Starting phenix.real_space_refine
on Thu Jan 16 16:57:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yjh_39342/01_2025/8yjh_39342.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yjh_39342/01_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_39342/01_2025/8yjh_39342.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yjh_39342/01_2025/8yjh_39342.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yjh_39342/01_2025/8yjh_39342.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yjh_39342/01_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-5571/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: 6.71, per 1000 atoms: 0.69
  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: 2.50
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      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: 3.39
  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: 3.54

  Time building geometry restraints manager: 2.87 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:             3.140
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.060
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     27.600
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.050
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.470
-------------------------------------------------------------------------------
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   9987  Z= 0.325
  Angle     :  1.042  11.331  13696  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 

*********************** 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  : 0.973 
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: 0.1868
  time to fit residues: 46.3752
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  : 1.114 
-------------------------------------------------------------------------------
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 = 34)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.110958 restraints weight = 14483.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.113653 restraints weight = 9719.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.115620 restraints weight = 7246.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
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   9987  Z= 0.248
  Angle     :  0.626   6.270  13696  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 

*********************** 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  : 0.944 
Fit side-chains
REVERT: B  177 ASN cc_start: 0.7810 (t0) cc_final: 0.7569 (t0)
REVERT: B  199 MET cc_start: 0.7436 (tmm) cc_final: 0.6777 (tmm)
REVERT: C    1 MET cc_start: 0.7599 (tpp) cc_final: 0.7384 (tpp)
REVERT: C  201 GLU cc_start: 0.7301 (pt0) cc_final: 0.7066 (pt0)
REVERT: A   68 MET cc_start: 0.7999 (ptp) cc_final: 0.7771 (ptp)
REVERT: A  135 CYS cc_start: 0.8079 (p) cc_final: 0.7806 (p)
REVERT: D  127 THR cc_start: 0.8905 (p) cc_final: 0.8631 (t)
REVERT: D  326 LYS cc_start: 0.8038 (pttm) cc_final: 0.7406 (mmtp)
  outliers start: 11
  outliers final: 8
  residues processed: 147
  average time/residue: 0.1816
  time to fit residues: 39.6857
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  : 1.092 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 46 optimal weight:    0.4980
   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:    0.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.6080

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

Flipped N/Q/H residues before XYZ refinement:
D  55 ASN
** 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 = 0.3914 r_free = 0.3914 target = 0.141599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.110133 restraints weight = 14676.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.112899 restraints weight = 9681.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.114841 restraints weight = 7244.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3570
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9987  Z= 0.205
  Angle     :  0.573   8.820  13696  Z= 0.303
  Chirality :  0.043   0.239   1578
  Planarity :  0.003   0.038   1583
  Dihedral  : 18.836  76.876   1802
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 9.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 10.94 %
    Favored  : 87.10 %
  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: -1.93 (0.23), residues: 1107
  helix: -0.00 (0.28), residues: 307
  sheet: -1.70 (0.26), residues: 349
  loop : -1.68 (0.26), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP D 274 
 HIS   0.004   0.001   HIS D 137 
 PHE   0.008   0.001   PHE D 126 
 TYR   0.013   0.002   TYR A 250 
 ARG   0.003   0.000   ARG A   5 

*********************** 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
  144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 0.990 
Fit side-chains
REVERT: B   36 ASN cc_start: 0.8472 (m-40) cc_final: 0.8212 (m-40)
REVERT: B  177 ASN cc_start: 0.7817 (t0) cc_final: 0.7581 (t0)
REVERT: B  184 GLN cc_start: 0.7159 (pp30) cc_final: 0.6786 (pp30)
REVERT: C  209 LEU cc_start: 0.8785 (mt) cc_final: 0.8582 (mt)
REVERT: A   68 MET cc_start: 0.7907 (ptp) cc_final: 0.7701 (ptp)
REVERT: A  135 CYS cc_start: 0.8139 (p) cc_final: 0.7791 (p)
REVERT: D   40 TYR cc_start: 0.7828 (m-10) cc_final: 0.7480 (m-10)
REVERT: D   44 ILE cc_start: 0.8724 (OUTLIER) cc_final: 0.8482 (mp)
REVERT: D  127 THR cc_start: 0.9009 (p) cc_final: 0.8723 (t)
REVERT: D  326 LYS cc_start: 0.8165 (pttm) cc_final: 0.7512 (mmtp)
  outliers start: 19
  outliers final: 13
  residues processed: 138
  average time/residue: 0.1836
  time to fit residues: 37.6957
Evaluate side-chains
  128 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.977 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue  186 SER
Chi-restraints excluded: chain C residue   23 ILE
Chi-restraints excluded: chain C residue  182 LEU
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
Chi-restraints excluded: chain D residue   55 ASN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0470
   chunk 88 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9980
   chunk 21 optimal weight:    0.9990
   chunk 84 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.5478

