Starting phenix.real_space_refine
on Mon Jul 28 04:47:29 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yjq_39346/07_2025/8yjq_39346.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yjq_39346/07_2025/8yjq_39346.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.51
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yjq_39346/07_2025/8yjq_39346.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yjq_39346/07_2025/8yjq_39346.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yjq_39346/07_2025/8yjq_39346.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yjq_39346/07_2025/8yjq_39346.cif"
  }
  resolution = 3.51
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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 300 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      58      5.49       5
     S      63      5.16       5
     C    6024      2.51       5
     N    1652      2.21       5
     O    2059      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9856
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "D"
      Number of atoms: 2769
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 351, 2769
          Classifications: {'peptide': 351}
          Link IDs: {'PTRANS': 15, 'TRANS': 335}
    Chain: "A"
      Number of atoms: 1955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1955
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 7, 'TRANS': 246}
    Chain: "C"
      Number of atoms: 1972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 256, 1972
          Classifications: {'peptide': 256}
          Link IDs: {'PTRANS': 7, 'TRANS': 248}
    Chain: "B"
      Number of atoms: 1955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1955
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 7, 'TRANS': 246}
    Chain: "J"
      Number of atoms: 344
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 344
          Classifications: {'DNA': 17}
          Link IDs: {'rna3p': 16}
    Chain: "E"
      Number of atoms: 576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 576
          Classifications: {'DNA': 28}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 27}
    Chain: "F"
      Number of atoms: 204
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 204
          Classifications: {'DNA': 10}
          Link IDs: {'rna3p': 9}
    Chain: "H"
      Number of atoms: 81
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 81
          Classifications: {'DNA': 4}
          Link IDs: {'rna3p': 3}
  Time building chain proxies: 6.55, per 1000 atoms: 0.66
  Number of scatterers: 9856
  At special positions: 0
  Unit cell: (106.24, 104.58, 104.58, 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      63     16.00
     P      58     15.00
     O    2059      8.00
     N    1652      7.00
     C    6024      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 135 " - pdb=" SG  CYS A 162 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 135 " - pdb=" SG  CYS C 162 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 135 " - pdb=" SG  CYS B 162 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.38
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2106

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 9 sheets defined
      28.3% alpha, 26.0% beta
      14 base pairs and 44 stacking pairs defined.
    Time for finding SS restraints: 3.22
  Creating SS restraints...
    Processing helix  chain 'D' and resid 5 through 12
    Processing helix  chain 'D' and resid 14 through 16
      No H-bonds generated for 'chain 'D' and resid 14 through 16'
    Processing helix  chain 'D' and resid 35 through 45
    Processing helix  chain 'D' and resid 61 through 77
    Processing helix  chain 'D' and resid 93 through 118
      removed outlier: 3.679A  pdb=" N   ALA D 107 " --> pdb=" O   ARG D 103 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   GLN D 112 " --> pdb=" O   GLU D 108 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLN D 113 " --> pdb=" O   LYS D 109 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ALA D 116 " --> pdb=" O   GLN D 112 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ALA D 117 " --> pdb=" O   GLN D 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 119 through 127
      removed outlier: 3.630A  pdb=" N   GLU D 124 " --> pdb=" O   GLU D 120 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   LYS D 125 " --> pdb=" O   GLN D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 128 through 131
      removed outlier: 3.744A  pdb=" N   VAL D 131 " --> pdb=" O   LYS D 128 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 128 through 131'
    Processing helix  chain 'D' and resid 135 through 140
      removed outlier: 3.564A  pdb=" N   GLU D 140 " --> pdb=" O   GLN D 136 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 141 through 149
      removed outlier: 3.819A  pdb=" N   LEU D 145 " --> pdb=" O   CYS D 141 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU D 147 " --> pdb=" O   HIS D 143 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   MET D 148 " --> pdb=" O   LEU D 144 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 158 through 169
      removed outlier: 3.595A  pdb=" N   ALA D 164 " --> pdb=" O   GLU D 160 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 180 through 186
      removed outlier: 3.950A  pdb=" N   THR D 184 " --> pdb=" O   MET D 180 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 217
    Processing helix  chain 'D' and resid 219 through 230
      removed outlier: 4.133A  pdb=" N   ASP D 225 " --> pdb=" O   GLU D 221 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU D 229 " --> pdb=" O   ASP D 225 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 243 through 253
      removed outlier: 3.668A  pdb=" N   VAL D 247 " --> pdb=" O   PRO D 243 " (cutoff:3.500A)
      removed outlier: 4.459A  pdb=" N   ASP D 248 " --> pdb=" O   LYS D 244 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   LEU D 249 " --> pdb=" O   ARG D 245 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 256 through 261
      removed outlier: 3.702A  pdb=" N   VAL D 260 " --> pdb=" O   ILE D 256 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   ARG D 261 " --> pdb=" O   GLU D 257 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 256 through 261'
    Processing helix  chain 'D' and resid 275 through 285
    Processing helix  chain 'D' and resid 304 through 310
      removed outlier: 3.744A  pdb=" N   LYS D 308 " --> pdb=" O   GLU D 304 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 317 through 330
