Starting phenix.real_space_refine
on Sun Jun  8 19:46:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bri_16215/06_2025/8bri_16215.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bri_16215/06_2025/8bri_16215.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bri_16215/06_2025/8bri_16215.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bri_16215/06_2025/8bri_16215.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bri_16215/06_2025/8bri_16215.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bri_16215/06_2025/8bri_16215.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.028
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      92      5.16       5
     C    6392      2.51       5
     N    1625      2.21       5
     O    1802      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 9911
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1880
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 250, 1880
          Classifications: {'peptide': 250}
          Link IDs: {'PTRANS': 6, 'TRANS': 243}
    Chain: "B"
      Number of atoms: 1761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1761
          Classifications: {'peptide': 233}
          Link IDs: {'PTRANS': 6, 'TRANS': 226}
    Chain: "C"
      Number of atoms: 1888
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 251, 1888
          Classifications: {'peptide': 251}
          Link IDs: {'PTRANS': 6, 'TRANS': 244}
    Chain: "D"
      Number of atoms: 1825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1825
          Classifications: {'peptide': 243}
          Link IDs: {'PTRANS': 6, 'TRANS': 236}
    Chain: "E"
      Number of atoms: 1761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 233, 1761
          Classifications: {'peptide': 233}
          Link IDs: {'PTRANS': 6, 'TRANS': 226}
    Chain: "F"
      Number of atoms: 398
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 398
          Classifications: {'peptide': 51}
          Link IDs: {'PTRANS': 3, 'TRANS': 47}
    Chain: "G"
      Number of atoms: 398
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 398
          Classifications: {'peptide': 51}
          Link IDs: {'PTRANS': 3, 'TRANS': 47}
  Time building chain proxies: 7.14, per 1000 atoms: 0.72
  Number of scatterers: 9911
  At special positions: 0
  Unit cell: (99.008, 109.824, 113.152, 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      92     16.00
     O    1802      8.00
     N    1625      7.00
     C    6392      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.80
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2362

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 1 sheets defined
      87.8% alpha, 0.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 21
    Processing helix  chain 'A' and resid 31 through 48
    Processing helix  chain 'A' and resid 51 through 68
    Processing helix  chain 'A' and resid 74 through 91
    Processing helix  chain 'A' and resid 92 through 95
    Processing helix  chain 'A' and resid 102 through 115
      removed outlier: 3.918A  pdb=" N   ASP A 114 " --> pdb=" O   ASP A 110 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   GLY A 115 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 167
      removed outlier: 3.578A  pdb=" N   VAL A 121 " --> pdb=" O   ASP A 117 " (cutoff:3.500A)
      Proline residue:  A 151  - end of helix
    Processing helix  chain 'A' and resid 174 through 196
      removed outlier: 4.006A  pdb=" N   THR A 185 " --> pdb=" O   VAL A 181 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   THR A 186 " --> pdb=" O   ALA A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 196 through 228
    Processing helix  chain 'A' and resid 230 through 240
      removed outlier: 3.761A  pdb=" N   ILE A 234 " --> pdb=" O   ASN A 230 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   SER A 236 " --> pdb=" O   ARG A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 243
      No H-bonds generated for 'chain 'A' and resid 241 through 243'
    Processing helix  chain 'A' and resid 246 through 251
      removed outlier: 3.551A  pdb=" N   ILE A 251 " --> pdb=" O   ARG A 247 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 50
    Processing helix  chain 'B' and resid 51 through 68
    Processing helix  chain 'B' and resid 72 through 90
    Processing helix  chain 'B' and resid 93 through 98
      removed outlier: 3.945A  pdb=" N   GLU B  96 " --> pdb=" O   LEU B  93 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   MET B  98 " --> pdb=" O   LEU B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 114
    Processing helix  chain 'B' and resid 117 through 168
      Proline residue:  B 151  - end of helix
    Processing helix  chain 'B' and resid 171 through 196
      removed outlier: 3.586A  pdb=" N   GLY B 176 " --> pdb=" O   PRO B 172 " (cutoff:3.500A)
      Proline residue:  B 177  - end of helix
      removed outlier: 3.554A  pdb=" N   THR B 186 " --> pdb=" O   ALA B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 196 through 227
    Processing helix  chain 'B' and resid 230 through 240
    Processing helix  chain 'B' and resid 241 through 244
      removed outlier: 3.805A  pdb=" N   GLU B 244 " --> pdb=" O   TYR B 241 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 241 through 244'
    Processing helix  chain 'B' and resid 245 through 251
      removed outlier: 3.946A  pdb=" N   LEU B 249 " --> pdb=" O   GLY B 245 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2 through 24
    Processing helix  chain 'C' and resid 31 through 50
      removed outlier: 3.743A  pdb=" N   LYS C  49 " --> pdb=" O   VAL C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 51 through 68
    Processing helix  chain 'C' and resid 72 through 91
    Processing helix  chain 'C' and resid 92 through 97
      removed outlier: 3.875A  pdb=" N   GLU C  96 " --> pdb=" O   LEU C  93 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   GLU C  97 " --> pdb=" O   ALA C  94 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 102 through 114
    Processing helix  chain 'C' and resid 117 through 168
      Proline residue:  C 151  - end of helix
    Processing helix  chain 'C' and resid 175 through 196
      removed outlier: 4.013A  pdb=" N   THR C 185 " --> pdb=" O   VAL C 181 " (cutoff:3.500A)
      removed outlier: 4.411A  pdb=" N   THR C 186 " --> pdb=" O   ALA C 182 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 228
    Processing helix  chain 'C' and resid 230 through 246
    Processing helix  chain 'D' and resid 2 through 23
      removed outlier: 3.654A  pdb=" N   GLY D  23 " --> pdb=" O   ALA D  19 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 26 through 30
      removed outlier: 3.582A  pdb=" N   VAL D  30 " --> pdb=" O   GLY D  27 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 31 through 47
    Processing helix  chain 'D' and resid 51 through 64
    Processing helix  chain 'D' and resid 72 through 90
      removed outlier: 3.519A  pdb=" N   LEU D  76 " --> pdb=" O   GLU D  72 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 91 through 98
      removed outlier: 3.545A  pdb=" N   GLU D  96 " --> pdb=" O   LEU D  93 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 102 through 114
    Processing helix  chain 'D' and resid 117 through 168
      Proline residue:  D 151  - end of helix
      removed outlier: 3.865A  pdb=" N   ASN D 168 " --> pdb=" O   ALA D 164 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 174 through 196
      removed outlier: 3.557A  pdb=" N   ALA D 178 " --> pdb=" O   ALA D 174 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   THR D 185 " --> pdb=" O   VAL D 181 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   THR D 186 " --> pdb=" O   ALA D 182 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 196 through 228
    Processing helix  chain 'D' and resid 230 through 243
    Processing helix  chain 'E' and resid 25 through 29
      removed outlier: 3.600A  pdb=" N   MET E  28 " --> pdb=" O   SER E  25 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 31 through 48
    Processing helix  chain 'E' and resid 51 through 68
    Processing helix  chain 'E' and resid 72 through 91
    Processing helix  chain 'E' and resid 102 through 113
    Processing helix  chain 'E' and resid 117 through 168
      Proline residue:  E 151  - end of helix
    Processing helix  chain 'E' and resid 171 through 196
      Proline residue:  E 177  - end of helix
      removed outlier: 3.704A  pdb=" N   THR E 186 " --> pdb=" O   ALA E 182 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 196 through 227
    Processing helix  chain 'E' and resid 230 through 243
      removed outlier: 3.671A  pdb=" N   SER E 236 " --> pdb=" O   ARG E 232 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASN E 240 " --> pdb=" O   SER E 236 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   TYR E 241 " --> pdb=" O   TYR E 237 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   LEU E 242 " --> pdb=" O   LEU E 238 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   ASN E 243 " --> pdb=" O   LYS E 239 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 245 through 250
      removed outlier: 3.591A  pdb=" N   ALA E 248 " --> pdb=" O   GLY E 245 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   LEU E 249 " --> pdb=" O   LYS E 246 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 16 through 39
      removed outlier: 3.886A  pdb=" N   GLY F  20 " --> pdb=" O   PRO F  16 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 43 through 58
      removed outlier: 3.666A  pdb=" N   LYS F  48 " --> pdb=" O   VAL F  44 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   GLN F  49 " --> pdb=" O   LEU F  45 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   ILE F  50 " --> pdb=" O   LYS F  46 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 17 through 39
      removed outlier: 4.523A  pdb=" N   THR G  21 " --> pdb=" O   LEU G  17 " (cutoff:3.500A)
      removed outlier: 4.001A  pdb=" N   PHE G  39 " --> pdb=" O   LEU G  35 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 43 through 58
    Processing sheet with id=AA1, first strand: chain 'F' and resid 40 through 42

    868 hydrogen bonds defined for protein.
