Starting phenix.real_space_refine
on Wed Apr 30 17:18:13 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yjh_39342/04_2025/8yjh_39342.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yjh_39342/04_2025/8yjh_39342.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.68
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yjh_39342/04_2025/8yjh_39342.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yjh_39342/04_2025/8yjh_39342.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yjh_39342/04_2025/8yjh_39342.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yjh_39342/04_2025/8yjh_39342.cif"
  }
  resolution = 3.68
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 55 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      53      5.49       5
     S      63      5.16       5
     C    5965      2.51       5
     N    1631      2.21       5
     O    2023      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9735
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "B"
      Number of atoms: 1963
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 1963
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 7, 'TRANS': 247}
    Chain: "C"
      Number of atoms: 1963
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 255, 1963
          Classifications: {'peptide': 255}
          Link IDs: {'PTRANS': 7, 'TRANS': 247}
    Chain: "A"
      Number of atoms: 1955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 1955
          Classifications: {'peptide': 254}
          Link IDs: {'PTRANS': 7, 'TRANS': 246}
    Chain: "D"
      Number of atoms: 2769
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 351, 2769
          Classifications: {'peptide': 351}
          Link IDs: {'PTRANS': 15, 'TRANS': 335}
    Chain: "J"
      Number of atoms: 308
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 308
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
    Chain: "E"
      Number of atoms: 512
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 512
          Classifications: {'DNA': 25}
          Link IDs: {'rna3p': 24}
    Chain: "F"
      Number of atoms: 205
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 205
          Classifications: {'DNA': 10}
          Link IDs: {'rna3p': 9}
    Chain: "H"
      Number of atoms: 60
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 60
          Classifications: {'DNA': 3}
          Link IDs: {'rna3p': 2}
  Time building chain proxies: 6.39, per 1000 atoms: 0.66
  Number of scatterers: 9735
  At special positions: 0
  Unit cell: (106.24, 95.45, 101.26, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      63     16.00
     P      53     15.00
     O    2023      8.00
     N    1631      7.00
     C    5965      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 135 " - pdb=" SG  CYS C 162 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.33
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      30 helices and 10 sheets defined
      28.9% alpha, 25.4% beta
      14 base pairs and 44 stacking pairs defined.
    Time for finding SS restraints: 3.84
  Creating SS restraints...
    Processing helix  chain 'B' and resid 8 through 19
      removed outlier: 4.262A  pdb=" N   LEU B  12 " --> pdb=" O   GLN B   8 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 72 through 81
    Processing helix  chain 'B' and resid 141 through 152
    Processing helix  chain 'B' and resid 209 through 217
    Processing helix  chain 'B' and resid 218 through 222
      removed outlier: 3.975A  pdb=" N   LEU B 221 " --> pdb=" O   ALA B 218 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER B 222 " --> pdb=" O   THR B 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 218 through 222'
    Processing helix  chain 'C' and resid 9 through 20
      removed outlier: 3.729A  pdb=" N   LYS C  13 " --> pdb=" O   GLY C   9 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 81
    Processing helix  chain 'C' and resid 141 through 153
    Processing helix  chain 'C' and resid 209 through 217
    Processing helix  chain 'C' and resid 218 through 222
      removed outlier: 3.528A  pdb=" N   LEU C 221 " --> pdb=" O   ALA C 218 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   SER C 222 " --> pdb=" O   THR C 219 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 218 through 222'
    Processing helix  chain 'A' and resid 8 through 19
      removed outlier: 4.365A  pdb=" N   LEU A  12 " --> pdb=" O   GLN A   8 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 80
    Processing helix  chain 'A' and resid 141 through 152
    Processing helix  chain 'A' and resid 209 through 216
    Processing helix  chain 'A' and resid 217 through 219
      No H-bonds generated for 'chain 'A' and resid 217 through 219'
    Processing helix  chain 'D' and resid 5 through 14
    Processing helix  chain 'D' and resid 35 through 45
      removed outlier: 3.744A  pdb=" N   ALA D  45 " --> pdb=" O   GLN D  41 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 61 through 76
    Processing helix  chain 'D' and resid 93 through 118
      removed outlier: 3.711A  pdb=" N   GLN D 112 " --> pdb=" O   GLU D 108 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   GLN D 113 " --> pdb=" O   LYS D 109 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 121 through 128
    Processing helix  chain 'D' and resid 134 through 149
      removed outlier: 3.561A  pdb=" N   GLY D 149 " --> pdb=" O   LEU D 145 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 158 through 169
      removed outlier: 3.767A  pdb=" N   SER D 162 " --> pdb=" O   GLU D 158 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 180 through 185
