Starting phenix.real_space_refine
on Mon Jan 13 21:37:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yvu_39614/01_2025/8yvu_39614.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yvu_39614/01_2025/8yvu_39614.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yvu_39614/01_2025/8yvu_39614.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yvu_39614/01_2025/8yvu_39614.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yvu_39614/01_2025/8yvu_39614.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yvu_39614/01_2025/8yvu_39614.cif"
  }
  resolution = 3.9
  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=   0.008 sd=   0.202
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    2828      2.51       5
     N     646      2.21       5
     O     712      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 4216
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 311
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 311
          Classifications: {'peptide': 37}
          Link IDs: {'PTRANS': 1, 'TRANS': 35}
    Chain: "B"
      Number of atoms: 1211
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 1211
          Classifications: {'peptide': 160}
          Link IDs: {'PTRANS': 1, 'TRANS': 158}
    Chain: "C"
      Number of atoms: 239
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 239
          Classifications: {'peptide': 29}
          Link IDs: {'TRANS': 28}
    Chain: "D"
      Number of atoms: 319
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 319
          Classifications: {'peptide': 39}
          Link IDs: {'TRANS': 38}
    Chain: "E"
      Number of atoms: 311
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 311
          Classifications: {'peptide': 37}
          Link IDs: {'PTRANS': 1, 'TRANS': 35}
    Chain: "F"
      Number of atoms: 1211
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 1211
          Classifications: {'peptide': 160}
          Link IDs: {'PTRANS': 1, 'TRANS': 158}
    Chain: "G"
      Number of atoms: 239
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 29, 239
          Classifications: {'peptide': 29}
          Link IDs: {'TRANS': 28}
    Chain: "H"
      Number of atoms: 319
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 319
          Classifications: {'peptide': 39}
          Link IDs: {'TRANS': 38}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'CLR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.28, per 1000 atoms: 0.78
  Number of scatterers: 4216
  At special positions: 0
  Unit cell: (71.742, 99.4605, 89.6775, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O     712      8.00
     N     646      7.00
     C    2828      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: 1.18
  Conformation dependent library (CDL) restraints added in 472.9 milliseconds
  

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  988

  Finding SS restraints...
    Secondary structure from input PDB file:
      19 helices and 0 sheets defined
      84.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 206 through 235
      removed outlier: 3.783A  pdb=" N   ILE A 214 " --> pdb=" O   LEU A 210 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   LYS A 235 " --> pdb=" O   THR A 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 57
    Processing helix  chain 'B' and resid 58 through 83
      removed outlier: 3.605A  pdb=" N   GLY B  62 " --> pdb=" O   GLN B  58 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   LEU B  73 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   CYS B  74 " --> pdb=" O   MET B  70 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   PHE B  75 " --> pdb=" O   ILE B  71 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   LEU B  83 " --> pdb=" O   VAL B  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 98
    Processing helix  chain 'B' and resid 99 through 104
    Processing helix  chain 'B' and resid 104 through 121
      removed outlier: 3.590A  pdb=" N   PHE B 108 " --> pdb=" O   GLY B 104 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   SER B 109 " --> pdb=" O   ALA B 105 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ILE B 110 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   GLU B 119 " --> pdb=" O   SER B 115 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ARG B 120 " --> pdb=" O   ILE B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 125 through 161
      removed outlier: 3.603A  pdb=" N   LEU B 131 " --> pdb=" O   VAL B 127 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR B 146 " --> pdb=" O   GLY B 142 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ILE B 161 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 205
      removed outlier: 3.565A  pdb=" N   SER B 176 " --> pdb=" O   CYS B 172 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ALA B 204 " --> pdb=" O   THR B 200 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   GLY B 205 " --> pdb=" O   ILE B 201 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 34
      removed outlier: 3.532A  pdb=" N   LEU C  32 " --> pdb=" O   LEU C  28 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LEU C  34 " --> pdb=" O   ALA C  30 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 34 through 53
    Processing helix  chain 'D' and resid 25 through 59
      removed outlier: 4.189A  pdb=" N   ILE D  31 " --> pdb=" O   ILE D  27 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   LEU D  32 " --> pdb=" O   LEU D  28 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   PHE D  33 " --> pdb=" O   ASP D  29 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   LEU D  34 " --> pdb=" O   ALA D  30 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   CYS D  44 " --> pdb=" O   THR D  40 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 206 through 234
      removed outlier: 3.524A  pdb=" N   LEU E 210 " --> pdb=" O   PHE E 206 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ILE E 214 " --> pdb=" O   LEU E 210 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 50 through 57
    Processing helix  chain 'F' and resid 58 through 83
      removed outlier: 3.669A  pdb=" N   GLY F  62 " --> pdb=" O   GLN F  58 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LEU F  73 " --> pdb=" O   ALA F  69 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   CYS F  74 " --> pdb=" O   MET F  70 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   PHE F  75 " --> pdb=" O   ILE F  71 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLY F  76 " --> pdb=" O   CYS F  72 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LEU F  83 " --> pdb=" O   VAL F  79 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 99 through 121
      removed outlier: 4.243A  pdb=" N   ILE F 106 " --> pdb=" O   PHE F 102 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   PHE F 107 " --> pdb=" O   TRP F 103 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 125 through 161
      removed outlier: 3.725A  pdb=" N   THR F 146 " --> pdb=" O   GLY F 142 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ALA F 157 " --> pdb=" O   LYS F 153 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   TYR F 158 " --> pdb=" O   LYS F 154 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ILE F 159 " --> pdb=" O   SER F 155 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 172 through 205
      removed outlier: 3.581A  pdb=" N   SER F 176 " --> pdb=" O   CYS F 172 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   SER F 195 " --> pdb=" O   LEU F 191 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   ALA F 204 " --> pdb=" O   THR F 200 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   GLY F 205 " --> pdb=" O   ILE F 201 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 27 through 53
      removed outlier: 3.683A  pdb=" N   ILE G  31 " --> pdb=" O   ILE G  27 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   LEU G  32 " --> pdb=" O   LEU G  28 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   LEU G  34 " --> pdb=" O   ALA G  30 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   TYR G  35 " --> pdb=" O   ILE G  31 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   GLY G  36 " --> pdb=" O   LEU G  32 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ILE G  37 " --> pdb=" O   PHE G  33 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 25 through 59
      removed outlier: 3.879A  pdb=" N   ILE H  31 " --> pdb=" O   ILE H  27 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LEU H  32 " --> pdb=" O   LEU H  28 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLU H  59 " --> pdb=" O   ILE H  55 " (cutoff:3.500A)

