Starting phenix.real_space_refine
on Thu Sep 18 15:03:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dwh_47246/09_2025/9dwh_47246.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dwh_47246/09_2025/9dwh_47246.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/9dwh_47246/09_2025/9dwh_47246.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dwh_47246/09_2025/9dwh_47246.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dwh_47246/09_2025/9dwh_47246.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dwh_47246/09_2025/9dwh_47246.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   1.009
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    8308      2.51       5
     N    2718      2.21       5
     O    3315      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14653
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 813
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 98, 805
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
      Conformer: "B"
        Number of residues, atoms: 98, 805
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
          bond proxies already assigned to first conformer: 808
    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: 732
      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: 800
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 800
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    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: 823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 823
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 725
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 725
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    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: 3.21, per 1000 atoms: 0.22
  Number of scatterers: 14653
  At special positions: 0
  Unit cell: (97.468, 152.397, 136.29, 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    3315      8.00
     N    2718      7.00
     C    8308      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: 0.83
  Conformation dependent library (CDL) restraints added in 517.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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
      67.9% alpha, 4.6% beta
      144 base pairs and 241 stacking pairs defined.
    Time for finding SS restraints: 1.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 4.139A  pdb=" N   GLU A  50 " --> pdb=" O   VAL A  46 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ARG A  53 " --> pdb=" O   ARG A  49 " (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
    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: 3.645A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.574A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.534A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
    Processing helix  chain 'C' and resid 90 through 97
      removed outlier: 3.500A  pdb=" N   ASN C  94 " --> pdb=" O   ASP C  90 " (cutoff:3.500A)
    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 123
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 4.835A  pdb=" N   GLU E  50 " --> pdb=" O   VAL E  46 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   ARG E  53 " --> pdb=" O   ARG E  49 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 77
      removed outlier: 3.659A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 132
    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: 4.163A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    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: 4.394A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
      removed outlier: 3.981A  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
      removed outlier: 3.543A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 124
    Processing helix  chain 'L' and resid 12 through 29
      removed outlier: 4.188A  pdb=" N   GLU L  21 " --> pdb=" O   ASP L  17 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   LEU L  22 " --> pdb=" O   MET L  18 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   ALA L  23 " --> pdb=" O   LEU L  19 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   ASN L  24 " --> pdb=" O   THR L  20 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 32 through 48
      removed outlier: 4.419A  pdb=" N   ALA L  38 " --> pdb=" O   HIS L  34 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 55 through 60
    Processing helix  chain 'L' and resid 66 through 80
      removed outlier: 3.692A  pdb=" N   ALA L  70 " --> pdb=" O   GLY L  66 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 82 through 90
    Processing helix  chain 'L' and resid 91 through 102
      removed outlier: 3.526A  pdb=" N   ARG L 102 " --> pdb=" O   ASN L  98 " (cutoff:3.500A)
    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: 3.576A  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: 3.608A  pdb=" N   VAL L 214 " --> pdb=" O   LEU L 210 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 261 through 274
      removed outlier: 4.640A  pdb=" N   TYR L 266 " --> pdb=" O   LYS L 262 " (cutoff:3.500A)
      removed outlier: 5.656A  pdb=" N   CYS L 267 " --> pdb=" O   ASP L 263 " (cutoff:3.500A)
      removed outlier: 3.809A  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: 3.519A  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: 7.087A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.518A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.447A  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: 7.150A  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: 7.185A  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: 3.697A  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: 3.593A  pdb=" N   SER L 188 " --> pdb=" O   ILE L 150 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 174 through 178
      removed outlier: 3.611A  pdb=" N   ILE L 174 " --> pdb=" O   THR L 196 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   ASP L 192 " --> pdb=" O   CYS L 178 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   VAL L 238 " --> pdb=" O   THR L 227 " (cutoff:3.500A)
      removed outlier: 5.924A  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

    530 hydrogen bonds defined for protein.
    1558 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      369 hydrogen bonds
      738 hydrogen bond angles
      0 basepair planarities
      144 basepair parallelities
      241 stacking parallelities
  Total time for adding SS restraints: 2.79