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.141276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.109889 restraints weight = 14337.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.112605 restraints weight = 9544.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.114572 restraints weight = 7156.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.2623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9987  Z= 0.194
  Angle     :  0.558   8.637  13696  Z= 0.295
  Chirality :  0.043   0.229   1578
  Planarity :  0.003   0.034   1583
  Dihedral  : 18.681  76.184   1802
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 12.69 %
    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: -1.62 (0.24), residues: 1107
  helix:  0.41 (0.29), residues: 308
  sheet: -1.80 (0.26), residues: 329
  loop : -1.40 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP D 274 
 HIS   0.004   0.001   HIS D 276 
 PHE   0.009   0.001   PHE D 126 
 TYR   0.013   0.001   TYR A 250 
 ARG   0.003   0.000   ARG D 211 

*********************** 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
  142 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 0.997 
Fit side-chains
REVERT: B  177 ASN cc_start: 0.7859 (t0) cc_final: 0.7629 (t0)
REVERT: A   68 MET cc_start: 0.7942 (ptp) cc_final: 0.7714 (ptp)
REVERT: A  135 CYS cc_start: 0.8138 (p) cc_final: 0.7759 (p)
REVERT: A  141 SER cc_start: 0.8311 (p) cc_final: 0.8111 (t)
REVERT: D   40 TYR cc_start: 0.7929 (m-10) cc_final: 0.7555 (m-10)
REVERT: D   44 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8291 (mp)
REVERT: D  326 LYS cc_start: 0.8183 (pttm) cc_final: 0.7538 (mmtp)
  outliers start: 22
  outliers final: 16
  residues processed: 135
  average time/residue: 0.1923
  time to fit residues: 38.6483
Evaluate side-chains
  131 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 114
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
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  137 VAL
Chi-restraints excluded: chain C residue  182 LEU
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  119 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  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  233 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 97 optimal weight:    0.6980
   chunk 6 optimal weight:    0.0270
   chunk 2 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 82 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 66 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 90 optimal weight:    0.6980
   overall best weight:    0.5838

-------------------------------------------------------------------------------
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 137 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 = 0.3901 r_free = 0.3901 target = 0.140634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.109182 restraints weight = 14356.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.111909 restraints weight = 9481.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.113843 restraints weight = 7119.476|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.2881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9987  Z= 0.199
  Angle     :  0.563   9.405  13696  Z= 0.295
  Chirality :  0.043   0.241   1578
  Planarity :  0.003   0.033   1583
  Dihedral  : 18.551  74.919   1802
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 11.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 13.83 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.45 (0.24), residues: 1107
  helix:  0.64 (0.29), residues: 307
  sheet: -1.80 (0.26), residues: 330
  loop : -1.28 (0.27), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP D 274 
 HIS   0.003   0.001   HIS D 276 
 PHE   0.012   0.001   PHE D 126 
 TYR   0.014   0.002   TYR A 250 
 ARG   0.002   0.000   ARG A   5 