      removed outlier: 3.609A  pdb=" N   ILE D 321 " --> pdb=" O   SER D 317 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ARG D 322 " --> pdb=" O   GLU D 318 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   SER D 323 " --> pdb=" O   GLU D 319 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LYS D 326 " --> pdb=" O   ARG D 322 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 339 through 343
      removed outlier: 3.646A  pdb=" N   ASP D 342 " --> pdb=" O   ARG D 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 9 through 20
      removed outlier: 3.600A  pdb=" N   ALA A  18 " --> pdb=" O   LYS A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 80
    Processing helix  chain 'A' and resid 141 through 152
      removed outlier: 3.902A  pdb=" N   ARG A 146 " --> pdb=" O   GLY A 142 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   ILE A 147 " --> pdb=" O   GLU A 143 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ARG A 149 " --> pdb=" O   ALA A 145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 194
      removed outlier: 3.734A  pdb=" N   ALA A 194 " --> pdb=" O   GLU A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 216
      removed outlier: 3.737A  pdb=" N   PHE A 214 " --> pdb=" O   ARG A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 219
      No H-bonds generated for 'chain 'A' and resid 217 through 219'
    Processing helix  chain 'C' and resid 9 through 17
      removed outlier: 3.657A  pdb=" N   LEU C  16 " --> pdb=" O   LEU C  12 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 80
    Processing helix  chain 'C' and resid 141 through 152
    Processing helix  chain 'C' and resid 209 through 216
    Processing helix  chain 'B' and resid 9 through 20
      removed outlier: 3.558A  pdb=" N   VAL B  15 " --> pdb=" O   ILE B  11 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU B  16 " --> pdb=" O   LEU B  12 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 80
    Processing helix  chain 'B' and resid 141 through 152
    Processing helix  chain 'B' and resid 209 through 216
      removed outlier: 3.852A  pdb=" N   PHE B 214 " --> pdb=" O   ARG B 210 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 18 through 21
      removed outlier: 6.572A  pdb=" N   ALA D 175 " --> pdb=" O   MET D 191 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   VAL D  31 " --> pdb=" O   VAL D  82 " (cutoff:3.500A)
      removed outlier: 7.446A  pdb=" N   VAL D  84 " --> pdb=" O   VAL D  31 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   ILE D  33 " --> pdb=" O   VAL D  84 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 336 through 337
      removed outlier: 4.007A  pdb=" N   THR D 336 " --> pdb=" O   ILE C 255 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 345 through 349
      removed outlier: 4.409A  pdb=" N   LYS D 345 " --> pdb=" O   GLY C 127 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   GLN C 125 " --> pdb=" O   THR D 347 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 59 through 61
      removed outlier: 3.601A  pdb=" N   THR A  59 " --> pdb=" O   ARG A   5 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ALA A   4 " --> pdb=" O   LEU A  90 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ALA A 100 " --> pdb=" O   ARG A  91 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   LEU A  99 " --> pdb=" O   MET A 116 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   GLY C 166 " --> pdb=" O   ALA C 163 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   SER C 172 " --> pdb=" O   ALA C 157 " (cutoff:3.500A)
      removed outlier: 5.315A  pdb=" N   ALA C 157 " --> pdb=" O   SER C 172 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 66 through 71
      removed outlier: 3.793A  pdb=" N   MET A  68 " --> pdb=" O   TRP A  28 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ALA A  26 " --> pdb=" O   VAL A  70 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   GLU A  25 " --> pdb=" O   MET A  40 " (cutoff:3.500A)
      removed outlier: 6.080A  pdb=" N   MET A  40 " --> pdb=" O   GLU A  25 " (cutoff:3.500A)
      removed outlier: 5.639A  pdb=" N   CYS A  27 " --> pdb=" O   GLN A  38 " (cutoff:3.500A)
      removed outlier: 4.649A  pdb=" N   GLN A  38 " --> pdb=" O   CYS A  27 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LEU A 251 " --> pdb=" O   LEU A 235 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   LEU A 235 " --> pdb=" O   LEU A 251 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   LYS A 240 " --> pdb=" O   THR A 224 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   THR A 224 " --> pdb=" O   LYS A 240 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 205 through 208
      removed outlier: 3.518A  pdb=" N   LEU A 205 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE A 180 " --> pdb=" O   PHE A 169 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   VAL B 111 " --> pdb=" O   LYS A 181 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   PHE B   2 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 59 through 61
      removed outlier: 3.937A  pdb=" N   SER B 172 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 5.022A  pdb=" N   ALA B 157 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   LEU B 205 " --> pdb=" O   ILE B 160 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 66 through 71
      removed outlier: 7.284A  pdb=" N   GLU C  25 " --> pdb=" O   MET C  40 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   MET C  40 " --> pdb=" O   GLU C  25 " (cutoff:3.500A)
      removed outlier: 6.200A  pdb=" N   CYS C  27 " --> pdb=" O   GLN C  38 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   GLN C  38 " --> pdb=" O   CYS C  27 " (cutoff:3.500A)
      removed outlier: 5.334A  pdb=" N   SER C 230 " --> pdb=" O   PRO C 234 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   LYS C 240 " --> pdb=" O   THR C 224 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   THR C 224 " --> pdb=" O   LYS C 240 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 66 through 71
      removed outlier: 3.647A  pdb=" N   MET B  68 " --> pdb=" O   TRP B  28 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   GLU B  25 " --> pdb=" O   MET B  40 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   MET B  40 " --> pdb=" O   GLU B  25 " (cutoff:3.500A)
      removed outlier: 7.200A  pdb=" N   CYS B  27 " --> pdb=" O   GLN B  38 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   GLN B  38 " --> pdb=" O   CYS B  27 " (cutoff:3.500A)

    388 hydrogen bonds defined for protein.
