Starting phenix.real_space_refine
on Mon May 19 00:24:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dwh_47246/05_2025/9dwh_47246.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dwh_47246/05_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_47246/05_2025/9dwh_47246.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dwh_47246/05_2025/9dwh_47246.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dwh_47246/05_2025/9dwh_47246.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dwh_47246/05_2025/9dwh_47246.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   1.009
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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 6.95, per 1000 atoms: 0.47
  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: 3.49
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 11 sheets defined
      67.9% alpha, 4.6% beta
      144 base pairs and 241 stacking pairs defined.
    Time for finding SS restraints: 6.22
  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: 6.19

  Time building geometry restraints manager: 4.17 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:             29.260
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          7.830
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     34.750
  Find NCS groups from input model:        0.300
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   75.110
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (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
 TRP   0.004   0.001   TRP L 325 
 HIS   0.009   0.001   HIS L 135 
 PHE   0.015   0.001   PHE L  25 
 TYR   0.023   0.002   TYR H  83 
 ARG   0.007   0.001   ARG F  23 

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

*********************** 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  : 1.157 
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: 0.3278
  time to fit residues: 72.3068
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  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 111 optimal weight:    9.9990
   chunk 100 optimal weight:    9.9990
   chunk 55 optimal weight:    0.9980
   chunk 34 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 103 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9980
   chunk 62 optimal weight:    6.9990
   chunk 77 optimal weight:    6.9990
   chunk 119 optimal weight:    7.9990
   overall best weight:    3.1986

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN
C 112 GLN
E 108 ASN
F  75 HIS
L  34 HIS
L 157 GLN
L 285 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.095353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.056856 restraints weight = 89453.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.2995 rms_B_bonded: 3.19
r_work: 0.2786 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.2786
-------------------------------------------------------------------------------
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 = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2782 r_free = 0.2782    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2782
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8758
moved from start:          0.1451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  15514  Z= 0.235
  Angle     :  0.580   6.917  22189  Z= 0.335
  Chirality :  0.037   0.191   2508
  Planarity :  0.004   0.043   1800
  Dihedral  : 29.271 163.479   4405
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  6.53 %
    Favored  : 92.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.26), residues: 1067
  helix:  2.11 (0.20), residues: 729
  sheet:  0.56 (0.75), residues: 30
  loop : -0.21 (0.36), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP L 325 
 HIS   0.004   0.001   HIS G  31 
 PHE   0.009   0.001   PHE L  25 
 TYR   0.037   0.002   TYR H  83 
 ARG   0.010   0.001   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04122 (  899)
  hydrogen bonds       : angle       3.41925 ( 2296)
  covalent geometry    : bond        0.00535 (15514)
  covalent geometry    : angle       0.58026 (22189)

*********************** 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
  128 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 1.223 
Fit side-chains
REVERT: A   97 GLU cc_start: 0.8239 (tm-30) cc_final: 0.8026 (tm-30)
REVERT: A  105 GLU cc_start: 0.8708 (tp30) cc_final: 0.8506 (mt-10)
REVERT: B   88 TYR cc_start: 0.8831 (m-10) cc_final: 0.8471 (m-10)
REVERT: D   83 TYR cc_start: 0.8662 (m-10) cc_final: 0.8323 (m-10)
REVERT: E   59 GLU cc_start: 0.8475 (pm20) cc_final: 0.8225 (pm20)
REVERT: L   11 LEU cc_start: 0.7853 (mp) cc_final: 0.7362 (tp)
REVERT: L   18 MET cc_start: 0.5701 (ppp) cc_final: 0.5101 (ppp)
REVERT: L  191 MET cc_start: 0.3895 (mmt) cc_final: 0.3456 (mmt)
REVERT: L  236 MET cc_start: 0.8867 (mmp) cc_final: 0.8594 (mmp)
  outliers start: 10
  outliers final: 7
  residues processed: 127
  average time/residue: 0.2948
  time to fit residues: 53.4630
Evaluate side-chains
  120 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 113
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
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 F residue   50 ILE
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain H residue  118 VAL
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 17 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9980
   chunk 119 optimal weight:    0.9990
   chunk 54 optimal weight:    0.1980
   chunk 129 optimal weight:    0.0010
   chunk 83 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 55 optimal weight:    0.7980
   chunk 124 optimal weight:   20.0000
   chunk 100 optimal weight:    9.9990
   chunk 27 optimal weight:    0.0970
   overall best weight:    0.4184

