Starting phenix.real_space_refine
on Fri Aug 22 19:35:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wp1_37707/08_2025/8wp1_37707_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wp1_37707/08_2025/8wp1_37707.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.15
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wp1_37707/08_2025/8wp1_37707_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wp1_37707/08_2025/8wp1_37707_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wp1_37707/08_2025/8wp1_37707.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wp1_37707/08_2025/8wp1_37707.map"
  }
  resolution = 3.15
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.002 sd=   0.117
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      52      5.16       5
     C    4685      2.51       5
     N    1232      2.21       5
     O    1357      1.98       5
     H       2      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7328
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 2481
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 304, 2481
          Classifications: {'peptide': 304}
          Link IDs: {'PTRANS': 12, 'TRANS': 291}
    Chain: "C"
      Number of atoms: 1834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1834
          Classifications: {'peptide': 228}
          Link IDs: {'PTRANS': 2, 'TRANS': 225}
          Chain breaks: 1
          Unresolved chain link dihedrals: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "D"
      Number of atoms: 2568
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2568
          Classifications: {'peptide': 334}
          Link IDs: {'PTRANS': 5, 'TRANS': 328}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 433
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 433
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "A"
      Number of atoms: 12
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 12
          Unusual residues: {'U9S': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 1.50, per 1000 atoms: 0.20
  Number of scatterers: 7328
  At special positions: 0
  Unit cell: (69.7, 103.7, 140.25, 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      52     16.00
     O    1357      8.00
     N    1232      7.00
     C    4685      6.00
     H       2      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  11 " - pdb=" SG  CYS A 268 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  95 " - pdb=" SG  CYS A 172 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.40
  Conformation dependent library (CDL) restraints added in 341.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1750

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 9 sheets defined
      44.3% alpha, 17.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 24
    Processing helix  chain 'A' and resid 24 through 50
    Processing helix  chain 'A' and resid 56 through 75
      removed outlier: 3.787A  pdb=" N   THR A  75 " --> pdb=" O   ALA A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 82
      removed outlier: 4.030A  pdb=" N   SER A  82 " --> pdb=" O   MET A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 121
      removed outlier: 3.849A  pdb=" N   ILE A 110 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   LEU A 111 " --> pdb=" O   TYR A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 134
    Processing helix  chain 'A' and resid 135 through 155
      removed outlier: 3.686A  pdb=" N   ILE A 140 " --> pdb=" O   LYS A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 162
      removed outlier: 3.636A  pdb=" N   ASN A 162 " --> pdb=" O   LEU A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 178
      removed outlier: 3.847A  pdb=" N   SER A 178 " --> pdb=" O   PHE A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 196
    Processing helix  chain 'A' and resid 196 through 219
    Processing helix  chain 'A' and resid 228 through 259
      removed outlier: 3.600A  pdb=" N   VAL A 238 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
      Proline residue:  A 247  - end of helix
      removed outlier: 3.675A  pdb=" N   ASN A 253 " --> pdb=" O   HIS A 249 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ARG A 259 " --> pdb=" O   ARG A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 285
      Proline residue:  A 282  - end of helix
      removed outlier: 3.967A  pdb=" N   PHE A 285 " --> pdb=" O   ARG A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 297
      removed outlier: 4.135A  pdb=" N   VAL A 289 " --> pdb=" O   PHE A 285 " (cutoff:3.500A)
      Proline residue:  A 292  - end of helix
    Processing helix  chain 'A' and resid 299 through 311
    Processing helix  chain 'C' and resid 6 through 31
    Processing helix  chain 'C' and resid 47 through 53
    Processing helix  chain 'C' and resid 207 through 216
      removed outlier: 3.833A  pdb=" N   TRP C 211 " --> pdb=" O   ARG C 208 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   ILE C 212 " --> pdb=" O   LYS C 209 " (cutoff:3.500A)
      removed outlier: 5.912A  pdb=" N   HIS C 213 " --> pdb=" O   LYS C 210 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 241 through 255
    Processing helix  chain 'C' and resid 273 through 279