    1086 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      28 hydrogen bonds
      56 hydrogen bond angles
      0 basepair planarities
      14 basepair parallelities
      44 stacking parallelities
  Total time for adding SS restraints: 3.26

  Time building geometry restraints manager: 2.83 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2964
        1.34 -     1.46: 2398
        1.46 -     1.58: 4546
        1.58 -     1.71: 113
        1.71 -     1.83: 102
  Bond restraints: 10123
  Sorted by residual:
  bond pdb=" CA  ALA D 176 "
       pdb=" CB  ALA D 176 "
    ideal  model  delta    sigma   weight residual
    1.524  1.486  0.037 1.30e-02 5.92e+03 8.14e+00
  bond pdb=" N   PHE D  85 "
       pdb=" CA  PHE D  85 "
    ideal  model  delta    sigma   weight residual
    1.454  1.487 -0.032 1.17e-02 7.31e+03 7.70e+00
  bond pdb=" N   ASP D  86 "
       pdb=" CA  ASP D  86 "
    ideal  model  delta    sigma   weight residual
    1.455  1.488 -0.033 1.30e-02 5.92e+03 6.29e+00
  bond pdb=" CB  ASN A  24 "
       pdb=" CG  ASN A  24 "
    ideal  model  delta    sigma   weight residual
    1.516  1.574 -0.058 2.50e-02 1.60e+03 5.39e+00
  bond pdb=" N   ALA B 242 "
       pdb=" CA  ALA B 242 "
    ideal  model  delta    sigma   weight residual
    1.457  1.484 -0.026 1.29e-02 6.01e+03 4.14e+00
  ... (remaining 10118 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 13489
        2.49 -     4.99: 332
        4.99 -     7.48: 58
        7.48 -     9.98: 23
        9.98 -    12.47: 4
  Bond angle restraints: 13906
  Sorted by residual:
  angle pdb=" C   ALA A 242 "
        pdb=" N   ASP A 243 "
        pdb=" CA  ASP A 243 "
      ideal   model   delta    sigma   weight residual
     121.54  134.01  -12.47 1.91e+00 2.74e-01 4.26e+01
  angle pdb=" C   LYS D 314 "
        pdb=" N   GLN D 315 "
        pdb=" CA  GLN D 315 "
      ideal   model   delta    sigma   weight residual
     122.36  129.01   -6.65 1.42e+00 4.96e-01 2.20e+01
  angle pdb=" C   ALA C 242 "
        pdb=" N   ASP C 243 "
        pdb=" CA  ASP C 243 "
      ideal   model   delta    sigma   weight residual
     122.08  128.51   -6.43 1.47e+00 4.63e-01 1.91e+01
  angle pdb=" N   THR A 219 "
        pdb=" CA  THR A 219 "
        pdb=" C   THR A 219 "
      ideal   model   delta    sigma   weight residual
     109.81  118.92   -9.11 2.21e+00 2.05e-01 1.70e+01
  angle pdb=" CB  MET A 119 "
        pdb=" CG  MET A 119 "
        pdb=" SD  MET A 119 "
      ideal   model   delta    sigma   weight residual
     112.70  124.81  -12.11 3.00e+00 1.11e-01 1.63e+01
  ... (remaining 13901 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 5046
       17.91 -    35.82: 722
       35.82 -    53.73: 285
       53.73 -    71.64: 64
       71.64 -    89.55: 12
  Dihedral angle restraints: 6129
    sinusoidal: 2883
      harmonic: 3246
  Sorted by residual:
  dihedral pdb=" CA  MET C 139 "
           pdb=" C   MET C 139 "
           pdb=" N   PRO C 140 "
           pdb=" CA  PRO C 140 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.26   23.74     0      5.00e+00 4.00e-02 2.25e+01
  dihedral pdb=" CA  PRO D  81 "
           pdb=" C   PRO D  81 "
           pdb=" N   VAL D  82 "
           pdb=" CA  VAL D  82 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.07   22.93     0      5.00e+00 4.00e-02 2.10e+01
  dihedral pdb=" CA  ILE D  33 "
           pdb=" C   ILE D  33 "
           pdb=" N   ASP D  34 "
           pdb=" CA  ASP D  34 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.48   22.52     0      5.00e+00 4.00e-02 2.03e+01
  ... (remaining 6126 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 1310
       0.061 -    0.121: 236
       0.121 -    0.182: 41
       0.182 -    0.243: 9
       0.243 -    0.303: 4
  Chirality restraints: 1600
  Sorted by residual:
  chirality pdb=" CB  ILE B 128 "
            pdb=" CA  ILE B 128 "
            pdb=" CG1 ILE B 128 "
            pdb=" CG2 ILE B 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.30 2.00e-01 2.50e+01 2.30e+00
  chirality pdb=" CB  ILE A 128 "
            pdb=" CA  ILE A 128 "
            pdb=" CG1 ILE A 128 "
            pdb=" CG2 ILE A 128 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" CA  ASP A 243 "
            pdb=" N   ASP A 243 "
            pdb=" C   ASP A 243 "
            pdb=" CB  ASP A 243 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.61e+00
  ... (remaining 1597 not shown)

  Planarity restraints: 1590
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 207 "   -0.015 2.00e-02 2.50e+03   2.49e-02 1.08e+01
        pdb=" CG  PHE B 207 "    0.052 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 207 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 207 "   -0.033 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 207 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 207 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 207 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 128 "   -0.053 5.00e-02 4.00e+02   8.09e-02 1.05e+01
        pdb=" N   PRO B 129 "    0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO B 129 "   -0.043 5.00e-02 4.00e+02
        pdb=" CD  PRO B 129 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 219 "    0.053 5.00e-02 4.00e+02   7.94e-02 1.01e+01
        pdb=" N   PRO A 220 "   -0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO A 220 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 220 "    0.045 5.00e-02 4.00e+02
  ... (remaining 1587 not shown)

  Histogram of nonbonded interaction distances:
        2.37 -     2.87: 3210
        2.87 -     3.38: 8198
        3.38 -     3.89: 17220
        3.89 -     4.39: 19050
        4.39 -     4.90: 32017
  Nonbonded interactions: 79695