    319 hydrogen bonds defined for protein.
    954 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.09

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1216
        1.34 -     1.46: 1021
        1.46 -     1.58: 2021
        1.58 -     1.69: 0
        1.69 -     1.81: 40
  Bond restraints: 4298
  Sorted by residual:
  bond pdb=" C13 CLR F 301 "
       pdb=" C17 CLR F 301 "
    ideal  model  delta    sigma   weight residual
    1.550  1.517  0.033 2.00e-02 2.50e+03 2.76e+00
  bond pdb=" C13 CLR A 301 "
       pdb=" C17 CLR A 301 "
    ideal  model  delta    sigma   weight residual
    1.550  1.517  0.033 2.00e-02 2.50e+03 2.68e+00
  bond pdb=" C13 CLR F 301 "
       pdb=" C14 CLR F 301 "
    ideal  model  delta    sigma   weight residual
    1.537  1.505  0.032 2.00e-02 2.50e+03 2.52e+00
  bond pdb=" C13 CLR A 301 "
       pdb=" C14 CLR A 301 "
    ideal  model  delta    sigma   weight residual
    1.537  1.505  0.032 2.00e-02 2.50e+03 2.50e+00
  bond pdb=" CA  LYS A 235 "
       pdb=" CB  LYS A 235 "
    ideal  model  delta    sigma   weight residual
    1.524  1.545 -0.022 1.41e-02 5.03e+03 2.37e+00
  ... (remaining 4293 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 5595
        1.59 -     3.17: 161
        3.17 -     4.76: 45
        4.76 -     6.35: 13
        6.35 -     7.93: 4
  Bond angle restraints: 5818
  Sorted by residual:
  angle pdb=" N   ILE B 106 "
        pdb=" CA  ILE B 106 "
        pdb=" C   ILE B 106 "
      ideal   model   delta    sigma   weight residual
     111.91  106.11    5.80 8.90e-01 1.26e+00 4.25e+01
  angle pdb=" N   PHE B 107 "
        pdb=" CA  PHE B 107 "
        pdb=" C   PHE B 107 "
      ideal   model   delta    sigma   weight residual
     112.93  106.87    6.06 1.33e+00 5.65e-01 2.08e+01
  angle pdb=" C   LEU D  24 "
        pdb=" N   CYS D  25 "
        pdb=" CA  CYS D  25 "
      ideal   model   delta    sigma   weight residual
     121.54  128.98   -7.44 1.91e+00 2.74e-01 1.52e+01
  angle pdb=" C   LYS F 166 "
        pdb=" CA  LYS F 166 "
        pdb=" CB  LYS F 166 "
      ideal   model   delta    sigma   weight residual
     116.34  110.97    5.37 1.40e+00 5.10e-01 1.47e+01
  angle pdb=" CA  LYS A 235 "
        pdb=" CB  LYS A 235 "
        pdb=" CG  LYS A 235 "
      ideal   model   delta    sigma   weight residual
     114.10  120.55   -6.45 2.00e+00 2.50e-01 1.04e+01
  ... (remaining 5813 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.97: 2339
       15.97 -    31.93: 195
       31.93 -    47.90: 58
       47.90 -    63.86: 10
       63.86 -    79.83: 6
  Dihedral angle restraints: 2608
    sinusoidal: 1076
      harmonic: 1532
  Sorted by residual:
  dihedral pdb=" CA  ILE F 161 "
           pdb=" C   ILE F 161 "
           pdb=" N   HIS F 162 "
           pdb=" CA  HIS F 162 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.32   20.68     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  ILE B 161 "
           pdb=" C   ILE B 161 "
           pdb=" N   HIS B 162 "
           pdb=" CA  HIS B 162 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.30   17.70     0      5.00e+00 4.00e-02 1.25e+01
  dihedral pdb=" CB  ARG B 121 "
           pdb=" CG  ARG B 121 "
           pdb=" CD  ARG B 121 "
           pdb=" NE  ARG B 121 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -110.72   50.72     3      1.50e+01 4.44e-03 8.93e+00
  ... (remaining 2605 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 612
       0.054 -    0.107: 98
       0.107 -    0.161: 10
       0.161 -    0.215: 4
       0.215 -    0.268: 2
  Chirality restraints: 726
  Sorted by residual:
  chirality pdb=" C13 CLR F 301 "
            pdb=" C12 CLR F 301 "
            pdb=" C14 CLR F 301 "
            pdb=" C17 CLR F 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.66   -0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" C13 CLR A 301 "
            pdb=" C12 CLR A 301 "
            pdb=" C14 CLR A 301 "
            pdb=" C17 CLR A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93   -2.67   -0.26 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" C10 CLR A 301 "
            pdb=" C1  CLR A 301 "
            pdb=" C5  CLR A 301 "
            pdb=" C9  CLR A 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.85   -2.65   -0.20 2.00e-01 2.50e+01 9.68e-01
  ... (remaining 723 not shown)