*********************** 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
  150 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 122
  time to evaluate  : 0.983 
Fit side-chains
REVERT: B  177 ASN cc_start: 0.7884 (t0) cc_final: 0.7683 (t0)
REVERT: B  199 MET cc_start: 0.7348 (tpp) cc_final: 0.6433 (tpp)
REVERT: C   91 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.6235 (mtm110)
REVERT: A  135 CYS cc_start: 0.8173 (p) cc_final: 0.7815 (p)
REVERT: A  141 SER cc_start: 0.8362 (p) cc_final: 0.8150 (t)
REVERT: D   40 TYR cc_start: 0.7938 (m-10) cc_final: 0.7566 (m-10)
REVERT: D   44 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8570 (mp)
REVERT: D  127 THR cc_start: 0.8965 (p) cc_final: 0.8693 (t)
REVERT: D  326 LYS cc_start: 0.8210 (pttm) cc_final: 0.7620 (mmtp)
  outliers start: 28
  outliers final: 20
  residues processed: 142
  average time/residue: 0.2014
  time to fit residues: 42.3251
Evaluate side-chains
  132 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 1.022 
-------------------------------------------------------------------------------
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  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  119 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  236 VAL
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue  256 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 102 optimal weight:    6.9990
   chunk 36 optimal weight:    1.9990
   chunk 98 optimal weight:    0.3980
   chunk 69 optimal weight:    3.9990
   chunk 90 optimal weight:    0.0980
   chunk 59 optimal weight:    0.8980
   chunk 70 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 137 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 = 0.3898 r_free = 0.3898 target = 0.140455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.109130 restraints weight = 14392.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.111882 restraints weight = 9491.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.113780 restraints weight = 7103.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3548
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.3100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9987  Z= 0.200
  Angle     :  0.561   9.973  13696  Z= 0.293
  Chirality :  0.043   0.243   1578
  Planarity :  0.003   0.032   1583
  Dihedral  : 18.429  73.407   1802
  Min Nonbonded Distance : 2.598

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 15.17 %
    Favored  : 82.04 %
  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: -1.34 (0.24), residues: 1107
  helix:  0.83 (0.29), residues: 305
  sheet: -1.81 (0.26), residues: 310
  loop : -1.27 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP D 274 
 HIS   0.004   0.001   HIS D 276 
 PHE   0.009   0.001   PHE D 126 
 TYR   0.015   0.001   TYR A 250 
 ARG   0.002   0.000   ARG A  64 

*********************** 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
  148 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 121
  time to evaluate  : 1.174 
Fit side-chains
REVERT: B  177 ASN cc_start: 0.7914 (t0) cc_final: 0.7706 (t0)
REVERT: B  184 GLN cc_start: 0.7084 (pp30) cc_final: 0.6854 (pp30)
REVERT: C   91 ARG cc_start: 0.7763 (OUTLIER) cc_final: 0.6215 (mtm110)
REVERT: A  135 CYS cc_start: 0.8137 (p) cc_final: 0.7865 (p)
REVERT: D   44 ILE cc_start: 0.8950 (OUTLIER) cc_final: 0.8575 (mp)
REVERT: D  127 THR cc_start: 0.8971 (p) cc_final: 0.8679 (t)
REVERT: D  326 LYS cc_start: 0.8323 (pttm) cc_final: 0.7688 (mmtp)
  outliers start: 27
  outliers final: 20
  residues processed: 138
  average time/residue: 0.1879
  time to fit residues: 38.7291
Evaluate side-chains
  133 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
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  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  119 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  236 VAL
Chi-restraints excluded: chain D residue   44 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 98 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0070
   chunk 79 optimal weight:    2.9990
   chunk 30 optimal weight:    0.1980
   chunk 108 optimal weight:    0.1980
   chunk 86 optimal weight:    7.9990
   chunk 44 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.3798

-------------------------------------------------------------------------------
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 137 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 = 0.4048 r_free = 0.4048 target = 0.150615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.120386 restraints weight = 14591.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.124186 restraints weight = 10393.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.125121 restraints weight = 7351.587|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7824
moved from start:          0.3184

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9987  Z= 0.168
  Angle     :  0.554  10.294  13696  Z= 0.289
  Chirality :  0.043   0.241   1578
  Planarity :  0.003   0.031   1583
  Dihedral  : 18.333  72.834   1802
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.00 %
    Favored  : 81.42 %
  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: -1.23 (0.25), residues: 1107
  helix:  0.96 (0.30), residues: 305
  sheet: -1.72 (0.27), residues: 310
  loop : -1.24 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D 276 
 PHE   0.009   0.001   PHE D 126 
 TYR   0.014   0.001   TYR A 250 
 ARG   0.002   0.000   ARG A   5 