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A  41 "
            pdb=" OG  SER A  43 "
     model   vdw
     2.366 3.040
  nonbonded pdb=" OE1 GLU D 158 "
            pdb=" OH  TYR D 234 "
     model   vdw
     2.378 3.040
  nonbonded pdb=" OG  SER A 222 "
            pdb=" O   THR A 224 "
     model   vdw
     2.379 3.040
  nonbonded pdb=" OG  SER A 141 "
            pdb=" O   SER A 222 "
     model   vdw
     2.392 3.040
  nonbonded pdb=" ND2 ASN D 302 "
            pdb=" OE1 GLU D 305 "
     model   vdw
     2.433 3.120
  ... (remaining 79690 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
  selection = (chain 'C' and resid 1 through 254)
}

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:             2.960
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     27.730
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.010
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7585
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  10126  Z= 0.227
  Angle     :  0.971  12.473  13912  Z= 0.492
  Chirality :  0.054   0.303   1600
  Planarity :  0.007   0.081   1590
  Dihedral  : 19.575  89.548   4014
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.80 (0.20), residues: 1107
  helix: -4.24 (0.13), residues: 289
  sheet: -1.66 (0.27), residues: 327
  loop : -1.82 (0.23), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A  28 
 HIS   0.002   0.001   HIS D 280 
 PHE   0.052   0.003   PHE B 207 
 TYR   0.054   0.003   TYR A 249 
 ARG   0.010   0.001   ARG D 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.27218 (  416)
  hydrogen bonds       : angle      10.98781 ( 1142)
  SS BOND              : bond        0.00272 (    3)
  SS BOND              : angle       0.60753 (    6)
  covalent geometry    : bond        0.00503 (10123)
  covalent geometry    : angle       0.97138 (13906)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.017 
Fit side-chains
REVERT: D   21 ASN cc_start: 0.7921 (m110) cc_final: 0.7675 (m-40)
REVERT: D  189 VAL cc_start: 0.9002 (t) cc_final: 0.8627 (p)
REVERT: A  125 GLN cc_start: 0.7939 (pp30) cc_final: 0.7665 (pp30)
REVERT: B   59 THR cc_start: 0.8043 (m) cc_final: 0.7586 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.1986
  time to fit residues: 41.4822
Evaluate side-chains
  107 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9980
   chunk 47 optimal weight:    0.2980
   chunk 29 optimal weight:    0.5980
   chunk 58 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
D 205 GLN
A 213 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.161264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.127949 restraints weight = 13974.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.133934 restraints weight = 7821.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.134754 restraints weight = 4691.970|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10126  Z= 0.165
  Angle     :  0.586   6.551  13912  Z= 0.323
  Chirality :  0.043   0.146   1600
  Planarity :  0.005   0.055   1590
  Dihedral  : 20.727  79.009   1871
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  8.26 %
    Favored  : 90.51 %
  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: -2.70 (0.22), residues: 1107
  helix: -2.21 (0.23), residues: 309
  sheet: -1.59 (0.27), residues: 322
  loop : -1.41 (0.25), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP D 274 
 HIS   0.003   0.001   HIS C  44 
 PHE   0.020   0.001   PHE D 207 
 TYR   0.014   0.002   TYR D  26 
 ARG   0.002   0.000   ARG D 103 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04469 (  416)
  hydrogen bonds       : angle       6.71171 ( 1142)
  SS BOND              : bond        0.00257 (    3)
  SS BOND              : angle       0.45855 (    6)
  covalent geometry    : bond        0.00368 (10123)
  covalent geometry    : angle       0.58647 (13906)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 1.004 
Fit side-chains
REVERT: B   75 MET cc_start: 0.8817 (tpp) cc_final: 0.7953 (ttt)
REVERT: B  143 GLU cc_start: 0.7559 (mm-30) cc_final: 0.7110 (mm-30)
  outliers start: 12
  outliers final: 7
  residues processed: 130
  average time/residue: 0.2148
  time to fit residues: 39.8026
Evaluate side-chains
  104 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   68 MET
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  206 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 4 optimal weight:    0.4980
   chunk 99 optimal weight:    0.6980
   chunk 93 optimal weight:    3.9990
   chunk 84 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   chunk 87 optimal weight:    0.9990
   chunk 100 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
D 137 HIS
C  38 GLN
C  71 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4170 r_free = 0.4170 target = 0.158591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.124845 restraints weight = 13960.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.130015 restraints weight = 7802.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.130679 restraints weight = 4979.663|
|-----------------------------------------------------------------------------|
r_work (final): 0.3806
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.2670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10126  Z= 0.157
  Angle     :  0.555   6.068  13912  Z= 0.303
  Chirality :  0.042   0.144   1600
  Planarity :  0.004   0.045   1590
  Dihedral  : 20.566  80.532   1871
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 11.66 %
    Favored  : 86.69 %
  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: -2.02 (0.23), residues: 1107
  helix: -0.83 (0.28), residues: 309
  sheet: -1.87 (0.25), residues: 330
  loop : -1.05 (0.27), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  28 
 HIS   0.003   0.001   HIS C  44 