  Planarity restraints: 666
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 227 "   -0.006 2.00e-02 2.50e+03   1.27e-02 1.62e+00
        pdb=" C   GLN A 227 "    0.022 2.00e-02 2.50e+03
        pdb=" O   GLN A 227 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   GLN A 228 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE F 168 "   -0.006 2.00e-02 2.50e+03   1.26e-02 1.58e+00
        pdb=" C   PHE F 168 "    0.022 2.00e-02 2.50e+03
        pdb=" O   PHE F 168 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   GLU F 169 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H  33 "   -0.011 2.00e-02 2.50e+03   8.20e-03 1.18e+00
        pdb=" CG  PHE H  33 "    0.018 2.00e-02 2.50e+03
        pdb=" CD1 PHE H  33 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD2 PHE H  33 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE H  33 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE H  33 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE H  33 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 663 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1046
        2.80 -     3.33: 4602
        3.33 -     3.85: 6699
        3.85 -     4.38: 7061
        4.38 -     4.90: 12096
  Nonbonded interactions: 31504
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 155 "
            pdb=" OG1 THR B 179 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" OE1 GLN A 227 "
            pdb=" NH2 ARG C  45 "
     model   vdw
     2.339 3.120
  nonbonded pdb=" CD1 LEU E 211 "
            pdb=" C26 CLR F 301 "
     model   vdw
     2.356 3.880
  nonbonded pdb=" O   SER B 115 "
            pdb=" OG  SER B 118 "
     model   vdw
     2.371 3.040
  nonbonded pdb=" NZ  LYS B  55 "
            pdb=" O   CYS B 202 "
     model   vdw
     2.412 3.120
  ... (remaining 31499 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 201 through 237)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 49 through 208)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.170
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6271
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      :  0.003   0.054   4298  Z= 0.206
  Angle     :  0.712   7.933   5818  Z= 0.380
  Chirality :  0.043   0.268    726
  Planarity :  0.003   0.022    666
  Dihedral  : 13.757  79.831   1620
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 12.74
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  4.09 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.38), residues: 514
  helix:  1.80 (0.26), residues: 408
  sheet:  None (None), residues: 0
  loop : -2.79 (0.57), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 103 
 HIS   0.002   0.000   HIS F  87 
 PHE   0.018   0.001   PHE H  33 
 TYR   0.012   0.002   TYR H  43 
 ARG   0.007   0.000   ARG D  51 

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

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

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.503 
Fit side-chains
REVERT: D   49 GLN cc_start: 0.8571 (tm-30) cc_final: 0.7998 (tm-30)
REVERT: E  214 ILE cc_start: 0.8801 (pt) cc_final: 0.8557 (pt)
REVERT: F   96 PHE cc_start: 0.8878 (m-80) cc_final: 0.8666 (m-80)
REVERT: F  158 TYR cc_start: 0.8155 (t80) cc_final: 0.7819 (t80)
REVERT: F  181 ILE cc_start: 0.9061 (mm) cc_final: 0.8781 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.1626
  time to fit residues: 26.7705
Evaluate side-chains
  108 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 12 optimal weight:    7.9990
   chunk 24 optimal weight:   10.0000
   chunk 19 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 14 optimal weight:    6.9990
   chunk 22 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A 229 GLN
** E 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4867 r_free = 0.4867 target = 0.254567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.200615 restraints weight = 5253.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.206723 restraints weight = 2829.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.210404 restraints weight = 1894.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.4523
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6556
moved from start:          0.1454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4298  Z= 0.215
  Angle     :  0.674   7.625   5818  Z= 0.345
  Chirality :  0.039   0.133    726
  Planarity :  0.003   0.026    666
  Dihedral  :  4.889  23.974    688
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  4.47 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 12.39 %
    Favored  : 84.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.38), residues: 514
  helix:  1.71 (0.25), residues: 418
  sheet:  None (None), residues: 0
  loop : -2.38 (0.65), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 103 
 HIS   0.002   0.000   HIS B 160 
 PHE   0.018   0.002   PHE F  60 
 TYR   0.018   0.002   TYR G  43 
 ARG   0.003   0.000   ARG D  51 

