Starting phenix.real_space_refine
on Wed Sep 17 17:19:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yjq_39346/09_2025/8yjq_39346.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yjq_39346/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yjq_39346/09_2025/8yjq_39346.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yjq_39346/09_2025/8yjq_39346.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yjq_39346/09_2025/8yjq_39346.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yjq_39346/09_2025/8yjq_39346.map"
  }
  resolution = 3.51
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 2.44, per 1000 atoms: 0.25
  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: 0.96
  Conformation dependent library (CDL) restraints added in 367.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 1.30
  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: 1.97

  Time building geometry restraints manager: 1.26 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:             4.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     12.040
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.970
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.010   0.001   ARG D 239 
 TYR   0.054   0.003   TYR A 249 
 PHE   0.052   0.003   PHE B 207 
 TRP   0.021   0.002   TRP A  28 
 HIS   0.002   0.001   HIS D 280 

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

*********************** 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  : 0.388 
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: 0.0949
  time to fit residues: 19.9515
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  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    0.4980
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
D 137 HIS
D 205 GLN
A 213 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.159779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.125981 restraints weight = 14003.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.130198 restraints weight = 7785.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.130994 restraints weight = 5581.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.131527 restraints weight = 4784.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.131918 restraints weight = 4512.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10126  Z= 0.182
  Angle     :  0.600   6.819  13912  Z= 0.330
  Chirality :  0.043   0.150   1600
  Planarity :  0.005   0.055   1590
  Dihedral  : 20.757  78.934   1871
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  :  8.26 %
    Favored  : 90.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.77 (0.22), residues: 1107
  helix: -2.29 (0.23), residues: 309
  sheet: -1.71 (0.27), residues: 314
  loop : -1.38 (0.25), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 339 
 TYR   0.016   0.002   TYR D  26 
 PHE   0.020   0.002   PHE D 207 
 TRP   0.007   0.001   TRP D 274 
 HIS   0.003   0.001   HIS C  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (10123)
  covalent geometry    : angle       0.60050 (13906)
  SS BOND              : bond        0.00328 (    3)
  SS BOND              : angle       0.40680 (    6)
  hydrogen bonds       : bond        0.04590 (  416)
  hydrogen bonds       : angle       6.75885 ( 1142)

*********************** 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: 13
    poor density    : 124
  time to evaluate  : 0.349 
Fit side-chains
REVERT: D   65 MET cc_start: 0.7222 (tmm) cc_final: 0.6992 (ptt)
REVERT: B   75 MET cc_start: 0.8826 (tpp) cc_final: 0.8009 (ttt)
  outliers start: 13
  outliers final: 7
  residues processed: 130
  average time/residue: 0.1013
  time to fit residues: 18.7219
Evaluate side-chains
  102 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
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 87 optimal weight:    0.6980
   chunk 78 optimal weight:    1.9990
   chunk 86 optimal weight:    0.5980
   chunk 64 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 89 optimal weight:    0.1980
   chunk 4 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0050
   chunk 21 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.4394

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

Flipped N/Q/H residues before XYZ refinement:
D  77 ASN
** A  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  38 GLN
C 108 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.160770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.127543 restraints weight = 13941.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.132783 restraints weight = 7562.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.133535 restraints weight = 5039.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.133763 restraints weight = 4313.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.133925 restraints weight = 4255.865|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10126  Z= 0.131
  Angle     :  0.533   5.895  13912  Z= 0.293
  Chirality :  0.042   0.141   1600
  Planarity :  0.004   0.046   1590
  Dihedral  : 20.562  79.230   1871
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 12.07 %
    Favored  : 86.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.06 (0.23), residues: 1107
  helix: -1.01 (0.28), residues: 307
  sheet: -1.71 (0.25), residues: 337
  loop : -1.09 (0.27), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 146 
 TYR   0.013   0.001   TYR D  26 
 PHE   0.018   0.001   PHE D 207 
 TRP   0.009   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (10123)
  covalent geometry    : angle       0.53263 (13906)
  SS BOND              : bond        0.00232 (    3)
  SS BOND              : angle       0.46922 (    6)
  hydrogen bonds       : bond        0.03601 (  416)
  hydrogen bonds       : angle       5.97291 ( 1142)