    2574 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: 2.96

  Time building geometry restraints manager: 3.26 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1778
        1.32 -     1.45: 2242
        1.45 -     1.57: 5854
        1.57 -     1.70: 0
        1.70 -     1.82: 182
  Bond restraints: 10056
  Sorted by residual:
  bond pdb=" CG  GLN D 210 "
       pdb=" CD  GLN D 210 "
    ideal  model  delta    sigma   weight residual
    1.516  1.459  0.057 2.50e-02 1.60e+03 5.14e+00
  bond pdb=" CB  ILE D 156 "
       pdb=" CG2 ILE D 156 "
    ideal  model  delta    sigma   weight residual
    1.521  1.452  0.069 3.30e-02 9.18e+02 4.34e+00
  bond pdb=" CB  VAL G  34 "
       pdb=" CG1 VAL G  34 "
    ideal  model  delta    sigma   weight residual
    1.521  1.455  0.066 3.30e-02 9.18e+02 4.03e+00
  bond pdb=" CG  MET F  30 "
       pdb=" SD  MET F  30 "
    ideal  model  delta    sigma   weight residual
    1.803  1.756  0.047 2.50e-02 1.60e+03 3.54e+00
  bond pdb=" CG  MET A 169 "
       pdb=" SD  MET A 169 "
    ideal  model  delta    sigma   weight residual
    1.803  1.756  0.047 2.50e-02 1.60e+03 3.49e+00
  ... (remaining 10051 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.31: 13307
        4.31 -     8.63: 190
        8.63 -    12.94: 31
       12.94 -    17.26: 12
       17.26 -    21.57: 1
  Bond angle restraints: 13541
  Sorted by residual:
  angle pdb=" O   PHE F  58 "
        pdb=" C   PHE F  58 "
        pdb=" N   GLY F  59 "
      ideal   model   delta    sigma   weight residual
     122.19  100.62   21.57 1.21e+00 6.83e-01 3.18e+02
  angle pdb=" CA  MET B 219 "
        pdb=" CB  MET B 219 "
        pdb=" CG  MET B 219 "
      ideal   model   delta    sigma   weight residual
     114.10  128.24  -14.14 2.00e+00 2.50e-01 5.00e+01
  angle pdb=" CA  MET D  83 "
        pdb=" CB  MET D  83 "
        pdb=" CG  MET D  83 "
      ideal   model   delta    sigma   weight residual
     114.10  128.10  -14.00 2.00e+00 2.50e-01 4.90e+01
  angle pdb=" CA  MET C 219 "
        pdb=" CB  MET C 219 "
        pdb=" CG  MET C 219 "
      ideal   model   delta    sigma   weight residual
     114.10  127.70  -13.60 2.00e+00 2.50e-01 4.62e+01
  angle pdb=" CA  MET C  83 "
        pdb=" CB  MET C  83 "
        pdb=" CG  MET C  83 "
      ideal   model   delta    sigma   weight residual
     114.10  126.60  -12.50 2.00e+00 2.50e-01 3.90e+01
  ... (remaining 13536 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 5201
       17.64 -    35.28: 670
       35.28 -    52.92: 152
       52.92 -    70.56: 18
       70.56 -    88.20: 15
  Dihedral angle restraints: 6056
    sinusoidal: 2374
      harmonic: 3682
  Sorted by residual:
  dihedral pdb=" CA  GLU D  99 "
           pdb=" C   GLU D  99 "
           pdb=" N   ILE D 100 "
           pdb=" CA  ILE D 100 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.69  -25.31     0      5.00e+00 4.00e-02 2.56e+01
  dihedral pdb=" N   GLN D 210 "
           pdb=" C   GLN D 210 "
           pdb=" CA  GLN D 210 "
           pdb=" CB  GLN D 210 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.25  -10.45     0      2.50e+00 1.60e-01 1.75e+01
  dihedral pdb=" N   MET E  83 "
           pdb=" C   MET E  83 "
           pdb=" CA  MET E  83 "
           pdb=" CB  MET E  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.11  -10.31     0      2.50e+00 1.60e-01 1.70e+01
  ... (remaining 6053 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.122: 1506
       0.122 -    0.243: 73
       0.243 -    0.365: 15
       0.365 -    0.487: 1
       0.487 -    0.608: 1
  Chirality restraints: 1596
  Sorted by residual:
  chirality pdb=" CB  ILE C 100 "
            pdb=" CA  ILE C 100 "
            pdb=" CG1 ILE C 100 "
            pdb=" CG2 ILE C 100 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.04    0.61 2.00e-01 2.50e+01 9.25e+00
  chirality pdb=" CG  LEU D 213 "
            pdb=" CB  LEU D 213 "
            pdb=" CD1 LEU D 213 "
            pdb=" CD2 LEU D 213 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.14   -0.45 2.00e-01 2.50e+01 5.04e+00
  chirality pdb=" CG  LEU D 166 "
            pdb=" CB  LEU D 166 "
            pdb=" CD1 LEU D 166 "
            pdb=" CD2 LEU D 166 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.27   -0.32 2.00e-01 2.50e+01 2.54e+00
  ... (remaining 1593 not shown)

  Planarity restraints: 1725
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE F  58 "    0.089 2.00e-02 2.50e+03   1.54e-01 2.39e+02
        pdb=" C   PHE F  58 "   -0.268 2.00e-02 2.50e+03
        pdb=" O   PHE F  58 "    0.095 2.00e-02 2.50e+03
        pdb=" N   GLY F  59 "    0.084 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE G  58 "    0.037 2.00e-02 2.50e+03   7.20e-02 5.19e+01
        pdb=" C   PHE G  58 "   -0.125 2.00e-02 2.50e+03
        pdb=" O   PHE G  58 "    0.046 2.00e-02 2.50e+03
        pdb=" N   GLY G  59 "    0.042 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D  44 "   -0.024 2.00e-02 2.50e+03   2.80e-02 1.37e+01
        pdb=" CG  PHE D  44 "    0.065 2.00e-02 2.50e+03
        pdb=" CD1 PHE D  44 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE D  44 "   -0.021 2.00e-02 2.50e+03
        pdb=" CE1 PHE D  44 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 PHE D  44 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE D  44 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1722 not shown)

  Histogram of nonbonded interaction distances:
        1.97 -     2.55: 84
        2.55 -     3.14: 8640
        3.14 -     3.73: 17280
        3.73 -     4.31: 21721
        4.31 -     4.90: 35416
  Nonbonded interactions: 83141
  Sorted by model distance:
  nonbonded pdb=" OG  SER D 193 "
            pdb=" OD1 ASN D 194 "
     model   vdw
     1.969 3.040
  nonbonded pdb=" O   PHE C  29 "
            pdb=" OH  TYR C 188 "
     model   vdw
     2.167 3.040
  nonbonded pdb=" O   PHE D  29 "
            pdb=" OH  TYR D 188 "
     model   vdw
     2.188 3.040
  nonbonded pdb=" OD1 ASN E 101 "
            pdb=" N   ASN E 102 "
     model   vdw
     2.189 3.120
  nonbonded pdb=" NZ  LYS C 107 "
            pdb=" OD2 ASP C 128 "
     model   vdw
     2.207 3.120
  ... (remaining 83136 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 20 through 243)
  selection = (chain 'B' and resid 20 through 243)
  selection = (chain 'C' and resid 20 through 243)
  selection = (chain 'D' and resid 20 through 243)
  selection = (chain 'E' and resid 20 through 243)
}
ncs_group {
  reference = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.860
  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:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     27.380
  Find NCS groups from input model:        0.530
  Set up NCS constraints:                  0.040
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  10056  Z= 0.243
  Angle     :  1.304  21.571  13541  Z= 0.665
  Chirality :  0.066   0.608   1596
  Planarity :  0.007   0.154   1725
  Dihedral  : 16.369  88.201   3694
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 24.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 30.13 %
    Favored  : 68.71 %
  Cbeta Deviations :  0.17 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.23), residues: 1298
  helix:  1.84 (0.16), residues: 1088
  sheet:  None (None), residues: 0
  loop : -1.03 (0.40), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.004   TRP G  18 
 HIS   0.003   0.001   HIS C 116 
 PHE   0.065   0.002   PHE D  44 