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

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

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.457 
Fit side-chains
REVERT: D   49 GLN cc_start: 0.8631 (tm-30) cc_final: 0.8024 (tm-30)
REVERT: E  214 ILE cc_start: 0.8773 (pt) cc_final: 0.8489 (pt)
REVERT: E  227 GLN cc_start: 0.8457 (tm-30) cc_final: 0.7992 (tp-100)
REVERT: E  228 GLN cc_start: 0.7196 (tm-30) cc_final: 0.6762 (tm-30)
REVERT: F   70 MET cc_start: 0.7022 (tpp) cc_final: 0.6762 (tpp)
REVERT: F   75 PHE cc_start: 0.8515 (m-80) cc_final: 0.7882 (m-80)
REVERT: F  158 TYR cc_start: 0.8181 (t80) cc_final: 0.7905 (t80)
REVERT: F  185 MET cc_start: 0.7497 (tpt) cc_final: 0.7262 (tpt)
REVERT: F  188 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8694 (pp)
REVERT: H   41 LEU cc_start: 0.7411 (tp) cc_final: 0.7186 (tp)
  outliers start: 16
  outliers final: 11
  residues processed: 118
  average time/residue: 0.1689
  time to fit residues: 24.7818
Evaluate side-chains
  113 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain B residue   50 TRP
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain D residue   31 ILE
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain E residue  211 LEU
Chi-restraints excluded: chain E residue  218 VAL
Chi-restraints excluded: chain E residue  219 ASP
Chi-restraints excluded: chain E residue  226 THR
Chi-restraints excluded: chain F residue  188 LEU
Chi-restraints excluded: chain H residue   50 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 30 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   chunk 36 optimal weight:    9.9990
   chunk 1 optimal weight:    0.5980
   chunk 28 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0980
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4853 r_free = 0.4853 target = 0.250452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4480 r_free = 0.4480 target = 0.201996 restraints weight = 4893.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.207267 restraints weight = 2621.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.210770 restraints weight = 1761.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.4557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6477
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4298  Z= 0.179
  Angle     :  0.623   8.495   5818  Z= 0.322
  Chirality :  0.037   0.130    726
  Planarity :  0.003   0.022    666
  Dihedral  :  4.825  34.729    688
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  4.09 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.61 %
    Allowed  : 16.30 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.38), residues: 514
  helix:  1.68 (0.25), residues: 420
  sheet:  None (None), residues: 0
  loop : -2.61 (0.63), residues: 94

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 103 
 HIS   0.001   0.000   HIS B 160 
 PHE   0.020   0.001   PHE F 177 
 TYR   0.022   0.002   TYR F 100 
 ARG   0.005   0.000   ARG D  51 

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

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

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.502 
Fit side-chains
REVERT: D   49 GLN cc_start: 0.8619 (tm-30) cc_final: 0.7969 (tm-30)
REVERT: E  214 ILE cc_start: 0.8737 (pt) cc_final: 0.8413 (pt)
REVERT: F   70 MET cc_start: 0.6989 (tpp) cc_final: 0.6648 (tpp)
REVERT: F   75 PHE cc_start: 0.8440 (m-80) cc_final: 0.7534 (m-80)
REVERT: F  158 TYR cc_start: 0.8094 (t80) cc_final: 0.7889 (t80)
REVERT: F  185 MET cc_start: 0.7349 (tpt) cc_final: 0.7073 (tpt)
REVERT: F  188 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8683 (pp)
REVERT: H   41 LEU cc_start: 0.7449 (tp) cc_final: 0.7228 (tp)
  outliers start: 12
  outliers final: 8
  residues processed: 119
  average time/residue: 0.1633
  time to fit residues: 24.4003
Evaluate side-chains
  110 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 TRP
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain D residue   31 ILE
Chi-restraints excluded: chain D residue   43 TYR
Chi-restraints excluded: chain E residue  211 LEU
Chi-restraints excluded: chain E residue  218 VAL
Chi-restraints excluded: chain E residue  226 THR
Chi-restraints excluded: chain F residue  188 LEU
Chi-restraints excluded: chain H residue   50 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 38 optimal weight:    0.3980
   chunk 24 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 30 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 37 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4814 r_free = 0.4814 target = 0.245293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4423 r_free = 0.4423 target = 0.195857 restraints weight = 5044.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4463 r_free = 0.4463 target = 0.200830 restraints weight = 2766.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4487 r_free = 0.4487 target = 0.204087 restraints weight = 1893.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.4500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6574
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4298  Z= 0.211
  Angle     :  0.642   8.764   5818  Z= 0.332
  Chirality :  0.038   0.136    726
  Planarity :  0.003   0.023    666
  Dihedral  :  4.704  27.352    688
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  4.47 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 19.78 %
    Favored  : 75.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.38), residues: 514
  helix:  1.69 (0.25), residues: 418
  sheet:  None (None), residues: 0
  loop : -2.72 (0.62), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 103 
 HIS   0.001   0.000   HIS B 160 
 PHE   0.014   0.001   PHE F 177 
 TYR   0.023   0.002   TYR F 100 
 ARG   0.005   0.000   ARG D  51 