*********************** 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
  126 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.373 
Fit side-chains
REVERT: A  146 ARG cc_start: 0.7884 (ptp90) cc_final: 0.7613 (ptp-170)
REVERT: A  196 THR cc_start: 0.7667 (m) cc_final: 0.7451 (p)
REVERT: B   75 MET cc_start: 0.8817 (tpp) cc_final: 0.7992 (ttt)
REVERT: B  143 GLU cc_start: 0.7718 (tp30) cc_final: 0.7448 (tp30)
  outliers start: 13
  outliers final: 6
  residues processed: 118
  average time/residue: 0.1160
  time to fit residues: 18.7189
Evaluate side-chains
  105 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   82 VAL
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  179 ASN
Chi-restraints excluded: chain B residue  206 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 6 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   chunk 74 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 93 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
C 108 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.156796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.122301 restraints weight = 13951.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.126599 restraints weight = 7475.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.129350 restraints weight = 5018.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.131105 restraints weight = 3825.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.132194 restraints weight = 3186.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.3024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10126  Z= 0.175
  Angle     :  0.562   5.898  13912  Z= 0.304
  Chirality :  0.043   0.146   1600
  Planarity :  0.003   0.043   1590
  Dihedral  : 20.465  77.823   1871
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 14.14 %
    Favored  : 83.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.82 (0.24), residues: 1107
  helix: -0.51 (0.29), residues: 312
  sheet: -1.94 (0.25), residues: 335
  loop : -0.86 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D  29 
 TYR   0.019   0.001   TYR D  26 
 PHE   0.016   0.001   PHE D 207 
 TRP   0.006   0.001   TRP C  28 
 HIS   0.013   0.001   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 (10123)
  covalent geometry    : angle       0.56183 (13906)
  SS BOND              : bond        0.00197 (    3)
  SS BOND              : angle       0.77076 (    6)
  hydrogen bonds       : bond        0.03517 (  416)
  hydrogen bonds       : angle       5.80304 ( 1142)

*********************** 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
  126 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.296 
Fit side-chains
REVERT: D   86 ASP cc_start: 0.7683 (OUTLIER) cc_final: 0.6747 (m-30)
REVERT: D  148 MET cc_start: 0.7269 (OUTLIER) cc_final: 0.5484 (mmt)
REVERT: A  196 THR cc_start: 0.7845 (m) cc_final: 0.7623 (p)
REVERT: C  115 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7391 (mt-10)
REVERT: B   75 MET cc_start: 0.8830 (tpp) cc_final: 0.8134 (ttt)
  outliers start: 20
  outliers final: 8
  residues processed: 116
  average time/residue: 0.1141
  time to fit residues: 18.3235
Evaluate side-chains
  110 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
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  148 MET
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  115 GLU
Chi-restraints excluded: chain C residue  179 ASN
Chi-restraints excluded: chain B residue  159 VAL
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 8 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 27 optimal weight:    5.9990
   chunk 107 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 4 optimal weight:    0.5980
   chunk 58 optimal weight:    0.3980
   chunk 34 optimal weight:    2.9990
   chunk 24 optimal weight:    0.3980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
C  38 GLN
C 108 GLN
C 246 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.157651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.123000 restraints weight = 13945.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.127312 restraints weight = 7487.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.130089 restraints weight = 5010.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.131861 restraints weight = 3815.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.133004 restraints weight = 3171.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.3184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10126  Z= 0.140
  Angle     :  0.531   6.655  13912  Z= 0.290
  Chirality :  0.042   0.152   1600
  Planarity :  0.003   0.044   1590
  Dihedral  : 20.400  76.462   1871
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 15.58 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.54 (0.24), residues: 1107
  helix: -0.19 (0.29), residues: 314
  sheet: -1.77 (0.25), residues: 342
  loop : -0.75 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  64 
 TYR   0.015   0.001   TYR D  26 
 PHE   0.015   0.001   PHE D 207 
 TRP   0.005   0.001   TRP C  28 
 HIS   0.007   0.001   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (10123)
  covalent geometry    : angle       0.53059 (13906)
  SS BOND              : bond        0.00150 (    3)
  SS BOND              : angle       0.43123 (    6)
  hydrogen bonds       : bond        0.03201 (  416)
  hydrogen bonds       : angle       5.61274 ( 1142)