      removed outlier: 3.967A  pdb=" N   THR D 184 " --> pdb=" O   MET D 180 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 216
    Processing helix  chain 'D' and resid 219 through 231
    Processing helix  chain 'D' and resid 242 through 252
      removed outlier: 3.650A  pdb=" N   VAL D 247 " --> pdb=" O   PRO D 243 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   ASP D 248 " --> pdb=" O   LYS D 244 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   LYS D 252 " --> pdb=" O   ASP D 248 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 255 through 263
      removed outlier: 3.744A  pdb=" N   ILE D 259 " --> pdb=" O   SER D 255 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 278 through 285
      removed outlier: 3.503A  pdb=" N   PHE D 283 " --> pdb=" O   ALA D 279 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 303 through 312
    Processing helix  chain 'D' and resid 317 through 332
      removed outlier: 3.836A  pdb=" N   ILE D 321 " --> pdb=" O   SER D 317 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 59 through 61
    Processing sheet with id=AA2, first strand: chain 'B' and resid 67 through 71
      removed outlier: 3.713A  pdb=" N   MET B  68 " --> pdb=" O   TRP B  28 " (cutoff:3.500A)
      removed outlier: 5.494A  pdb=" N   CYS B  27 " --> pdb=" O   GLN B  38 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   GLN B  38 " --> pdb=" O   CYS B  27 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   GLY B  34 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU B  47 " --> pdb=" O   TYR B 250 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLU B 238 " --> pdb=" O   THR B 226 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   LYS B 240 " --> pdb=" O   THR B 224 " (cutoff:3.500A)
      removed outlier: 6.184A  pdb=" N   THR B 224 " --> pdb=" O   LYS B 240 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 110 through 112
      removed outlier: 3.563A  pdb=" N   VAL B 111 " --> pdb=" O   LYS A 181 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LEU A 205 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 206 through 207
      removed outlier: 4.523A  pdb=" N   ALA B 157 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   SER B 172 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   VAL B 167 " --> pdb=" O   LEU B 182 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ILE C  88 " --> pdb=" O   LEU C   6 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 67 through 71
      removed outlier: 3.863A  pdb=" N   ALA C  26 " --> pdb=" O   VAL C  70 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   GLU C  25 " --> pdb=" O   MET C  40 " (cutoff:3.500A)
      removed outlier: 5.530A  pdb=" N   MET C  40 " --> pdb=" O   GLU C  25 " (cutoff:3.500A)
      removed outlier: 5.275A  pdb=" N   CYS C  27 " --> pdb=" O   GLN C  38 " (cutoff:3.500A)
      removed outlier: 4.477A  pdb=" N   GLN C  38 " --> pdb=" O   CYS C  27 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLY C 245 " --> pdb=" O   ILE C 241 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LEU C 251 " --> pdb=" O   LEU C 235 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLU C 238 " --> pdb=" O   THR C 226 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   LYS C 240 " --> pdb=" O   THR C 224 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   THR C 224 " --> pdb=" O   LYS C 240 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL C 136 " --> pdb=" O   GLU C 198 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   GLU C 198 " --> pdb=" O   VAL C 136 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 124 through 127
      removed outlier: 3.753A  pdb=" N   GLY D 348 " --> pdb=" O   GLN C 125 " (cutoff:3.500A)
      removed outlier: 6.093A  pdb=" N   GLY C 127 " --> pdb=" O   VAL D 346 " (cutoff:3.500A)
      removed outlier: 6.363A  pdb=" N   VAL D 346 " --> pdb=" O   GLY C 127 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 204 through 208
      removed outlier: 4.863A  pdb=" N   ALA C 157 " --> pdb=" O   SER C 172 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   SER C 172 " --> pdb=" O   ALA C 157 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   LEU A  99 " --> pdb=" O   MET A 116 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   THR A  59 " --> pdb=" O   ARG A   5 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 67 through 71
      removed outlier: 3.620A  pdb=" N   MET A  68 " --> pdb=" O   TRP A  28 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   GLY A  34 " --> pdb=" O   SER A  31 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   GLY A 245 " --> pdb=" O   ILE A 241 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   TYR A 249 " --> pdb=" O   VAL A 237 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   SER A 228 " --> pdb=" O   VAL A 236 " (cutoff:3.500A)
      removed outlier: 4.497A  pdb=" N   LYS A 240 " --> pdb=" O   THR A 224 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   THR A 224 " --> pdb=" O   LYS A 240 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL A 136 " --> pdb=" O   GLU A 198 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   GLU A 198 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 18 through 21
      removed outlier: 3.571A  pdb=" N   ARG D  19 " --> pdb=" O   GLU D 206 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ILE D 204 " --> pdb=" O   ASN D  21 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 152 through 154
      removed outlier: 6.799A  pdb=" N   LYS D  30 " --> pdb=" O   ALA D 174 " (cutoff:3.500A)
      removed outlier: 7.133A  pdb=" N   ALA D 176 " --> pdb=" O   LYS D  30 " (cutoff:3.500A)
      removed outlier: 5.619A  pdb=" N   ALA D  32 " --> pdb=" O   ALA D 176 " (cutoff:3.500A)