 TYR   0.042   0.003   TYR B 237 
 ARG   0.010   0.001   ARG E 144 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11201 (  868)
  hydrogen bonds       : angle       5.35186 ( 2574)
  covalent geometry    : bond        0.00545 (10056)
  covalent geometry    : angle       1.30375 (13541)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 286
  time to evaluate  : 1.152 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  134 GLU cc_start: 0.7302 (tm-30) cc_final: 0.6890 (tm-30)
REVERT: B  138 GLN cc_start: 0.8692 (OUTLIER) cc_final: 0.8432 (mm-40)
REVERT: C  169 MET cc_start: 0.7424 (tmm) cc_final: 0.7222 (tmm)
REVERT: C  208 ARG cc_start: 0.8236 (ttp-110) cc_final: 0.7957 (ttp-110)
REVERT: D  134 GLU cc_start: 0.8411 (pp20) cc_final: 0.7583 (pp20)
REVERT: E   39 VAL cc_start: 0.7848 (t) cc_final: 0.7645 (p)
REVERT: E  169 MET cc_start: 0.8246 (ppp) cc_final: 0.7884 (ttp)
  outliers start: 12
  outliers final: 4
  residues processed: 290
  average time/residue: 0.2534
  time to fit residues: 102.0514
Evaluate side-chains
  269 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 264
  time to evaluate  : 1.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  133 ASP
Chi-restraints excluded: chain B residue  138 GLN
Chi-restraints excluded: chain D residue  165 MET
Chi-restraints excluded: chain E residue   99 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 33 optimal weight:    4.9990
   chunk 66 optimal weight:    0.6980
   chunk 52 optimal weight:    1.9990
   chunk 101 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 61 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9990
   chunk 118 optimal weight:    0.8980
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 240 ASN
** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 214 ASN
** F  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.124952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.093077 restraints weight = 29843.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.095126 restraints weight = 21598.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.096837 restraints weight = 13399.206|
|-----------------------------------------------------------------------------|
r_work (final): 0.3631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.1323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10056  Z= 0.166
  Angle     :  0.806   9.901  13541  Z= 0.402
  Chirality :  0.045   0.257   1596
  Planarity :  0.005   0.040   1725
  Dihedral  :  5.212  60.378   1383
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 16.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.93 %
    Favored  : 98.07 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 21.21 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.23), residues: 1298
  helix:  1.46 (0.15), residues: 1104
  sheet:  None (None), residues: 0
  loop : -1.08 (0.40), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP G  18 
 HIS   0.002   0.001   HIS A 136 
 PHE   0.029   0.002   PHE F  32 
 TYR   0.034   0.002   TYR B 237 
 ARG   0.007   0.001   ARG C 215 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04437 (  868)
  hydrogen bonds       : angle       4.49462 ( 2574)
  covalent geometry    : bond        0.00360 (10056)
  covalent geometry    : angle       0.80634 (13541)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 289
  time to evaluate  : 0.947 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.8748 (mpp) cc_final: 0.8518 (mpp)
REVERT: B  134 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7287 (tm-30)
REVERT: B  138 GLN cc_start: 0.9044 (mm-40) cc_final: 0.8821 (mm-40)
REVERT: C   44 PHE cc_start: 0.8575 (t80) cc_final: 0.8357 (t80)
REVERT: C   56 PHE cc_start: 0.7178 (m-80) cc_final: 0.6877 (m-80)
REVERT: D   15 PHE cc_start: 0.8299 (m-80) cc_final: 0.8089 (m-80)
REVERT: D   83 MET cc_start: 0.9340 (mmm) cc_final: 0.9102 (mmm)
REVERT: D  166 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9158 (mm)
REVERT: D  211 GLU cc_start: 0.9045 (tp30) cc_final: 0.8844 (tp30)
REVERT: E   68 PHE cc_start: 0.7767 (m-80) cc_final: 0.7394 (m-10)
REVERT: E  117 ASP cc_start: 0.8276 (OUTLIER) cc_final: 0.7726 (p0)
REVERT: E  153 MET cc_start: 0.8828 (mmm) cc_final: 0.8473 (tpp)
REVERT: E  165 MET cc_start: 0.8405 (mtm) cc_final: 0.8168 (ttm)
REVERT: F   19 MET cc_start: 0.8407 (tpt) cc_final: 0.8187 (tpt)
  outliers start: 45
  outliers final: 23
  residues processed: 312
  average time/residue: 0.2116
  time to fit residues: 92.1828
Evaluate side-chains
  288 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 263
  time to evaluate  : 1.051 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain C residue    1 MET
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   48 MET
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain D residue   33 THR
Chi-restraints excluded: chain D residue  166 LEU
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue  117 ASP
Chi-restraints excluded: chain E residue  133 ASP
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain G residue   35 LEU
Chi-restraints excluded: chain G residue   60 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 116 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 55 optimal weight:    4.9990
   chunk 47 optimal weight:    0.5980
   chunk 90 optimal weight:    5.9990
   chunk 127 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 229 GLN
** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 138 GLN
** G  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.123826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.091829 restraints weight = 30282.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.094335 restraints weight = 17796.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.096087 restraints weight = 12939.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  10056  Z= 0.162
  Angle     :  0.781  11.577  13541  Z= 0.387
  Chirality :  0.043   0.219   1596
  Planarity :  0.004   0.036   1725
  Dihedral  :  4.439  55.251   1372
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  4.41 %
    Allowed  : 24.09 %
    Favored  : 71.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.23), residues: 1298
  helix:  1.40 (0.15), residues: 1113
  sheet:  None (None), residues: 0
  loop : -1.21 (0.42), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.002   TRP G  18 
 HIS   0.002   0.001   HIS D 136 
 PHE   0.025   0.002   PHE F  39 
 TYR   0.024   0.002   TYR B 237 
 ARG   0.007   0.001   ARG A 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04078 (  868)
  hydrogen bonds       : angle       4.37872 ( 2574)
  covalent geometry    : bond        0.00363 (10056)
  covalent geometry    : angle       0.78071 (13541)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  320 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 274
  time to evaluate  : 1.045 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.4184 (mtp) cc_final: 0.3878 (mtt)
REVERT: A  230 ASN cc_start: 0.8830 (t0) cc_final: 0.8433 (p0)
REVERT: B  134 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7089 (tm-30)
REVERT: B  138 GLN cc_start: 0.8977 (mm-40) cc_final: 0.8731 (mm-40)
REVERT: B  153 MET cc_start: 0.8542 (tpp) cc_final: 0.7950 (tpp)
REVERT: C   56 PHE cc_start: 0.7185 (m-80) cc_final: 0.6864 (m-10)
REVERT: C  208 ARG cc_start: 0.8325 (ttp-110) cc_final: 0.7779 (ttp-110)
REVERT: D   83 MET cc_start: 0.9373 (mmm) cc_final: 0.9132 (mmm)
REVERT: D  211 GLU cc_start: 0.8977 (tp30) cc_final: 0.8629 (tp30)