  Time building geometry restraints manager: 1.25 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2777
        1.33 -     1.45: 4862
        1.45 -     1.57: 7256
        1.57 -     1.69: 584
        1.69 -     1.81: 35
  Bond restraints: 15514
  Sorted by residual:
  bond pdb=" P    DC K 119 "
       pdb=" OP3  DC K 119 "
    ideal  model  delta    sigma   weight residual
    1.480  1.611 -0.131 2.00e-02 2.50e+03 4.29e+01
  bond pdb=" CA  LYS L  35 "
       pdb=" C   LYS L  35 "
    ideal  model  delta    sigma   weight residual
    1.522  1.491  0.031 9.30e-03 1.16e+04 1.11e+01
  bond pdb=" N   ARG A  49 "
       pdb=" CA  ARG A  49 "
    ideal  model  delta    sigma   weight residual
    1.459  1.501 -0.043 1.28e-02 6.10e+03 1.10e+01
  bond pdb=" N   ILE L  69 "
       pdb=" CA  ILE L  69 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.035 1.21e-02 6.83e+03 8.24e+00
  bond pdb=" CA  GLY L  64 "
       pdb=" C   GLY L  64 "
    ideal  model  delta    sigma   weight residual
    1.514  1.474  0.039 1.39e-02 5.18e+03 7.97e+00
  ... (remaining 15509 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.19: 21793
        2.19 -     4.38: 346
        4.38 -     6.57: 39
        6.57 -     8.77: 8
        8.77 -    10.96: 3
  Bond angle restraints: 22189
  Sorted by residual:
  angle pdb=" C   GLY L  64 "
        pdb=" N   VAL L  65 "
        pdb=" CA  VAL L  65 "
      ideal   model   delta    sigma   weight residual
     121.65  113.27    8.38 9.40e-01 1.13e+00 7.95e+01
  angle pdb=" N   LYS L  35 "
        pdb=" CA  LYS L  35 "
        pdb=" C   LYS L  35 "
      ideal   model   delta    sigma   weight residual
     112.12  102.49    9.63 1.34e+00 5.57e-01 5.17e+01
  angle pdb=" N   PRO L  63 "
        pdb=" CA  PRO L  63 "
        pdb=" C   PRO L  63 "
      ideal   model   delta    sigma   weight residual
     111.21  100.25   10.96 1.59e+00 3.96e-01 4.75e+01
  angle pdb=" N   VAL L  65 "
        pdb=" CA  VAL L  65 "
        pdb=" CB  VAL L  65 "
      ideal   model   delta    sigma   weight residual
     112.28  118.38   -6.10 1.00e+00 1.00e+00 3.72e+01
  angle pdb=" N   VAL L  65 "
        pdb=" CA  VAL L  65 "
        pdb=" C   VAL L  65 "
      ideal   model   delta    sigma   weight residual
     106.21   99.71    6.50 1.07e+00 8.73e-01 3.69e+01
  ... (remaining 22184 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.26: 7146
       33.26 -    66.52: 1429
       66.52 -    99.79: 38
       99.79 -   133.05: 1
      133.05 -   166.31: 5
  Dihedral angle restraints: 8619
    sinusoidal: 5468
      harmonic: 3151
  Sorted by residual:
  dihedral pdb=" CD  ARG G  71 "
           pdb=" NE  ARG G  71 "
           pdb=" CZ  ARG G  71 "
           pdb=" NH1 ARG G  71 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   72.24  -72.24     1      1.00e+01 1.00e-02 6.67e+01
  dihedral pdb=" C   ASP G  72 "
           pdb=" N   ASP G  72 "
           pdb=" CA  ASP G  72 "
           pdb=" CB  ASP G  72 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -133.91   11.31     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  157.89   22.11     0      5.00e+00 4.00e-02 1.96e+01
  ... (remaining 8616 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.125: 2484
       0.125 -    0.250: 21
       0.250 -    0.374: 1
       0.374 -    0.499: 1
       0.499 -    0.624: 1
  Chirality restraints: 2508
  Sorted by residual:
  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 9.73e+00
  chirality pdb=" CA  ASP G  72 "
            pdb=" N   ASP G  72 "
            pdb=" C   ASP G  72 "
            pdb=" CB  ASP G  72 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.42e+00
  chirality pdb=" CA  LYS L  35 "
            pdb=" N   LYS L  35 "
            pdb=" C   LYS L  35 "
            pdb=" CB  LYS L  35 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.04e+00
  ... (remaining 2505 not shown)