    403 hydrogen bonds defined for protein.
    1152 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      28 hydrogen bonds
      56 hydrogen bond angles
      0 basepair planarities
      14 basepair parallelities
      44 stacking parallelities
  Total time for adding SS restraints: 3.57

  Time building geometry restraints manager: 2.75 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2732
        1.34 -     1.46: 2131
        1.46 -     1.58: 4920
        1.58 -     1.70: 102
        1.70 -     1.82: 102
  Bond restraints: 9987
  Sorted by residual:
  bond pdb=" C   THR C 219 "
       pdb=" N   PRO C 220 "
    ideal  model  delta    sigma   weight residual
    1.335  1.362 -0.027 9.40e-03 1.13e+04 8.22e+00
  bond pdb=" CB  ASP C 113 "
       pdb=" CG  ASP C 113 "
    ideal  model  delta    sigma   weight residual
    1.516  1.570 -0.054 2.50e-02 1.60e+03 4.66e+00
  bond pdb=" CB  GLU B 132 "
       pdb=" CG  GLU B 132 "
    ideal  model  delta    sigma   weight residual
    1.520  1.579 -0.059 3.00e-02 1.11e+03 3.91e+00
  bond pdb=" CB  ASP A 113 "
       pdb=" CG  ASP A 113 "
    ideal  model  delta    sigma   weight residual
    1.516  1.562 -0.046 2.50e-02 1.60e+03 3.38e+00
  bond pdb=" CB  GLU B 174 "
       pdb=" CG  GLU B 174 "
    ideal  model  delta    sigma   weight residual
    1.520  1.566 -0.046 3.00e-02 1.11e+03 2.31e+00
  ... (remaining 9982 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.27: 13130
        2.27 -     4.53: 441
        4.53 -     6.80: 78
        6.80 -     9.06: 37
        9.06 -    11.33: 10
  Bond angle restraints: 13696
  Sorted by residual:
  angle pdb=" CA  GLU B 132 "
        pdb=" CB  GLU B 132 "
        pdb=" CG  GLU B 132 "
      ideal   model   delta    sigma   weight residual
     114.10  123.74   -9.64 2.00e+00 2.50e-01 2.32e+01
  angle pdb=" C   ALA A 242 "
        pdb=" N   ASP A 243 "
        pdb=" CA  ASP A 243 "
      ideal   model   delta    sigma   weight residual
     121.54  130.43   -8.89 1.91e+00 2.74e-01 2.16e+01
  angle pdb=" O   GLN A 131 "
        pdb=" C   GLN A 131 "
        pdb=" N   GLU A 132 "
      ideal   model   delta    sigma   weight residual
     122.39  128.16   -5.77 1.29e+00 6.01e-01 2.00e+01
  angle pdb=" C   LYS B 254 "
        pdb=" N   ILE B 255 "
        pdb=" CA  ILE B 255 "
      ideal   model   delta    sigma   weight residual
     121.70  129.65   -7.95 1.80e+00 3.09e-01 1.95e+01
  angle pdb=" CA  GLU A 132 "
        pdb=" CB  GLU A 132 "
        pdb=" CG  GLU A 132 "
      ideal   model   delta    sigma   weight residual
     114.10  122.26   -8.16 2.00e+00 2.50e-01 1.66e+01
  ... (remaining 13691 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.60: 5024
       17.60 -    35.19: 688
       35.19 -    52.79: 280
       52.79 -    70.38: 48
       70.38 -    87.98: 13
  Dihedral angle restraints: 6053
    sinusoidal: 2807
      harmonic: 3246
  Sorted by residual:
  dihedral pdb=" CA  MET C 199 "
           pdb=" C   MET C 199 "
           pdb=" N   ASN C 200 "
           pdb=" CA  ASN C 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.09   23.91     0      5.00e+00 4.00e-02 2.29e+01
  dihedral pdb=" CA  ASN B  71 "
           pdb=" C   ASN B  71 "
           pdb=" N   LEU B  72 "
           pdb=" CA  LEU B  72 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.78  -23.22     0      5.00e+00 4.00e-02 2.16e+01
  dihedral pdb=" CA  ILE D  33 "
           pdb=" C   ILE D  33 "
           pdb=" N   ASP D  34 "
           pdb=" CA  ASP D  34 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.56   22.44     0      5.00e+00 4.00e-02 2.01e+01
  ... (remaining 6050 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1181
       0.054 -    0.108: 290
       0.108 -    0.162: 80
       0.162 -    0.216: 21
       0.216 -    0.270: 6
  Chirality restraints: 1578
  Sorted by residual:
  chirality pdb=" CA  THR A 219 "
            pdb=" N   THR A 219 "
            pdb=" C   THR A 219 "
            pdb=" CB  THR A 219 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.26    0.27 2.00e-01 2.50e+01 1.82e+00
  chirality pdb=" CB  VAL A 236 "
            pdb=" CA  VAL A 236 "
            pdb=" CG1 VAL A 236 "
            pdb=" CG2 VAL A 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CB  ILE D  44 "
            pdb=" CA  ILE D  44 "
            pdb=" CG1 ILE D  44 "
            pdb=" CG2 ILE D  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.24 2.00e-01 2.50e+01 1.45e+00
  ... (remaining 1575 not shown)

