Starting phenix.real_space_refine
on Wed Mar  4 03:22:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7kzx_23092/03_2026/7kzx_23092.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7kzx_23092/03_2026/7kzx_23092.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7kzx_23092/03_2026/7kzx_23092.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7kzx_23092/03_2026/7kzx_23092.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7kzx_23092/03_2026/7kzx_23092.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7kzx_23092/03_2026/7kzx_23092.cif"
  }
  resolution = 4.0
  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=   0.001 sd=   0.044
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    6658      2.51       5
     N    1754      2.21       5
     O    1992      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 75 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10432
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2163
          Classifications: {'peptide': 281}
          Link IDs: {'PTRANS': 6, 'TRANS': 274}
    Chain: "B"
      Number of atoms: 2163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2163
          Classifications: {'peptide': 281}
          Link IDs: {'PTRANS': 6, 'TRANS': 274}
    Chain: "C"
      Number of atoms: 1460
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1460
          Classifications: {'peptide': 190}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 179}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1589
          Classifications: {'peptide': 209}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 1468
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 191, 1468
          Classifications: {'peptide': 191}
          Link IDs: {'PCIS': 2, 'PTRANS': 8, 'TRANS': 180}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1589
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 209, 1589
          Classifications: {'peptide': 209}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 196}
          Chain breaks: 2
  Time building chain proxies: 2.55, per 1000 atoms: 0.24
  Number of scatterers: 10432
  At special positions: 0
  Unit cell: (75.555, 151.11, 150.075, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      28     16.00
     O    1992      8.00
     N    1754      7.00
     C    6658      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  24 " - pdb=" SG  CYS C  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 136 " - pdb=" SG  CYS C 196 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  24 " - pdb=" SG  CYS E  89 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 136 " - pdb=" SG  CYS E 196 " 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: 0.87
  Conformation dependent library (CDL) restraints added in 477.9 milliseconds
  

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2550

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 24 sheets defined
      32.0% alpha, 27.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 35
      removed outlier: 3.579A  pdb=" N   VAL A  19 " --> pdb=" O   SER A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 38 through 64
    Processing helix  chain 'A' and resid 80 through 107
      removed outlier: 3.788A  pdb=" N   ALA A  84 " --> pdb=" O   ALA A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 138
      removed outlier: 3.557A  pdb=" N   LYS A 138 " --> pdb=" O   VAL A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 149 through 175
      removed outlier: 3.826A  pdb=" N   SER A 153 " --> pdb=" O   VAL A 149 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   LEU A 160 " --> pdb=" O   TYR A 156 " (cutoff:3.500A)
      removed outlier: 4.814A  pdb=" N   PHE A 161 " --> pdb=" O   LYS A 157 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   LEU A 172 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   TYR A 175 " --> pdb=" O   VAL A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 177 through 208
      removed outlier: 4.183A  pdb=" N   GLY A 182 " --> pdb=" O   TRP A 178 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   LEU A 183 " --> pdb=" O   TRP A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 225
    Processing helix  chain 'A' and resid 258 through 277
    Processing helix  chain 'B' and resid 13 through 35
      removed outlier: 3.723A  pdb=" N   TYR B  35 " --> pdb=" O   LEU B  31 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 39 through 64
      removed outlier: 3.846A  pdb=" N   ALA B  43 " --> pdb=" O   ALA B  39 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 109
      removed outlier: 3.686A  pdb=" N   ALA B  84 " --> pdb=" O   ALA B  80 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ALA B  85 " --> pdb=" O   GLU B  81 " (cutoff:3.500A)
      removed outlier: 4.705A  pdb=" N   GLY B 104 " --> pdb=" O   LEU B 100 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   ASN B 109 " --> pdb=" O   GLU B 105 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 138
      removed outlier: 3.704A  pdb=" N   LYS B 138 " --> pdb=" O   VAL B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 175
      removed outlier: 4.872A  pdb=" N   LEU B 160 " --> pdb=" O   TYR B 156 " (cutoff:3.500A)
      removed outlier: 4.745A  pdb=" N   PHE B 161 " --> pdb=" O   LYS B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 208
      removed outlier: 4.357A  pdb=" N   ASP B 181 " --> pdb=" O   TRP B 177 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   GLY B 182 " --> pdb=" O   TRP B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 226
    Processing helix  chain 'B' and resid 258 through 277
    Processing helix  chain 'C' and resid 80 through 84
    Processing helix  chain 'C' and resid 123 through 128
    Processing helix  chain 'C' and resid 185 through 189
    Processing helix  chain 'D' and resid 65 through 68
    Processing helix  chain 'D' and resid 90 through 94
      removed outlier: 3.709A  pdb=" N   THR D  94 " --> pdb=" O   ALA D  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 218 through 221
    Processing helix  chain 'E' and resid 80 through 84
    Processing helix  chain 'E' and resid 123 through 129
    Processing helix  chain 'E' and resid 186 through 190
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 211
      removed outlier: 4.511A  pdb=" N   ASP A 235 " --> pdb=" O   HIS A 250 " (cutoff:3.500A)
      removed outlier: 5.865A  pdb=" N   VAL A 245 " --> pdb=" O   GLU A 281 " (cutoff:3.500A)
      removed outlier: 7.558A  pdb=" N   ILE A 283 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
      removed outlier: 6.197A  pdb=" N   ILE A 247 " --> pdb=" O   ILE A 283 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 253 through 254
      removed outlier: 6.543A  pdb=" N   LEU A 253 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 232 through 233
    Processing sheet with id=AA4, first strand: chain 'B' and resid 232 through 233
      removed outlier: 6.201A  pdb=" N   VAL B 245 " --> pdb=" O   GLU B 281 " (cutoff:3.500A)
      removed outlier: 7.579A  pdb=" N   ILE B 283 " --> pdb=" O   VAL B 245 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   ILE B 247 " --> pdb=" O   ILE B 283 " (cutoff:3.500A)
      removed outlier: 7.538A  pdb=" N   HIS B 285 " --> pdb=" O   ILE B 247 " (cutoff:3.500A)
      removed outlier: 6.043A  pdb=" N   PHE B 249 " --> pdb=" O   HIS B 285 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 6 through 8
    Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 14
      removed outlier: 6.409A  pdb=" N   LEU C  12 " --> pdb=" O   GLU C 107 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 54 through 55
      removed outlier: 5.270A  pdb=" N   LEU C  47 " --> pdb=" O   GLN C  38 " (cutoff:3.500A)
      removed outlier: 5.561A  pdb=" N   GLN C  38 " --> pdb=" O   LEU C  47 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 118 through 120
      removed outlier: 3.949A  pdb=" N   ALA C 132 " --> pdb=" O   LEU C 183 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   LEU C 183 " --> pdb=" O   ALA C 132 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   VAL C 134 " --> pdb=" O   LEU C 181 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASN C 140 " --> pdb=" O   TYR C 175 " (cutoff:3.500A)
      removed outlier: 6.131A  pdb=" N   TYR C 175 " --> pdb=" O   ASN C 140 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 8 through 9
    Processing sheet with id=AB1, first strand: chain 'D' and resid 60 through 63
      removed outlier: 5.200A  pdb=" N   TRP D  50 " --> pdb=" O   ARG D  41 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   ARG D  41 " --> pdb=" O   TRP D  50 " (cutoff:3.500A)
      removed outlier: 4.594A  pdb=" N   TYR D 120 " --> pdb=" O   ARG D 101 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'D' and resid 60 through 63
      removed outlier: 5.200A  pdb=" N   TRP D  50 " --> pdb=" O   ARG D  41 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   ARG D  41 " --> pdb=" O   TRP D  50 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 106 through 108
      removed outlier: 3.518A  pdb=" N   SER D 108 " --> pdb=" O   HIS D 112 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   HIS D 112 " --> pdb=" O   SER D 108 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 137 through 140
      removed outlier: 3.616A  pdb=" N   ASP D 161 " --> pdb=" O   TYR D 193 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   TYR D 193 " --> pdb=" O   ASP D 161 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 137 through 140
      removed outlier: 3.616A  pdb=" N   ASP D 161 " --> pdb=" O   TYR D 193 " (cutoff:3.500A)
      removed outlier: 6.933A  pdb=" N   TYR D 193 " --> pdb=" O   ASP D 161 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 213 through 217
    Processing sheet with id=AB7, first strand: chain 'E' and resid 5 through 8
      removed outlier: 3.538A  pdb=" N   VAL E  20 " --> pdb=" O   ILE E  76 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'E' and resid 12 through 14
      removed outlier: 6.910A  pdb=" N   VAL E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.857A  pdb=" N   TYR E  50 " --> pdb=" O   VAL E  34 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   TRP E  36 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   SER E  54 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'E' and resid 118 through 120
      removed outlier: 5.844A  pdb=" N   TYR E 175 " --> pdb=" O   ASN E 140 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'F' and resid 7 through 10
    Processing sheet with id=AC2, first strand: chain 'F' and resid 13 through 14
      removed outlier: 6.898A  pdb=" N   ILE F  37 " --> pdb=" O   SER F  53 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   SER F  53 " --> pdb=" O   ILE F  37 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   TRP F  39 " --> pdb=" O   VAL F  51 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'F' and resid 106 through 107
    Processing sheet with id=AC4, first strand: chain 'F' and resid 137 through 139
      removed outlier: 3.512A  pdb=" N   ASP F 161 " --> pdb=" O   TYR F 193 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   TYR F 193 " --> pdb=" O   ASP F 161 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'F' and resid 137 through 139
      removed outlier: 3.512A  pdb=" N   ASP F 161 " --> pdb=" O   TYR F 193 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   TYR F 193 " --> pdb=" O   ASP F 161 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   LEU F 192 " --> pdb=" O   GLN F 188 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'F' and resid 168 through 171
      removed outlier: 3.555A  pdb=" N   SER F 170 " --> pdb=" O   ASN F 214 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   ASN F 214 " --> pdb=" O   SER F 170 " (cutoff:3.500A)