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

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

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.452 
Fit side-chains
REVERT: B   58 GLN cc_start: 0.8032 (tm-30) cc_final: 0.7625 (tm-30)
REVERT: C   41 LEU cc_start: 0.7542 (tt) cc_final: 0.7292 (tt)
REVERT: D   49 GLN cc_start: 0.8660 (tm-30) cc_final: 0.7973 (tm-30)
REVERT: E  214 ILE cc_start: 0.8770 (pt) cc_final: 0.8428 (pt)
REVERT: F   70 MET cc_start: 0.7012 (tpp) cc_final: 0.6643 (tpp)
REVERT: F   75 PHE cc_start: 0.8495 (m-80) cc_final: 0.7554 (m-80)
REVERT: F  158 TYR cc_start: 0.8142 (t80) cc_final: 0.7935 (t80)
REVERT: F  177 PHE cc_start: 0.9080 (t80) cc_final: 0.8742 (t80)
REVERT: F  185 MET cc_start: 0.7345 (tpt) cc_final: 0.7141 (tpt)
REVERT: F  188 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8677 (pp)
REVERT: H   37 ILE cc_start: 0.8171 (mt) cc_final: 0.7961 (tp)
REVERT: H   41 LEU cc_start: 0.7651 (tp) cc_final: 0.7431 (tp)
REVERT: H   49 GLN cc_start: 0.8350 (tp-100) cc_final: 0.8093 (tp-100)
REVERT: H   52 LYS cc_start: 0.8541 (mmtp) cc_final: 0.8238 (mmtp)
REVERT: H   59 GLU cc_start: 0.6101 (pp20) cc_final: 0.5699 (tm-30)
  outliers start: 23
  outliers final: 11
  residues processed: 129
  average time/residue: 0.1602
  time to fit residues: 25.8129
Evaluate side-chains
  124 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 112
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 TRP
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain C residue   32 LEU
Chi-restraints excluded: chain D residue   31 ILE
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue   43 TYR
Chi-restraints excluded: chain E residue  218 VAL
Chi-restraints excluded: chain E residue  226 THR
Chi-restraints excluded: chain F residue  186 LEU
Chi-restraints excluded: chain F residue  188 LEU
Chi-restraints excluded: chain H residue   50 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 10 optimal weight:   10.0000
   chunk 31 optimal weight:    0.2980
   chunk 47 optimal weight:    0.4980
   chunk 25 optimal weight:    0.2980
   chunk 18 optimal weight:    7.9990
   chunk 4 optimal weight:    0.8980
   chunk 34 optimal weight:    6.9990
   chunk 30 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 228 GLN
E 229 GLN
** G  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4826 r_free = 0.4826 target = 0.245666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.194463 restraints weight = 5467.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.199872 restraints weight = 3039.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4478 r_free = 0.4478 target = 0.203117 restraints weight = 2070.896|
|-----------------------------------------------------------------------------|
r_work (final): 0.4475
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6621
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4298  Z= 0.208
  Angle     :  0.646   9.182   5818  Z= 0.334
  Chirality :  0.037   0.136    726
  Planarity :  0.003   0.022    666
  Dihedral  :  4.600  22.345    688
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  4.47 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 21.30 %
    Favored  : 73.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.38), residues: 514
  helix:  1.70 (0.25), residues: 418
  sheet:  None (None), residues: 0
  loop : -2.72 (0.62), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 103 
 HIS   0.001   0.000   HIS B 160 
 PHE   0.012   0.001   PHE F 177 
 TYR   0.024   0.002   TYR F 100 
 ARG   0.005   0.000   ARG D  51 

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

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

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.486 
Fit side-chains
REVERT: C   41 LEU cc_start: 0.7564 (tt) cc_final: 0.7360 (tt)
REVERT: D   49 GLN cc_start: 0.8668 (tm-30) cc_final: 0.7996 (tm-30)
REVERT: E  214 ILE cc_start: 0.8763 (pt) cc_final: 0.8443 (pt)
REVERT: E  227 GLN cc_start: 0.8600 (tm-30) cc_final: 0.8064 (tp-100)
REVERT: F   70 MET cc_start: 0.7092 (tpp) cc_final: 0.6693 (tpp)
REVERT: F   75 PHE cc_start: 0.8551 (m-80) cc_final: 0.8078 (m-80)
REVERT: F  158 TYR cc_start: 0.8344 (t80) cc_final: 0.8048 (t80)
REVERT: F  185 MET cc_start: 0.7345 (tpt) cc_final: 0.7056 (tpt)
REVERT: F  188 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.8679 (pp)
REVERT: H   41 LEU cc_start: 0.7655 (tp) cc_final: 0.7437 (tp)
REVERT: H   49 GLN cc_start: 0.8458 (tp-100) cc_final: 0.8188 (tp-100)
REVERT: H   50 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8434 (p)
  outliers start: 23
  outliers final: 14
  residues processed: 128
  average time/residue: 0.1520
  time to fit residues: 24.4587
Evaluate side-chains
  130 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 114
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain B residue   50 TRP
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain C residue   32 LEU
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain D residue   31 ILE
Chi-restraints excluded: chain D residue   43 TYR
Chi-restraints excluded: chain E residue  218 VAL
Chi-restraints excluded: chain E residue  226 THR
Chi-restraints excluded: chain F residue  186 LEU
Chi-restraints excluded: chain F residue  188 LEU
Chi-restraints excluded: chain H residue   50 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 4 optimal weight:    0.5980
   chunk 33 optimal weight:    7.9990
   chunk 29 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0570
   chunk 26 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 43 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.5698

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4847 r_free = 0.4847 target = 0.251634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.198802 restraints weight = 5310.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.204353 restraints weight = 2906.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.208141 restraints weight = 1993.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.4505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6590
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4298  Z= 0.177
  Angle     :  0.641   9.190   5818  Z= 0.327
  Chirality :  0.037   0.136    726
  Planarity :  0.003   0.019    666
  Dihedral  :  4.467  24.345    688
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  4.47 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 21.74 %
    Favored  : 73.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.38), residues: 514
  helix:  1.75 (0.25), residues: 418
  sheet:  None (None), residues: 0
  loop : -2.82 (0.59), residues: 96

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B 103 
 HIS   0.001   0.000   HIS B 160 
 PHE   0.010   0.001   PHE F 177 
 TYR   0.029   0.002   TYR G  43 
 ARG   0.005   0.000   ARG D  51 