  Planarity restraints: 1583
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP D 274 "   -0.020 2.00e-02 2.50e+03   2.32e-02 1.35e+01
        pdb=" CG  TRP D 274 "    0.062 2.00e-02 2.50e+03
        pdb=" CD1 TRP D 274 "   -0.032 2.00e-02 2.50e+03
        pdb=" CD2 TRP D 274 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP D 274 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP D 274 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP D 274 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ2 TRP D 274 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP D 274 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP D 274 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 132 "    0.015 2.00e-02 2.50e+03   2.99e-02 8.92e+00
        pdb=" C   GLU A 132 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   GLU A 132 "    0.020 2.00e-02 2.50e+03
        pdb=" N   TYR A 133 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A   5 "   -0.236 9.50e-02 1.11e+02   1.07e-01 8.83e+00
        pdb=" NE  ARG A   5 "    0.023 2.00e-02 2.50e+03
        pdb=" CZ  ARG A   5 "   -0.021 2.00e-02 2.50e+03
        pdb=" NH1 ARG A   5 "    0.010 2.00e-02 2.50e+03
        pdb=" NH2 ARG A   5 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1580 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1834
        2.79 -     3.31: 8023
        3.31 -     3.84: 17211
        3.84 -     4.37: 19369
        4.37 -     4.90: 32874
  Nonbonded interactions: 79311
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 192 "
            pdb=" OG  SER A 223 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" O   MET D  67 "
            pdb=" OG1 THR D  71 "
     model   vdw
     2.306 3.040
  nonbonded pdb=" O   THR C 216 "
            pdb=" OG1 THR C 219 "
     model   vdw
     2.352 3.040
  nonbonded pdb=" OH  TYR C 211 "
            pdb=" O   SER D  25 "
     model   vdw
     2.357 3.040
  nonbonded pdb=" O   ASN B  71 "
            pdb=" OG  SER B  74 "
     model   vdw
     2.366 3.040
  ... (remaining 79306 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.430
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     28.680
  Find NCS groups from input model:        0.290
  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:   35.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
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   0.062   9988  Z= 0.237
  Angle     :  1.042  11.331  13698  Z= 0.537
  Chirality :  0.056   0.270   1578
  Planarity :  0.007   0.107   1583
  Dihedral  : 18.972  87.975   3944
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 4.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  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: -3.68 (0.21), residues: 1107
  helix: -2.74 (0.20), residues: 307
  sheet: -2.02 (0.27), residues: 331
  loop : -2.36 (0.23), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.062   0.004   TRP D 274 
 HIS   0.007   0.001   HIS D  63 
 PHE   0.037   0.003   PHE D  27 
 TYR   0.022   0.003   TYR B 133 
 ARG   0.024   0.001   ARG A   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19943 (  431)
  hydrogen bonds       : angle       9.94013 ( 1208)
  SS BOND              : bond        0.00363 (    1)
  SS BOND              : angle       2.40126 (    2)
  covalent geometry    : bond        0.00511 ( 9987)
  covalent geometry    : angle       1.04158 (13696)

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

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 1.023 
Fit side-chains
REVERT: B   87 ILE cc_start: 0.8076 (mp) cc_final: 0.7636 (mt)
REVERT: B  184 GLN cc_start: 0.6862 (tm-30) cc_final: 0.6492 (tm-30)
REVERT: C  201 GLU cc_start: 0.7192 (pt0) cc_final: 0.6919 (pt0)
  outliers start: 0
  outliers final: 0
  residues processed: 162
  average time/residue: 0.1671
  time to fit residues: 41.2570
Evaluate side-chains
  126 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.9990
   chunk 86 optimal weight:    6.9990
   chunk 47 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 89 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 103 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
C 246 HIS
** D  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.142415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.110958 restraints weight = 14483.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.113650 restraints weight = 9719.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.115583 restraints weight = 7251.586|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9988  Z= 0.178
  Angle     :  0.626   6.270  13698  Z= 0.338
  Chirality :  0.045   0.166   1578
  Planarity :  0.004   0.036   1583
  Dihedral  : 19.320  72.526   1802
  Min Nonbonded Distance : 2.588

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  8.57 %
    Favored  : 90.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.43 (0.22), residues: 1107
  helix: -0.72 (0.27), residues: 304
  sheet: -1.77 (0.27), residues: 327
  loop : -1.96 (0.24), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP D 274 
 HIS   0.009   0.001   HIS D 137 
 PHE   0.012   0.001   PHE D 126 
 TYR   0.015   0.002   TYR B 133 
 ARG   0.008   0.001   ARG A   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04056 (  431)
  hydrogen bonds       : angle       6.58455 ( 1208)
  SS BOND              : bond        0.00319 (    1)
  SS BOND              : angle       1.10093 (    2)
  covalent geometry    : bond        0.00393 ( 9987)
  covalent geometry    : angle       0.62615 (13696)

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

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 141
  time to evaluate  : 1.035 
Fit side-chains
REVERT: B  177 ASN cc_start: 0.7826 (t0) cc_final: 0.7571 (t0)
REVERT: B  199 MET cc_start: 0.7437 (tmm) cc_final: 0.6775 (tmm)
REVERT: C    1 MET cc_start: 0.7600 (tpp) cc_final: 0.7366 (tpp)
REVERT: C  201 GLU cc_start: 0.7355 (pt0) cc_final: 0.7117 (pt0)
REVERT: A   68 MET cc_start: 0.8039 (ptp) cc_final: 0.7809 (ptp)
REVERT: A  135 CYS cc_start: 0.8117 (p) cc_final: 0.7835 (p)
REVERT: D  127 THR cc_start: 0.8934 (p) cc_final: 0.8664 (t)
REVERT: D  326 LYS cc_start: 0.8083 (pttm) cc_final: 0.7420 (mmtp)
  outliers start: 11
  outliers final: 8
  residues processed: 147
  average time/residue: 0.1871
  time to fit residues: 40.8879
Evaluate side-chains
  130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 122
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  251 LEU
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain D residue  256 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 86 optimal weight:    5.9990
   chunk 31 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 73 optimal weight:    0.0470
   chunk 83 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.9280