    570 hydrogen bonds defined for protein.
    1539 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.27

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3322
        1.34 -     1.46: 2067
        1.46 -     1.57: 5233
        1.57 -     1.69: 0
        1.69 -     1.81: 38
  Bond restraints: 10660
  Sorted by residual:
  bond pdb=" C   LYS E  43 "
       pdb=" N   ALA E  44 "
    ideal  model  delta    sigma   weight residual
    1.331  1.287  0.045 1.63e-02 3.76e+03 7.46e+00
  bond pdb=" CA  ARG C 144 "
       pdb=" C   ARG C 144 "
    ideal  model  delta    sigma   weight residual
    1.524  1.471  0.053 2.25e-02 1.98e+03 5.46e+00
  bond pdb=" C   LYS F 218 "
       pdb=" N   PRO F 219 "
    ideal  model  delta    sigma   weight residual
    1.336  1.358 -0.022 1.08e-02 8.57e+03 4.16e+00
  bond pdb=" C   GLN C  39 "
       pdb=" N   LYS C  40 "
    ideal  model  delta    sigma   weight residual
    1.330  1.305  0.025 1.47e-02 4.63e+03 2.98e+00
  bond pdb=" CB  TRP E  93 "
       pdb=" CG  TRP E  93 "
    ideal  model  delta    sigma   weight residual
    1.498  1.445  0.053 3.10e-02 1.04e+03 2.89e+00
  ... (remaining 10655 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 13391
        1.38 -     2.75: 919
        2.75 -     4.13: 157
        4.13 -     5.50: 28
        5.50 -     6.88: 16
  Bond angle restraints: 14511
  Sorted by residual:
  angle pdb=" N   ILE A  66 "
        pdb=" CA  ILE A  66 "
        pdb=" C   ILE A  66 "
      ideal   model   delta    sigma   weight residual
     113.00  107.36    5.64 1.30e+00 5.92e-01 1.88e+01
  angle pdb=" C   VAL B 149 "
        pdb=" N   GLU B 150 "
        pdb=" CA  GLU B 150 "
      ideal   model   delta    sigma   weight residual
     121.54  127.41   -5.87 1.91e+00 2.74e-01 9.45e+00
  angle pdb=" C   VAL F  51 "
        pdb=" N   ALA F  52 "
        pdb=" CA  ALA F  52 "
      ideal   model   delta    sigma   weight residual
     121.63  115.87    5.76 1.92e+00 2.71e-01 9.01e+00
  angle pdb=" CA  ARG F 111 "
        pdb=" CB  ARG F 111 "
        pdb=" CG  ARG F 111 "
      ideal   model   delta    sigma   weight residual
     114.10  119.82   -5.72 2.00e+00 2.50e-01 8.18e+00
  angle pdb=" N   GLY F 179 "
        pdb=" CA  GLY F 179 "
        pdb=" C   GLY F 179 "
      ideal   model   delta    sigma   weight residual
     113.18  106.45    6.73 2.37e+00 1.78e-01 8.06e+00
  ... (remaining 14506 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.18: 5765
       18.18 -    36.35: 412
       36.35 -    54.53: 79
       54.53 -    72.71: 45
       72.71 -    90.88: 20
  Dihedral angle restraints: 6321
    sinusoidal: 2362
      harmonic: 3959
  Sorted by residual:
  dihedral pdb=" CA  SER C  94 "
           pdb=" C   SER C  94 "
           pdb=" N   TRP C  95 "
           pdb=" CA  TRP C  95 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.91  -26.09     0      5.00e+00 4.00e-02 2.72e+01
  dihedral pdb=" CA  CYS C 196 "
           pdb=" C   CYS C 196 "
           pdb=" N   GLU C 197 "
           pdb=" CA  GLU C 197 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -154.40  -25.60     0      5.00e+00 4.00e-02 2.62e+01
  dihedral pdb=" CA  PRO B 228 "
           pdb=" C   PRO B 228 "
           pdb=" N   ARG B 229 "
           pdb=" CA  ARG B 229 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.35   24.65     0      5.00e+00 4.00e-02 2.43e+01
  ... (remaining 6318 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 1257
       0.047 -    0.094: 341
       0.094 -    0.141: 82
       0.141 -    0.188: 8
       0.188 -    0.235: 1
  Chirality restraints: 1689
  Sorted by residual:
  chirality pdb=" CB  ILE B 284 "
            pdb=" CA  ILE B 284 "
            pdb=" CG1 ILE B 284 "
            pdb=" CG2 ILE B 284 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CA  ARG D 111 "
            pdb=" N   ARG D 111 "
            pdb=" C   ARG D 111 "
            pdb=" CB  ARG D 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.71e-01
  chirality pdb=" CB  VAL A 230 "
            pdb=" CA  VAL A 230 "
            pdb=" CG1 VAL A 230 "
            pdb=" CG2 VAL A 230 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.45e-01
  ... (remaining 1686 not shown)

  Planarity restraints: 1826
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU F 165 "   -0.053 5.00e-02 4.00e+02   8.02e-02 1.03e+01
        pdb=" N   PRO F 166 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO F 166 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO F 166 "   -0.040 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP D  76 "    0.011 2.00e-02 2.50e+03   2.17e-02 4.71e+00
        pdb=" C   ASP D  76 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   ASP D  76 "    0.014 2.00e-02 2.50e+03
        pdb=" N   THR D  77 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B 195 "   -0.010 2.00e-02 2.50e+03   2.06e-02 4.24e+00
        pdb=" C   GLN B 195 "    0.036 2.00e-02 2.50e+03
        pdb=" O   GLN B 195 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ALA B 196 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1823 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 141
        2.61 -     3.18: 10116
        3.18 -     3.75: 16628
        3.75 -     4.33: 22413
        4.33 -     4.90: 35955
  Nonbonded interactions: 85253
  Sorted by model distance:
  nonbonded pdb=" O   SER F  34 "
            pdb=" OH  TYR F 104 "
     model   vdw
     2.031 3.040
  nonbonded pdb=" OG  SER C  94 "
            pdb=" O   LEU C  97 "
     model   vdw
     2.113 3.040
  nonbonded pdb=" OH  TYR F 162 "
            pdb=" OE1 GLU F 165 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" O   ASP C  83 "
            pdb=" OH  TYR C  87 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" O   LEU B 212 "
            pdb=" NH1 ARG B 217 "
     model   vdw
     2.165 3.120
  ... (remaining 85248 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'
}
ncs_group {
  reference = (chain 'C' and resid 2 through 202)
  selection = (chain 'E' and (resid 2 through 149 or resid 162 through 202))
}
ncs_group {
  reference = chain 'D'
  selection = chain 'F'
}

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:             3.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     9.750
  Find NCS groups from input model:        0.140
  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:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8024
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      :  0.006   0.053  10664  Z= 0.299
  Angle     :  0.807   6.881  14519  Z= 0.457
  Chirality :  0.045   0.235   1689
  Planarity :  0.006   0.080   1826
  Dihedral  : 15.745  90.882   3759
  Min Nonbonded Distance : 2.031

Molprobity Statistics.
  All-atom Clashscore : 19.32
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  9.27 %
    Favored  : 90.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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 are not related in a simple way.
  whole: -2.29 (0.22), residues: 1337
  helix: -0.18 (0.25), residues: 398
  sheet: -1.17 (0.27), residues: 338
  loop : -2.68 (0.23), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 229 
 TYR   0.028   0.002   TYR F 104 
 PHE   0.015   0.002   PHE C  72 
 TRP   0.030   0.003   TRP B 179 
 HIS   0.008   0.002   HIS B 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00615 (10660)
  covalent geometry    : angle       0.80710 (14511)
  SS BOND              : bond        0.00311 (    4)
  SS BOND              : angle       1.17005 (    8)
  hydrogen bonds       : bond        0.15515 (  534)
  hydrogen bonds       : angle       7.24276 ( 1539)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 MET cc_start: 0.8504 (ttm) cc_final: 0.8280 (ttt)
REVERT: A   99 LEU cc_start: 0.9405 (mt) cc_final: 0.9166 (mt)
REVERT: B  190 CYS cc_start: 0.9491 (t) cc_final: 0.9168 (m)
REVERT: D   50 TRP cc_start: 0.8398 (t60) cc_final: 0.7994 (t60)
REVERT: D   93 ASP cc_start: 0.7952 (m-30) cc_final: 0.7429 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1151
  time to fit residues: 18.5688
Evaluate side-chains
  56 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0170
   chunk 10 optimal weight:    7.9990
   chunk 66 optimal weight:    0.7980
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    8.9990
   overall best weight:    1.1622