REVERT: E   68 PHE cc_start: 0.7770 (m-80) cc_final: 0.7136 (m-10)
REVERT: E  117 ASP cc_start: 0.8194 (OUTLIER) cc_final: 0.7651 (p0)
REVERT: E  209 ASP cc_start: 0.9289 (t0) cc_final: 0.9089 (t0)
REVERT: E  210 GLN cc_start: 0.9045 (mt0) cc_final: 0.8805 (mt0)
REVERT: E  214 ASN cc_start: 0.8900 (m-40) cc_final: 0.8489 (p0)
  outliers start: 46
  outliers final: 28
  residues processed: 298
  average time/residue: 0.2152
  time to fit residues: 90.2765
Evaluate side-chains
  284 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 255
  time to evaluate  : 1.010 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  200 ILE
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  179 MET
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   48 MET
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain D residue   22 LEU
Chi-restraints excluded: chain D residue   33 THR
Chi-restraints excluded: chain D residue  156 ILE
Chi-restraints excluded: chain D residue  193 SER
Chi-restraints excluded: chain D residue  216 ARG
Chi-restraints excluded: chain E residue   20 MET
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue  117 ASP
Chi-restraints excluded: chain E residue  133 ASP
Chi-restraints excluded: chain F residue   25 LEU
Chi-restraints excluded: chain G residue   35 LEU
Chi-restraints excluded: chain G residue   60 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 16 optimal weight:    5.9990
   chunk 7 optimal weight:   10.0000
   chunk 88 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 86 optimal weight:    0.5980
   chunk 118 optimal weight:   10.0000
   chunk 98 optimal weight:    0.0980
   chunk 28 optimal weight:    0.9990
   chunk 47 optimal weight:    6.9990
   overall best weight:    0.6584

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 GLN
B 229 GLN
** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 194 ASN
** E  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.123448 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.092333 restraints weight = 29819.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.094971 restraints weight = 17086.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.096713 restraints weight = 12154.502|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.2251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10056  Z= 0.146
  Angle     :  0.760   9.090  13541  Z= 0.375
  Chirality :  0.042   0.201   1596
  Planarity :  0.004   0.035   1725
  Dihedral  :  4.451  55.469   1372
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 14.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 24.47 %
    Favored  : 70.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.23), residues: 1298
  helix:  1.42 (0.16), residues: 1106
  sheet:  None (None), residues: 0
  loop : -1.10 (0.42), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP G  18 
 HIS   0.002   0.001   HIS A 136 
 PHE   0.043   0.002   PHE D  15 
 TYR   0.019   0.001   TYR B 237 
 ARG   0.007   0.000   ARG A 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03966 (  868)
  hydrogen bonds       : angle       4.33611 ( 2574)
  covalent geometry    : bond        0.00319 (10056)
  covalent geometry    : angle       0.75963 (13541)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  332 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 282
  time to evaluate  : 1.415 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.4219 (mtp) cc_final: 0.3955 (mtt)
REVERT: A  230 ASN cc_start: 0.8820 (t0) cc_final: 0.8429 (p0)
REVERT: B  134 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7185 (tm-30)
REVERT: B  138 GLN cc_start: 0.8970 (mm-40) cc_final: 0.8701 (mm-40)
REVERT: B  153 MET cc_start: 0.8620 (tpp) cc_final: 0.7945 (tpp)
REVERT: B  169 MET cc_start: 0.7008 (tmm) cc_final: 0.6762 (tmm)
REVERT: C   52 MET cc_start: 0.8398 (tpp) cc_final: 0.8173 (tpp)
REVERT: C   56 PHE cc_start: 0.7290 (m-80) cc_final: 0.6981 (m-10)
REVERT: C  208 ARG cc_start: 0.8397 (ttp-110) cc_final: 0.7735 (ttp-110)
REVERT: D   15 PHE cc_start: 0.8448 (m-80) cc_final: 0.8169 (m-80)
REVERT: D   83 MET cc_start: 0.9409 (mmm) cc_final: 0.9025 (mmm)
REVERT: D  211 GLU cc_start: 0.9037 (tp30) cc_final: 0.8687 (tp30)
REVERT: D  226 GLN cc_start: 0.8842 (mm110) cc_final: 0.8528 (mm110)
REVERT: E   68 PHE cc_start: 0.7791 (m-80) cc_final: 0.7250 (m-10)
REVERT: E  117 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7600 (p0)
REVERT: E  165 MET cc_start: 0.8486 (mtm) cc_final: 0.8249 (ttm)
REVERT: E  210 GLN cc_start: 0.9076 (mt0) cc_final: 0.8761 (mt0)
REVERT: E  211 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8421 (mm-30)
REVERT: E  214 ASN cc_start: 0.9004 (m-40) cc_final: 0.8706 (m110)
REVERT: G   42 MET cc_start: 0.8651 (tmm) cc_final: 0.8428 (tmm)
  outliers start: 50
  outliers final: 36
  residues processed: 305
  average time/residue: 0.2069
  time to fit residues: 88.8953
Evaluate side-chains
  299 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 262
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  200 ILE
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  179 MET
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  200 ILE
Chi-restraints excluded: chain B residue  226 GLN
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   48 MET
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain C residue  200 ILE
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain D residue   33 THR
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  156 ILE
Chi-restraints excluded: chain D residue  193 SER
Chi-restraints excluded: chain E residue   20 MET
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   76 LEU
Chi-restraints excluded: chain E residue  117 ASP
Chi-restraints excluded: chain E residue  133 ASP
Chi-restraints excluded: chain F residue   50 ILE
Chi-restraints excluded: chain G residue   29 LEU
Chi-restraints excluded: chain G residue   35 LEU
Chi-restraints excluded: chain G residue   60 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 97 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 112 optimal weight:    4.9990
   chunk 11 optimal weight:    0.2980
   chunk 52 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 84 optimal weight:    8.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 GLN
** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 101 ASN
** D 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 194 ASN
** E  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 138 GLN
** G  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.123049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.090756 restraints weight = 29926.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.093322 restraints weight = 17640.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.094894 restraints weight = 12821.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10056  Z= 0.165
  Angle     :  0.790  12.820  13541  Z= 0.392
  Chirality :  0.044   0.273   1596
  Planarity :  0.004   0.034   1725
  Dihedral  :  4.438  55.355   1372
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  5.76 %
    Allowed  : 24.38 %
    Favored  : 69.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.45 (0.23), residues: 1298
  helix:  1.36 (0.16), residues: 1109
  sheet:  None (None), residues: 0
  loop : -1.20 (0.42), residues: 189

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP G  18 
 HIS   0.002   0.001   HIS A 136 
 PHE   0.029   0.002   PHE D  15 