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

Flipped N/Q/H residues before XYZ refinement:
** D  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.138681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.106821 restraints weight = 14694.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.109541 restraints weight = 9753.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.111431 restraints weight = 7326.322|
|-----------------------------------------------------------------------------|
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.2655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9988  Z= 0.189
  Angle     :  0.611   9.754  13698  Z= 0.321
  Chirality :  0.044   0.257   1578
  Planarity :  0.004   0.039   1583
  Dihedral  : 18.833  75.826   1802
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 11.46 %
    Favored  : 86.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.00 (0.23), residues: 1107
  helix: -0.05 (0.28), residues: 307
  sheet: -1.79 (0.26), residues: 329
  loop : -1.72 (0.25), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP D 274 
 HIS   0.005   0.001   HIS D 137 
 PHE   0.010   0.002   PHE D 126 
 TYR   0.016   0.002   TYR B 133 
 ARG   0.003   0.000   ARG A   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03776 (  431)
  hydrogen bonds       : angle       6.11091 ( 1208)
  SS BOND              : bond        0.00155 (    1)
  SS BOND              : angle       0.82111 (    2)
  covalent geometry    : bond        0.00432 ( 9987)
  covalent geometry    : angle       0.61071 (13696)

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

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 1.143 
Fit side-chains
REVERT: B   36 ASN cc_start: 0.8483 (m-40) cc_final: 0.8224 (m-40)
REVERT: B  177 ASN cc_start: 0.7841 (t0) cc_final: 0.7574 (t0)
REVERT: B  184 GLN cc_start: 0.7349 (pp30) cc_final: 0.7013 (pp30)
REVERT: B  199 MET cc_start: 0.7344 (tmm) cc_final: 0.7102 (tmm)
REVERT: C    1 MET cc_start: 0.7641 (tpp) cc_final: 0.7366 (tpp)
REVERT: C  201 GLU cc_start: 0.7380 (pt0) cc_final: 0.7166 (pt0)
REVERT: A   68 MET cc_start: 0.8050 (ptp) cc_final: 0.7833 (ptp)
REVERT: A  135 CYS cc_start: 0.8174 (p) cc_final: 0.7830 (p)
REVERT: D   40 TYR cc_start: 0.7886 (m-10) cc_final: 0.7528 (m-10)
REVERT: D   44 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8328 (mp)
REVERT: D  139 ASP cc_start: 0.6993 (m-30) cc_final: 0.6764 (m-30)
REVERT: D  326 LYS cc_start: 0.8244 (pttm) cc_final: 0.7578 (mmtp)
  outliers start: 19
  outliers final: 13
  residues processed: 140
  average time/residue: 0.2005
  time to fit residues: 41.3352
Evaluate side-chains
  130 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 116
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   38 GLN
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue  123 VAL
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain A residue  116 MET
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain D residue   44 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 88 optimal weight:    4.9990
   chunk 47 optimal weight:    0.6980
   chunk 103 optimal weight:    0.1980
   chunk 21 optimal weight:    0.5980
   chunk 84 optimal weight:    0.8980
   chunk 64 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9990
   chunk 18 optimal weight:    0.6980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 184 GLN
** D  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.139551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.108060 restraints weight = 14350.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.110825 restraints weight = 9500.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.112736 restraints weight = 7119.016|
|-----------------------------------------------------------------------------|
r_work (final): 0.3535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.2807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9988  Z= 0.146
  Angle     :  0.569   8.672  13698  Z= 0.301
  Chirality :  0.043   0.234   1578
  Planarity :  0.003   0.033   1583
  Dihedral  : 18.690  75.787   1802
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 11.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 12.49 %
    Favored  : 85.04 %
  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: -1.68 (0.24), residues: 1107
  helix:  0.37 (0.29), residues: 308
  sheet: -1.88 (0.27), residues: 301
  loop : -1.47 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP D 274 
 HIS   0.004   0.001   HIS D 137 
 PHE   0.009   0.001   PHE D 126 
 TYR   0.015   0.002   TYR A 250 
 ARG   0.003   0.000   ARG D 211 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03179 (  431)
  hydrogen bonds       : angle       5.80534 ( 1208)
  SS BOND              : bond        0.00059 (    1)
  SS BOND              : angle       0.74801 (    2)
  covalent geometry    : bond        0.00332 ( 9987)
  covalent geometry    : angle       0.56938 (13696)

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

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 121
  time to evaluate  : 1.102 
Fit side-chains
REVERT: B  177 ASN cc_start: 0.7897 (t0) cc_final: 0.7651 (t0)
REVERT: A  135 CYS cc_start: 0.8142 (p) cc_final: 0.7857 (p)
REVERT: D   40 TYR cc_start: 0.7979 (m-10) cc_final: 0.7586 (m-10)
REVERT: D   44 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8550 (mp)
REVERT: D  127 THR cc_start: 0.8944 (p) cc_final: 0.8642 (t)
REVERT: D  326 LYS cc_start: 0.8251 (pttm) cc_final: 0.7659 (mmtp)
  outliers start: 24
  outliers final: 16
  residues processed: 139
  average time/residue: 0.1933
  time to fit residues: 39.8842
Evaluate side-chains
  132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   67 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 4 optimal weight:    3.9990
   chunk 97 optimal weight:    0.5980
   chunk 6 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   chunk 82 optimal weight:    0.0040
   chunk 24 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0570
   chunk 26 optimal weight:    0.9990
   chunk 99 optimal weight:    0.9990
   chunk 90 optimal weight:    0.0060
   overall best weight:    0.2926