 PHE   0.018   0.001   PHE D 207 
 TYR   0.016   0.001   TYR D  26 
 ARG   0.002   0.000   ARG A 146 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03718 (  416)
  hydrogen bonds       : angle       5.92778 ( 1142)
  SS BOND              : bond        0.00285 (    3)
  SS BOND              : angle       0.57975 (    6)
  covalent geometry    : bond        0.00356 (10123)
  covalent geometry    : angle       0.55541 (13906)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 1.068 
Fit side-chains
REVERT: D   86 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.6734 (m-30)
REVERT: A  124 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6781 (tm-30)
REVERT: A  146 ARG cc_start: 0.7906 (ptp90) cc_final: 0.7637 (ptp-170)
REVERT: B   75 MET cc_start: 0.8842 (tpp) cc_final: 0.8119 (ttt)
REVERT: B  143 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7392 (tp30)
  outliers start: 16
  outliers final: 8
  residues processed: 121
  average time/residue: 0.2527
  time to fit residues: 41.8165
Evaluate side-chains
  105 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 1.015 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue  258 GLU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   68 MET
Chi-restraints excluded: chain A residue   85 GLU
Chi-restraints excluded: chain A residue  124 GLU
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain C residue  179 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 21 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 50 optimal weight:    0.2980
   chunk 10 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.7986

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

Flipped N/Q/H residues before XYZ refinement:
** C  38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 108 GLN
C 177 ASN
C 246 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.156639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.122162 restraints weight = 13742.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.126468 restraints weight = 7453.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.129144 restraints weight = 4983.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7804
moved from start:          0.3104

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  10126  Z= 0.172
  Angle     :  0.558   5.972  13912  Z= 0.304
  Chirality :  0.043   0.149   1600
  Planarity :  0.003   0.044   1590
  Dihedral  : 20.488  77.469   1871
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 13.62 %
    Favored  : 84.21 %
  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: -1.80 (0.24), residues: 1107
  helix: -0.49 (0.29), residues: 316
  sheet: -1.89 (0.25), residues: 332
  loop : -0.91 (0.28), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 274 
 HIS   0.005   0.001   HIS D 276 
 PHE   0.018   0.001   PHE D 207 
 TYR   0.016   0.001   TYR D  26 
 ARG   0.007   0.000   ARG B  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03429 (  416)
  hydrogen bonds       : angle       5.82647 ( 1142)
  SS BOND              : bond        0.00260 (    3)
  SS BOND              : angle       0.63585 (    6)
  covalent geometry    : bond        0.00395 (10123)
  covalent geometry    : angle       0.55826 (13906)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.823 
Fit side-chains
REVERT: D  148 MET cc_start: 0.7375 (OUTLIER) cc_final: 0.5624 (mmt)
REVERT: C  115 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7441 (mt-10)
REVERT: B   75 MET cc_start: 0.8840 (tpp) cc_final: 0.8134 (ttt)
  outliers start: 21
  outliers final: 11
  residues processed: 113
  average time/residue: 0.2267
  time to fit residues: 35.9825
Evaluate side-chains
  110 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 97
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  148 MET
Chi-restraints excluded: chain D residue  258 GLU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   68 MET
Chi-restraints excluded: chain A residue   85 GLU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  179 ASN
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  206 THR
Chi-restraints excluded: chain B residue  244 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 83 optimal weight:    0.0870
   chunk 37 optimal weight:    2.9990
   chunk 63 optimal weight:    0.7980
   chunk 0 optimal weight:    2.9990
   chunk 80 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 88 optimal weight:    0.9980
   chunk 57 optimal weight:    0.3980
   chunk 18 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.157202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.122758 restraints weight = 13720.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.127111 restraints weight = 7369.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.129816 restraints weight = 4902.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.3283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10126  Z= 0.143
  Angle     :  0.532   6.276  13912  Z= 0.289
  Chirality :  0.042   0.146   1600
  Planarity :  0.003   0.044   1590
  Dihedral  : 20.383  76.315   1871
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 15.07 %
    Favored  : 82.87 %
  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: -1.50 (0.24), residues: 1107
  helix: -0.09 (0.30), residues: 310
  sheet: -1.80 (0.25), residues: 345
  loop : -0.73 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  28 
 HIS   0.002   0.001   HIS D 276 
 PHE   0.015   0.001   PHE D 207 
 TYR   0.015   0.001   TYR D  26 
 ARG   0.004   0.000   ARG D  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03176 (  416)
  hydrogen bonds       : angle       5.59102 ( 1142)
  SS BOND              : bond        0.00129 (    3)
  SS BOND              : angle       0.46263 (    6)