  Planarity restraints: 1800
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG G  71 "   -1.055 9.50e-02 1.11e+02   4.73e-01 1.35e+02
        pdb=" NE  ARG G  71 "    0.063 2.00e-02 2.50e+03
        pdb=" CZ  ARG G  71 "    0.013 2.00e-02 2.50e+03
        pdb=" NH1 ARG G  71 "   -0.007 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  HIS L  34 "    0.017 2.00e-02 2.50e+03   3.57e-02 1.27e+01
        pdb=" C   HIS L  34 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   HIS L  34 "    0.024 2.00e-02 2.50e+03
        pdb=" N   LYS L  35 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN G  68 "   -0.017 2.00e-02 2.50e+03   3.43e-02 1.18e+01
        pdb=" C   ASN G  68 "    0.059 2.00e-02 2.50e+03
        pdb=" O   ASN G  68 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   ALA G  69 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1797 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2432
        2.78 -     3.31: 13006
        3.31 -     3.84: 28608
        3.84 -     4.37: 31837
        4.37 -     4.90: 47177
  Nonbonded interactions: 123060
  Sorted by model distance:
  nonbonded pdb=" OP1  DC J  34 "
            pdb=" OG1 THR L 233 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   THR C  16 "
            pdb=" OG  SER C  19 "
     model   vdw
     2.297 3.040
  nonbonded pdb=" OG  SER C  18 "
            pdb=" O   LEU C  23 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OG  SER G  18 "
            pdb=" O   LEU G  23 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" OG  SER L 275 "
            pdb=" O   SER L 334 "
     model   vdw
     2.311 3.040
  ... (remaining 123055 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' and (resid 38 through 128 or resid 130 through 134))
  selection = (chain 'E' and (resid 38 through 128 or resid 130 through 134))
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 14 through 119)
  selection = (chain 'G' and resid 14 through 119)
}
ncs_group {
  reference = (chain 'D' and (resid 32 through 81 or resid 83 through 124))
  selection = (chain 'H' and (resid 32 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:                  0.000
  Normalize map: mean=0, sd=1:             19.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.970
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     14.560
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.810
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
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   0.131  15514  Z= 0.195
  Angle     :  0.656  10.956  22189  Z= 0.401
  Chirality :  0.042   0.624   2508
  Planarity :  0.012   0.473   1800
  Dihedral  : 26.100 166.309   6589
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  :  0.33 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.26), residues: 1067
  helix:  1.91 (0.20), residues: 714
  sheet:  1.19 (0.82), residues: 29
  loop : -0.26 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  23 
 TYR   0.023   0.002   TYR H  83 
 PHE   0.015   0.001   PHE L  25 
 TRP   0.004   0.001   TRP L 325 
 HIS   0.009   0.001   HIS L 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (15514)
  covalent geometry    : angle       0.65609 (22189)
  hydrogen bonds       : bond        0.11342 (  899)
  hydrogen bonds       : angle       4.16907 ( 2296)

*********************** 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
  162 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 160
  time to evaluate  : 0.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8329 (m-10) cc_final: 0.7940 (m-10)
REVERT: E   60 LEU cc_start: 0.8042 (mm) cc_final: 0.7782 (mm)
REVERT: L   11 LEU cc_start: 0.7427 (mp) cc_final: 0.7030 (tp)
REVERT: L  236 MET cc_start: 0.8834 (mmp) cc_final: 0.8598 (mmp)
  outliers start: 2
  outliers final: 0
  residues processed: 161
  average time/residue: 0.1493
  time to fit residues: 33.1308
Evaluate side-chains
  116 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:   10.0000
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    7.9990
   chunk 130 optimal weight:   30.0000
   chunk 124 optimal weight:   50.0000
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    6.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  55 GLN
C  38 ASN
C  73 ASN
C 112 GLN
E 108 ASN
F  75 HIS
L  34 HIS
** L 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.093297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.054323 restraints weight = 107891.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 3.48
r_work: 0.2730 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2713
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2713 r_free = 0.2713    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2713 r_free = 0.2713    target_work(ls_wunit_k1) = 0.043         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2713
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8820
moved from start:          0.1976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.056  15514  Z= 0.344
  Angle     :  0.661   7.547  22189  Z= 0.376
  Chirality :  0.041   0.194   2508
  Planarity :  0.005   0.057   1800
  Dihedral  : 29.555 162.362   4405
  Min Nonbonded Distance : 2.331

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  7.07 %
    Favored  : 91.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.85 (0.26), residues: 1067
  helix:  1.92 (0.19), residues: 729
  sheet:  0.89 (0.72), residues: 29
  loop : -0.35 (0.36), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D  79 
 TYR   0.037   0.003   TYR H  83 
 PHE   0.010   0.001   PHE L  25 
 TRP   0.001   0.000   TRP L 325 
 HIS   0.006   0.002   HIS G  31 