-------------------------------------------------------------------------------
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 = 0.4001 r_free = 0.4001 target = 0.097423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.059122 restraints weight = 98215.031|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 3.42
r_work: 0.2863 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.2863
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2850
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2850 r_free = 0.2850    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2850 r_free = 0.2850    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2850
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.1476

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= 0.131
  Angle     :  0.516   6.039  22189  Z= 0.303
  Chirality :  0.034   0.172   2508
  Planarity :  0.003   0.043   1800
  Dihedral  : 29.085 164.365   4405
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 6.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  7.94 %
    Favored  : 90.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.38 (0.27), residues: 1067
  helix:  2.33 (0.20), residues: 730
  sheet:  0.49 (0.78), residues: 30
  loop : -0.13 (0.37), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP L 325 
 HIS   0.004   0.001   HIS L 135 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.027   0.001   TYR H  83 
 ARG   0.006   0.000   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03251 (  899)
  hydrogen bonds       : angle       3.03107 ( 2296)
  covalent geometry    : bond        0.00275 (15514)
  covalent geometry    : angle       0.51578 (22189)

*********************** 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
  141 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 1.519 
Fit side-chains
REVERT: A   97 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7865 (tm-30)
REVERT: B   84 MET cc_start: 0.8797 (mmm) cc_final: 0.8422 (mmm)
REVERT: B   88 TYR cc_start: 0.8830 (m-10) cc_final: 0.8126 (m-10)
REVERT: D   83 TYR cc_start: 0.8617 (m-10) cc_final: 0.8137 (m-10)
REVERT: E   59 GLU cc_start: 0.8278 (pm20) cc_final: 0.8002 (pm20)
REVERT: E   60 LEU cc_start: 0.8537 (mm) cc_final: 0.8277 (mm)
REVERT: L   11 LEU cc_start: 0.7844 (mp) cc_final: 0.7373 (tp)
REVERT: L   18 MET cc_start: 0.5476 (ppp) cc_final: 0.5013 (ppp)
REVERT: L  155 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7819 (mpp)
REVERT: L  236 MET cc_start: 0.8789 (mmp) cc_final: 0.8472 (mmp)
REVERT: L  282 MET cc_start: 0.5164 (mmm) cc_final: 0.4818 (mmm)
  outliers start: 10
  outliers final: 5
  residues processed: 136
  average time/residue: 0.3126
  time to fit residues: 60.9940
Evaluate side-chains
  127 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 121
  time to evaluate  : 1.301 
-------------------------------------------------------------------------------
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 C residue  100 VAL
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain L residue  155 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 109 optimal weight:    4.9990
   chunk 52 optimal weight:    0.6980
   chunk 114 optimal weight:    5.9990
   chunk 89 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 110 optimal weight:    7.9990
   chunk 50 optimal weight:    0.7980
   chunk 78 optimal weight:    7.9990
   chunk 81 optimal weight:    7.9990
   chunk 126 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    2.0986

-------------------------------------------------------------------------------
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 = 0.095687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.057198 restraints weight = 82225.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.3006 rms_B_bonded: 3.19
r_work: 0.2799 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2788
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2788 r_free = 0.2788    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2788
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8715
moved from start:          0.1816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  15514  Z= 0.181
  Angle     :  0.530   7.436  22189  Z= 0.310
  Chirality :  0.035   0.167   2508
  Planarity :  0.003   0.038   1800
  Dihedral  : 29.243 165.420   4405
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  8.71 %
    Favored  : 90.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.45 (0.27), residues: 1067
  helix:  2.36 (0.20), residues: 733
  sheet:  0.62 (0.77), residues: 30
  loop : -0.09 (0.37), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP L 325 
 HIS   0.003   0.001   HIS B  75 
 PHE   0.007   0.001   PHE E  67 
 TYR   0.030   0.002   TYR D  40 
 ARG   0.006   0.000   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03651 (  899)
  hydrogen bonds       : angle       3.08310 ( 2296)
  covalent geometry    : bond        0.00409 (15514)
  covalent geometry    : angle       0.52985 (22189)