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

Flipped N/Q/H residues before XYZ refinement:
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 184 GLN
D  55 ASN
** D  63 HIS ** 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 = 0.3923 r_free = 0.3923 target = 0.142509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.111545 restraints weight = 14349.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.114357 restraints weight = 9420.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.116308 restraints weight = 7028.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3581
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7798
moved from start:          0.2920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9988  Z= 0.112
  Angle     :  0.553   9.272  13698  Z= 0.290
  Chirality :  0.042   0.234   1578
  Planarity :  0.003   0.028   1583
  Dihedral  : 18.467  76.098   1802
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 10.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 14.34 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.34 (0.25), residues: 1107
  helix:  0.79 (0.30), residues: 307
  sheet: -1.72 (0.26), residues: 331
  loop : -1.27 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP D 274 
 HIS   0.004   0.001   HIS D  63 
 PHE   0.008   0.001   PHE D 126 
 TYR   0.012   0.001   TYR A 250 
 ARG   0.003   0.000   ARG A   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02894 (  431)
  hydrogen bonds       : angle       5.44912 ( 1208)
  SS BOND              : bond        0.00067 (    1)
  SS BOND              : angle       0.52187 (    2)
  covalent geometry    : bond        0.00250 ( 9987)
  covalent geometry    : angle       0.55269 (13696)

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

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 132
  time to evaluate  : 0.999 
Fit side-chains
REVERT: C   91 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.6276 (mtm110)
REVERT: A  141 SER cc_start: 0.8300 (p) cc_final: 0.8088 (t)
REVERT: D   40 TYR cc_start: 0.7858 (m-10) cc_final: 0.7504 (m-10)
REVERT: D   44 ILE cc_start: 0.8900 (OUTLIER) cc_final: 0.8537 (mp)
REVERT: D  127 THR cc_start: 0.9007 (p) cc_final: 0.8709 (t)
REVERT: D  326 LYS cc_start: 0.8299 (pttm) cc_final: 0.7678 (mmtp)
  outliers start: 22
  outliers final: 15
  residues processed: 146
  average time/residue: 0.1735
  time to fit residues: 38.0815
Evaluate side-chains
  135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   91 ARG
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   55 ASN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 102 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9990
   chunk 98 optimal weight:    4.9990
   chunk 69 optimal weight:    0.0040
   chunk 90 optimal weight:    1.9990
   chunk 59 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    1.1998

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

Flipped N/Q/H residues before XYZ refinement:
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 184 GLN
** D  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.144414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.112722 restraints weight = 14817.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.115793 restraints weight = 9825.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.117863 restraints weight = 7338.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.3375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9988  Z= 0.226
  Angle     :  0.634  10.525  13698  Z= 0.330
  Chirality :  0.046   0.249   1578
  Planarity :  0.003   0.031   1583
  Dihedral  : 18.569  71.837   1802
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 13.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 15.79 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.24), residues: 1107
  helix:  0.54 (0.29), residues: 307
  sheet: -1.88 (0.27), residues: 305
  loop : -1.24 (0.27), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP D 274 
 HIS   0.004   0.001   HIS D 137 
 PHE   0.013   0.002   PHE D 126 
 TYR   0.020   0.002   TYR B 133 
 ARG   0.002   0.000   ARG A 149 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03744 (  431)
  hydrogen bonds       : angle       5.77788 ( 1208)
  SS BOND              : bond        0.00049 (    1)
  SS BOND              : angle       1.54288 (    2)
  covalent geometry    : bond        0.00519 ( 9987)
  covalent geometry    : angle       0.63421 (13696)

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

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 130
  time to evaluate  : 1.097 
Fit side-chains
REVERT: B  119 MET cc_start: 0.7561 (pmm) cc_final: 0.7282 (pmm)
REVERT: B  184 GLN cc_start: 0.7313 (pp30) cc_final: 0.7015 (pp30)
REVERT: C   91 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.6221 (mtm110)
REVERT: A  135 CYS cc_start: 0.8168 (p) cc_final: 0.7901 (p)
REVERT: A  146 ARG cc_start: 0.7730 (tpm170) cc_final: 0.7447 (ttm-80)
REVERT: D   44 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8594 (mp)
REVERT: D  127 THR cc_start: 0.9086 (p) cc_final: 0.8838 (t)
REVERT: D  152 TYR cc_start: 0.8616 (p90) cc_final: 0.8220 (p90)
REVERT: D  326 LYS cc_start: 0.8461 (pttm) cc_final: 0.7743 (mmtp)
  outliers start: 30
  outliers final: 23
  residues processed: 150
  average time/residue: 0.1958
  time to fit residues: 43.1561
Evaluate side-chains
  145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 1.065 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  159 VAL
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   91 ARG
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain C residue  255 ILE
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   68 MET
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  256 ILE
Chi-restraints excluded: chain D residue  284 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 38 optimal weight:    0.8980
   chunk 98 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 108 optimal weight:    0.6980
   chunk 86 optimal weight:    0.0770
   chunk 44 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   chunk 51 optimal weight:    0.5980
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.5138