Details of bonding type rmsd
  covalent geometry    : bond        0.00795 (15514)
  covalent geometry    : angle       0.66134 (22189)
  hydrogen bonds       : bond        0.05086 (  899)
  hydrogen bonds       : angle       3.62321 ( 2296)

*********************** 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 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 119
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8277 (tm-30)
REVERT: A  105 GLU cc_start: 0.8794 (tp30) cc_final: 0.8539 (mt-10)
REVERT: B   88 TYR cc_start: 0.8939 (m-10) cc_final: 0.8481 (m-10)
REVERT: D   71 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8733 (tm-30)
REVERT: D   83 TYR cc_start: 0.8695 (m-10) cc_final: 0.8323 (m-10)
REVERT: E   81 ASP cc_start: 0.8500 (t70) cc_final: 0.8269 (t70)
REVERT: L   11 LEU cc_start: 0.7903 (mp) cc_final: 0.7393 (tp)
REVERT: L   18 MET cc_start: 0.5947 (ppp) cc_final: 0.5412 (ppp)
REVERT: L  191 MET cc_start: 0.4208 (mmt) cc_final: 0.3763 (mmt)
REVERT: L  236 MET cc_start: 0.8879 (mmp) cc_final: 0.8607 (mmp)
  outliers start: 15
  outliers final: 10
  residues processed: 130
  average time/residue: 0.1384
  time to fit residues: 25.3318
Evaluate side-chains
  126 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 116
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue  118 VAL
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain L residue  158 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 21 optimal weight:    0.6980
   chunk 69 optimal weight:    3.9990
   chunk 37 optimal weight:    6.9990
   chunk 104 optimal weight:   30.0000
   chunk 9 optimal weight:    0.9980
   chunk 129 optimal weight:    4.9990
   chunk 54 optimal weight:    0.2980
   chunk 43 optimal weight:    0.8980
   chunk 122 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3972 r_free = 0.3972 target = 0.095748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.057279 restraints weight = 95702.421|
|-----------------------------------------------------------------------------|
r_work (start): 0.3007 rms_B_bonded: 3.48
r_work: 0.2810 rms_B_bonded: 4.81 restraints_weight: 0.5000
r_work (final): 0.2810
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2796
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2796 r_free = 0.2796    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2796 r_free = 0.2796    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2796
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8701
moved from start:          0.1808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15514  Z= 0.141
  Angle     :  0.526   5.480  22189  Z= 0.310
  Chirality :  0.034   0.171   2508
  Planarity :  0.004   0.044   1800
  Dihedral  : 29.236 163.538   4405
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  :  8.60 %
    Favored  : 90.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.27 (0.26), residues: 1067
  helix:  2.24 (0.20), residues: 731
  sheet:  0.47 (0.75), residues: 30
  loop : -0.15 (0.37), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  79 
 TYR   0.030   0.001   TYR H  83 
 PHE   0.008   0.001   PHE A  67 
 TRP   0.006   0.002   TRP L 325 
 HIS   0.004   0.001   HIS L 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (15514)
  covalent geometry    : angle       0.52603 (22189)
  hydrogen bonds       : bond        0.03443 (  899)
  hydrogen bonds       : angle       3.06970 ( 2296)

*********************** 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
  138 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7932 (tm-30)
REVERT: E   59 GLU cc_start: 0.8208 (pm20) cc_final: 0.7866 (pm20)
REVERT: H   34 LYS cc_start: 0.8568 (mmtm) cc_final: 0.8347 (mmtm)
REVERT: L   18 MET cc_start: 0.5843 (ppp) cc_final: 0.5440 (ppp)
REVERT: L  155 MET cc_start: 0.8151 (mpp) cc_final: 0.7904 (mpp)
REVERT: L  236 MET cc_start: 0.8820 (mmp) cc_final: 0.8493 (mmp)
REVERT: L  282 MET cc_start: 0.5265 (mmm) cc_final: 0.4928 (mmm)
  outliers start: 12
  outliers final: 8
  residues processed: 134
  average time/residue: 0.1315
  time to fit residues: 25.2386
Evaluate side-chains
  128 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain L residue  214 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 8 optimal weight:    0.8980
   chunk 85 optimal weight:    9.9990
   chunk 58 optimal weight:    3.9990
   chunk 56 optimal weight:    0.4980
   chunk 19 optimal weight:    5.9990
   chunk 129 optimal weight:   20.0000
   chunk 98 optimal weight:   10.0000
   chunk 64 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    2.4786