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

Flipped N/Q/H residues before XYZ refinement:
** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 248 GLN
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 168 GLN
D 188 GLN
** E  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 188 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.078593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.058727 restraints weight = 52184.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.060429 restraints weight = 28927.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.061524 restraints weight = 19832.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.062210 restraints weight = 15574.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.062538 restraints weight = 13330.001|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.1649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10664  Z= 0.170
  Angle     :  0.691  10.357  14519  Z= 0.364
  Chirality :  0.044   0.179   1689
  Planarity :  0.005   0.057   1826
  Dihedral  :  5.810  37.994   1461
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 14.22
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.55 %
    Favored  : 92.37 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  : 11.22 %
    Favored  : 87.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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 are not related in a simple way.
  whole: -1.66 (0.22), residues: 1337
  helix:  0.48 (0.26), residues: 401
  sheet: -0.82 (0.28), residues: 316
  loop : -2.37 (0.23), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C  19 
 TYR   0.024   0.002   TYR F 104 
 PHE   0.018   0.001   PHE F 130 
 TRP   0.021   0.002   TRP E  93 
 HIS   0.007   0.001   HIS B  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (10660)
  covalent geometry    : angle       0.68909 (14511)
  SS BOND              : bond        0.00318 (    4)
  SS BOND              : angle       2.45392 (    8)
  hydrogen bonds       : bond        0.04842 (  534)
  hydrogen bonds       : angle       5.63115 ( 1539)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   41 MET cc_start: 0.8882 (ttm) cc_final: 0.8586 (ttt)
REVERT: A   93 MET cc_start: 0.8781 (mmm) cc_final: 0.8538 (tpp)
REVERT: A   99 LEU cc_start: 0.9537 (mt) cc_final: 0.9296 (mt)
REVERT: B   93 MET cc_start: 0.9224 (mmm) cc_final: 0.8995 (mmm)
REVERT: B  190 CYS cc_start: 0.9266 (t) cc_final: 0.8953 (m)
REVERT: C    5 MET cc_start: 0.8185 (mmm) cc_final: 0.7556 (mmm)
REVERT: C  167 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7929 (tp30)
REVERT: D   50 TRP cc_start: 0.8405 (t60) cc_final: 0.8003 (t60)
REVERT: D   92 GLU cc_start: 0.8071 (tp30) cc_final: 0.7713 (tp30)
REVERT: D  193 TYR cc_start: 0.7458 (m-80) cc_final: 0.6942 (m-10)
REVERT: E  102 GLN cc_start: 0.7798 (mm110) cc_final: 0.7481 (tp40)
  outliers start: 10
  outliers final: 7
  residues processed: 97
  average time/residue: 0.0890
  time to fit residues: 12.7810
Evaluate side-chains
  62 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   28 ILE
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain C residue  180 THR
Chi-restraints excluded: chain D residue  123 GLN
Chi-restraints excluded: chain D residue  224 VAL
Chi-restraints excluded: chain F residue  141 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 106 optimal weight:   10.0000
   chunk 112 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0070
   chunk 77 optimal weight:    5.9990
   chunk 27 optimal weight:    0.8980
   chunk 1 optimal weight:    6.9990
   chunk 126 optimal weight:    0.3980
   chunk 14 optimal weight:    5.9990
   chunk 4 optimal weight:    9.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    0.6200

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

Flipped N/Q/H residues before XYZ refinement:
** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.079707 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.060985 restraints weight = 52333.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.061960 restraints weight = 29163.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.062824 restraints weight = 20404.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.062819 restraints weight = 19497.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.062804 restraints weight = 16347.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10664  Z= 0.138
  Angle     :  0.638   9.359  14519  Z= 0.333
  Chirality :  0.043   0.171   1689
  Planarity :  0.005   0.051   1826
  Dihedral  :  5.346  28.083   1461
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.13 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 14.02 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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 are not related in a simple way.
  whole: -1.36 (0.22), residues: 1337
  helix:  0.75 (0.25), residues: 404
  sheet: -0.79 (0.27), residues: 334
  loop : -2.15 (0.24), residues: 599

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F  90 
 TYR   0.017   0.001   TYR B 156 
 PHE   0.018   0.001   PHE E 120 
 TRP   0.014   0.001   TRP E  93 
 HIS   0.005   0.001   HIS B  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (10660)
  covalent geometry    : angle       0.63549 (14511)
  SS BOND              : bond        0.00253 (    4)
  SS BOND              : angle       2.40442 (    8)
  hydrogen bonds       : bond        0.04281 (  534)
  hydrogen bonds       : angle       5.16496 ( 1539)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 76
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 MET cc_start: 0.8743 (mmm) cc_final: 0.8436 (tpp)
REVERT: B   45 LEU cc_start: 0.9042 (tt) cc_final: 0.8781 (tp)
REVERT: B  190 CYS cc_start: 0.9268 (t) cc_final: 0.8935 (m)
REVERT: C    5 MET cc_start: 0.8092 (mmm) cc_final: 0.7673 (mmm)
REVERT: C  167 GLU cc_start: 0.8259 (mt-10) cc_final: 0.7974 (tp30)
REVERT: D   50 TRP cc_start: 0.8313 (t60) cc_final: 0.8030 (t60)
REVERT: D  226 LYS cc_start: 0.8181 (tptt) cc_final: 0.7819 (mtmm)
REVERT: E  102 GLN cc_start: 0.7601 (mm110) cc_final: 0.7352 (tp40)
  outliers start: 25
  outliers final: 8
  residues processed: 97
  average time/residue: 0.0891
  time to fit residues: 12.8616
Evaluate side-chains
  65 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain C residue  180 THR
Chi-restraints excluded: chain D residue   87 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 71 optimal weight:    7.9990
   chunk 61 optimal weight:    5.9990
   chunk 97 optimal weight:    0.3980
   chunk 48 optimal weight:    0.7980
   chunk 133 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0570
   chunk 77 optimal weight:    4.9990
   chunk 40 optimal weight:    9.9990
   chunk 117 optimal weight:    0.2980
   chunk 63 optimal weight:    1.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.7100