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

Flipped N/Q/H residues before XYZ refinement:
C 184 GLN
** D  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.147554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.117263 restraints weight = 14819.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.121928 restraints weight = 10938.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.122432 restraints weight = 7470.911|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.3332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9988  Z= 0.136
  Angle     :  0.567   7.753  13698  Z= 0.299
  Chirality :  0.043   0.185   1578
  Planarity :  0.003   0.031   1583
  Dihedral  : 18.437  72.613   1802
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 17.03 %
    Favored  : 80.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.32 (0.25), residues: 1107
  helix:  0.78 (0.29), residues: 307
  sheet: -1.88 (0.27), residues: 302
  loop : -1.16 (0.28), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D 274 
 HIS   0.003   0.001   HIS D  63 
 PHE   0.009   0.001   PHE D 126 
 TYR   0.016   0.001   TYR A 250 
 ARG   0.002   0.000   ARG B  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03035 (  431)
  hydrogen bonds       : angle       5.52466 ( 1208)
  SS BOND              : bond        0.00025 (    1)
  SS BOND              : angle       0.82657 (    2)
  covalent geometry    : bond        0.00312 ( 9987)
  covalent geometry    : angle       0.56697 (13696)

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

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 124
  time to evaluate  : 1.172 
Fit side-chains
REVERT: B  119 MET cc_start: 0.7437 (pmm) cc_final: 0.6382 (pmm)
REVERT: B  184 GLN cc_start: 0.7252 (pp30) cc_final: 0.6934 (pp30)
REVERT: C   91 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.6173 (mtm110)
REVERT: C  209 LEU cc_start: 0.8749 (mt) cc_final: 0.7910 (tt)
REVERT: A  141 SER cc_start: 0.8282 (p) cc_final: 0.8038 (t)
REVERT: D   44 ILE cc_start: 0.8970 (OUTLIER) cc_final: 0.8565 (mp)
REVERT: D  127 THR cc_start: 0.9043 (p) cc_final: 0.8797 (t)
  outliers start: 28
  outliers final: 21
  residues processed: 142
  average time/residue: 0.1906
  time to fit residues: 40.0247
Evaluate side-chains
  139 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 116
  time to evaluate  : 1.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   91 ARG
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain D residue   40 TYR
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   82 VAL
Chi-restraints excluded: chain D residue  270 VAL
Chi-restraints excluded: chain D residue  284 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 3 optimal weight:    2.9990
   chunk 84 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0970
   chunk 90 optimal weight:    4.9990
   chunk 52 optimal weight:    0.1980
   chunk 6 optimal weight:    0.9980
   chunk 96 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
C 184 GLN
** D  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.148047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.116864 restraints weight = 14928.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.120036 restraints weight = 10432.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.121440 restraints weight = 7760.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.3426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9988  Z= 0.138
  Angle     :  0.584   9.702  13698  Z= 0.306
  Chirality :  0.043   0.189   1578
  Planarity :  0.003   0.030   1583
  Dihedral  : 18.355  73.352   1802
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 18.27 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.26 (0.25), residues: 1107
  helix:  0.84 (0.30), residues: 307
  sheet: -1.84 (0.27), residues: 307
  loop : -1.11 (0.28), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D  63 
 PHE   0.009   0.001   PHE D 126 
 TYR   0.014   0.002   TYR A 250 
 ARG   0.002   0.000   ARG D 322 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03089 (  431)
  hydrogen bonds       : angle       5.43164 ( 1208)
  SS BOND              : bond        0.00019 (    1)
  SS BOND              : angle       0.59136 (    2)
  covalent geometry    : bond        0.00315 ( 9987)
  covalent geometry    : angle       0.58360 (13696)

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

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 119
  time to evaluate  : 0.998 
Fit side-chains
REVERT: B  119 MET cc_start: 0.7467 (pmm) cc_final: 0.7230 (pmm)
REVERT: C   91 ARG cc_start: 0.7809 (OUTLIER) cc_final: 0.6188 (mtm110)
REVERT: C  209 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.7866 (tt)
REVERT: A  141 SER cc_start: 0.8288 (p) cc_final: 0.8031 (t)
REVERT: D   44 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8599 (mp)
REVERT: D  127 THR cc_start: 0.9046 (p) cc_final: 0.8806 (t)
REVERT: D  326 LYS cc_start: 0.8416 (pttt) cc_final: 0.7471 (mmtp)
  outliers start: 27
  outliers final: 18
  residues processed: 136
  average time/residue: 0.1843
  time to fit residues: 37.2011
Evaluate side-chains
  138 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 117
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   91 ARG
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  209 LEU
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain D residue   40 TYR
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue  284 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 84 optimal weight:    0.6980
   chunk 95 optimal weight:    2.9990
   chunk 59 optimal weight:    3.9990
   chunk 20 optimal weight:    0.1980
   chunk 3 optimal weight:    2.9990
   chunk 28 optimal weight:    0.4980
   chunk 25 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 53 optimal weight:    0.5980
   chunk 58 optimal weight:    0.0770
   overall best weight:    0.4138

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

Flipped N/Q/H residues before XYZ refinement:
C 184 GLN
** D  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.149311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.118363 restraints weight = 14812.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.121948 restraints weight = 10401.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.122863 restraints weight = 7499.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.3472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9988  Z= 0.125
  Angle     :  0.577  10.575  13698  Z= 0.301
  Chirality :  0.043   0.192   1578
  Planarity :  0.003   0.030   1583
  Dihedral  : 18.292  73.886   1802
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 18.58 %
    Favored  : 78.84 %
  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: -1.16 (0.25), residues: 1107
  helix:  0.89 (0.30), residues: 311
  sheet: -1.70 (0.27), residues: 315
  loop : -1.09 (0.29), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D  63 
 PHE   0.009   0.001   PHE A 169 
 TYR   0.014   0.001   TYR A 250 
 ARG   0.002   0.000   ARG A   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02943 (  431)
  hydrogen bonds       : angle       5.33850 ( 1208)
  SS BOND              : bond        0.00011 (    1)
  SS BOND              : angle       0.66276 (    2)
  covalent geometry    : bond        0.00285 ( 9987)
  covalent geometry    : angle       0.57663 (13696)