-------------------------------------------------------------------------------
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 = 0.3943 r_free = 0.3943 target = 0.094290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.055508 restraints weight = 122370.964|
|-----------------------------------------------------------------------------|
r_work (start): 0.2953 rms_B_bonded: 3.89
r_work (final): 0.2953
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2952
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2952 r_free = 0.2952    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2953 r_free = 0.2953    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2953
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.2110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  15514  Z= 0.199
  Angle     :  0.546   5.472  22189  Z= 0.320
  Chirality :  0.035   0.166   2508
  Planarity :  0.003   0.038   1800
  Dihedral  : 29.381 164.744   4405
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  9.47 %
    Favored  : 88.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.33 (0.27), residues: 1067
  helix:  2.27 (0.20), residues: 733
  sheet:  0.83 (0.69), residues: 36
  loop : -0.19 (0.38), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  79 
 TYR   0.040   0.002   TYR H  83 
 PHE   0.007   0.001   PHE G  25 
 TRP   0.001   0.000   TRP L 325 
 HIS   0.003   0.001   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (15514)
  covalent geometry    : angle       0.54616 (22189)
  hydrogen bonds       : bond        0.03980 (  899)
  hydrogen bonds       : angle       3.16089 ( 2296)

*********************** 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
  137 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.393 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.7546 (tm-30) cc_final: 0.7227 (tm-30)
REVERT: B   88 TYR cc_start: 0.8520 (m-10) cc_final: 0.8199 (m-10)
REVERT: L   11 LEU cc_start: 0.8225 (OUTLIER) cc_final: 0.7574 (tp)
REVERT: L   18 MET cc_start: 0.6124 (ppp) cc_final: 0.5799 (ppp)
REVERT: L  236 MET cc_start: 0.8689 (mmp) cc_final: 0.8366 (mmp)
REVERT: L  282 MET cc_start: 0.5371 (mmm) cc_final: 0.5086 (mmm)
  outliers start: 15
  outliers final: 10
  residues processed: 133
  average time/residue: 0.1371
  time to fit residues: 25.7988
Evaluate side-chains
  130 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue  155 MET
Chi-restraints excluded: chain L residue  214 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 93 optimal weight:    7.9990
   chunk 14 optimal weight:    0.8980
   chunk 68 optimal weight:    0.7980
   chunk 126 optimal weight:    6.9990
   chunk 120 optimal weight:    1.9990
   chunk 124 optimal weight:   10.0000
   chunk 47 optimal weight:    0.1980
   chunk 123 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    0.9784

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.095677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.057116 restraints weight = 106451.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3000 rms_B_bonded: 3.64
r_work: 0.2797 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2786
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2786 r_free = 0.2786    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2786 r_free = 0.2786    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2786
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8706
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15514  Z= 0.138
  Angle     :  0.516   5.425  22189  Z= 0.305
  Chirality :  0.034   0.166   2508
  Planarity :  0.003   0.041   1800
  Dihedral  : 29.267 164.514   4405
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  :  9.47 %
    Favored  : 88.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.53 (0.27), residues: 1067
  helix:  2.43 (0.20), residues: 732
  sheet:  0.86 (0.68), residues: 36
  loop : -0.12 (0.38), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  71 
 TYR   0.035   0.001   TYR H  83 
 PHE   0.008   0.001   PHE A  67 
 TRP   0.003   0.001   TRP L 325 
 HIS   0.004   0.001   HIS L 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (15514)
  covalent geometry    : angle       0.51622 (22189)
  hydrogen bonds       : bond        0.03362 (  899)
  hydrogen bonds       : angle       2.96395 ( 2296)