*********************** 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
  118 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 103
  time to evaluate  : 0.333 
Fit side-chains
REVERT: D   86 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.6627 (m-30)
REVERT: C  115 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7393 (mt-10)
  outliers start: 15
  outliers final: 8
  residues processed: 112
  average time/residue: 0.1035
  time to fit residues: 16.2856
Evaluate side-chains
  108 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
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  134 THR
Chi-restraints excluded: chain A residue   85 GLU
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  206 THR
Chi-restraints excluded: chain B residue  244 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0060
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 81 optimal weight:    0.2980
   chunk 0 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 8 optimal weight:    0.7980
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
C 108 GLN
C 125 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.160170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.126011 restraints weight = 14221.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.130358 restraints weight = 7653.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.133140 restraints weight = 5099.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.134898 restraints weight = 3878.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.135913 restraints weight = 3222.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.3420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10126  Z= 0.140
  Angle     :  0.528   6.649  13912  Z= 0.287
  Chirality :  0.042   0.146   1600
  Planarity :  0.003   0.044   1590
  Dihedral  : 20.310  75.059   1871
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 15.89 %
    Favored  : 81.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.27 (0.25), residues: 1107
  helix:  0.12 (0.30), residues: 310
  sheet: -1.47 (0.24), residues: 373
  loop : -0.71 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  64 
 TYR   0.014   0.001   TYR D  26 
 PHE   0.015   0.001   PHE D 207 
 TRP   0.006   0.001   TRP C  28 
 HIS   0.007   0.001   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 (10123)
  covalent geometry    : angle       0.52782 (13906)
  SS BOND              : bond        0.00150 (    3)
  SS BOND              : angle       0.41852 (    6)
  hydrogen bonds       : bond        0.03154 (  416)
  hydrogen bonds       : angle       5.46971 ( 1142)

*********************** 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
  125 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.388 
Fit side-chains
REVERT: D   86 ASP cc_start: 0.7626 (OUTLIER) cc_final: 0.6622 (m-30)
REVERT: D  148 MET cc_start: 0.7389 (OUTLIER) cc_final: 0.5676 (mmt)
REVERT: A   59 THR cc_start: 0.7818 (OUTLIER) cc_final: 0.7586 (p)
REVERT: C  115 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7368 (mt-10)
REVERT: B  198 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7384 (mp0)
  outliers start: 21
  outliers final: 8
  residues processed: 115
  average time/residue: 0.1078
  time to fit residues: 17.3043
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  : 0.325 
-------------------------------------------------------------------------------
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  134 THR
Chi-restraints excluded: chain D residue  148 MET
Chi-restraints excluded: chain D residue  255 SER
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  179 ASN
Chi-restraints excluded: chain B residue  159 VAL
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 82 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 26 optimal weight:    0.4980
   chunk 34 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 88 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 90 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
D 315 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.140538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.105774 restraints weight = 14670.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.109905 restraints weight = 8451.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.110802 restraints weight = 5551.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.110992 restraints weight = 5389.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.111247 restraints weight = 4900.442|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.3710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035  10126  Z= 0.197
  Angle     :  0.576   6.444  13912  Z= 0.309
  Chirality :  0.044   0.145   1600
  Planarity :  0.003   0.043   1590
  Dihedral  : 20.362  74.533   1871
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 16.10 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.30 (0.25), residues: 1107
  helix:  0.08 (0.30), residues: 310
  sheet: -1.54 (0.25), residues: 360
  loop : -0.70 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  64 
 TYR   0.017   0.002   TYR D  26 
 PHE   0.017   0.002   PHE D 207 
 TRP   0.005   0.001   TRP C  28 
 HIS   0.005   0.001   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00452 (10123)
  covalent geometry    : angle       0.57586 (13906)
  SS BOND              : bond        0.00180 (    3)
  SS BOND              : angle       0.58128 (    6)
  hydrogen bonds       : bond        0.03368 (  416)
  hydrogen bonds       : angle       5.65545 ( 1142)