*********************** 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
  132 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 1.152 
Fit side-chains
REVERT: A   97 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7911 (tm-30)
REVERT: B   88 TYR cc_start: 0.8898 (m-10) cc_final: 0.8320 (m-10)
REVERT: D   83 TYR cc_start: 0.8616 (m-10) cc_final: 0.8148 (m-10)
REVERT: E   59 GLU cc_start: 0.8414 (pm20) cc_final: 0.8064 (pm20)
REVERT: G   91 GLU cc_start: 0.8727 (tp30) cc_final: 0.8513 (tp30)
REVERT: L   18 MET cc_start: 0.5657 (ppp) cc_final: 0.5292 (ppp)
REVERT: L  155 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7729 (mpp)
REVERT: L  236 MET cc_start: 0.8809 (mmp) cc_final: 0.8485 (mmp)
REVERT: L  282 MET cc_start: 0.5414 (mmm) cc_final: 0.5120 (mmm)
  outliers start: 10
  outliers final: 6
  residues processed: 129
  average time/residue: 0.2913
  time to fit residues: 53.4243
Evaluate side-chains
  126 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 119
  time to evaluate  : 1.242 
-------------------------------------------------------------------------------
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  108 LEU
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain L residue  155 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 132
   random chunks:
   chunk 117 optimal weight:    5.9990
   chunk 41 optimal weight:    6.9990
   chunk 96 optimal weight:    7.9990
   chunk 58 optimal weight:    1.9990
   chunk 64 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 78 optimal weight:    6.9990
   chunk 16 optimal weight:    2.9990
   chunk 77 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9980
   chunk 85 optimal weight:   10.0000
   overall best weight:    2.7988

-------------------------------------------------------------------------------
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 = 0.3946 r_free = 0.3946 target = 0.094414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.055845 restraints weight = 81118.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.2970 rms_B_bonded: 3.15
r_work: 0.2776 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2761
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2761 r_free = 0.2761    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2761 r_free = 0.2761    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2761
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8740
moved from start:          0.2157

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= 0.209
  Angle     :  0.550   8.299  22189  Z= 0.321
  Chirality :  0.036   0.161   2508
  Planarity :  0.003   0.037   1800
  Dihedral  : 29.382 164.862   4405
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  :  9.79 %
    Favored  : 88.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.44 (0.26), residues: 1067
  helix:  2.34 (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
 TRP   0.003   0.001   TRP L 325 
 HIS   0.004   0.001   HIS L 135 
 PHE   0.007   0.001   PHE E  67 
 TYR   0.030   0.002   TYR L  39 
 ARG   0.004   0.000   ARG D  79 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04019 (  899)
  hydrogen bonds       : angle       3.12446 ( 2296)
  covalent geometry    : bond        0.00475 (15514)
  covalent geometry    : angle       0.54968 (22189)

