm)
REVERT: C   36 LYS cc_start: 0.9123 (mtpt) cc_final: 0.8857 (ttmt)
REVERT: C   61 GLU cc_start: 0.8867 (tp30) cc_final: 0.8612 (tp30)
REVERT: E   59 GLU cc_start: 0.8266 (pm20) cc_final: 0.7869 (pm20)
REVERT: G   36 LYS cc_start: 0.9147 (tppt) cc_final: 0.8632 (tttt)
REVERT: G  110 ASN cc_start: 0.8941 (t0) cc_final: 0.8563 (t0)
REVERT: L  236 MET cc_start: 0.9085 (mpp) cc_final: 0.8831 (mmp)
REVERT: L  325 TRP cc_start: 0.7813 (t-100) cc_final: 0.7543 (t-100)
  outliers start: 7
  outliers final: 5
  residues processed: 128
  average time/residue: 0.4812
  time to fit residues: 86.5626
Evaluate side-chains
  123 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 118
  time to evaluate  : 1.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  102 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 63 optimal weight:    5.9990
   chunk 126 optimal weight:   20.0000
   chunk 37 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9990
   chunk 124 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 92 optimal weight:    6.9990
   chunk 54 optimal weight:    0.9980
   chunk 131 optimal weight:   10.0000
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
E  39 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.094350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.055988 restraints weight = 89579.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.2972 rms_B_bonded: 3.26
r_work: 0.2792 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2778
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2778 r_free = 0.2778    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2778 r_free = 0.2778    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2778
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8759
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15522  Z= 0.140
  Angle     :  0.505   6.590  22198  Z= 0.300
  Chirality :  0.033   0.141   2507
  Planarity :  0.004   0.050   1802
  Dihedral  : 28.913 147.159   4406
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.91 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  9.13 %
    Favored  : 89.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.62 (0.26), residues: 1067
  helix:  2.54 (0.19), residues: 727
  sheet:  1.58 (0.72), residues: 29
  loop : -0.22 (0.36), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP L 325 
 HIS   0.005   0.001   HIS G  31 
 PHE   0.007   0.001   PHE A  67 
 TYR   0.031   0.001   TYR H  83 
 ARG   0.009   0.000   ARG G  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03230 (  892)
  hydrogen bonds       : angle       2.83745 ( 2283)
  covalent geometry    : bond        0.00304 (15522)
  covalent geometry    : angle       0.50524 (22198)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 125
  time to evaluate  : 1.363 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8927 (mt-10) cc_final: 0.8707 (mt-10)
REVERT: A  120 MET cc_start: 0.8593 (mtm) cc_final: 0.8360 (mtp)
REVERT: C   36 LYS cc_start: 0.9133 (mtpt) cc_final: 0.8876 (ttmt)
REVERT: C   41 GLU cc_start: 0.8031 (pp20) cc_final: 0.7763 (pp20)
REVERT: E   59 GLU cc_start: 0.8238 (pm20) cc_final: 0.7793 (pm20)
REVERT: G   36 LYS cc_start: 0.9146 (tppt) cc_final: 0.8611 (tmmt)
REVERT: G  110 ASN cc_start: 0.8928 (t0) cc_final: 0.8547 (t0)
REVERT: L  236 MET cc_start: 0.9122 (mpp) cc_final: 0.8887 (mmp)
REVERT: L  325 TRP cc_start: 0.7864 (t-100) cc_final: 0.7606 (t-100)
  outliers start: 11
  outliers final: 6
  residues processed: 132
  average time/residue: 0.3363
  time to fit residues: 61.3017
Evaluate side-chains
  127 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 121
  time to evaluate  : 1.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   34 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 92 optimal weight:    7.9990
   chunk 31 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 121 optimal weight:   50.0000
   chunk 95 optimal weight:    6.9990
   chunk 104 optimal weight:    3.9990
   chunk 116 optimal weight:    5.9990
   chunk 85 optimal weight:   10.0000
   chunk 61 optimal weight:    4.9990
   chunk 88 optimal weight:   10.0000
   overall best weight:    4.3990

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

Flipped N/Q/H residues before XYZ refinement:
A  76 GLN
D  67 ASN
E  39 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.090813 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.051543 restraints weight = 75534.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.2859 rms_B_bonded: 2.96
r_work: 0.2686 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2672
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2672 r_free = 0.2672    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2672 r_free = 0.2672    target_work(ls_wunit_k1) = 0.041         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2672
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8859
moved from start:          0.2206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.047  15522  Z= 0.306
  Angle     :  0.626   7.666  22198  Z= 0.361
  Chirality :  0.039   0.139   2507
  Planarity :  0.004   0.044   1802
  Dihedral  : 29.423 150.142   4406
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.66 %
    Favored  : 96.24 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 10.22 %
    Favored  : 88.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.26), residues: 1067
  helix:  2.24 (0.19), residues: 726
  sheet:  1.67 (0.78), residues: 29
  loop : -0.45 (0.36), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP L 325 
 HIS   0.006   0.001   HIS L 135 
 PHE   0.009   0.001   PHE H  65 
 TYR   0.048   0.003   TYR D  83 