*********************** 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
  121 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 0.379 
Fit side-chains
REVERT: D   86 ASP cc_start: 0.7619 (OUTLIER) cc_final: 0.6770 (m-30)
REVERT: D  148 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.6068 (mmt)
REVERT: A   59 THR cc_start: 0.7979 (OUTLIER) cc_final: 0.7741 (p)
REVERT: C  115 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7491 (mt-10)
REVERT: B  198 GLU cc_start: 0.8373 (OUTLIER) cc_final: 0.7411 (mp0)
  outliers start: 22
  outliers final: 12
  residues processed: 113
  average time/residue: 0.1104
  time to fit residues: 17.4911
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  : 0.356 
-------------------------------------------------------------------------------
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 D residue  255 SER
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  179 ASN
Chi-restraints excluded: chain B residue   22 LEU
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 60 optimal weight:    0.7980
   chunk 66 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 88 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 91 optimal weight:    0.5980
   chunk 102 optimal weight:    4.9990
   chunk 2 optimal weight:    0.6980
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C 108 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.141492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.106722 restraints weight = 14610.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.111894 restraints weight = 8532.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.112405 restraints weight = 5229.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.112615 restraints weight = 4928.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.112749 restraints weight = 4650.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.3776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10126  Z= 0.165
  Angle     :  0.562   6.879  13912  Z= 0.304
  Chirality :  0.043   0.145   1600
  Planarity :  0.003   0.043   1590
  Dihedral  : 20.361  74.257   1871
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 12.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 16.41 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.17 (0.25), residues: 1107
  helix:  0.35 (0.31), residues: 300
  sheet: -1.57 (0.24), residues: 369
  loop : -0.60 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  64 
 TYR   0.016   0.001   TYR D  26 
 PHE   0.016   0.001   PHE D 207 
 TRP   0.006   0.001   TRP C  28 
 HIS   0.006   0.001   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (10123)
  covalent geometry    : angle       0.56222 (13906)
  SS BOND              : bond        0.00156 (    3)
  SS BOND              : angle       0.38878 (    6)
  hydrogen bonds       : bond        0.03223 (  416)
  hydrogen bonds       : angle       5.58933 ( 1142)

*********************** 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
  118 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.305 
Fit side-chains
REVERT: D   86 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.6644 (m-30)
REVERT: D  148 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.6190 (mmt)
REVERT: A   59 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7747 (p)
REVERT: A  239 TYR cc_start: 0.9010 (m-80) cc_final: 0.8635 (m-80)
REVERT: C  115 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7402 (mt-10)
REVERT: B  198 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7390 (mp0)
  outliers start: 20
  outliers final: 11
  residues processed: 109
  average time/residue: 0.0995
  time to fit residues: 15.4552
Evaluate side-chains
  112 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 96
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
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 D residue  255 SER
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  179 ASN
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain B residue  167 VAL
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 112 optimal weight:    3.9990
   chunk 53 optimal weight:    0.3980
   chunk 74 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0870
   chunk 7 optimal weight:    0.8980
   chunk 104 optimal weight:    4.9990
   chunk 103 optimal weight:    3.9990
   chunk 3 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 63 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   overall best weight:    0.8160

-------------------------------------------------------------------------------
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 = 0.3941 r_free = 0.3941 target = 0.140730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.106371 restraints weight = 14625.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.109453 restraints weight = 11634.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.111039 restraints weight = 6655.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.111675 restraints weight = 5524.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.112092 restraints weight = 5339.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.3928

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10126  Z= 0.177
  Angle     :  0.573   6.884  13912  Z= 0.308
  Chirality :  0.043   0.145   1600
  Planarity :  0.003   0.044   1590
  Dihedral  : 20.352  75.801   1871
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 12.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 17.13 %
    Favored  : 80.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.15 (0.25), residues: 1107
  helix:  0.34 (0.31), residues: 299
  sheet: -1.56 (0.24), residues: 363
  loop : -0.58 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  64 
 TYR   0.016   0.002   TYR D  26 
 PHE   0.016   0.001   PHE D 207 
 TRP   0.005   0.001   TRP D 274 
 HIS   0.004   0.001   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 (10123)
  covalent geometry    : angle       0.57338 (13906)
  SS BOND              : bond        0.00152 (    3)
  SS BOND              : angle       0.50214 (    6)
  hydrogen bonds       : bond        0.03280 (  416)
  hydrogen bonds       : angle       5.61603 ( 1142)

*********************** 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
  119 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.380 
Fit side-chains
REVERT: D  148 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.6462 (mmt)
REVERT: A   59 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7790 (p)
REVERT: A  146 ARG cc_start: 0.7854 (ttm110) cc_final: 0.7318 (ttm110)
REVERT: A  150 ASP cc_start: 0.7483 (m-30) cc_final: 0.7261 (m-30)
REVERT: A  239 TYR cc_start: 0.9009 (m-80) cc_final: 0.8628 (m-80)
REVERT: C  115 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.7264 (mt-10)
REVERT: B    8 GLN cc_start: 0.7157 (pm20) cc_final: 0.6954 (pm20)
REVERT: B  198 GLU cc_start: 0.8386 (OUTLIER) cc_final: 0.7437 (mp0)
  outliers start: 20
  outliers final: 15
  residues processed: 110
  average time/residue: 0.1178
  time to fit residues: 18.1112
Evaluate side-chains
  116 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
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  255 SER
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  206 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
Chi-restraints excluded: chain B residue  244 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 102 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 22 optimal weight:    0.0670
   chunk 109 optimal weight:    0.9980
   chunk 107 optimal weight:    0.5980
   chunk 77 optimal weight:    3.9990
   chunk 55 optimal weight:    0.4980
   chunk 103 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9980
   overall best weight:    0.6318