      removed outlier: 4.491A  pdb=" N   LYS C 279 " --> pdb=" O   GLU C 275 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 282 through 286
    Processing helix  chain 'C' and resid 295 through 309
      removed outlier: 3.809A  pdb=" N   ALA C 301 " --> pdb=" O   GLU C 297 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 330 through 351
    Processing helix  chain 'D' and resid 4 through 24
      removed outlier: 3.774A  pdb=" N   GLU D  10 " --> pdb=" O   GLN D   6 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 32 through 36
      removed outlier: 4.406A  pdb=" N   ASN D  36 " --> pdb=" O   ILE D  33 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 10 through 23
      removed outlier: 3.897A  pdb=" N   LYS E  14 " --> pdb=" O   ALA E  10 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 33 through 44
    Processing sheet with id=AA1, first strand: chain 'A' and resid 164 through 166
    Processing sheet with id=AA2, first strand: chain 'C' and resid 185 through 190
      removed outlier: 6.369A  pdb=" N   VAL C  34 " --> pdb=" O   LYS C 197 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   PHE C 199 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   LEU C  36 " --> pdb=" O   PHE C 199 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   ALA C 220 " --> pdb=" O   LYS C  35 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ILE C 221 " --> pdb=" O   ILE C 265 " (cutoff:3.500A)
      removed outlier: 7.275A  pdb=" N   PHE C 267 " --> pdb=" O   ILE C 221 " (cutoff:3.500A)
      removed outlier: 6.585A  pdb=" N   PHE C 223 " --> pdb=" O   PHE C 267 " (cutoff:3.500A)
      removed outlier: 7.077A  pdb=" N   ASN C 269 " --> pdb=" O   PHE C 223 " (cutoff:3.500A)
      removed outlier: 6.681A  pdb=" N   VAL C 225 " --> pdb=" O   ASN C 269 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 47 through 51
      removed outlier: 3.779A  pdb=" N   CYS D 317 " --> pdb=" O   GLY D 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 58 through 62
      removed outlier: 6.944A  pdb=" N   ALA D  73 " --> pdb=" O   TYR D  59 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   MET D  61 " --> pdb=" O   VAL D  71 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   VAL D  71 " --> pdb=" O   MET D  61 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   SER D  74 " --> pdb=" O   LYS D  78 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   LYS D  78 " --> pdb=" O   SER D  74 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 100 through 105
      removed outlier: 6.823A  pdb=" N   GLY D 115 " --> pdb=" O   MET D 101 " (cutoff:3.500A)
      removed outlier: 4.604A  pdb=" N   CYS D 103 " --> pdb=" O   ALA D 113 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   ALA D 113 " --> pdb=" O   CYS D 103 " (cutoff:3.500A)
      removed outlier: 5.304A  pdb=" N   TYR D 105 " --> pdb=" O   TYR D 111 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   TYR D 111 " --> pdb=" O   TYR D 105 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   ASN D 125 " --> pdb=" O   VAL D 135 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   VAL D 135 " --> pdb=" O   ASN D 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 146 through 151
      removed outlier: 6.704A  pdb=" N   SER D 160 " --> pdb=" O   SER D 147 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   CYS D 149 " --> pdb=" O   VAL D 158 " (cutoff:3.500A)
      removed outlier: 6.620A  pdb=" N   VAL D 158 " --> pdb=" O   CYS D 149 " (cutoff:3.500A)
      removed outlier: 4.279A  pdb=" N   ILE D 157 " --> pdb=" O   TRP D 169 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   THR D 165 " --> pdb=" O   SER D 161 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 187 through 192
      removed outlier: 6.807A  pdb=" N   GLY D 202 " --> pdb=" O   MET D 188 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   LEU D 190 " --> pdb=" O   VAL D 200 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   VAL D 200 " --> pdb=" O   LEU D 190 " (cutoff:3.500A)
      removed outlier: 5.241A  pdb=" N   LEU D 192 " --> pdb=" O   LEU D 198 " (cutoff:3.500A)
      removed outlier: 7.397A  pdb=" N   LEU D 198 " --> pdb=" O   LEU D 192 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   SER D 207 " --> pdb=" O   ALA D 203 " (cutoff:3.500A)
      removed outlier: 6.637A  pdb=" N   ALA D 208 " --> pdb=" O   THR D 221 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   THR D 221 " --> pdb=" O   ALA D 208 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   LEU D 210 " --> pdb=" O   ARG D 219 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 229 through 234
      removed outlier: 3.536A  pdb=" N   MET D 262 " --> pdb=" O   LEU D 252 " (cutoff:3.500A)
      removed outlier: 6.145A  pdb=" N   ASP D 254 " --> pdb=" O   GLU D 260 " (cutoff:3.500A)
      removed outlier: 5.956A  pdb=" N   GLU D 260 " --> pdb=" O   ASP D 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 273 through 278
      removed outlier: 3.762A  pdb=" N   SER D 275 " --> pdb=" O   GLY D 288 " (cutoff:3.500A)
      removed outlier: 6.154A  pdb=" N   ASP D 298 " --> pdb=" O   ARG D 304 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   ARG D 304 " --> pdb=" O   ASP D 298 " (cutoff:3.500A)

    359 hydrogen bonds defined for protein.