  covalent geometry    : bond        0.00326 (10123)
  covalent geometry    : angle       0.53169 (13906)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 105
  time to evaluate  : 1.120 
Fit side-chains
REVERT: D  148 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.5705 (mmt)
REVERT: A  196 THR cc_start: 0.7899 (m) cc_final: 0.7635 (p)
REVERT: C  115 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7360 (mt-10)
  outliers start: 20
  outliers final: 10
  residues processed: 115
  average time/residue: 0.2406
  time to fit residues: 39.1750
Evaluate side-chains
  114 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 102
  time to evaluate  : 0.984 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  134 THR
Chi-restraints excluded: chain D residue  148 MET
Chi-restraints excluded: chain D residue  258 GLU
Chi-restraints excluded: chain A residue   85 GLU
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain C residue    8 GLN
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  179 ASN
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  206 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 103 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 105 optimal weight:    0.3980
   chunk 109 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   chunk 100 optimal weight:    0.9980
   chunk 108 optimal weight:    1.9990
   chunk 39 optimal weight:    0.7980
   chunk 32 optimal weight:    4.9990
   chunk 104 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 315 GLN
C  38 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.155921 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.121450 restraints weight = 13815.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.125711 restraints weight = 7533.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.128356 restraints weight = 5074.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.3555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10126  Z= 0.162
  Angle     :  0.545   6.546  13912  Z= 0.295
  Chirality :  0.042   0.144   1600
  Planarity :  0.003   0.043   1590
  Dihedral  : 20.349  75.348   1871
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 15.48 %
    Favored  : 82.15 %
  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 (0.25), residues: 1107
  helix:  0.07 (0.30), residues: 310
  sheet: -1.84 (0.24), residues: 339
  loop : -0.63 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  28 
 HIS   0.003   0.001   HIS C  44 
 PHE   0.016   0.001   PHE D 207 
 TYR   0.016   0.001   TYR D  26 
 ARG   0.003   0.000   ARG D  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03241 (  416)
  hydrogen bonds       : angle       5.58777 ( 1142)
  SS BOND              : bond        0.00124 (    3)
  SS BOND              : angle       0.47778 (    6)
  covalent geometry    : bond        0.00371 (10123)
  covalent geometry    : angle       0.54541 (13906)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 0.980 
Fit side-chains
REVERT: D  148 MET cc_start: 0.7640 (OUTLIER) cc_final: 0.5991 (mmt)
REVERT: A   59 THR cc_start: 0.7875 (p) cc_final: 0.7645 (p)
REVERT: C  115 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7410 (mt-10)
REVERT: B  198 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7474 (mp0)
  outliers start: 23
  outliers final: 11
  residues processed: 116
  average time/residue: 0.2241
  time to fit residues: 36.6658
Evaluate side-chains
  112 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  134 THR
Chi-restraints excluded: chain D residue  148 MET
Chi-restraints excluded: chain D residue  258 GLU
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  179 ASN
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  206 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 24 optimal weight:    4.9990
   chunk 32 optimal weight:    4.9990
   chunk 113 optimal weight:    5.9990
   chunk 46 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** D 276 HIS ** 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 = 0.3939 r_free = 0.3939 target = 0.140724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.106132 restraints weight = 14899.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.110418 restraints weight = 10387.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.111221 restraints weight = 6053.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.3718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  10126  Z= 0.176
  Angle     :  0.557   6.583  13912  Z= 0.300
  Chirality :  0.043   0.144   1600
  Planarity :  0.003   0.043   1590
  Dihedral  : 20.356  74.770   1871
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 16.20 %
    Favored  : 81.53 %
  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: -1.31 (0.25), residues: 1107
  helix:  0.12 (0.30), residues: 310
  sheet: -1.75 (0.25), residues: 330
  loop : -0.66 (0.29), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  28 
 HIS   0.003   0.001   HIS D 276 
 PHE   0.016   0.001   PHE D 207 
 TYR   0.016   0.002   TYR D  26 
 ARG   0.003   0.000   ARG A 146 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03264 (  416)
  hydrogen bonds       : angle       5.61593 ( 1142)
  SS BOND              : bond        0.00181 (    3)
  SS BOND              : angle       0.48422 (    6)
  covalent geometry    : bond        0.00405 (10123)
  covalent geometry    : angle       0.55735 (13906)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 1.200 
Fit side-chains
REVERT: D  148 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.6180 (mmt)
REVERT: A   59 THR cc_start: 0.7991 (OUTLIER) cc_final: 0.7758 (p)
REVERT: C  115 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7498 (mt-10)