*********************** 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
  138 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.8268 (tm-30) cc_final: 0.7851 (tm-30)
REVERT: B   88 TYR cc_start: 0.8864 (m-10) cc_final: 0.8549 (m-10)
REVERT: H   34 LYS cc_start: 0.8494 (mmtm) cc_final: 0.8290 (mmtm)
REVERT: L   11 LEU cc_start: 0.8200 (mp) cc_final: 0.7541 (tp)
REVERT: L   18 MET cc_start: 0.5872 (ppp) cc_final: 0.5610 (ppp)
REVERT: L  155 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7644 (mpp)
REVERT: L  236 MET cc_start: 0.8800 (mmp) cc_final: 0.8454 (mmp)
  outliers start: 15
  outliers final: 13
  residues processed: 136
  average time/residue: 0.1354
  time to fit residues: 26.2704
Evaluate side-chains
  131 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 117
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain L residue  155 MET
Chi-restraints excluded: chain L residue  214 VAL
Chi-restraints excluded: chain L residue  292 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 27 optimal weight:    5.9990
   chunk 128 optimal weight:   40.0000
   chunk 57 optimal weight:    4.9990
   chunk 67 optimal weight:    0.8980
   chunk 41 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 23 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   chunk 86 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9980
   chunk 103 optimal weight:    8.9990
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
F  75 HIS
H  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.094700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.056501 restraints weight = 74083.800|
|-----------------------------------------------------------------------------|
r_work (start): 0.2985 rms_B_bonded: 3.02
r_work: 0.2794 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2783
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2783 r_free = 0.2783    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2783 r_free = 0.2783    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2783
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  15514  Z= 0.181
  Angle     :  0.535   5.580  22189  Z= 0.313
  Chirality :  0.035   0.161   2508
  Planarity :  0.003   0.038   1800
  Dihedral  : 29.327 165.418   4405
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  :  9.58 %
    Favored  : 88.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.54 (0.27), residues: 1067
  helix:  2.43 (0.20), residues: 733
  sheet:  0.93 (0.69), residues: 36
  loop : -0.10 (0.38), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  23 
 TYR   0.046   0.002   TYR H  83 
 PHE   0.007   0.001   PHE E  67 
 TRP   0.001   0.000   TRP L 325 
 HIS   0.003   0.001   HIS L 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (15514)
  covalent geometry    : angle       0.53477 (22189)
  hydrogen bonds       : bond        0.03704 (  899)
  hydrogen bonds       : angle       3.04565 ( 2296)

*********************** 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
  138 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 119
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7836 (tm-30)
REVERT: B   88 TYR cc_start: 0.8847 (m-10) cc_final: 0.8482 (m-10)
REVERT: G   91 GLU cc_start: 0.8830 (tp30) cc_final: 0.8618 (tp30)
REVERT: L   11 LEU cc_start: 0.8218 (mp) cc_final: 0.7548 (tp)
REVERT: L   18 MET cc_start: 0.5952 (ppp) cc_final: 0.5732 (ppp)
REVERT: L  155 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.7548 (mpp)
REVERT: L  236 MET cc_start: 0.8773 (mmp) cc_final: 0.8421 (mmp)
REVERT: L  282 MET cc_start: 0.5100 (mmp) cc_final: 0.4895 (mmm)
  outliers start: 19
  outliers final: 15
  residues processed: 134
  average time/residue: 0.1379
  time to fit residues: 26.4505
Evaluate side-chains
  132 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 116
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   96 SER
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain L residue  155 MET
Chi-restraints excluded: chain L residue  214 VAL
Chi-restraints excluded: chain L residue  292 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 17 optimal weight:   10.0000
   chunk 12 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 100 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 54 optimal weight:    4.9990
   chunk 13 optimal weight:    0.6980
   chunk 72 optimal weight:    4.9990
   chunk 73 optimal weight:   10.0000
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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 = 0.3966 r_free = 0.3966 target = 0.095400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.056798 restraints weight = 121698.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 3.86
r_work (final): 0.2986
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2986
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2986 r_free = 0.2986    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2986 r_free = 0.2986    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2986
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.2282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  15514  Z= 0.148
  Angle     :  0.528   9.820  22189  Z= 0.309
  Chirality :  0.034   0.161   2508
  Planarity :  0.003   0.039   1800
  Dihedral  : 29.287 165.098   4405
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 10.12 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.60 (0.27), residues: 1067
  helix:  2.47 (0.20), residues: 732
  sheet:  0.82 (0.69), residues: 36
  loop : -0.03 (0.38), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG G  71 
 TYR   0.045   0.002   TYR H  83 
 PHE   0.007   0.001   PHE E  67 
 TRP   0.001   0.000   TRP L 325 
 HIS   0.004   0.001   HIS L 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (15514)
  covalent geometry    : angle       0.52818 (22189)
  hydrogen bonds       : bond        0.03429 (  899)
  hydrogen bonds       : angle       2.95952 ( 2296)