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

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

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

  2134 Ramachandran restraints generated.
    1067 Oldfield, 0 Emsley, 1067 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 119
  time to evaluate  : 1.266 
Fit side-chains
REVERT: B   88 TYR cc_start: 0.8919 (m-10) cc_final: 0.8285 (m-10)
REVERT: D   83 TYR cc_start: 0.8599 (m-10) cc_final: 0.8201 (m-10)
REVERT: E   59 GLU cc_start: 0.8388 (pm20) cc_final: 0.8136 (pm20)
REVERT: L   11 LEU cc_start: 0.8227 (mp) cc_final: 0.7571 (tp)
REVERT: L   18 MET cc_start: 0.5943 (ppp) cc_final: 0.5654 (ppp)
REVERT: L  155 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7655 (mpp)
REVERT: L  236 MET cc_start: 0.8802 (mmp) cc_final: 0.8466 (mmp)
  outliers start: 14
  outliers final: 10
  residues processed: 130
  average time/residue: 0.3081
  time to fit residues: 56.9397
Evaluate side-chains
  125 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 1.185 
-------------------------------------------------------------------------------
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   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 G residue   64 GLU
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain L residue  155 MET
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 50 optimal weight:    0.7980
   chunk 66 optimal weight:    4.9990
   chunk 11 optimal weight:    3.9990
   chunk 65 optimal weight:    4.9990
   chunk 63 optimal weight:    0.0040
   chunk 15 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 95 optimal weight:    6.9990
   chunk 88 optimal weight:   10.0000
   overall best weight:    0.7192

-------------------------------------------------------------------------------
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 = 0.3976 r_free = 0.3976 target = 0.096136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.058021 restraints weight = 81312.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3028 rms_B_bonded: 3.18
r_work: 0.2836 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2824
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2824 r_free = 0.2824    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2824
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8680
moved from start:          0.2162

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= 0.134
  Angle     :  0.515   8.064  22189  Z= 0.304
  Chirality :  0.034   0.161   2508
  Planarity :  0.003   0.040   1800
  Dihedral  : 29.206 165.691   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 :  1.52 %
    Allowed  : 10.23 %
    Favored  : 88.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.62 (0.27), residues: 1067
  helix:  2.47 (0.20), residues: 732
  sheet:  0.84 (0.68), residues: 36
  loop : -0.01 (0.38), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP L 325 
 HIS   0.004   0.001   HIS L 135 
 PHE   0.008   0.001   PHE A  67 
 TYR   0.027   0.001   TYR H  40 
 ARG   0.004   0.000   ARG G  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03356 (  899)
  hydrogen bonds       : angle       2.92312 ( 2296)
  covalent geometry    : bond        0.00285 (15514)
  covalent geometry    : angle       0.51488 (22189)

*********************** 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
  139 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 125
  time to evaluate  : 1.170 
Fit side-chains
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8888 (m-10) cc_final: 0.8141 (m-10)
REVERT: D   83 TYR cc_start: 0.8519 (m-10) cc_final: 0.8108 (m-10)
REVERT: E   59 GLU cc_start: 0.8327 (pm20) cc_final: 0.8086 (pm20)
REVERT: L   11 LEU cc_start: 0.8174 (mp) cc_final: 0.7520 (tp)
REVERT: L   18 MET cc_start: 0.5841 (ppp) cc_final: 0.5585 (ppp)
REVERT: L  155 MET cc_start: 0.7942 (OUTLIER) cc_final: 0.7624 (mpp)
REVERT: L  236 MET cc_start: 0.8764 (mmp) cc_final: 0.8407 (mmp)
REVERT: L  282 MET cc_start: 0.5056 (mmp) cc_final: 0.4851 (mmm)
  outliers start: 14
  outliers final: 10
  residues processed: 135
  average time/residue: 0.3295
  time to fit residues: 63.7825
Evaluate side-chains
  131 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 1.276 
-------------------------------------------------------------------------------
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   16 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain E residue   96 SER
Chi-restraints excluded: chain G residue   18 SER
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain L residue  155 MET
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 46 optimal weight:    7.9990
   chunk 80 optimal weight:    7.9990
   chunk 103 optimal weight:    0.5980
   chunk 8 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 18 optimal weight:    0.2980
   chunk 111 optimal weight:   20.0000
   chunk 86 optimal weight:   10.0000
   chunk 68 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 17 optimal weight:    9.9990
   overall best weight:    1.7584