*********************** 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
  153 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 0.988 
Fit side-chains
REVERT: B   87 ILE cc_start: 0.8567 (mp) cc_final: 0.8288 (mp)
REVERT: B  119 MET cc_start: 0.7389 (pmm) cc_final: 0.7129 (pmm)
REVERT: B  184 GLN cc_start: 0.7099 (pp30) cc_final: 0.6810 (pp30)
REVERT: C   91 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.6186 (mtm110)
REVERT: D   44 ILE cc_start: 0.8922 (OUTLIER) cc_final: 0.8575 (mp)
REVERT: D  127 THR cc_start: 0.8919 (p) cc_final: 0.8623 (t)
REVERT: D  326 LYS cc_start: 0.8349 (pttm) cc_final: 0.7721 (mmtp)
  outliers start: 25
  outliers final: 18
  residues processed: 140
  average time/residue: 0.1825
  time to fit residues: 38.2699
Evaluate side-chains
  134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 0.985 
-------------------------------------------------------------------------------
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  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  119 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  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
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 90 optimal weight:    5.9990
   chunk 52 optimal weight:    0.0970
   chunk 6 optimal weight:    0.8980
   chunk 96 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 36 optimal weight:    0.7980
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.7178

-------------------------------------------------------------------------------
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 131 GLN
C 184 GLN
** D  55 ASN ** 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: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.148007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.117835 restraints weight = 14949.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.121476 restraints weight = 11042.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.122404 restraints weight = 8039.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.3378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9987  Z= 0.228
  Angle     :  0.584  10.737  13696  Z= 0.304
  Chirality :  0.044   0.228   1578
  Planarity :  0.003   0.028   1583
  Dihedral  : 18.322  72.290   1802
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 17.44 %
    Favored  : 79.88 %
  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: -1.21 (0.25), residues: 1107
  helix:  0.92 (0.30), residues: 305
  sheet: -1.72 (0.26), residues: 317
  loop : -1.16 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP D 274 
 HIS   0.004   0.001   HIS D 276 
 PHE   0.010   0.001   PHE D 126 
 TYR   0.013   0.002   TYR A 250 
 ARG   0.002   0.000   ARG D 211 

*********************** 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
  145 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 0.989 
Fit side-chains
REVERT: B   87 ILE cc_start: 0.8642 (mp) cc_final: 0.8349 (mp)
REVERT: B  119 MET cc_start: 0.7405 (pmm) cc_final: 0.7167 (pmm)
REVERT: C   91 ARG cc_start: 0.7800 (OUTLIER) cc_final: 0.6192 (mtm110)
REVERT: D   44 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8573 (mp)
REVERT: D  127 THR cc_start: 0.8917 (p) cc_final: 0.8611 (t)
REVERT: D  326 LYS cc_start: 0.8347 (pttm) cc_final: 0.7737 (mmtp)
  outliers start: 26
  outliers final: 21
  residues processed: 135
  average time/residue: 0.1919
  time to fit residues: 38.6440
Evaluate side-chains
  135 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
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  199 MET
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  119 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  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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 84 optimal weight:    0.5980
   chunk 95 optimal weight:    0.6980
   chunk 59 optimal weight:    0.2980
   chunk 20 optimal weight:    0.0270
   chunk 3 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0770
   chunk 25 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.3396

-------------------------------------------------------------------------------
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 137 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 = 0.4046 r_free = 0.4046 target = 0.150743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.121052 restraints weight = 14801.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.124448 restraints weight = 10626.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.125292 restraints weight = 7703.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.3713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.3380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9987  Z= 0.169
  Angle     :  0.561   9.887  13696  Z= 0.294
  Chirality :  0.043   0.203   1578
  Planarity :  0.003   0.029   1583
  Dihedral  : 18.237  72.334   1802
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 11.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 17.85 %
    Favored  : 79.67 %
  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: -1.11 (0.25), residues: 1107
  helix:  1.02 (0.30), residues: 307
  sheet: -1.64 (0.26), residues: 321
  loop : -1.12 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 274 
 HIS   0.003   0.001   HIS D 276 
 PHE   0.009   0.001   PHE B 215 
 TYR   0.012   0.001   TYR A 250 
 ARG   0.002   0.000   ARG A   5 