*********************** 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
  136 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7090 (tm-30)
REVERT: B   88 TYR cc_start: 0.8512 (m-10) cc_final: 0.8129 (m-10)
REVERT: L   11 LEU cc_start: 0.8295 (mp) cc_final: 0.7624 (tp)
REVERT: L   18 MET cc_start: 0.6169 (ppp) cc_final: 0.5942 (ppp)
REVERT: L  155 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7622 (mpp)
REVERT: L  236 MET cc_start: 0.8679 (mmp) cc_final: 0.8329 (mmp)
  outliers start: 16
  outliers final: 13
  residues processed: 134
  average time/residue: 0.1433
  time to fit residues: 27.5837
Evaluate side-chains
  132 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.500 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   31 LYS
Chi-restraints excluded: chain B residue   49 LEU
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain L residue  155 MET
Chi-restraints excluded: chain L residue  214 VAL
Chi-restraints excluded: chain L residue  292 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 129 optimal weight:    8.9990
   chunk 17 optimal weight:   10.0000
   chunk 131 optimal weight:    7.9990
   chunk 21 optimal weight:    3.9990
   chunk 109 optimal weight:    0.2980
   chunk 119 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 95 optimal weight:    7.9990
   chunk 98 optimal weight:   10.0000
   chunk 128 optimal weight:    9.9990
   overall best weight:    2.6386

-------------------------------------------------------------------------------
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 = 0.3945 r_free = 0.3945 target = 0.094553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.056612 restraints weight = 63981.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.2991 rms_B_bonded: 2.67
r_work: 0.2790 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2789
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8742
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033  15514  Z= 0.203
  Angle     :  0.556   6.121  22189  Z= 0.324
  Chirality :  0.036   0.156   2508
  Planarity :  0.003   0.036   1800
  Dihedral  : 29.418 165.439   4405
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 10.99 %
    Favored  : 87.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.53 (0.27), residues: 1067
  helix:  2.40 (0.19), residues: 733
  sheet:  0.80 (0.69), residues: 36
  loop : -0.04 (0.39), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG G  71 
 TYR   0.043   0.002   TYR H  83 
 PHE   0.007   0.001   PHE L 278 
 TRP   0.001   0.000   TRP L 325 
 HIS   0.005   0.001   HIS L 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 (15514)
  covalent geometry    : angle       0.55559 (22189)
  hydrogen bonds       : bond        0.03977 (  899)
  hydrogen bonds       : angle       3.11431 ( 2296)

*********************** 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
  133 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7850 (tm-30)
REVERT: B   88 TYR cc_start: 0.8852 (m-10) cc_final: 0.8531 (m-10)
REVERT: L   11 LEU cc_start: 0.8308 (mp) cc_final: 0.7630 (tp)
REVERT: L  155 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7348 (mpp)
REVERT: L  236 MET cc_start: 0.8746 (mmp) cc_final: 0.8371 (mmp)
  outliers start: 15
  outliers final: 11
  residues processed: 131
  average time/residue: 0.1428
  time to fit residues: 26.7249
Evaluate side-chains
  128 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain L residue  155 MET
Chi-restraints excluded: chain L residue  214 VAL
Chi-restraints excluded: chain L residue  292 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 124 optimal weight:   20.0000
   chunk 123 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 60 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9990
   chunk 97 optimal weight:   10.0000
   chunk 28 optimal weight:    4.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3984 r_free = 0.3984 target = 0.096641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.058577 restraints weight = 88357.543|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 3.19
r_work: 0.2831 rms_B_bonded: 4.64 restraints_weight: 0.5000
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2824
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2824
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8704
moved from start:          0.2492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15514  Z= 0.141
  Angle     :  0.532   5.684  22189  Z= 0.311
  Chirality :  0.034   0.157   2508
  Planarity :  0.003   0.041   1800
  Dihedral  : 29.198 166.166   4405
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 11.21 %
    Favored  : 87.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.64 (0.27), residues: 1067
  helix:  2.47 (0.20), residues: 734
  sheet:  0.79 (0.68), residues: 36
  loop :  0.06 (0.39), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G  71 
 TYR   0.044   0.001   TYR H  83 
 PHE   0.008   0.001   PHE E  67 
 TRP   0.002   0.001   TRP L 325 
 HIS   0.004   0.001   HIS L 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (15514)
  covalent geometry    : angle       0.53187 (22189)
  hydrogen bonds       : bond        0.03326 (  899)
  hydrogen bonds       : angle       2.93151 ( 2296)