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

Flipped N/Q/H residues before XYZ refinement:
** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.079830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.060310 restraints weight = 53176.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.062013 restraints weight = 29244.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.063104 restraints weight = 19925.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.063765 restraints weight = 15539.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.064091 restraints weight = 13278.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10664  Z= 0.132
  Angle     :  0.641  11.997  14519  Z= 0.329
  Chirality :  0.043   0.169   1689
  Planarity :  0.004   0.054   1826
  Dihedral  :  5.146  34.313   1461
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.53 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 14.55 %
    Favored  : 83.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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 are not related in a simple way.
  whole: -1.04 (0.23), residues: 1337
  helix:  1.03 (0.26), residues: 400
  sheet: -0.65 (0.27), residues: 336
  loop : -1.92 (0.25), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  90 
 TYR   0.019   0.001   TYR C 175 
 PHE   0.016   0.001   PHE B 101 
 TRP   0.038   0.001   TRP A  33 
 HIS   0.003   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (10660)
  covalent geometry    : angle       0.63934 (14511)
  SS BOND              : bond        0.00238 (    4)
  SS BOND              : angle       2.00571 (    8)
  hydrogen bonds       : bond        0.04118 (  534)
  hydrogen bonds       : angle       4.93149 ( 1539)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 72
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 MET cc_start: 0.8658 (mmm) cc_final: 0.8366 (tpp)
REVERT: B   45 LEU cc_start: 0.9013 (tt) cc_final: 0.8721 (tp)
REVERT: B   93 MET cc_start: 0.9013 (mmm) cc_final: 0.8768 (mmm)
REVERT: B  101 PHE cc_start: 0.7743 (t80) cc_final: 0.6953 (t80)
REVERT: C    5 MET cc_start: 0.8139 (mmm) cc_final: 0.7741 (mmm)
REVERT: C  167 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7944 (tp30)
REVERT: D   50 TRP cc_start: 0.8345 (t60) cc_final: 0.8073 (t60)
  outliers start: 24
  outliers final: 16
  residues processed: 91
  average time/residue: 0.0860
  time to fit residues: 11.6962
Evaluate side-chains
  74 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 58
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  156 TYR
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain C residue  180 THR
Chi-restraints excluded: chain D residue   87 ASN
Chi-restraints excluded: chain D residue   99 CYS
Chi-restraints excluded: chain D residue  224 VAL
Chi-restraints excluded: chain E residue  165 VAL
Chi-restraints excluded: chain F residue    8 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 5 optimal weight:   20.0000
   chunk 0 optimal weight:   30.0000
   chunk 13 optimal weight:    3.9990
   chunk 117 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 29 optimal weight:    8.9990
   chunk 27 optimal weight:    6.9990
   chunk 23 optimal weight:    3.9990
   chunk 120 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   chunk 41 optimal weight:    0.0770
   overall best weight:    2.2144

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

Flipped N/Q/H residues before XYZ refinement:
** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  91 GLN
** F  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.077845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.060982 restraints weight = 52837.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.061214 restraints weight = 36508.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.061628 restraints weight = 32762.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.061923 restraints weight = 24783.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.062149 restraints weight = 22657.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.2774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  10664  Z= 0.221
  Angle     :  0.668  12.778  14519  Z= 0.347
  Chirality :  0.043   0.180   1689
  Planarity :  0.005   0.056   1826
  Dihedral  :  5.204  31.351   1461
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 14.61
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.18 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 15.25 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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 are not related in a simple way.
  whole: -0.93 (0.23), residues: 1337
  helix:  1.08 (0.26), residues: 400
  sheet: -0.51 (0.28), residues: 318
  loop : -1.85 (0.25), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  22 
 TYR   0.022   0.002   TYR C 175 
 PHE   0.019   0.002   PHE E 120 
 TRP   0.049   0.002   TRP A  33 
 HIS   0.005   0.001   HIS C 200 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 (10660)
  covalent geometry    : angle       0.66600 (14511)
  SS BOND              : bond        0.00175 (    4)
  SS BOND              : angle       2.30424 (    8)
  hydrogen bonds       : bond        0.04210 (  534)
  hydrogen bonds       : angle       4.95229 ( 1539)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 57
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 MET cc_start: 0.8767 (mmm) cc_final: 0.8493 (tpp)
REVERT: C  167 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7990 (tp30)
REVERT: D   50 TRP cc_start: 0.8421 (t60) cc_final: 0.7996 (t60)
REVERT: D  171 TRP cc_start: 0.7557 (OUTLIER) cc_final: 0.7335 (m100)
REVERT: E    5 MET cc_start: 0.8566 (mmt) cc_final: 0.8263 (mmt)
  outliers start: 37
  outliers final: 23
  residues processed: 90
  average time/residue: 0.0762
  time to fit residues: 10.6871
Evaluate side-chains
  77 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 53
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  215 ASP
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  156 TYR
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain B residue  247 ILE
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain C residue  180 THR
Chi-restraints excluded: chain D residue   87 ASN
Chi-restraints excluded: chain D residue   99 CYS
Chi-restraints excluded: chain D residue  123 GLN
Chi-restraints excluded: chain D residue  171 TRP
Chi-restraints excluded: chain D residue  221 ASN
Chi-restraints excluded: chain D residue  224 VAL
Chi-restraints excluded: chain E residue  165 VAL
Chi-restraints excluded: chain F residue    8 VAL
Chi-restraints excluded: chain F residue   37 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 109 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 67 optimal weight:   10.0000
   chunk 99 optimal weight:    1.9990
   chunk 56 optimal weight:    0.2980
   chunk 84 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 126 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9980
   chunk 75 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  85 GLN
** E  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.078540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.059915 restraints weight = 53242.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.060912 restraints weight = 29400.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.061982 restraints weight = 21331.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.061918 restraints weight = 19379.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.061831 restraints weight = 15961.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.3025