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

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

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 118
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
REVERT: C   41 LEU cc_start: 0.7535 (tt) cc_final: 0.7322 (tt)
REVERT: D   49 GLN cc_start: 0.8403 (tm-30) cc_final: 0.7814 (tm-30)
REVERT: E  214 ILE cc_start: 0.8734 (pt) cc_final: 0.8407 (pt)
REVERT: F   70 MET cc_start: 0.7625 (tpp) cc_final: 0.7043 (tpp)
REVERT: F   75 PHE cc_start: 0.8615 (m-80) cc_final: 0.8274 (m-80)
REVERT: F  158 TYR cc_start: 0.8360 (t80) cc_final: 0.8059 (t80)
REVERT: F  185 MET cc_start: 0.7362 (tpt) cc_final: 0.7031 (tpt)
REVERT: F  188 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8677 (pp)
REVERT: H   49 GLN cc_start: 0.8456 (tp-100) cc_final: 0.8233 (tp-100)
REVERT: H   50 VAL cc_start: 0.8617 (OUTLIER) cc_final: 0.8378 (p)
REVERT: H   52 LYS cc_start: 0.8659 (mmtp) cc_final: 0.8291 (mmtp)
  outliers start: 20
  outliers final: 11
  residues processed: 131
  average time/residue: 0.1468
  time to fit residues: 24.3429
Evaluate side-chains
  127 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain B residue   50 TRP
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain C residue   32 LEU
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain D residue   43 TYR
Chi-restraints excluded: chain E residue  218 VAL
Chi-restraints excluded: chain E residue  226 THR
Chi-restraints excluded: chain F residue  186 LEU
Chi-restraints excluded: chain F residue  188 LEU
Chi-restraints excluded: chain H residue   50 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 30 optimal weight:    6.9990
   chunk 37 optimal weight:    9.9990
   chunk 8 optimal weight:    0.0870
   chunk 29 optimal weight:    1.9990
   chunk 42 optimal weight:   20.0000
   chunk 13 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 24 optimal weight:   10.9990
   chunk 0 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    1.3964

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

Flipped N/Q/H residues before XYZ refinement:
B  58 GLN
** G  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4788 r_free = 0.4788 target = 0.243216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.191474 restraints weight = 5070.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4412 r_free = 0.4412 target = 0.196385 restraints weight = 2878.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.199441 restraints weight = 2001.650|
|-----------------------------------------------------------------------------|
r_work (final): 0.4441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6687
moved from start:          0.2834

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   4298  Z= 0.251
  Angle     :  0.712   9.904   5818  Z= 0.364
  Chirality :  0.039   0.146    726
  Planarity :  0.003   0.023    666
  Dihedral  :  4.694  20.381    688
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  5.06 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 23.04 %
    Favored  : 71.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.37), residues: 514
  helix:  1.74 (0.25), residues: 406
  sheet:  None (None), residues: 0
  loop : -2.40 (0.58), residues: 108

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 103 
 HIS   0.001   0.000   HIS B 160 
 PHE   0.024   0.002   PHE F  60 
 TYR   0.025   0.002   TYR F 100 
 ARG   0.005   0.000   ARG D  51 

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

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

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.462 
Fit side-chains
REVERT: B   58 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.8174 (tt0)
REVERT: D   49 GLN cc_start: 0.8703 (tm-30) cc_final: 0.8024 (tm-30)
REVERT: E  214 ILE cc_start: 0.8836 (pt) cc_final: 0.8502 (pt)
REVERT: E  227 GLN cc_start: 0.8587 (tm-30) cc_final: 0.8104 (tp-100)
REVERT: F   58 GLN cc_start: 0.7889 (mt0) cc_final: 0.7129 (pm20)
REVERT: F   70 MET cc_start: 0.7080 (tpp) cc_final: 0.6662 (tpp)
REVERT: F   75 PHE cc_start: 0.8634 (m-80) cc_final: 0.8326 (m-80)
REVERT: F  158 TYR cc_start: 0.8277 (t80) cc_final: 0.7998 (t80)
REVERT: F  185 MET cc_start: 0.7337 (tpt) cc_final: 0.7000 (tpt)
REVERT: F  188 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8691 (pp)
REVERT: H   49 GLN cc_start: 0.8380 (tp-100) cc_final: 0.8126 (tp-100)
REVERT: H   52 LYS cc_start: 0.8664 (mmtp) cc_final: 0.8231 (mmtp)
  outliers start: 23
  outliers final: 19
  residues processed: 135
  average time/residue: 0.1549
  time to fit residues: 26.2860
Evaluate side-chains
  135 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain B residue   50 TRP
Chi-restraints excluded: chain B residue   58 GLN
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  183 VAL
Chi-restraints excluded: chain C residue   32 LEU
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain D residue   31 ILE
Chi-restraints excluded: chain D residue   38 VAL
Chi-restraints excluded: chain D residue   43 TYR
Chi-restraints excluded: chain E residue  218 VAL
Chi-restraints excluded: chain E residue  226 THR
Chi-restraints excluded: chain F residue   64 THR
Chi-restraints excluded: chain F residue  186 LEU
Chi-restraints excluded: chain F residue  188 LEU
Chi-restraints excluded: chain F residue  190 ILE
Chi-restraints excluded: chain F residue  191 LEU
Chi-restraints excluded: chain H residue   50 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 27 optimal weight:    0.2980
   chunk 29 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 3 optimal weight:    0.4980
   chunk 31 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  58 GLN
** G  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4795 r_free = 0.4795 target = 0.243218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.197335 restraints weight = 4983.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4454 r_free = 0.4454 target = 0.200640 restraints weight = 3644.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.203743 restraints weight = 2048.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.4503
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6593
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   4298  Z= 0.220
  Angle     :  0.694   9.024   5818  Z= 0.352
  Chirality :  0.038   0.136    726
  Planarity :  0.003   0.022    666
  Dihedral  :  4.572  22.652    688
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.39 %
    Allowed  :  4.28 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  5.00 %
    Allowed  : 24.57 %
    Favored  : 70.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.37), residues: 514
  helix:  1.68 (0.25), residues: 412
  sheet:  None (None), residues: 0
  loop : -2.79 (0.56), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 103 
 HIS   0.001   0.000   HIS B 160 
 PHE   0.022   0.001   PHE F  60 
 TYR   0.027   0.002   TYR F 100 
 ARG   0.005   0.000   ARG D  51 