*********************** 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
  140 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.516 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8850 (m-10) cc_final: 0.8517 (m-10)
REVERT: E   60 LEU cc_start: 0.8429 (mm) cc_final: 0.8216 (mm)
REVERT: L   11 LEU cc_start: 0.8323 (mp) cc_final: 0.7661 (tp)
REVERT: L  155 MET cc_start: 0.7846 (OUTLIER) cc_final: 0.7309 (mpp)
REVERT: L  236 MET cc_start: 0.8752 (mmp) cc_final: 0.8379 (mmp)
  outliers start: 13
  outliers final: 12
  residues processed: 138
  average time/residue: 0.1388
  time to fit residues: 27.6611
Evaluate side-chains
  133 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain E residue  107 THR
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain L residue  155 MET
Chi-restraints excluded: chain L residue  214 VAL
Chi-restraints excluded: chain L residue  292 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 20 optimal weight:    0.6980
   chunk 125 optimal weight:   40.0000
   chunk 121 optimal weight:    9.9990
   chunk 55 optimal weight:    0.8980
   chunk 17 optimal weight:   10.0000
   chunk 22 optimal weight:    0.6980
   chunk 15 optimal weight:    0.8980
   chunk 123 optimal weight:   10.0000
   chunk 106 optimal weight:    5.9990
   chunk 99 optimal weight:   10.0000
   chunk 113 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
H  84 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.096836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.058374 restraints weight = 91596.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3033 rms_B_bonded: 3.25
r_work: 0.2833 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2826
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2826 r_free = 0.2826    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2826 r_free = 0.2826    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2826
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15514  Z= 0.142
  Angle     :  0.549  12.870  22189  Z= 0.316
  Chirality :  0.035   0.191   2508
  Planarity :  0.003   0.041   1800
  Dihedral  : 29.199 166.585   4405
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.08 %
    Favored  : 86.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.69 (0.27), residues: 1067
  helix:  2.50 (0.20), residues: 728
  sheet:  0.83 (0.69), residues: 36
  loop :  0.13 (0.39), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  71 
 TYR   0.042   0.001   TYR H  83 
 PHE   0.008   0.001   PHE L 223 
 TRP   0.001   0.000   TRP L 325 
 HIS   0.005   0.001   HIS L 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (15514)
  covalent geometry    : angle       0.54857 (22189)
  hydrogen bonds       : bond        0.03342 (  899)
  hydrogen bonds       : angle       2.97743 ( 2296)

********************** 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
  137 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 124
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8848 (m-10) cc_final: 0.8511 (m-10)
REVERT: L   11 LEU cc_start: 0.8324 (mp) cc_final: 0.7651 (tp)
REVERT: L   18 MET cc_start: 0.7038 (tmm) cc_final: 0.6508 (tpt)
REVERT: L  155 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.7385 (mpp)
REVERT: L  236 MET cc_start: 0.8750 (mmp) cc_final: 0.8379 (mmp)
  outliers start: 13
  outliers final: 11
  residues processed: 134
  average time/residue: 0.1397
  time to fit residues: 26.8026
Evaluate side-chains
  134 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 122
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   30 THR
Chi-restraints excluded: chain B residue   96 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain E residue   51 ILE
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain F residue   82 THR
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain G residue   79 ILE
Chi-restraints excluded: chain L residue  155 MET
Chi-restraints excluded: chain L residue  214 VAL
Chi-restraints excluded: chain L residue  292 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 120 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 107 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9980
   chunk 79 optimal weight:    6.9990
   chunk 71 optimal weight:    0.0170
   chunk 23 optimal weight:    9.9990
   chunk 114 optimal weight:    9.9990
   chunk 66 optimal weight:    4.9990
   chunk 59 optimal weight:    0.0970
   overall best weight:    0.9618

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

Flipped N/Q/H residues before XYZ refinement:
H  84 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.097026 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.058510 restraints weight = 97839.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 3.35
r_work: 0.2824 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2824
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2824
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8706
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  15514  Z= 0.139
  Angle     :  0.539   9.715  22189  Z= 0.313
  Chirality :  0.034   0.183   2508
  Planarity :  0.003   0.042   1800
  Dihedral  : 29.186 166.648   4405
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 11.75 %
    Favored  : 86.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.69 (0.27), residues: 1067
  helix:  2.50 (0.20), residues: 728
  sheet:  0.82 (0.68), residues: 36
  loop :  0.16 (0.39), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG G  71 
 TYR   0.042   0.001   TYR H  83 
 PHE   0.008   0.001   PHE L 223 
 TRP   0.001   0.000   TRP L 325 
 HIS   0.005   0.001   HIS L 135 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 (15514)
  covalent geometry    : angle       0.53946 (22189)
  hydrogen bonds       : bond        0.03323 (  899)
  hydrogen bonds       : angle       2.97044 ( 2296)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5294.64 seconds
wall clock time: 90 minutes 46.16 seconds (5446.16 seconds total)