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10664  Z= 0.168
  Angle     :  0.642  11.526  14519  Z= 0.333
  Chirality :  0.042   0.181   1689
  Planarity :  0.004   0.053   1826
  Dihedral  :  5.095  31.870   1461
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.43 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 16.39 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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 are not related in a simple way.
  whole: -0.87 (0.23), residues: 1337
  helix:  1.13 (0.26), residues: 400
  sheet: -0.55 (0.27), residues: 354
  loop : -1.82 (0.26), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG F  22 
 TYR   0.015   0.001   TYR D 162 
 PHE   0.012   0.001   PHE F  71 
 TRP   0.059   0.002   TRP A  33 
 HIS   0.005   0.001   HIS B  71 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 (10660)
  covalent geometry    : angle       0.64081 (14511)
  SS BOND              : bond        0.00239 (    4)
  SS BOND              : angle       2.00629 (    8)
  hydrogen bonds       : bond        0.04091 (  534)
  hydrogen bonds       : angle       4.83168 ( 1539)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 56
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 MET cc_start: 0.8724 (mmm) cc_final: 0.8499 (tpp)
REVERT: B   93 MET cc_start: 0.8942 (mmm) cc_final: 0.8616 (mmm)
REVERT: C  167 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7858 (tp30)
REVERT: D   50 TRP cc_start: 0.8516 (t60) cc_final: 0.8090 (t60)
REVERT: D  171 TRP cc_start: 0.7586 (OUTLIER) cc_final: 0.7165 (m100)
REVERT: D  223 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7397 (tptp)
REVERT: E    5 MET cc_start: 0.8396 (mmt) cc_final: 0.8154 (mmt)
REVERT: E   82 GLU cc_start: 0.8904 (pm20) cc_final: 0.7743 (pp20)
REVERT: F   92 GLU cc_start: 0.8292 (pm20) cc_final: 0.8089 (pp20)
  outliers start: 32
  outliers final: 22
  residues processed: 84
  average time/residue: 0.0806
  time to fit residues: 10.6517
Evaluate side-chains
  76 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 52
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  215 ASP
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  156 TYR
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain C residue  180 THR
Chi-restraints excluded: chain D residue   87 ASN
Chi-restraints excluded: chain D residue   99 CYS
Chi-restraints excluded: chain D residue  123 GLN
Chi-restraints excluded: chain D residue  171 TRP
Chi-restraints excluded: chain D residue  221 ASN
Chi-restraints excluded: chain D residue  223 LYS
Chi-restraints excluded: chain D residue  224 VAL
Chi-restraints excluded: chain E residue  165 VAL
Chi-restraints excluded: chain F residue    8 VAL
Chi-restraints excluded: chain F residue   37 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 56 optimal weight:    0.0570
   chunk 16 optimal weight:    1.9990
   chunk 70 optimal weight:    3.9990
   chunk 9 optimal weight:    9.9990
   chunk 67 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0870
   chunk 73 optimal weight:    7.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:    7.9990
   chunk 17 optimal weight:    3.9990
   chunk 4 optimal weight:   10.0000
   overall best weight:    1.8282