 TYR   0.039   0.002   TYR B 237 
 ARG   0.007   0.001   ARG A 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03916 (  868)
  hydrogen bonds       : angle       4.40200 ( 2574)
  covalent geometry    : bond        0.00367 (10056)
  covalent geometry    : angle       0.78954 (13541)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 276
  time to evaluate  : 1.092 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.8691 (mpp) cc_final: 0.8429 (mpp)
REVERT: A   98 MET cc_start: 0.4172 (mtp) cc_final: 0.3839 (mtt)
REVERT: A  195 MET cc_start: 0.8996 (mmm) cc_final: 0.8604 (mtt)
REVERT: A  230 ASN cc_start: 0.8852 (t0) cc_final: 0.8431 (p0)
REVERT: B  122 ARG cc_start: 0.9010 (ttp80) cc_final: 0.8734 (ttp80)
REVERT: B  134 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7181 (tm-30)
REVERT: B  138 GLN cc_start: 0.8946 (mm-40) cc_final: 0.8713 (mm-40)
REVERT: B  153 MET cc_start: 0.8584 (tpp) cc_final: 0.7903 (tpp)
REVERT: B  194 ASN cc_start: 0.7938 (m-40) cc_final: 0.7538 (m-40)
REVERT: C   52 MET cc_start: 0.8460 (tpp) cc_final: 0.8226 (tpp)
REVERT: C   56 PHE cc_start: 0.7325 (m-80) cc_final: 0.7002 (m-80)
REVERT: D   15 PHE cc_start: 0.8450 (m-80) cc_final: 0.8200 (m-80)
REVERT: D   83 MET cc_start: 0.9376 (mmm) cc_final: 0.9157 (mmm)
REVERT: D  106 GLN cc_start: 0.9087 (mm-40) cc_final: 0.8629 (mm-40)
REVERT: D  208 ARG cc_start: 0.8799 (ttp80) cc_final: 0.8161 (ttp80)
REVERT: D  211 GLU cc_start: 0.9045 (tp30) cc_final: 0.8791 (tp30)
REVERT: D  219 MET cc_start: 0.8956 (ppp) cc_final: 0.8698 (ppp)
REVERT: D  226 GLN cc_start: 0.8866 (mm110) cc_final: 0.8570 (mm110)
REVERT: E   68 PHE cc_start: 0.7822 (m-80) cc_final: 0.7278 (m-10)
REVERT: E   83 MET cc_start: 0.9001 (mpp) cc_final: 0.8748 (mpp)
REVERT: E  117 ASP cc_start: 0.8127 (OUTLIER) cc_final: 0.7593 (p0)
REVERT: E  210 GLN cc_start: 0.9080 (mt0) cc_final: 0.8865 (mt0)
REVERT: E  211 GLU cc_start: 0.8732 (mm-30) cc_final: 0.8414 (mm-30)
REVERT: E  214 ASN cc_start: 0.8976 (m-40) cc_final: 0.8645 (m110)
REVERT: E  218 ILE cc_start: 0.8604 (mt) cc_final: 0.8339 (mm)
REVERT: F   26 MET cc_start: 0.9276 (mmt) cc_final: 0.8985 (mmm)
  outliers start: 60
  outliers final: 43
  residues processed: 308
  average time/residue: 0.2037
  time to fit residues: 88.5236
Evaluate side-chains
  306 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 262
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  200 ILE
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  158 THR
Chi-restraints excluded: chain B residue  179 MET
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  226 GLN
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue   48 MET
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain C residue  200 ILE
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain D residue   33 THR
Chi-restraints excluded: chain D residue  101 ASN
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  156 ILE
Chi-restraints excluded: chain D residue  166 LEU
Chi-restraints excluded: chain D residue  193 SER
Chi-restraints excluded: chain E residue   20 MET
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   76 LEU
Chi-restraints excluded: chain E residue  105 MET
Chi-restraints excluded: chain E residue  117 ASP
Chi-restraints excluded: chain E residue  133 ASP
Chi-restraints excluded: chain E residue  160 VAL
Chi-restraints excluded: chain G residue   29 LEU
Chi-restraints excluded: chain G residue   35 LEU
Chi-restraints excluded: chain G residue   60 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 112 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 118 optimal weight:    0.9980
   chunk 66 optimal weight:    0.6980
   chunk 76 optimal weight:    0.5980
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 GLN
B 229 GLN
** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 106 GLN
** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 194 ASN
D 229 GLN
** E  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  49 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.123679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.091333 restraints weight = 30248.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.093962 restraints weight = 17809.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.095625 restraints weight = 12864.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.2783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10056  Z= 0.150
  Angle     :  0.796  14.409  13541  Z= 0.391
  Chirality :  0.044   0.299   1596
  Planarity :  0.004   0.036   1725
  Dihedral  :  4.480  55.802   1372
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 15.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  5.57 %
    Allowed  : 24.86 %
    Favored  : 69.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.48 (0.23), residues: 1298
  helix:  1.37 (0.16), residues: 1112
  sheet:  None (None), residues: 0
  loop : -1.16 (0.44), residues: 186

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP G  18 
 HIS   0.002   0.001   HIS C 116 
 PHE   0.026   0.002   PHE F  39 
 TYR   0.037   0.002   TYR B 237 
 ARG   0.009   0.001   ARG A 122 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03905 (  868)
  hydrogen bonds       : angle       4.37409 ( 2574)
  covalent geometry    : bond        0.00335 (10056)
  covalent geometry    : angle       0.79569 (13541)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 277
  time to evaluate  : 1.102 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.8762 (mpp) cc_final: 0.8419 (mpp)
REVERT: A   98 MET cc_start: 0.4157 (mtp) cc_final: 0.3777 (mtt)
REVERT: A  195 MET cc_start: 0.9038 (mmm) cc_final: 0.8613 (mtt)
REVERT: A  230 ASN cc_start: 0.8836 (t0) cc_final: 0.8496 (p0)
REVERT: B  122 ARG cc_start: 0.9026 (ttp80) cc_final: 0.8748 (ttp80)
REVERT: B  134 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7162 (tm-30)
REVERT: B  138 GLN cc_start: 0.8927 (mm-40) cc_final: 0.8673 (mm-40)
REVERT: B  153 MET cc_start: 0.8567 (tpp) cc_final: 0.7947 (tpp)
REVERT: B  210 GLN cc_start: 0.8780 (tt0) cc_final: 0.8188 (pp30)
REVERT: B  211 GLU cc_start: 0.8671 (tp30) cc_final: 0.8340 (tp30)
REVERT: C   52 MET cc_start: 0.8485 (tpp) cc_final: 0.8255 (tpp)
REVERT: C   56 PHE cc_start: 0.7299 (m-80) cc_final: 0.6926 (m-80)
REVERT: D   15 PHE cc_start: 0.8405 (m-80) cc_final: 0.8165 (m-80)
REVERT: D  106 GLN cc_start: 0.9125 (mm110) cc_final: 0.8825 (mm-40)
REVERT: D  208 ARG cc_start: 0.8778 (ttp80) cc_final: 0.8105 (ttp80)
REVERT: D  211 GLU cc_start: 0.9042 (tp30) cc_final: 0.8744 (tp30)
REVERT: D  216 ARG cc_start: 0.9354 (ttt180) cc_final: 0.8994 (tpp80)
REVERT: D  219 MET cc_start: 0.8887 (ppp) cc_final: 0.8605 (ppp)
REVERT: D  226 GLN cc_start: 0.8849 (mm110) cc_final: 0.8576 (mm110)
REVERT: E   68 PHE cc_start: 0.7820 (m-80) cc_final: 0.7286 (m-10)
REVERT: E  117 ASP cc_start: 0.8073 (OUTLIER) cc_final: 0.7550 (p0)
REVERT: E  210 GLN cc_start: 0.9075 (mt0) cc_final: 0.8875 (mt0)
REVERT: E  214 ASN cc_start: 0.9053 (m-40) cc_final: 0.8717 (m110)
REVERT: E  218 ILE cc_start: 0.8593 (mt) cc_final: 0.8217 (mm)
REVERT: F   26 MET cc_start: 0.9248 (mmt) cc_final: 0.9010 (mmm)
REVERT: G   42 MET cc_start: 0.8552 (tmm) cc_final: 0.7993 (tmm)
  outliers start: 58
  outliers final: 38
  residues processed: 308
  average time/residue: 0.2046
  time to fit residues: 89.0978
Evaluate side-chains
  307 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 268
  time to evaluate  : 1.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  158 THR