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

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

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
REVERT: D   49 GLN cc_start: 0.8434 (tm-30) cc_final: 0.7830 (tm-30)
REVERT: E  214 ILE cc_start: 0.8798 (pt) cc_final: 0.8424 (pt)
REVERT: E  227 GLN cc_start: 0.8521 (tm-30) cc_final: 0.8228 (tp-100)
REVERT: E  228 GLN cc_start: 0.7023 (tm-30) cc_final: 0.6493 (tm-30)
REVERT: F   58 GLN cc_start: 0.7621 (mt0) cc_final: 0.7059 (pm20)
REVERT: F   70 MET cc_start: 0.7335 (tpp) cc_final: 0.6680 (tpp)
REVERT: F   75 PHE cc_start: 0.8598 (m-80) cc_final: 0.8348 (m-80)
REVERT: F  188 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8634 (pp)
REVERT: H   49 GLN cc_start: 0.8207 (tp-100) cc_final: 0.7941 (tp-100)
REVERT: H   50 VAL cc_start: 0.8635 (OUTLIER) cc_final: 0.8377 (p)
REVERT: H   52 LYS cc_start: 0.8558 (mmtp) cc_final: 0.8067 (mmtp)
  outliers start: 23
  outliers final: 17
  residues processed: 128
  average time/residue: 0.1480
  time to fit residues: 24.1664
Evaluate side-chains
  131 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain B residue   50 TRP
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain C residue   32 LEU
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain D residue   31 ILE
Chi-restraints excluded: chain D residue   43 TYR
Chi-restraints excluded: chain E residue  218 VAL
Chi-restraints excluded: chain E residue  226 THR
Chi-restraints excluded: chain F residue   64 THR
Chi-restraints excluded: chain F residue  177 PHE
Chi-restraints excluded: chain F residue  186 LEU
Chi-restraints excluded: chain F residue  188 LEU
Chi-restraints excluded: chain F residue  191 LEU
Chi-restraints excluded: chain H residue   27 ILE
Chi-restraints excluded: chain H residue   50 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 26 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 38 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9990
   chunk 24 optimal weight:   10.0000
   chunk 7 optimal weight:    0.8980
   chunk 17 optimal weight:    4.9990
   chunk 42 optimal weight:   10.0000
   chunk 22 optimal weight:    0.3980
   chunk 43 optimal weight:    0.3980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** G  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4816 r_free = 0.4816 target = 0.245825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.193413 restraints weight = 5096.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4435 r_free = 0.4435 target = 0.198597 restraints weight = 2856.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4461 r_free = 0.4461 target = 0.201938 restraints weight = 1981.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.4471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6645
moved from start:          0.3065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   4298  Z= 0.216
  Angle     :  0.706   9.244   5818  Z= 0.355
  Chirality :  0.038   0.144    726
  Planarity :  0.003   0.021    666
  Dihedral  :  4.585  24.171    688
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 10.67
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.67 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 26.30 %
    Favored  : 69.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.37), residues: 514
  helix:  1.70 (0.25), residues: 412
  sheet:  None (None), residues: 0
  loop : -2.84 (0.55), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 103 
 HIS   0.001   0.000   HIS B 160 
 PHE   0.021   0.001   PHE F 102 
 TYR   0.025   0.002   TYR F 100 
 ARG   0.005   0.000   ARG D  51 