 ARG   0.016   0.001   ARG G  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04604 (  892)
  hydrogen bonds       : angle       3.24310 ( 2283)
  covalent geometry    : bond        0.00708 (15522)
  covalent geometry    : angle       0.62624 (22198)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9167 (mtpt) cc_final: 0.8907 (ttmt)
REVERT: C   41 GLU cc_start: 0.8479 (pp20) cc_final: 0.8271 (tm-30)
REVERT: C   61 GLU cc_start: 0.8916 (tp30) cc_final: 0.8657 (tp30)
REVERT: C  110 ASN cc_start: 0.9147 (t0) cc_final: 0.8898 (t0)
REVERT: E   59 GLU cc_start: 0.8483 (pm20) cc_final: 0.8267 (pm20)
REVERT: F   84 MET cc_start: 0.8881 (tpp) cc_final: 0.8637 (mmm)
REVERT: L  236 MET cc_start: 0.9163 (mpp) cc_final: 0.8859 (mmp)
REVERT: L  325 TRP cc_start: 0.7826 (t-100) cc_final: 0.7541 (t-100)
  outliers start: 13
  outliers final: 9
  residues processed: 128
  average time/residue: 0.3432
  time to fit residues: 61.5636
Evaluate side-chains
  124 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 115
  time to evaluate  : 1.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain F residue   21 VAL
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   44 LYS
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  101 THR
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   34 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 32 optimal weight:    0.8980
   chunk 17 optimal weight:   10.0000
   chunk 94 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9990
   chunk 100 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 41 optimal weight:    0.6980
   chunk 80 optimal weight:    5.9990
   chunk 73 optimal weight:   10.0000
   chunk 113 optimal weight:    6.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
L 135 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.093608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.054701 restraints weight = 74593.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.2934 rms_B_bonded: 3.03
r_work: 0.2769 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.2769
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2757
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2757
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8771
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15522  Z= 0.145
  Angle     :  0.536   7.372  22198  Z= 0.316
  Chirality :  0.034   0.144   2507
  Planarity :  0.003   0.048   1802
  Dihedral  : 29.089 150.994   4406
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.72 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 11.63 %
    Favored  : 87.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.53 (0.26), residues: 1067
  helix:  2.52 (0.20), residues: 721
  sheet:  1.47 (0.75), residues: 29
  loop : -0.30 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP L 325 
 HIS   0.006   0.001   HIS L 135 
 PHE   0.010   0.001   PHE A  67 
 TYR   0.046   0.002   TYR D  83 
 ARG   0.010   0.000   ARG G  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03354 (  892)
  hydrogen bonds       : angle       2.85986 ( 2283)
  covalent geometry    : bond        0.00313 (15522)
  covalent geometry    : angle       0.53641 (22198)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 1.180 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9136 (mtpt) cc_final: 0.8884 (ttmt)
REVERT: C   61 GLU cc_start: 0.8864 (tp30) cc_final: 0.8622 (tp30)
REVERT: E   59 GLU cc_start: 0.8251 (pm20) cc_final: 0.7722 (pm20)
REVERT: L  236 MET cc_start: 0.9150 (mpp) cc_final: 0.8899 (mmp)
REVERT: L  325 TRP cc_start: 0.7888 (t-100) cc_final: 0.7458 (t-100)
  outliers start: 12
  outliers final: 6
  residues processed: 127
  average time/residue: 0.3485
  time to fit residues: 60.8262
Evaluate side-chains
  123 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   34 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 129 optimal weight:    8.9990
   chunk 78 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 104 optimal weight:    5.9990
   chunk 12 optimal weight:    0.3980
   chunk 7 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 112 optimal weight:    6.9990
   chunk 11 optimal weight:    5.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    2.2788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.092798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.053680 restraints weight = 74707.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.2908 rms_B_bonded: 2.99
r_work: 0.2743 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2731
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2731 r_free = 0.2731    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2731 r_free = 0.2731    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2731
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8800
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  15522  Z= 0.191
  Angle     :  0.551   6.937  22198  Z= 0.325
  Chirality :  0.035   0.141   2507
  Planarity :  0.004   0.046   1802
  Dihedral  : 29.174 151.003   4406
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.38 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 12.83 %
    Favored  : 86.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.43 (0.26), residues: 1067
  helix:  2.44 (0.20), residues: 721
  sheet:  1.39 (0.76), residues: 29
  loop : -0.33 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP L 325 
 HIS   0.006   0.001   HIS L 135 
 PHE   0.007   0.001   PHE A  67 
 TYR   0.060   0.002   TYR D  83 
 ARG   0.009   0.000   ARG G  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03748 (  892)
  hydrogen bonds       : angle       2.95381 ( 2283)