Chi-restraints excluded: chain B residue  179 MET
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  226 GLN
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain C residue  200 ILE
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain D residue   33 THR
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  156 ILE
Chi-restraints excluded: chain D residue  165 MET
Chi-restraints excluded: chain D residue  166 LEU
Chi-restraints excluded: chain D residue  193 SER
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   76 LEU
Chi-restraints excluded: chain E residue  105 MET
Chi-restraints excluded: chain E residue  117 ASP
Chi-restraints excluded: chain E residue  133 ASP
Chi-restraints excluded: chain E residue  160 VAL
Chi-restraints excluded: chain G residue   29 LEU
Chi-restraints excluded: chain G residue   35 LEU
Chi-restraints excluded: chain G residue   60 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 89 optimal weight:    0.0670
   chunk 25 optimal weight:    9.9990
   chunk 27 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 78 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 47 optimal weight:    4.9990
   chunk 15 optimal weight:    0.7980
   chunk 3 optimal weight:    0.9980
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 GLN
** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 101 ASN
** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 194 ASN
** E  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.123670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.091460 restraints weight = 30512.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.093961 restraints weight = 17866.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.095688 restraints weight = 12962.304|
|-----------------------------------------------------------------------------|
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10056  Z= 0.156
  Angle     :  0.822  13.918  13541  Z= 0.405
  Chirality :  0.044   0.244   1596
  Planarity :  0.004   0.038   1725
  Dihedral  :  4.521  55.756   1372
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 16.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 25.82 %
    Favored  : 69.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.23), residues: 1298
  helix:  1.35 (0.16), residues: 1111
  sheet:  None (None), residues: 0
  loop : -1.30 (0.43), residues: 187

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP G  18 
 HIS   0.002   0.001   HIS C 116 
 PHE   0.026   0.001   PHE F  39 
 TYR   0.034   0.002   TYR B 237 
 ARG   0.008   0.000   ARG C 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03920 (  868)
  hydrogen bonds       : angle       4.40577 ( 2574)
  covalent geometry    : bond        0.00354 (10056)
  covalent geometry    : angle       0.82185 (13541)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  328 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 278
  time to evaluate  : 1.067 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   83 MET cc_start: 0.8782 (mpp) cc_final: 0.8468 (mpp)
REVERT: A   98 MET cc_start: 0.4278 (mtp) cc_final: 0.3858 (mtt)
REVERT: A  195 MET cc_start: 0.9031 (mmm) cc_final: 0.8633 (mtt)
REVERT: B  122 ARG cc_start: 0.9046 (ttp80) cc_final: 0.8803 (ttp80)
REVERT: B  134 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7183 (tm-30)
REVERT: B  138 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8646 (mm-40)
REVERT: B  153 MET cc_start: 0.8566 (tpp) cc_final: 0.7940 (tpp)
REVERT: C  169 MET cc_start: 0.7603 (tmm) cc_final: 0.7363 (tmm)
REVERT: C  208 ARG cc_start: 0.8444 (ttp-110) cc_final: 0.8224 (ttm170)
REVERT: D   15 PHE cc_start: 0.8404 (m-80) cc_final: 0.8171 (m-80)
REVERT: D  106 GLN cc_start: 0.9075 (mm110) cc_final: 0.8691 (mm-40)
REVERT: D  208 ARG cc_start: 0.8820 (ttp80) cc_final: 0.8113 (ttp80)
REVERT: D  211 GLU cc_start: 0.9023 (tp30) cc_final: 0.8738 (tp30)
REVERT: D  216 ARG cc_start: 0.9375 (ttt180) cc_final: 0.8974 (tpp80)
REVERT: D  226 GLN cc_start: 0.8880 (mm110) cc_final: 0.8638 (mm110)
REVERT: E   68 PHE cc_start: 0.7800 (m-80) cc_final: 0.7204 (m-10)
REVERT: E  105 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8566 (mmm)
REVERT: E  117 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7471 (p0)
REVERT: E  210 GLN cc_start: 0.9066 (mt0) cc_final: 0.8862 (mt0)
REVERT: E  214 ASN cc_start: 0.9047 (m-40) cc_final: 0.8758 (m110)
REVERT: E  218 ILE cc_start: 0.8726 (mt) cc_final: 0.8427 (mm)
REVERT: F   26 MET cc_start: 0.9241 (mmt) cc_final: 0.9027 (mmm)
  outliers start: 50
  outliers final: 37
  residues processed: 304
  average time/residue: 0.2181
  time to fit residues: 93.3867
Evaluate side-chains
  307 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 268
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  226 GLN
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain C residue  200 ILE
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain D residue   33 THR
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  156 ILE
Chi-restraints excluded: chain D residue  165 MET
Chi-restraints excluded: chain D residue  166 LEU
Chi-restraints excluded: chain D residue  193 SER
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   76 LEU
Chi-restraints excluded: chain E residue  105 MET
Chi-restraints excluded: chain E residue  117 ASP
Chi-restraints excluded: chain E residue  133 ASP
Chi-restraints excluded: chain E residue  160 VAL
Chi-restraints excluded: chain G residue   29 LEU
Chi-restraints excluded: chain G residue   35 LEU
Chi-restraints excluded: chain G residue   60 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 126 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 119 optimal weight:    0.6980
   chunk 96 optimal weight:    5.9990
   chunk 123 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 GLN
** C 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 194 ASN
** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 138 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.122926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.090414 restraints weight = 30319.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.093007 restraints weight = 17874.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.094674 restraints weight = 12968.428|
|-----------------------------------------------------------------------------|
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.3167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10056  Z= 0.169
  Angle     :  0.870  15.295  13541  Z= 0.425
  Chirality :  0.046   0.288   1596
  Planarity :  0.004   0.038   1725
  Dihedral  :  4.561  55.745   1372
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 17.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 26.58 %
    Favored  : 68.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.23), residues: 1298
  helix:  1.32 (0.16), residues: 1113
  sheet:  None (None), residues: 0
  loop : -1.38 (0.42), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP G  18 
 HIS   0.002   0.001   HIS D 136 
 PHE   0.031   0.002   PHE F  32 
 TYR   0.031   0.002   TYR B 237 
 ARG   0.007   0.001   ARG C 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03964 (  868)
  hydrogen bonds       : angle       4.45448 ( 2574)
  covalent geometry    : bond        0.00389 (10056)
  covalent geometry    : angle       0.86970 (13541)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 274
  time to evaluate  : 1.177 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.4185 (mtp) cc_final: 0.3941 (mtt)