-------------------------------------------------------------------------------
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 = 0.3961 r_free = 0.3961 target = 0.095352 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.056985 restraints weight = 87594.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 3.21
r_work: 0.2807 rms_B_bonded: 4.64 restraints_weight: 0.5000
r_work (final): 0.2807
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2797
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2797 r_free = 0.2797    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2797 r_free = 0.2797    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2797
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8719
moved from start:          0.2253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  15514  Z= 0.163
  Angle     :  0.529   8.447  22189  Z= 0.310
  Chirality :  0.034   0.157   2508
  Planarity :  0.003   0.038   1800
  Dihedral  : 29.244 166.053   4405
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 10.45 %
    Favored  : 87.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.61 (0.27), residues: 1067
  helix:  2.46 (0.20), residues: 733
  sheet:  0.81 (0.69), residues: 36
  loop :  0.02 (0.38), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP L 325 
 HIS   0.004   0.001   HIS L 135 
 PHE   0.006   0.001   PHE E  67 
 TYR   0.034   0.002   TYR D  40 
 ARG   0.004   0.000   ARG G  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03585 (  899)
  hydrogen bonds       : angle       2.99612 ( 2296)
  covalent geometry    : bond        0.00362 (15514)
  covalent geometry    : angle       0.52866 (22189)

*********************** 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: 15
    poor density    : 121
  time to evaluate  : 1.280 
Fit side-chains
REVERT: B   88 TYR cc_start: 0.8907 (m-10) cc_final: 0.8229 (m-10)
REVERT: D   83 TYR cc_start: 0.8562 (m-10) cc_final: 0.8213 (m-10)
REVERT: E   59 GLU cc_start: 0.8443 (pm20) cc_final: 0.8217 (pm20)
REVERT: L   11 LEU cc_start: 0.8208 (mp) cc_final: 0.7547 (tp)
REVERT: L   18 MET cc_start: 0.5911 (ppp) cc_final: 0.5684 (ppp)
REVERT: L  155 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.7644 (mpp)
REVERT: L  236 MET cc_start: 0.8760 (mmp) cc_final: 0.8393 (mmp)
  outliers start: 15
  outliers final: 11
  residues processed: 133
  average time/residue: 0.2906
  time to fit residues: 55.2253
Evaluate side-chains
  131 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
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   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 G residue   64 GLU
Chi-restraints excluded: chain H residue   88 THR
Chi-restraints excluded: chain L residue  155 MET
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 66 optimal weight:    5.9990
   chunk 6 optimal weight:    2.9990
   chunk 100 optimal weight:    6.9990
   chunk 101 optimal weight:    5.9990
   chunk 76 optimal weight:    8.9990
   chunk 79 optimal weight:    6.9990
   chunk 87 optimal weight:   10.0000
   chunk 115 optimal weight:    7.9990
   chunk 86 optimal weight:   10.0000
   chunk 50 optimal weight:    2.9990
   chunk 112 optimal weight:    3.9990
   overall best weight:    4.3990

-------------------------------------------------------------------------------
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 = 0.3917 r_free = 0.3917 target = 0.093256 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.053606 restraints weight = 109534.006|
|-----------------------------------------------------------------------------|
r_work (start): 0.2924 rms_B_bonded: 3.79
r_work: 0.2738 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2727
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2727 r_free = 0.2727    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2727 r_free = 0.2727    target_work(ls_wunit_k1) = 0.042         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2727
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8816
moved from start:          0.2753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050  15514  Z= 0.298
  Angle     :  0.623   9.658  22189  Z= 0.356
  Chirality :  0.039   0.152   2508
  Planarity :  0.004   0.035   1800
  Dihedral  : 29.659 165.053   4405
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 11.10 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.25 (0.26), residues: 1067
  helix:  2.18 (0.19), residues: 733
  sheet:  1.15 (0.68), residues: 35
  loop : -0.16 (0.38), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.001   TRP L 325 
 HIS   0.004   0.001   HIS B  75 
 PHE   0.009   0.001   PHE L 278 
 TYR   0.050   0.003   TYR D  40 
 ARG   0.005   0.000   ARG G  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04754 (  899)
  hydrogen bonds       : angle       3.36804 ( 2296)
  covalent geometry    : bond        0.00686 (15514)
  covalent geometry    : angle       0.62294 (22189)