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

Flipped N/Q/H residues before XYZ refinement:
** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.077901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.059268 restraints weight = 52787.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.060225 restraints weight = 29316.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.061166 restraints weight = 21706.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.061141 restraints weight = 20050.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.061083 restraints weight = 16296.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.3089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10664  Z= 0.194
  Angle     :  0.654  10.829  14519  Z= 0.338
  Chirality :  0.042   0.186   1689
  Planarity :  0.004   0.053   1826
  Dihedral  :  5.090  30.252   1461
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 13.50
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.33 %
    Favored  : 92.60 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 16.48 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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 are not related in a simple way.
  whole: -0.79 (0.23), residues: 1337
  helix:  1.20 (0.26), residues: 400
  sheet: -0.40 (0.29), residues: 330
  loop : -1.81 (0.25), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F  22 
 TYR   0.016   0.002   TYR D 162 
 PHE   0.016   0.001   PHE E 120 
 TRP   0.081   0.002   TRP A  33 
 HIS   0.004   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 (10660)
  covalent geometry    : angle       0.65267 (14511)
  SS BOND              : bond        0.00352 (    4)
  SS BOND              : angle       1.96984 (    8)
  hydrogen bonds       : bond        0.04143 (  534)
  hydrogen bonds       : angle       4.83722 ( 1539)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 55
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 TRP cc_start: 0.7804 (OUTLIER) cc_final: 0.7318 (t60)
REVERT: A   93 MET cc_start: 0.8786 (mmm) cc_final: 0.8542 (tpp)
REVERT: B   93 MET cc_start: 0.8910 (mmm) cc_final: 0.8682 (mmm)
REVERT: B   98 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9180 (mp)
REVERT: B  101 PHE cc_start: 0.7145 (t80) cc_final: 0.6592 (t80)
REVERT: C  167 GLU cc_start: 0.8237 (mt-10) cc_final: 0.7922 (tp30)
REVERT: D   50 TRP cc_start: 0.8525 (t60) cc_final: 0.8106 (t60)
REVERT: D  157 CYS cc_start: 0.6261 (p) cc_final: 0.5450 (p)
REVERT: D  171 TRP cc_start: 0.7757 (OUTLIER) cc_final: 0.7030 (m100)
REVERT: F   92 GLU cc_start: 0.8288 (pm20) cc_final: 0.7937 (pp20)
  outliers start: 35
  outliers final: 25
  residues processed: 86
  average time/residue: 0.0893
  time to fit residues: 11.6590
Evaluate side-chains
  81 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 53
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 TRP
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  215 ASP
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain A residue  265 ILE
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  156 TYR
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain C residue    3 ILE
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain C residue  180 THR
Chi-restraints excluded: chain C residue  191 HIS
Chi-restraints excluded: chain D residue   37 ILE
Chi-restraints excluded: chain D residue   87 ASN
Chi-restraints excluded: chain D residue   99 CYS
Chi-restraints excluded: chain D residue  123 GLN
Chi-restraints excluded: chain D residue  171 TRP
Chi-restraints excluded: chain D residue  221 ASN
Chi-restraints excluded: chain D residue  224 VAL
Chi-restraints excluded: chain D residue  229 GLU
Chi-restraints excluded: chain F residue    8 VAL
Chi-restraints excluded: chain F residue   37 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   chunk 121 optimal weight:    0.1980
   chunk 74 optimal weight:   10.0000
   chunk 64 optimal weight:    0.9990
   chunk 57 optimal weight:    5.9990
   chunk 125 optimal weight:    0.9990
   chunk 110 optimal weight:    6.9990
   chunk 123 optimal weight:    0.7980
   chunk 40 optimal weight:    5.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  39 GLN
** F  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.079480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.061133 restraints weight = 52807.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.061953 restraints weight = 30052.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.062281 restraints weight = 23084.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.062554 restraints weight = 20637.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.062651 restraints weight = 17151.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.3436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10664  Z= 0.132
  Angle     :  0.633  10.465  14519  Z= 0.324
  Chirality :  0.042   0.204   1689
  Planarity :  0.004   0.052   1826
  Dihedral  :  4.882  28.982   1461
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 12.40
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.53 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 17.70 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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 are not related in a simple way.
  whole: -0.66 (0.24), residues: 1337
  helix:  1.32 (0.26), residues: 400
  sheet: -0.39 (0.28), residues: 342
  loop : -1.71 (0.26), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 229 
 TYR   0.011   0.001   TYR F  55 
 PHE   0.015   0.001   PHE E 120 
 TRP   0.071   0.002   TRP A  33 
 HIS   0.004   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (10660)
  covalent geometry    : angle       0.63189 (14511)
  SS BOND              : bond        0.00390 (    4)
  SS BOND              : angle       1.69210 (    8)
  hydrogen bonds       : bond        0.03968 (  534)
  hydrogen bonds       : angle       4.75229 ( 1539)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 65
  time to evaluate  : 0.288 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 TRP cc_start: 0.7742 (OUTLIER) cc_final: 0.7076 (t60)