REVERT: A  195 MET cc_start: 0.9157 (mmm) cc_final: 0.8794 (mtt)
REVERT: B  122 ARG cc_start: 0.9075 (ttp80) cc_final: 0.8853 (ttp80)
REVERT: B  134 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7161 (tm-30)
REVERT: B  138 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8640 (mm-40)
REVERT: B  153 MET cc_start: 0.8576 (tpp) cc_final: 0.7941 (tpp)
REVERT: B  194 ASN cc_start: 0.7978 (m-40) cc_final: 0.7481 (m-40)
REVERT: B  210 GLN cc_start: 0.8765 (tt0) cc_final: 0.8259 (pp30)
REVERT: B  211 GLU cc_start: 0.8761 (tp30) cc_final: 0.8415 (tp30)
REVERT: C   56 PHE cc_start: 0.7260 (m-80) cc_final: 0.6963 (m-80)
REVERT: C   61 ILE cc_start: 0.8760 (tp) cc_final: 0.8533 (tp)
REVERT: C  135 ARG cc_start: 0.8661 (tpp-160) cc_final: 0.8157 (tpp-160)
REVERT: C  169 MET cc_start: 0.7659 (tmm) cc_final: 0.7432 (tmm)
REVERT: D   15 PHE cc_start: 0.8387 (m-80) cc_final: 0.8155 (m-80)
REVERT: D   99 GLU cc_start: 0.8518 (mp0) cc_final: 0.8107 (pm20)
REVERT: D  106 GLN cc_start: 0.9084 (mm110) cc_final: 0.8791 (mm-40)
REVERT: D  208 ARG cc_start: 0.8805 (ttp80) cc_final: 0.8093 (ttp80)
REVERT: D  211 GLU cc_start: 0.9029 (tp30) cc_final: 0.8753 (tp30)
REVERT: D  216 ARG cc_start: 0.9345 (ttt180) cc_final: 0.9064 (tpp80)
REVERT: D  226 GLN cc_start: 0.8872 (mm110) cc_final: 0.8637 (mm110)
REVERT: E   68 PHE cc_start: 0.7881 (m-80) cc_final: 0.7329 (m-10)
REVERT: E  105 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8437 (tpp)
REVERT: E  117 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7368 (p0)
REVERT: E  153 MET cc_start: 0.8790 (mmm) cc_final: 0.8372 (tpp)
REVERT: E  214 ASN cc_start: 0.9056 (m-40) cc_final: 0.8755 (m110)
REVERT: E  218 ILE cc_start: 0.8755 (mt) cc_final: 0.8256 (mm)
REVERT: F   26 MET cc_start: 0.9237 (mmt) cc_final: 0.9020 (mmm)
REVERT: G   42 MET cc_start: 0.8570 (tmm) cc_final: 0.8332 (tmm)
  outliers start: 47
  outliers final: 39
  residues processed: 298
  average time/residue: 0.2034
  time to fit residues: 85.7473
Evaluate side-chains
  310 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 269
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  158 THR
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  206 LEU
Chi-restraints excluded: chain B residue  226 GLN
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain C residue  200 ILE
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain D residue   33 THR
Chi-restraints excluded: chain D residue   82 GLU
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  156 ILE
Chi-restraints excluded: chain D residue  165 MET
Chi-restraints excluded: chain D residue  166 LEU
Chi-restraints excluded: chain D residue  193 SER
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   59 THR
Chi-restraints excluded: chain E residue   76 LEU
Chi-restraints excluded: chain E residue  105 MET
Chi-restraints excluded: chain E residue  117 ASP
Chi-restraints excluded: chain E residue  133 ASP
Chi-restraints excluded: chain G residue   35 LEU
Chi-restraints excluded: chain G residue   37 LEU
Chi-restraints excluded: chain G residue   45 LEU
Chi-restraints excluded: chain G residue   60 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 46 optimal weight:    0.5980
   chunk 122 optimal weight:    0.6980
   chunk 114 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 40 optimal weight:    0.7980
   chunk 99 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0870
   chunk 11 optimal weight:    0.3980
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 GLN
B 229 GLN
C 194 ASN
** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 194 ASN
** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.123471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.091892 restraints weight = 30328.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.094489 restraints weight = 17603.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.096126 restraints weight = 12634.095|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.3263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10056  Z= 0.158
  Angle     :  0.901  14.742  13541  Z= 0.436
  Chirality :  0.047   0.319   1596
  Planarity :  0.004   0.038   1725
  Dihedral  :  4.597  55.571   1372
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 16.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  : 27.26 %
    Favored  : 68.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.23), residues: 1298
  helix:  1.31 (0.16), residues: 1113
  sheet:  None (None), residues: 0
  loop : -1.48 (0.40), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP F  18 
 HIS   0.002   0.001   HIS D 136 
 PHE   0.047   0.002   PHE F  32 
 TYR   0.031   0.002   TYR B 237 
 ARG   0.008   0.001   ARG C 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03977 (  868)
  hydrogen bonds       : angle       4.47609 ( 2574)
  covalent geometry    : bond        0.00354 (10056)
  covalent geometry    : angle       0.90089 (13541)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  326 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 282
  time to evaluate  : 1.150 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 MET cc_start: 0.9179 (mmm) cc_final: 0.8445 (mtt)
REVERT: B  122 ARG cc_start: 0.9052 (ttp80) cc_final: 0.8835 (ttp80)
REVERT: B  134 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7180 (tm-30)
REVERT: B  138 GLN cc_start: 0.8907 (mm-40) cc_final: 0.8624 (mm-40)
REVERT: B  153 MET cc_start: 0.8564 (tpp) cc_final: 0.7884 (tpp)
REVERT: B  194 ASN cc_start: 0.7848 (m-40) cc_final: 0.7357 (m-40)
REVERT: B  210 GLN cc_start: 0.8741 (tt0) cc_final: 0.8237 (pp30)
REVERT: B  211 GLU cc_start: 0.8732 (tp30) cc_final: 0.8393 (tp30)
REVERT: C   56 PHE cc_start: 0.7275 (m-80) cc_final: 0.7019 (m-80)
REVERT: C   61 ILE cc_start: 0.8736 (tp) cc_final: 0.8474 (tp)
REVERT: C  169 MET cc_start: 0.7542 (tmm) cc_final: 0.7339 (tmm)
REVERT: D   15 PHE cc_start: 0.8309 (m-80) cc_final: 0.8099 (m-80)
REVERT: D   28 MET cc_start: 0.7437 (ppp) cc_final: 0.6877 (tmm)
REVERT: D   99 GLU cc_start: 0.8437 (mp0) cc_final: 0.8049 (pm20)
REVERT: D  106 GLN cc_start: 0.9076 (mm110) cc_final: 0.8750 (mm-40)
REVERT: D  208 ARG cc_start: 0.8775 (ttp80) cc_final: 0.8078 (ttp80)
REVERT: D  211 GLU cc_start: 0.9026 (tp30) cc_final: 0.8747 (tp30)
REVERT: D  216 ARG cc_start: 0.9333 (ttt180) cc_final: 0.9045 (tpp80)
REVERT: D  226 GLN cc_start: 0.8843 (mm110) cc_final: 0.8620 (mm110)
REVERT: E   68 PHE cc_start: 0.7904 (m-80) cc_final: 0.6316 (m-80)
REVERT: E  105 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8458 (tpp)
REVERT: E  117 ASP cc_start: 0.7990 (OUTLIER) cc_final: 0.7467 (p0)
REVERT: E  153 MET cc_start: 0.8819 (mmm) cc_final: 0.8379 (tpp)
REVERT: E  168 ASN cc_start: 0.8235 (m-40) cc_final: 0.7725 (t0)
  outliers start: 44
  outliers final: 35
  residues processed: 305
  average time/residue: 0.2216
  time to fit residues: 95.8910
Evaluate side-chains
  308 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 271
  time to evaluate  : 1.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  226 GLN
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain C residue  200 ILE
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain D residue   33 THR
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  156 ILE
Chi-restraints excluded: chain D residue  165 MET
Chi-restraints excluded: chain D residue  166 LEU
Chi-restraints excluded: chain D residue  193 SER