*********************** 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
  127 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 1.135 
Fit side-chains
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8933 (m-10) cc_final: 0.8271 (m-10)
REVERT: D   71 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8744 (tm-30)
REVERT: D   83 TYR cc_start: 0.8651 (m-10) cc_final: 0.8143 (m-10)
REVERT: L   11 LEU cc_start: 0.8579 (mp) cc_final: 0.7935 (tp)
REVERT: L  155 MET cc_start: 0.7812 (mpp) cc_final: 0.7456 (mpp)
REVERT: L  236 MET cc_start: 0.8862 (mmp) cc_final: 0.8515 (mmp)
  outliers start: 14
  outliers final: 12
  residues processed: 125
  average time/residue: 0.3010
  time to fit residues: 53.2254
Evaluate side-chains
  123 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 111
  time to evaluate  : 1.194 
-------------------------------------------------------------------------------
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   96 THR
Chi-restraints excluded: chain C residue   16 THR
Chi-restraints excluded: chain C residue  108 LEU
Chi-restraints excluded: chain D residue  115 THR
Chi-restraints excluded: chain E residue   51 ILE
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  135 HIS
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 40 optimal weight:    0.8980
   chunk 102 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 121 optimal weight:    6.9990
   chunk 91 optimal weight:    6.9990
   chunk 49 optimal weight:    0.5980
   chunk 120 optimal weight:    0.9990
   chunk 122 optimal weight:   10.0000
   chunk 99 optimal weight:   10.0000
   overall best weight:    1.2584

-------------------------------------------------------------------------------
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 = 0.3965 r_free = 0.3965 target = 0.095451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.056690 restraints weight = 101059.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.2993 rms_B_bonded: 3.45
r_work: 0.2790 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2784
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2784 r_free = 0.2784    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2784
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8755
moved from start:          0.2592

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  15514  Z= 0.149
  Angle     :  0.548   9.427  22189  Z= 0.318
  Chirality :  0.035   0.155   2508
  Planarity :  0.003   0.039   1800
  Dihedral  : 29.387 166.189   4405
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 11.32 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.52 (0.27), residues: 1067
  helix:  2.38 (0.20), residues: 732
  sheet:  1.11 (0.67), residues: 35
  loop : -0.05 (0.38), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP L 325 
 HIS   0.004   0.001   HIS L 135 
 PHE   0.009   0.001   PHE E  67 
 TYR   0.034   0.002   TYR D  40 
 ARG   0.005   0.000   ARG G  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03627 (  899)
  hydrogen bonds       : angle       3.02362 ( 2296)
  covalent geometry    : bond        0.00324 (15514)
  covalent geometry    : angle       0.54839 (22189)

*********************** 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
  135 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 1.127 
Fit side-chains
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8928 (m-10) cc_final: 0.8188 (m-10)
REVERT: D   83 TYR cc_start: 0.8568 (m-10) cc_final: 0.8216 (m-10)
REVERT: L   11 LEU cc_start: 0.8396 (mp) cc_final: 0.7711 (tt)
REVERT: L  155 MET cc_start: 0.7819 (mpp) cc_final: 0.7434 (mpp)
REVERT: L  236 MET cc_start: 0.8780 (mmp) cc_final: 0.8407 (mmp)
  outliers start: 12
  outliers final: 11
  residues processed: 132
  average time/residue: 0.2886
  time to fit residues: 54.2509
Evaluate side-chains
  131 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 120
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
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   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 G residue   16 THR
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain H residue   88 THR
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 73 optimal weight:   10.0000
   chunk 42 optimal weight:    0.8980
   chunk 52 optimal weight:    1.9990
   chunk 89 optimal weight:   10.0000
   chunk 48 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 128 optimal weight:    5.9990
   chunk 70 optimal weight:    2.9990
   chunk 92 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    1.1186