REVERT: B   45 LEU cc_start: 0.8968 (tt) cc_final: 0.8690 (tp)
REVERT: B   93 MET cc_start: 0.8857 (mmm) cc_final: 0.8615 (mmm)
REVERT: B   98 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9126 (mp)
REVERT: B  101 PHE cc_start: 0.7108 (t80) cc_final: 0.6742 (t80)
REVERT: B  184 PHE cc_start: 0.9043 (m-80) cc_final: 0.8781 (m-80)
REVERT: C   95 TRP cc_start: 0.7788 (t-100) cc_final: 0.7287 (t-100)
REVERT: C  167 GLU cc_start: 0.8186 (mt-10) cc_final: 0.7876 (tp30)
REVERT: D   50 TRP cc_start: 0.8396 (t60) cc_final: 0.8009 (t60)
REVERT: D  157 CYS cc_start: 0.6168 (p) cc_final: 0.5308 (p)
REVERT: D  171 TRP cc_start: 0.7631 (OUTLIER) cc_final: 0.6971 (m100)
REVERT: E   82 GLU cc_start: 0.8816 (pm20) cc_final: 0.7581 (pp20)
REVERT: F   40 VAL cc_start: 0.9503 (t) cc_final: 0.9297 (m)
REVERT: F   92 GLU cc_start: 0.8243 (pm20) cc_final: 0.8010 (pp20)
  outliers start: 27
  outliers final: 18
  residues processed: 87
  average time/residue: 0.0828
  time to fit residues: 10.8171
Evaluate side-chains
  81 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 60
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 TRP
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  215 ASP
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  156 TYR
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain C residue  180 THR
Chi-restraints excluded: chain C residue  191 HIS
Chi-restraints excluded: chain D residue   87 ASN
Chi-restraints excluded: chain D residue  171 TRP
Chi-restraints excluded: chain D residue  221 ASN
Chi-restraints excluded: chain D residue  224 VAL
Chi-restraints excluded: chain E residue  119 ILE
Chi-restraints excluded: chain F residue    8 VAL
Chi-restraints excluded: chain F residue   37 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 99 optimal weight:    0.3980
   chunk 58 optimal weight:    1.9990
   chunk 113 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 128 optimal weight:    0.7980
   chunk 131 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 111 optimal weight:    4.9990
   chunk 42 optimal weight:    7.9990
   chunk 103 optimal weight:    0.8980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  91 GLN
** F  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.079625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.062699 restraints weight = 52598.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.063360 restraints weight = 35561.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.063563 restraints weight = 25861.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.063754 restraints weight = 22335.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.063898 restraints weight = 20324.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.3606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10664  Z= 0.133
  Angle     :  0.638  10.239  14519  Z= 0.326
  Chirality :  0.042   0.210   1689
  Planarity :  0.004   0.055   1826
  Dihedral  :  4.756  26.520   1461
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.13 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 18.23 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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 are not related in a simple way.
  whole: -0.63 (0.24), residues: 1337
  helix:  1.25 (0.26), residues: 408
  sheet: -0.22 (0.28), residues: 341
  loop : -1.77 (0.26), residues: 588

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 229 
 TYR   0.013   0.001   TYR C 142 
 PHE   0.017   0.001   PHE E 120 
 TRP   0.070   0.002   TRP A  33 
 HIS   0.004   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 (10660)
  covalent geometry    : angle       0.63710 (14511)
  SS BOND              : bond        0.00275 (    4)
  SS BOND              : angle       1.69954 (    8)
  hydrogen bonds       : bond        0.03945 (  534)
  hydrogen bonds       : angle       4.68598 ( 1539)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 66
  time to evaluate  : 0.322 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 TRP cc_start: 0.7287 (OUTLIER) cc_final: 0.6673 (t60)
REVERT: B   45 LEU cc_start: 0.8789 (tt) cc_final: 0.8517 (tp)
REVERT: B   98 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9067 (mp)
REVERT: B  101 PHE cc_start: 0.6706 (t80) cc_final: 0.6456 (t80)
REVERT: B  225 LYS cc_start: 0.8775 (pttm) cc_final: 0.7924 (tptp)
REVERT: C   95 TRP cc_start: 0.7751 (t-100) cc_final: 0.7277 (t-100)
REVERT: D   50 TRP cc_start: 0.8202 (t60) cc_final: 0.7828 (t60)
REVERT: D  118 MET cc_start: 0.9288 (mmm) cc_final: 0.8521 (mtt)
REVERT: D  157 CYS cc_start: 0.5574 (p) cc_final: 0.4939 (p)
REVERT: D  171 TRP cc_start: 0.7703 (OUTLIER) cc_final: 0.7119 (m100)
REVERT: E  172 ASP cc_start: 0.7922 (p0) cc_final: 0.7603 (p0)
  outliers start: 27
  outliers final: 18
  residues processed: 87
  average time/residue: 0.0917
  time to fit residues: 11.9533
Evaluate side-chains
  82 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 61
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 TRP
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  215 ASP
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  156 TYR
Chi-restraints excluded: chain B residue  183 LEU
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   91 GLN
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain C residue  180 THR
Chi-restraints excluded: chain C residue  191 HIS
Chi-restraints excluded: chain D residue   87 ASN
Chi-restraints excluded: chain D residue  171 TRP
Chi-restraints excluded: chain F residue    8 VAL
Chi-restraints excluded: chain F residue   37 ILE
Chi-restraints excluded: chain F residue  112 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 12 optimal weight:    6.9990
   chunk 118 optimal weight:    0.0670
   chunk 95 optimal weight:    2.9990
   chunk 109 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 67 optimal weight:   10.0000
   chunk 78 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 16 optimal weight:    4.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    1.2922