REVERT: B  198 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7494 (mp0)
  outliers start: 22
  outliers final: 13
  residues processed: 112
  average time/residue: 0.2493
  time to fit residues: 39.7493
Evaluate side-chains
  113 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   74 MET
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  134 THR
Chi-restraints excluded: chain D residue  148 MET
Chi-restraints excluded: chain D residue  258 GLU
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  179 ASN
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  206 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0000
   chunk 84 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.6584

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

Flipped N/Q/H residues before XYZ refinement:
** D 276 HIS ** 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 = 0.3950 r_free = 0.3950 target = 0.141558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.107016 restraints weight = 14878.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.111450 restraints weight = 9826.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.112191 restraints weight = 5836.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.3825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10126  Z= 0.153
  Angle     :  0.544   7.079  13912  Z= 0.294
  Chirality :  0.042   0.143   1600
  Planarity :  0.003   0.043   1590
  Dihedral  : 20.311  74.075   1871
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 17.03 %
    Favored  : 81.11 %
  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: -1.18 (0.25), residues: 1107
  helix:  0.24 (0.30), residues: 309
  sheet: -1.60 (0.25), residues: 337
  loop : -0.62 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  28 
 HIS   0.002   0.001   HIS D 276 
 PHE   0.015   0.001   PHE D 207 
 TYR   0.014   0.001   TYR D  26 
 ARG   0.003   0.000   ARG D  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03152 (  416)
  hydrogen bonds       : angle       5.52816 ( 1142)
  SS BOND              : bond        0.00170 (    3)
  SS BOND              : angle       0.40827 (    6)
  covalent geometry    : bond        0.00354 (10123)
  covalent geometry    : angle       0.54393 (13906)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 1.115 
Fit side-chains
REVERT: D  148 MET cc_start: 0.7830 (OUTLIER) cc_final: 0.6190 (mmt)
REVERT: A   59 THR cc_start: 0.8021 (OUTLIER) cc_final: 0.7774 (p)
REVERT: A  196 THR cc_start: 0.7915 (m) cc_final: 0.7587 (p)
REVERT: A  239 TYR cc_start: 0.9003 (m-80) cc_final: 0.8639 (m-80)
REVERT: C  115 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7373 (mt-10)
REVERT: B  198 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7454 (mp0)
  outliers start: 18
  outliers final: 12
  residues processed: 105
  average time/residue: 0.2721
  time to fit residues: 40.6495
Evaluate side-chains
  109 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 93
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   74 MET
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  134 THR
Chi-restraints excluded: chain D residue  148 MET
Chi-restraints excluded: chain D residue  259 ILE
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  179 ASN
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  206 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 111 optimal weight:    6.9990
   chunk 112 optimal weight:    3.9990
   chunk 105 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 107 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 42 optimal weight:    0.3980
   chunk 30 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 89 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:
** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 GLN
** B   8 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 = 0.3921 r_free = 0.3921 target = 0.139180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.104289 restraints weight = 14904.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.109381 restraints weight = 9221.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.109856 restraints weight = 5376.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3515
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.3996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  10126  Z= 0.203
  Angle     :  0.590  11.221  13912  Z= 0.313
  Chirality :  0.044   0.152   1600
  Planarity :  0.003   0.043   1590
  Dihedral  : 20.371  73.821   1871
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 12.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 17.65 %
    Favored  : 80.29 %
  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: -1.28 (0.25), residues: 1107
  helix:  0.19 (0.30), residues: 308
  sheet: -1.79 (0.25), residues: 332
  loop : -0.61 (0.29), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  28 
 HIS   0.004   0.001   HIS C  44 
 PHE   0.017   0.002   PHE D 207 
 TYR   0.017   0.002   TYR D  26 
 ARG   0.003   0.000   ARG A 146 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03349 (  416)
  hydrogen bonds       : angle       5.67980 ( 1142)
  SS BOND              : bond        0.00209 (    3)
  SS BOND              : angle       0.58387 (    6)
  covalent geometry    : bond        0.00468 (10123)
  covalent geometry    : angle       0.59030 (13906)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 1.255 
Fit side-chains
REVERT: D   86 ASP cc_start: 0.7606 (OUTLIER) cc_final: 0.6724 (m-30)
REVERT: D  148 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.6377 (mmt)
REVERT: A   59 THR cc_start: 0.8053 (OUTLIER) cc_final: 0.7820 (p)
REVERT: C  115 GLU cc_start: 0.7629 (OUTLIER) cc_final: 0.7370 (mt-10)
REVERT: C  244 MET cc_start: 0.8898 (tpp) cc_final: 0.8628 (ttm)