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   76 LEU
Chi-restraints excluded: chain E residue  105 MET
Chi-restraints excluded: chain E residue  117 ASP
Chi-restraints excluded: chain E residue  133 ASP
Chi-restraints excluded: chain G residue   35 LEU
Chi-restraints excluded: chain G residue   45 LEU
Chi-restraints excluded: chain G residue   60 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 73 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9980
   chunk 66 optimal weight:    0.5980
   chunk 43 optimal weight:    0.5980
   chunk 87 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 110 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 GLN
** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 194 ASN
** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.123476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.091774 restraints weight = 30368.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.094279 restraints weight = 17531.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.096055 restraints weight = 12590.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.3445

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10056  Z= 0.167
  Angle     :  0.947  14.656  13541  Z= 0.462
  Chirality :  0.047   0.327   1596
  Planarity :  0.004   0.038   1725
  Dihedral  :  4.660  54.825   1372
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 17.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 28.79 %
    Favored  : 67.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.23), residues: 1298
  helix:  1.26 (0.16), residues: 1113
  sheet:  None (None), residues: 0
  loop : -1.45 (0.41), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP F  18 
 HIS   0.002   0.001   HIS D 136 
 PHE   0.043   0.002   PHE C  44 
 TYR   0.031   0.002   TYR B 237 
 ARG   0.009   0.000   ARG C 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04118 (  868)
  hydrogen bonds       : angle       4.57196 ( 2574)
  covalent geometry    : bond        0.00375 (10056)
  covalent geometry    : angle       0.94658 (13541)

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

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

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2596 Ramachandran restraints generated.
    1298 Oldfield, 0 Emsley, 1298 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 272
  time to evaluate  : 1.138 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 MET cc_start: 0.9181 (mmm) cc_final: 0.8506 (mtt)
REVERT: B   72 GLU cc_start: 0.8272 (tp30) cc_final: 0.7971 (mp0)
REVERT: B   83 MET cc_start: 0.8849 (mpp) cc_final: 0.8505 (mmt)
REVERT: B  122 ARG cc_start: 0.9020 (ttp80) cc_final: 0.8804 (ttp80)
REVERT: B  134 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7184 (tm-30)
REVERT: B  138 GLN cc_start: 0.8902 (mm-40) cc_final: 0.8619 (mm-40)
REVERT: B  153 MET cc_start: 0.8600 (tpp) cc_final: 0.7926 (tpp)
REVERT: B  194 ASN cc_start: 0.7881 (m-40) cc_final: 0.7391 (m-40)
REVERT: C   56 PHE cc_start: 0.7299 (m-80) cc_final: 0.7075 (m-80)
REVERT: C  208 ARG cc_start: 0.8516 (ttp-110) cc_final: 0.8241 (ttp80)
REVERT: D   28 MET cc_start: 0.7642 (ppp) cc_final: 0.7306 (ppp)
REVERT: D   99 GLU cc_start: 0.8450 (mp0) cc_final: 0.8020 (pm20)
REVERT: D  106 GLN cc_start: 0.9091 (mm110) cc_final: 0.8788 (mm-40)
REVERT: D  134 GLU cc_start: 0.8305 (pp20) cc_final: 0.7418 (pp20)
REVERT: D  208 ARG cc_start: 0.8779 (ttp80) cc_final: 0.8092 (ttp80)
REVERT: D  211 GLU cc_start: 0.9043 (tp30) cc_final: 0.8759 (tp30)
REVERT: D  216 ARG cc_start: 0.9334 (ttt180) cc_final: 0.9051 (tpp80)
REVERT: D  226 GLN cc_start: 0.8853 (mm110) cc_final: 0.8616 (mm110)
REVERT: E  105 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8471 (tpp)
REVERT: E  117 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7431 (p0)
REVERT: E  153 MET cc_start: 0.8828 (mmm) cc_final: 0.8431 (tpp)
REVERT: E  210 GLN cc_start: 0.9265 (mt0) cc_final: 0.8970 (mp10)
  outliers start: 40
  outliers final: 33
  residues processed: 293
  average time/residue: 0.2218
  time to fit residues: 92.9670
Evaluate side-chains
  300 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 265
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 LEU
Chi-restraints excluded: chain A residue   15 PHE
Chi-restraints excluded: chain A residue  120 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  192 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain B residue   20 MET
Chi-restraints excluded: chain B residue   30 VAL
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   33 THR
Chi-restraints excluded: chain B residue   67 MET
Chi-restraints excluded: chain B residue  193 SER
Chi-restraints excluded: chain B residue  204 LEU
Chi-restraints excluded: chain B residue  226 GLN
Chi-restraints excluded: chain B residue  249 LEU
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain C residue  140 THR
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain C residue  200 ILE
Chi-restraints excluded: chain C residue  202 ASP
Chi-restraints excluded: chain C residue  206 LEU
Chi-restraints excluded: chain D residue   33 THR
Chi-restraints excluded: chain D residue  140 THR
Chi-restraints excluded: chain D residue  156 ILE
Chi-restraints excluded: chain D residue  193 SER
Chi-restraints excluded: chain D residue  195 MET
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   76 LEU
Chi-restraints excluded: chain E residue  105 MET
Chi-restraints excluded: chain E residue  117 ASP
Chi-restraints excluded: chain G residue   35 LEU
Chi-restraints excluded: chain G residue   45 LEU
Chi-restraints excluded: chain G residue   60 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9980
   chunk 35 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 8 optimal weight:    9.9990
   chunk 52 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 67 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 226 GLN
** D 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 194 ASN
** D 229 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.123449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.090941 restraints weight = 30231.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.093475 restraints weight = 17804.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.095078 restraints weight = 12951.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
moved from start:          0.3569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10056  Z= 0.172
  Angle     :  0.953  14.601  13541  Z= 0.465
  Chirality :  0.048   0.322   1596
  Planarity :  0.004   0.037   1725
  Dihedral  :  4.681  54.587   1372
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 17.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 29.17 %
    Favored  : 66.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.23), residues: 1298
  helix:  1.21 (0.16), residues: 1113
  sheet:  None (None), residues: 0
  loop : -1.55 (0.40), residues: 185

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP F  18 
 HIS   0.002   0.001   HIS D 136 
 PHE   0.041   0.002   PHE D  15 
 TYR   0.030   0.002   TYR B 237 
 ARG   0.009   0.000   ARG C 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04177 (  868)
  hydrogen bonds       : angle       4.62770 ( 2574)
  covalent geometry    : bond        0.00389 (10056)
  covalent geometry    : angle       0.95329 (13541)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3789.13 seconds
wall clock time: 67 minutes 25.94 seconds (4045.94 seconds total)