  covalent geometry    : bond        0.00431 (15522)
  covalent geometry    : angle       0.55129 (22198)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 1.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9158 (mtpt) cc_final: 0.8905 (ttmt)
REVERT: E   59 GLU cc_start: 0.8391 (pm20) cc_final: 0.7841 (pm20)
REVERT: L  236 MET cc_start: 0.9160 (mpp) cc_final: 0.8919 (mmp)
REVERT: L  325 TRP cc_start: 0.7852 (t-100) cc_final: 0.7490 (t-100)
  outliers start: 10
  outliers final: 8
  residues processed: 123
  average time/residue: 0.3451
  time to fit residues: 58.4825
Evaluate side-chains
  125 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 117
  time to evaluate  : 1.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain F residue   44 LYS
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   34 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 17 optimal weight:   10.0000
   chunk 49 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 83 optimal weight:   20.0000
   chunk 129 optimal weight:    9.9990
   chunk 65 optimal weight:    3.9990
   chunk 82 optimal weight:   10.0000
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
L 135 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.092992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.054640 restraints weight = 60148.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 2.64
r_work: 0.2782 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2782
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2770
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2770 r_free = 0.2770    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2770 r_free = 0.2770    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2770
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8766
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  15522  Z= 0.161
  Angle     :  0.545   8.091  22198  Z= 0.321
  Chirality :  0.034   0.141   2507
  Planarity :  0.004   0.048   1802
  Dihedral  : 29.155 151.347   4406
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.29 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 12.83 %
    Favored  : 85.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.26), residues: 1067
  helix:  2.44 (0.19), residues: 721
  sheet:  1.34 (0.76), residues: 29
  loop : -0.30 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP L 325 
 HIS   0.005   0.001   HIS L 135 
 PHE   0.007   0.001   PHE A  67 
 TYR   0.051   0.002   TYR D  83 
 ARG   0.012   0.000   ARG G  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03548 (  892)
  hydrogen bonds       : angle       2.90774 ( 2283)
  covalent geometry    : bond        0.00355 (15522)
  covalent geometry    : angle       0.54521 (22198)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 1.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9136 (mtpt) cc_final: 0.8885 (ttmt)
REVERT: E   59 GLU cc_start: 0.8292 (pm20) cc_final: 0.7734 (pm20)
REVERT: L  236 MET cc_start: 0.9153 (mpp) cc_final: 0.8912 (mmp)
REVERT: L  325 TRP cc_start: 0.7856 (t-100) cc_final: 0.7493 (t-100)
  outliers start: 11
  outliers final: 8
  residues processed: 128
  average time/residue: 0.3485
  time to fit residues: 61.7295
Evaluate side-chains
  126 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 118
  time to evaluate  : 1.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   34 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 42 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 59 optimal weight:    7.9990
   chunk 18 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9990
   chunk 74 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.0984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.093851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.054898 restraints weight = 71508.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.2946 rms_B_bonded: 2.96
r_work: 0.2776 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2762
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2762 r_free = 0.2762    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2762 r_free = 0.2762    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2762
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8777
moved from start:          0.2181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15522  Z= 0.148
  Angle     :  0.545   7.857  22198  Z= 0.321
  Chirality :  0.034   0.141   2507
  Planarity :  0.004   0.049   1802
  Dihedral  : 29.112 151.421   4406
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.38 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 13.04 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.47 (0.26), residues: 1067
  helix:  2.46 (0.20), residues: 721
  sheet:  1.33 (0.76), residues: 29
  loop : -0.29 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP L 325 
 HIS   0.007   0.001   HIS L 135 
 PHE   0.007   0.001   PHE A  67 
 TYR   0.043   0.002   TYR D  83 
 ARG   0.011   0.000   ARG G  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03457 (  892)
  hydrogen bonds       : angle       2.86832 ( 2283)
  covalent geometry    : bond        0.00320 (15522)
  covalent geometry    : angle       0.54468 (22198)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 1.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ASP cc_start: 0.8546 (t0) cc_final: 0.8205 (p0)
REVERT: C   36 LYS cc_start: 0.9131 (mtpt) cc_final: 0.8879 (ttmt)
REVERT: C   61 GLU cc_start: 0.8793 (tp30) cc_final: 0.8368 (tp30)
REVERT: E   58 THR cc_start: 0.9081 (p) cc_final: 0.8699 (p)
REVERT: E   59 GLU cc_start: 0.8317 (pm20) cc_final: 0.7773 (pm20)
REVERT: L  236 MET cc_start: 0.9169 (mpp) cc_final: 0.8936 (mmp)