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

Flipped N/Q/H residues before XYZ refinement:
A 163 ASN
** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.079168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.060774 restraints weight = 52382.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.061406 restraints weight = 29956.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.062733 restraints weight = 22179.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.062677 restraints weight = 18885.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.062594 restraints weight = 16014.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.3682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  10664  Z= 0.159
  Angle     :  0.666  10.884  14519  Z= 0.342
  Chirality :  0.042   0.226   1689
  Planarity :  0.004   0.052   1826
  Dihedral  :  4.762  25.969   1461
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.91 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 18.49 %
    Favored  : 79.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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 are not related in a simple way.
  whole: -0.66 (0.23), residues: 1337
  helix:  1.14 (0.26), residues: 405
  sheet: -0.20 (0.28), residues: 353
  loop : -1.76 (0.26), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 229 
 TYR   0.015   0.001   TYR D 162 
 PHE   0.018   0.001   PHE F  71 
 TRP   0.068   0.002   TRP A  33 
 HIS   0.004   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (10660)
  covalent geometry    : angle       0.66455 (14511)
  SS BOND              : bond        0.00172 (    4)
  SS BOND              : angle       1.80362 (    8)
  hydrogen bonds       : bond        0.04025 (  534)
  hydrogen bonds       : angle       4.74358 ( 1539)

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

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

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2674 Ramachandran restraints generated.
    1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 62
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 TRP cc_start: 0.7648 (OUTLIER) cc_final: 0.7021 (t60)
REVERT: A   93 MET cc_start: 0.9115 (tpp) cc_final: 0.8848 (tpp)
REVERT: B   45 LEU cc_start: 0.9008 (tt) cc_final: 0.8738 (tp)
REVERT: B   93 MET cc_start: 0.8792 (mmm) cc_final: 0.8560 (mmm)
REVERT: B   98 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9129 (mp)
REVERT: B  101 PHE cc_start: 0.7092 (t80) cc_final: 0.6702 (t80)
REVERT: B  225 LYS cc_start: 0.8774 (pttm) cc_final: 0.7934 (tptp)
REVERT: C   95 TRP cc_start: 0.7771 (t-100) cc_final: 0.7280 (t-100)
REVERT: D   50 TRP cc_start: 0.8420 (t60) cc_final: 0.7990 (t60)
REVERT: D  118 MET cc_start: 0.9260 (mmm) cc_final: 0.8560 (mtt)
REVERT: D  157 CYS cc_start: 0.6192 (p) cc_final: 0.5419 (p)
REVERT: D  171 TRP cc_start: 0.7721 (OUTLIER) cc_final: 0.7109 (m100)
REVERT: E   82 GLU cc_start: 0.8693 (pm20) cc_final: 0.7462 (pp20)
REVERT: E   91 GLN cc_start: 0.8268 (pp30) cc_final: 0.7865 (pp30)
  outliers start: 22
  outliers final: 18
  residues processed: 79
  average time/residue: 0.0887
  time to fit residues: 10.5804
Evaluate side-chains
  79 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 58
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 TRP
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  215 ASP
Chi-restraints excluded: chain A residue  230 VAL
Chi-restraints excluded: chain B residue   98 LEU
Chi-restraints excluded: chain B residue   99 LEU
Chi-restraints excluded: chain B residue  156 TYR
Chi-restraints excluded: chain B residue  230 VAL
Chi-restraints excluded: chain B residue  245 VAL
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue  129 SER
Chi-restraints excluded: chain C residue  180 THR
Chi-restraints excluded: chain C residue  191 HIS
Chi-restraints excluded: chain D residue   87 ASN
Chi-restraints excluded: chain D residue  171 TRP
Chi-restraints excluded: chain D residue  224 VAL
Chi-restraints excluded: chain D residue  226 LYS
Chi-restraints excluded: chain F residue    8 VAL
Chi-restraints excluded: chain F residue   37 ILE
Chi-restraints excluded: chain F residue  112 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   chunk 85 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0030
   chunk 30 optimal weight:    0.0050
   chunk 103 optimal weight:    0.9990
   chunk 74 optimal weight:    8.9990
   chunk 100 optimal weight:    0.0370
   chunk 95 optimal weight:    0.8980
   chunk 63 optimal weight:    0.0470
   overall best weight:    0.1980

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

Flipped N/Q/H residues before XYZ refinement:
** B 250 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 285 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.080561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.063592 restraints weight = 52524.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.064041 restraints weight = 32567.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.064406 restraints weight = 24785.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.064582 restraints weight = 21718.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.064674 restraints weight = 19901.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.3977

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10664  Z= 0.126
  Angle     :  0.655  11.379  14519  Z= 0.334
  Chirality :  0.042   0.219   1689
  Planarity :  0.004   0.052   1826
  Dihedral  :  4.623  23.548   1461
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  5.16 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 19.02 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.29 %
    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 are not related in a simple way.
  whole: -0.58 (0.23), residues: 1337
  helix:  1.14 (0.26), residues: 405
  sheet:  0.02 (0.28), residues: 343
  loop : -1.75 (0.26), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 229 
 TYR   0.010   0.001   TYR F  55 
 PHE   0.024   0.001   PHE E 120 
 TRP   0.066   0.002   TRP A  33 
 HIS   0.004   0.001   HIS A 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 (10660)
  covalent geometry    : angle       0.65391 (14511)
  SS BOND              : bond        0.00295 (    4)
  SS BOND              : angle       2.00956 (    8)
  hydrogen bonds       : bond        0.03928 (  534)
  hydrogen bonds       : angle       4.66617 ( 1539)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1681.98 seconds
wall clock time: 29 minutes 58.31 seconds (1798.31 seconds total)