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

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

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
REVERT: D   49 GLN cc_start: 0.8453 (tm-30) cc_final: 0.7863 (tm-30)
REVERT: E  214 ILE cc_start: 0.8811 (pt) cc_final: 0.8486 (pt)
REVERT: E  227 GLN cc_start: 0.8578 (tm-30) cc_final: 0.8257 (tp-100)
REVERT: E  228 GLN cc_start: 0.7081 (tm-30) cc_final: 0.6539 (tm-30)
REVERT: F   58 GLN cc_start: 0.7854 (mt0) cc_final: 0.7097 (pm20)
REVERT: F   70 MET cc_start: 0.7516 (tpp) cc_final: 0.6956 (tpp)
REVERT: F   75 PHE cc_start: 0.8588 (m-80) cc_final: 0.7933 (m-80)
REVERT: F  188 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8685 (pp)
REVERT: H   49 GLN cc_start: 0.8356 (tp-100) cc_final: 0.8074 (tp-100)
REVERT: H   50 VAL cc_start: 0.8718 (OUTLIER) cc_final: 0.8454 (p)
REVERT: H   52 LYS cc_start: 0.8629 (mmtp) cc_final: 0.8279 (mmtp)
  outliers start: 21
  outliers final: 16
  residues processed: 124
  average time/residue: 0.1534
  time to fit residues: 24.1512
Evaluate side-chains
  130 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 112
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain B residue   50 TRP
Chi-restraints excluded: chain B residue   85 ILE
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain C residue   32 LEU
Chi-restraints excluded: chain C residue   38 VAL
Chi-restraints excluded: chain D residue   31 ILE
Chi-restraints excluded: chain D residue   43 TYR
Chi-restraints excluded: chain E residue  218 VAL
Chi-restraints excluded: chain E residue  226 THR
Chi-restraints excluded: chain F residue   64 THR
Chi-restraints excluded: chain F residue  177 PHE
Chi-restraints excluded: chain F residue  186 LEU
Chi-restraints excluded: chain F residue  188 LEU
Chi-restraints excluded: chain F residue  191 LEU
Chi-restraints excluded: chain H residue   50 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 8 optimal weight:    0.1980
   chunk 12 optimal weight:    4.9990
   chunk 32 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 34 optimal weight:    8.9990
   chunk 35 optimal weight:    0.8980
   chunk 43 optimal weight:    0.1980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4834 r_free = 0.4834 target = 0.248319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.200145 restraints weight = 5006.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.204521 restraints weight = 3614.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4497 r_free = 0.4497 target = 0.206552 restraints weight = 2142.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.4505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6561
moved from start:          0.3097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   4298  Z= 0.188
  Angle     :  0.694   9.626   5818  Z= 0.346
  Chirality :  0.037   0.141    726
  Planarity :  0.003   0.020    666
  Dihedral  :  4.427  26.274    688
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.28 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 27.83 %
    Favored  : 69.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.37), residues: 514
  helix:  1.79 (0.25), residues: 412
  sheet:  None (None), residues: 0
  loop : -2.85 (0.54), residues: 102

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 103 
 HIS   0.001   0.000   HIS B 160 
 PHE   0.020   0.001   PHE F  60 
 TYR   0.025   0.002   TYR F 100 
 ARG   0.007   0.000   ARG D  51 

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

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

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1028 Ramachandran restraints generated.
    514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.523 
Fit side-chains
   revert: symmetry clash
REVERT: C   52 LYS cc_start: 0.8321 (tptp) cc_final: 0.7069 (mttp)
REVERT: D   49 GLN cc_start: 0.8487 (tm-30) cc_final: 0.7888 (tm-30)
REVERT: E  214 ILE cc_start: 0.8789 (pt) cc_final: 0.8435 (pt)
REVERT: E  227 GLN cc_start: 0.8490 (tm-30) cc_final: 0.8220 (tp-100)
REVERT: E  228 GLN cc_start: 0.7140 (tm-30) cc_final: 0.6906 (tm-30)
REVERT: F   58 GLN cc_start: 0.7613 (mt0) cc_final: 0.7187 (pm20)
REVERT: F   70 MET cc_start: 0.7479 (tpp) cc_final: 0.7117 (tpp)
REVERT: F  188 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8643 (pp)
REVERT: H   49 GLN cc_start: 0.8242 (tp-100) cc_final: 0.7991 (tp-100)
REVERT: H   52 LYS cc_start: 0.8698 (mmtp) cc_final: 0.8321 (mmtp)
  outliers start: 14
  outliers final: 11
  residues processed: 118
  average time/residue: 0.1466
  time to fit residues: 21.8583
Evaluate side-chains
  119 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  212 VAL
Chi-restraints excluded: chain A residue  233 LEU
Chi-restraints excluded: chain B residue   50 TRP
Chi-restraints excluded: chain B residue  152 LEU
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain C residue   32 LEU
Chi-restraints excluded: chain D residue   31 ILE
Chi-restraints excluded: chain D residue   43 TYR
Chi-restraints excluded: chain E residue  218 VAL
Chi-restraints excluded: chain F residue   64 THR
Chi-restraints excluded: chain F residue  186 LEU
Chi-restraints excluded: chain F residue  188 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 48
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0670
   chunk 15 optimal weight:    0.9980
   chunk 24 optimal weight:   10.0000
   chunk 43 optimal weight:    0.0470
   chunk 14 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 19 optimal weight:    0.2980
   chunk 22 optimal weight:    0.5980
   chunk 2 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   overall best weight:    0.3816

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

Flipped N/Q/H residues before XYZ refinement:
** A 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4860 r_free = 0.4860 target = 0.251123 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4517 r_free = 0.4517 target = 0.203596 restraints weight = 4979.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4520 r_free = 0.4520 target = 0.210229 restraints weight = 3316.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4530 r_free = 0.4530 target = 0.210954 restraints weight = 1906.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.4539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6508
moved from start:          0.3186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4298  Z= 0.180
  Angle     :  0.695   9.264   5818  Z= 0.344
  Chirality :  0.037   0.138    726
  Planarity :  0.003   0.020    666
  Dihedral  :  4.444  26.330    688
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 9.64
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  4.28 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 28.04 %
    Favored  : 69.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.37), residues: 514
  helix:  1.90 (0.25), residues: 408
  sheet:  None (None), residues: 0
  loop : -2.58 (0.56), residues: 106

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 103 
 HIS   0.001   0.000   HIS B 160 
 PHE   0.019   0.001   PHE F  60 
 TYR   0.022   0.002   TYR F 100 
 ARG   0.006   0.000   ARG D  51 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1620.34 seconds
wall clock time: 29 minutes 48.35 seconds (1788.35 seconds total)