-------------------------------------------------------------------------------
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 = 0.3971 r_free = 0.3971 target = 0.095870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.057735 restraints weight = 85049.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 3.12
r_work: 0.2830 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2818
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2818 r_free = 0.2818    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 = 0.2818 r_free = 0.2818    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2818
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8706
moved from start:          0.2610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  15514  Z= 0.145
  Angle     :  0.544  11.163  22189  Z= 0.315
  Chirality :  0.034   0.153   2508
  Planarity :  0.003   0.040   1800
  Dihedral  : 29.307 166.495   4405
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 11.32 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.58 (0.27), residues: 1067
  helix:  2.43 (0.20), residues: 732
  sheet:  0.79 (0.69), residues: 36
  loop :  0.01 (0.38), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.001   0.000   TRP L 325 
 HIS   0.004   0.001   HIS L 135 
 PHE   0.007   0.001   PHE E  67 
 TYR   0.030   0.002   TYR D  40 
 ARG   0.006   0.000   ARG G  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03420 (  899)
  hydrogen bonds       : angle       2.99550 ( 2296)
  covalent geometry    : bond        0.00316 (15514)
  covalent geometry    : angle       0.54368 (22189)

********************** 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
  138 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 1.230 
Fit side-chains
   revert: symmetry clash
REVERT: B   88 TYR cc_start: 0.8897 (m-10) cc_final: 0.8127 (m-10)
REVERT: D   71 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8703 (tp30)
REVERT: D   83 TYR cc_start: 0.8531 (m-10) cc_final: 0.8152 (m-10)
REVERT: E   59 GLU cc_start: 0.8350 (pm20) cc_final: 0.8112 (pm20)
REVERT: L   11 LEU cc_start: 0.8385 (mp) cc_final: 0.7704 (tt)
REVERT: L   18 MET cc_start: 0.6541 (ppp) cc_final: 0.5760 (ppp)
REVERT: L  155 MET cc_start: 0.7850 (mpp) cc_final: 0.7409 (mpp)
REVERT: L  236 MET cc_start: 0.8740 (mmp) cc_final: 0.8363 (mmp)
  outliers start: 12
  outliers final: 11
  residues processed: 136
  average time/residue: 0.2970
  time to fit residues: 57.7891
Evaluate side-chains
  133 residues out of total 915 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 1.339 
-------------------------------------------------------------------------------
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   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 G residue   16 THR
Chi-restraints excluded: chain G residue   64 GLU
Chi-restraints excluded: chain H residue   88 THR
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 105 optimal weight:    0.0010
   chunk 34 optimal weight:    0.6980
   chunk 112 optimal weight:    6.9990
   chunk 22 optimal weight:    0.7980
   chunk 4 optimal weight:    5.9990
   chunk 64 optimal weight:    0.8980
   chunk 42 optimal weight:    0.7980
   chunk 13 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.5786

-------------------------------------------------------------------------------
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
L 279 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.097206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.059130 restraints weight = 97652.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.3066 rms_B_bonded: 3.37
r_work: 0.2872 rms_B_bonded: 4.79 restraints_weight: 0.5000
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2856
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2856 r_free = 0.2856    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2856 r_free = 0.2856    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2856
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8670
moved from start:          0.2616

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= 0.133
  Angle     :  0.556  18.256  22189  Z= 0.316
  Chirality :  0.034   0.238   2508
  Planarity :  0.003   0.043   1800
  Dihedral  : 29.152 167.348   4405
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 12.08 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.63 (0.27), residues: 1067
  helix:  2.47 (0.20), residues: 727
  sheet:  0.67 (0.69), residues: 36
  loop :  0.10 (0.38), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP L 325 
 HIS   0.005   0.001   HIS G  31 
 PHE   0.009   0.001   PHE L 223 
 TYR   0.026   0.001   TYR D  40 
 ARG   0.006   0.000   ARG G  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03202 (  899)
  hydrogen bonds       : angle       2.91097 ( 2296)
  covalent geometry    : bond        0.00283 (15514)
  covalent geometry    : angle       0.55574 (22189)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10325.29 seconds
wall clock time: 179 minutes 33.80 seconds (10773.80 seconds total)