REVERT: L  325 TRP cc_start: 0.7885 (t-100) cc_final: 0.7530 (t-100)
  outliers start: 11
  outliers final: 9
  residues processed: 127
  average time/residue: 0.3363
  time to fit residues: 59.0837
Evaluate side-chains
  128 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 1.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain F residue   22 LEU
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  102 ILE
Chi-restraints excluded: chain H residue   34 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 94 optimal weight:    6.9990
   chunk 105 optimal weight:    4.9990
   chunk 79 optimal weight:    6.9990
   chunk 67 optimal weight:    2.9990
   chunk 20 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0040
   chunk 112 optimal weight:    6.9990
   chunk 85 optimal weight:   10.0000
   chunk 99 optimal weight:    8.9990
   chunk 82 optimal weight:   10.0000
   overall best weight:    1.9596

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

Flipped N/Q/H residues before XYZ refinement:
L 135 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.093404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.054506 restraints weight = 64472.147|
|-----------------------------------------------------------------------------|
r_work (start): 0.2939 rms_B_bonded: 2.79
r_work: 0.2771 rms_B_bonded: 4.23 restraints_weight: 0.5000
r_work (final): 0.2771
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2756
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2756 r_free = 0.2756    target_work(ls_wunit_k1) = 0.044         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2756
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8785
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  15522  Z= 0.178
  Angle     :  0.557   7.782  22198  Z= 0.327
  Chirality :  0.034   0.141   2507
  Planarity :  0.004   0.048   1802
  Dihedral  : 29.129 151.209   4406
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.47 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  : 13.48 %
    Favored  : 85.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.26), residues: 1067
  helix:  2.40 (0.20), residues: 721
  sheet:  1.39 (0.77), residues: 29
  loop : -0.31 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP L 325 
 HIS   0.005   0.001   HIS L 135 
 PHE   0.007   0.001   PHE A  67 
 TYR   0.043   0.002   TYR D  83 
 ARG   0.011   0.000   ARG G  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03646 (  892)
  hydrogen bonds       : angle       2.93138 ( 2283)
  covalent geometry    : bond        0.00399 (15522)
  covalent geometry    : angle       0.55673 (22198)

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 1.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 LYS cc_start: 0.9126 (mtpt) cc_final: 0.8872 (ttmt)
REVERT: E   59 GLU cc_start: 0.8338 (pm20) cc_final: 0.7770 (pm20)
REVERT: L  236 MET cc_start: 0.9162 (mpp) cc_final: 0.8911 (mmp)
REVERT: L  325 TRP cc_start: 0.7862 (t-100) cc_final: 0.7510 (t-100)
  outliers start: 10
  outliers final: 6
  residues processed: 127
  average time/residue: 0.3356
  time to fit residues: 59.1744
Evaluate side-chains
  126 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 120
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   43 VAL
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain G residue   49 VAL
Chi-restraints excluded: chain G residue   95 LYS
Chi-restraints excluded: chain G residue  102 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 5 optimal weight:    0.8980
   chunk 18 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0870
   chunk 52 optimal weight:    0.9980
   chunk 61 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 96 optimal weight:    8.9990
   chunk 8 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 108 optimal weight:    5.9990
   chunk 99 optimal weight:   10.0000
   overall best weight:    0.7360

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.094827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.056681 restraints weight = 62257.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.2987 rms_B_bonded: 2.72
r_work: 0.2829 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.2829
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2818
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2818 r_free = 0.2818    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2818 r_free = 0.2818    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2818
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8720
moved from start:          0.2295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15522  Z= 0.140
  Angle     :  0.549   9.964  22198  Z= 0.322
  Chirality :  0.033   0.140   2507
  Planarity :  0.004   0.052   1802
  Dihedral  : 29.028 151.461   4406
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.47 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 14.02 %
    Favored  : 85.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.46 (0.27), residues: 1067
  helix:  2.44 (0.20), residues: 721
  sheet:  1.36 (0.78), residues: 29
  loop : -0.25 (0.36), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP L 325 
 HIS   0.005   0.001   HIS D  82 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.044   0.002   TYR H  83 
 ARG   0.011   0.000   ARG G  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03431 (  892)
  hydrogen bonds       : angle       2.85874 ( 2283)
  covalent geometry    : bond        0.00299 (15522)
  covalent geometry    : angle       0.54929 (22198)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 17505.29 seconds
wall clock time: 308 minutes 13.58 seconds (18493.58 seconds total)