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

Flipped N/Q/H residues before XYZ refinement:
C 108 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.141961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.107755 restraints weight = 14676.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.111282 restraints weight = 11051.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.112658 restraints weight = 6333.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.113200 restraints weight = 5423.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.113484 restraints weight = 5235.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.3571
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.3961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10126  Z= 0.151
  Angle     :  0.557   7.114  13912  Z= 0.300
  Chirality :  0.043   0.165   1600
  Planarity :  0.003   0.044   1590
  Dihedral  : 20.362  76.663   1871
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 12.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 17.44 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.07 (0.25), residues: 1107
  helix:  0.41 (0.31), residues: 299
  sheet: -1.50 (0.25), residues: 363
  loop : -0.55 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  64 
 TYR   0.014   0.001   TYR D  26 
 PHE   0.015   0.001   PHE D 207 
 TRP   0.006   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (10123)
  covalent geometry    : angle       0.55717 (13906)
  SS BOND              : bond        0.00135 (    3)
  SS BOND              : angle       0.41726 (    6)
  hydrogen bonds       : bond        0.03189 (  416)
  hydrogen bonds       : angle       5.52593 ( 1142)

********************** 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
  121 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 0.426 
Fit side-chains
REVERT: D   86 ASP cc_start: 0.7607 (OUTLIER) cc_final: 0.6682 (m-30)
REVERT: D  148 MET cc_start: 0.8004 (OUTLIER) cc_final: 0.6363 (mmt)
REVERT: A   59 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7846 (p)
REVERT: A  146 ARG cc_start: 0.7854 (ttm110) cc_final: 0.7301 (ttm110)
REVERT: A  150 ASP cc_start: 0.7462 (m-30) cc_final: 0.7247 (m-30)
REVERT: A  239 TYR cc_start: 0.8992 (m-80) cc_final: 0.8622 (m-80)
REVERT: C  115 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7175 (mt-10)
REVERT: B  198 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7441 (mp0)
  outliers start: 20
  outliers final: 13
  residues processed: 111
  average time/residue: 0.1113
  time to fit residues: 17.3233
Evaluate side-chains
  119 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
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 D residue  255 SER
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  206 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  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 10 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 41 optimal weight:    1.9990
   chunk 102 optimal weight:    0.9980
   chunk 42 optimal weight:    0.6980
   chunk 1 optimal weight:    0.0470
   chunk 93 optimal weight:    3.9990
   chunk 111 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.7280

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

Flipped N/Q/H residues before XYZ refinement:
C  38 GLN
C 108 GLN
** B   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.141467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.107407 restraints weight = 14749.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.110737 restraints weight = 11174.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.112155 restraints weight = 6409.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.112739 restraints weight = 5436.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.113020 restraints weight = 5256.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3566
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.4026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10126  Z= 0.163
  Angle     :  0.567   7.073  13912  Z= 0.304
  Chirality :  0.043   0.185   1600
  Planarity :  0.003   0.044   1590
  Dihedral  : 20.371  77.115   1871
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.65 %
    Favored  : 80.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.25), residues: 1107
  helix:  0.30 (0.31), residues: 305
  sheet: -1.50 (0.25), residues: 363
  loop : -0.59 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  64 
 TYR   0.014   0.001   TYR D  26 
 PHE   0.015   0.001   PHE D 207 
 TRP   0.005   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 (10123)
  covalent geometry    : angle       0.56710 (13906)
  SS BOND              : bond        0.00144 (    3)
  SS BOND              : angle       0.49748 (    6)
  hydrogen bonds       : bond        0.03241 (  416)
  hydrogen bonds       : angle       5.54355 ( 1142)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1661.65 seconds
wall clock time: 29 minutes 33.12 seconds (1773.12 seconds total)