REVERT: B  198 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.7466 (mp0)
  outliers start: 20
  outliers final: 12
  residues processed: 102
  average time/residue: 0.3716
  time to fit residues: 56.0160
Evaluate side-chains
  107 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 1.867 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   74 MET
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue   86 ASP
Chi-restraints excluded: chain D residue  134 THR
Chi-restraints excluded: chain D residue  148 MET
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  116 MET
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  179 ASN
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  206 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 60 optimal weight:    0.4980
   chunk 42 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 96 optimal weight:    0.1980
   chunk 59 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** D 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B   8 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 = 0.3942 r_free = 0.3942 target = 0.140762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.105733 restraints weight = 14750.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.109638 restraints weight = 8206.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.111995 restraints weight = 5653.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.4035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10126  Z= 0.160
  Angle     :  0.567  10.229  13912  Z= 0.301
  Chirality :  0.043   0.168   1600
  Planarity :  0.003   0.044   1590
  Dihedral  : 20.384  75.753   1871
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 17.75 %
    Favored  : 80.29 %
  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: -1.20 (0.25), residues: 1107
  helix:  0.27 (0.30), residues: 308
  sheet: -1.69 (0.26), residues: 335
  loop : -0.61 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D 276 
 PHE   0.015   0.001   PHE D 207 
 TYR   0.015   0.001   TYR D  26 
 ARG   0.003   0.000   ARG B  64 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03180 (  416)
  hydrogen bonds       : angle       5.60958 ( 1142)
  SS BOND              : bond        0.00142 (    3)
  SS BOND              : angle       0.47224 (    6)
  covalent geometry    : bond        0.00369 (10123)
  covalent geometry    : angle       0.56738 (13906)

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.962 
Fit side-chains
REVERT: D  148 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.6280 (mmt)
REVERT: D  258 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7066 (pt0)
REVERT: A   59 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7850 (p)
REVERT: A  239 TYR cc_start: 0.9008 (m-80) cc_final: 0.8631 (m-80)
REVERT: C  115 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7283 (mt-10)
REVERT: B  198 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7499 (mp0)
  outliers start: 19
  outliers final: 12
  residues processed: 103
  average time/residue: 0.2193
  time to fit residues: 31.8656
Evaluate side-chains
  108 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   74 MET
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  134 THR
Chi-restraints excluded: chain D residue  148 MET
Chi-restraints excluded: chain D residue  258 GLU
Chi-restraints excluded: chain D residue  311 CYS
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain C residue  115 GLU
Chi-restraints excluded: chain C residue  121 LEU
Chi-restraints excluded: chain C residue  179 ASN
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  196 THR
Chi-restraints excluded: chain B residue  198 GLU
Chi-restraints excluded: chain B residue  206 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 83 optimal weight:    0.1980
   chunk 113 optimal weight:    5.9990
   chunk 90 optimal weight:    0.9990
   chunk 36 optimal weight:    0.1980
   chunk 22 optimal weight:    0.9980
   chunk 25 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0050
   chunk 53 optimal weight:    0.8980
   chunk 98 optimal weight:    3.9990
   overall best weight:    0.4194

-------------------------------------------------------------------------------
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 = 0.3964 r_free = 0.3964 target = 0.142525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.107958 restraints weight = 14744.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.112361 restraints weight = 8989.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.113035 restraints weight = 5651.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.4057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10126  Z= 0.128
  Angle     :  0.556  10.853  13912  Z= 0.294
  Chirality :  0.042   0.189   1600
  Planarity :  0.003   0.044   1590
  Dihedral  : 20.367  78.068   1871
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 18.06 %
    Favored  : 80.29 %
  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: -1.07 (0.25), residues: 1107
  helix:  0.35 (0.31), residues: 305
  sheet: -1.57 (0.26), residues: 340
  loop : -0.53 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP D 298 
 HIS   0.002   0.000   HIS C  44 
 PHE   0.014   0.001   PHE D 207 
 TYR   0.012   0.001   TYR D  26 
 ARG   0.003   0.000   ARG D  29 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03124 (  416)
  hydrogen bonds       : angle       5.46912 ( 1142)
  SS BOND              : bond        0.00250 (    3)
  SS BOND              : angle       0.56944 (    6)
  covalent geometry    : bond        0.00292 (10123)
  covalent geometry    : angle       0.55551 (13906)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3389.37 seconds
wall clock time: 61 minutes 50.93 seconds (3710.93 seconds total)