*********************** 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
  144 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 1.078 
Fit side-chains
REVERT: B   87 ILE cc_start: 0.8594 (mp) cc_final: 0.8308 (mp)
REVERT: B  119 MET cc_start: 0.7311 (pmm) cc_final: 0.7083 (pmm)
REVERT: C   91 ARG cc_start: 0.7716 (OUTLIER) cc_final: 0.6165 (mtm110)
REVERT: D   44 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8611 (mp)
REVERT: D  127 THR cc_start: 0.8901 (p) cc_final: 0.8609 (t)
  outliers start: 24
  outliers final: 16
  residues processed: 134
  average time/residue: 0.1879
  time to fit residues: 37.8635
Evaluate side-chains
  134 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
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   91 ARG
Chi-restraints excluded: chain C residue  137 VAL
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  119 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   67 MET
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:    0.6980
   chunk 2 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 66 optimal weight:    0.3980
   chunk 102 optimal weight:    0.8980
   chunk 98 optimal weight:    0.9980
   chunk 28 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 56 optimal weight:    0.5980
   chunk 92 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 184 GLN
** D  55 ASN ** 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: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.148185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.117550 restraints weight = 14723.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.120882 restraints weight = 10649.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.121709 restraints weight = 7721.457|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.3505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9987  Z= 0.228
  Angle     :  0.596  10.200  13696  Z= 0.310
  Chirality :  0.044   0.192   1578
  Planarity :  0.003   0.027   1583
  Dihedral  : 18.265  72.771   1802
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 18.16 %
    Favored  : 79.67 %
  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: -1.13 (0.25), residues: 1107
  helix:  0.94 (0.30), residues: 305
  sheet: -1.66 (0.26), residues: 321
  loop : -1.09 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP D 274 
 HIS   0.004   0.001   HIS D 276 
 PHE   0.010   0.001   PHE D  68 
 TYR   0.020   0.002   TYR A 133 
 ARG   0.003   0.000   ARG D 322 

********************** 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
  137 residues out of total 969 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.924 
Fit side-chains
REVERT: B   87 ILE cc_start: 0.8637 (mp) cc_final: 0.8338 (mp)
REVERT: B  119 MET cc_start: 0.7376 (pmm) cc_final: 0.7158 (pmm)
REVERT: C   40 MET cc_start: 0.8523 (ttm) cc_final: 0.8221 (ttm)
REVERT: C   91 ARG cc_start: 0.7764 (OUTLIER) cc_final: 0.6201 (mtm110)
REVERT: D   44 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8633 (mp)
REVERT: D  127 THR cc_start: 0.8902 (p) cc_final: 0.8603 (t)
REVERT: D  326 LYS cc_start: 0.8330 (pttt) cc_final: 0.7436 (mmtp)
  outliers start: 21
  outliers final: 15
  residues processed: 129
  average time/residue: 0.1879
  time to fit residues: 36.0266
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  : 1.080 
-------------------------------------------------------------------------------
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  219 THR
Chi-restraints excluded: chain C residue  235 LEU
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue  119 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  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:    0.9980
   chunk 32 optimal weight:    2.9990
   chunk 96 optimal weight:    0.6980
   chunk 98 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 16 optimal weight:    0.6980
   chunk 69 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 41 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 5 optimal weight:    0.0980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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**
** D  55 ASN ** 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 = 0.4024 r_free = 0.4024 target = 0.148818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.118307 restraints weight = 14607.963|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.122455 restraints weight = 10396.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.123212 restraints weight = 7158.090|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.3553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9987  Z= 0.206
  Angle     :  0.585   9.868  13696  Z= 0.305
  Chirality :  0.043   0.185   1578
  Planarity :  0.003   0.029   1583
  Dihedral  : 18.233  72.826   1802
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 18.47 %
    Favored  : 79.77 %
  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:  0.97 (0.30), residues: 307
  sheet: -1.65 (0.26), residues: 319
  loop : -1.07 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP D 274 
 HIS   0.004   0.001   HIS D 276 
 PHE   0.010   0.001   PHE D 126 
 TYR   0.019   0.002   TYR A 133 
 ARG   0.002   0.000   ARG A  64 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2728.87 seconds
wall clock time: 50 minutes 23.62 seconds (3023.62 seconds total)