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

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 1.171 
Fit side-chains
REVERT: B   86 ASP cc_start: 0.7267 (t0) cc_final: 0.7061 (t0)
REVERT: B  119 MET cc_start: 0.7397 (pmm) cc_final: 0.7174 (pmm)
REVERT: C   91 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6265 (mtm110)
REVERT: C  209 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.7779 (tt)
REVERT: D   44 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8600 (mp)
REVERT: D  127 THR cc_start: 0.9034 (p) cc_final: 0.8808 (t)
REVERT: D  326 LYS cc_start: 0.8461 (pttt) cc_final: 0.7484 (mmtp)
  outliers start: 25
  outliers final: 20
  residues processed: 139
  average time/residue: 0.2010
  time to fit residues: 41.5316
Evaluate side-chains
  141 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 1.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   91 ARG
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  209 LEU
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   68 MET
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  219 THR
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain D residue   40 TYR
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue  284 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 2 optimal weight:    0.4980
   chunk 86 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   chunk 66 optimal weight:    0.1980
   chunk 102 optimal weight:    2.9990
   chunk 98 optimal weight:    0.4980
   chunk 28 optimal weight:    0.6980
   chunk 88 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 92 optimal weight:    2.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 184 GLN
** D  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.148670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.117552 restraints weight = 14902.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.121260 restraints weight = 10537.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.122428 restraints weight = 7455.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.3548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9988  Z= 0.138
  Angle     :  0.586  10.408  13698  Z= 0.304
  Chirality :  0.043   0.196   1578
  Planarity :  0.003   0.028   1583
  Dihedral  : 18.269  74.370   1802
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 18.37 %
    Favored  : 79.26 %
  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: -1.10 (0.25), residues: 1107
  helix:  0.91 (0.30), residues: 311
  sheet: -1.64 (0.27), residues: 317
  loop : -1.05 (0.29), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D  63 
 PHE   0.010   0.001   PHE B 215 
 TYR   0.014   0.001   TYR A 250 
 ARG   0.002   0.000   ARG B  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03051 (  431)
  hydrogen bonds       : angle       5.34345 ( 1208)
  SS BOND              : bond        0.00072 (    1)
  SS BOND              : angle       0.82650 (    2)
  covalent geometry    : bond        0.00319 ( 9987)
  covalent geometry    : angle       0.58633 (13696)

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

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 0.985 
Fit side-chains
REVERT: B  119 MET cc_start: 0.7418 (pmm) cc_final: 0.7188 (pmm)
REVERT: C   40 MET cc_start: 0.8474 (ttm) cc_final: 0.8165 (ttm)
REVERT: C   91 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.6283 (mtm110)
REVERT: C  209 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.7835 (tt)
REVERT: D   44 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8600 (mp)
REVERT: D  127 THR cc_start: 0.9038 (p) cc_final: 0.8796 (t)
REVERT: D  326 LYS cc_start: 0.8497 (pttt) cc_final: 0.7522 (mmtp)
  outliers start: 23
  outliers final: 19
  residues processed: 137
  average time/residue: 0.1830
  time to fit residues: 37.4239
Evaluate side-chains
  140 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue   35 VAL
Chi-restraints excluded: chain C residue   91 ARG
Chi-restraints excluded: chain C residue  137 VAL
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  209 LEU
Chi-restraints excluded: chain C residue  216 THR
Chi-restraints excluded: chain C residue  219 THR
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   68 MET
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  196 THR
Chi-restraints excluded: chain A residue  203 VAL
Chi-restraints excluded: chain A residue  228 SER
Chi-restraints excluded: chain A residue  235 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain D residue   40 TYR
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue  284 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 96 optimal weight:    0.8980
   chunk 98 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 69 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C 184 GLN
** D  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.147173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.116498 restraints weight = 14851.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.119289 restraints weight = 9985.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.120248 restraints weight = 7367.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.3665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9988  Z= 0.163
  Angle     :  0.608  12.155  13698  Z= 0.312
  Chirality :  0.044   0.267   1578
  Planarity :  0.003   0.031   1583
  Dihedral  : 18.286  74.710   1802
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 18.47 %
    Favored  : 79.26 %
  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: -1.16 (0.25), residues: 1107
  helix:  0.82 (0.30), residues: 311
  sheet: -1.56 (0.27), residues: 331
  loop : -1.12 (0.29), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 274 
 HIS   0.002   0.001   HIS D 137 
 PHE   0.011   0.001   PHE B 215 
 TYR   0.015   0.002   TYR A 250 
 ARG   0.002   0.000   ARG B  91 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03162 (  431)
  hydrogen bonds       : angle       5.46635 ( 1208)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       0.99529 (    2)
  covalent geometry    : bond        0.00376 ( 9987)
  covalent geometry    : angle       0.60766 (13696)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3460.16 seconds
wall clock time: 61 minutes 36.57 seconds (3696.57 seconds total)