    1026 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.93

  Time building geometry restraints manager: 0.52 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 2
        1.03 -     1.23: 34
        1.23 -     1.42: 3122
        1.42 -     1.62: 4245
        1.62 -     1.81: 74
  Bond restraints: 7477
  Sorted by residual:
  bond pdb=" C   THR D 274 "
       pdb=" O   THR D 274 "
    ideal  model  delta    sigma   weight residual
    1.236  1.137  0.099 1.39e-02 5.18e+03 5.05e+01
  bond pdb=" C   VAL D 315 "
       pdb=" O   VAL D 315 "
    ideal  model  delta    sigma   weight residual
    1.237  1.156  0.081 1.19e-02 7.06e+03 4.66e+01
  bond pdb=" C   ASN C 255 "
       pdb=" O   ASN C 255 "
    ideal  model  delta    sigma   weight residual
    1.235  1.158  0.077 1.33e-02 5.65e+03 3.35e+01
  bond pdb=" N   THR D 274 "
       pdb=" CA  THR D 274 "
    ideal  model  delta    sigma   weight residual
    1.455  1.395  0.060 1.33e-02 5.65e+03 2.03e+01
  bond pdb=" C   GLU E  58 "
       pdb=" O   GLU E  58 "
    ideal  model  delta    sigma   weight residual
    1.236  1.178  0.058 1.31e-02 5.83e+03 1.96e+01
  ... (remaining 7472 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.67: 9894
        1.67 -     3.33: 186
        3.33 -     5.00: 37
        5.00 -     6.67: 6
        6.67 -     8.33: 5
  Bond angle restraints: 10128
  Sorted by residual:
  angle pdb=" N   ASN C 255 "
        pdb=" CA  ASN C 255 "
        pdb=" CB  ASN C 255 "
      ideal   model   delta    sigma   weight residual
     110.47  102.14    8.33 1.45e+00 4.76e-01 3.30e+01
  angle pdb=" O   SER E  57 "
        pdb=" C   SER E  57 "
        pdb=" N   GLU E  58 "
      ideal   model   delta    sigma   weight residual
     121.87  127.56   -5.69 1.05e+00 9.07e-01 2.94e+01
  angle pdb=" CA  SER E  57 "
        pdb=" C   SER E  57 "
        pdb=" N   GLU E  58 "
      ideal   model   delta    sigma   weight residual
     118.87  113.02    5.85 1.18e+00 7.18e-01 2.46e+01
  angle pdb=" CA  THR D 274 "
        pdb=" C   THR D 274 "
        pdb=" N   SER D 275 "
      ideal   model   delta    sigma   weight residual
     118.40  124.47   -6.07 1.28e+00 6.10e-01 2.25e+01
  angle pdb=" C   VAL D 315 "
        pdb=" CA  VAL D 315 "
        pdb=" CB  VAL D 315 "
      ideal   model   delta    sigma   weight residual
     111.32  116.98   -5.66 1.21e+00 6.83e-01 2.19e+01
  ... (remaining 10123 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 3832
       17.59 -    35.18: 476
       35.18 -    52.77: 117
       52.77 -    70.36: 19
       70.36 -    87.95: 10
  Dihedral angle restraints: 4454
    sinusoidal: 1753
      harmonic: 2701
  Sorted by residual:
  dihedral pdb=" CB  CYS A  95 "
           pdb=" SG  CYS A  95 "
           pdb=" SG  CYS A 172 "
           pdb=" CB  CYS A 172 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -166.83   80.83     1      1.00e+01 1.00e-02 8.07e+01
  dihedral pdb=" CB  CYS A  11 "
           pdb=" SG  CYS A  11 "
           pdb=" SG  CYS A 268 "
           pdb=" CB  CYS A 268 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -126.03   40.03     1      1.00e+01 1.00e-02 2.25e+01
  dihedral pdb=" N   ASN C 255 "
           pdb=" C   ASN C 255 "
           pdb=" CA  ASN C 255 "
           pdb=" CB  ASN C 255 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  111.97   10.83     0      2.50e+00 1.60e-01 1.88e+01
  ... (remaining 4451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 906
       0.046 -    0.092: 200
       0.092 -    0.138: 48
       0.138 -    0.184: 1
       0.184 -    0.230: 4
  Chirality restraints: 1159
  Sorted by residual:
  chirality pdb=" C04 U9S A 401 "
            pdb=" C02 U9S A 401 "
            pdb=" C05 U9S A 401 "
            pdb=" O09 U9S A 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.16    2.39   -0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CB  THR D 274 "
            pdb=" CA  THR D 274 "
            pdb=" OG1 THR D 274 "
            pdb=" CG2 THR D 274 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.33    0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CA  VAL D 315 "
            pdb=" N   VAL D 315 "
            pdb=" C   VAL D 315 "
            pdb=" CB  VAL D 315 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.23    0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 1156 not shown)

  Planarity restraints: 1278
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  76 "    0.038 5.00e-02 4.00e+02   5.78e-02 5.35e+00
        pdb=" N   PRO A  77 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A  77 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A  77 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D 235 "   -0.032 5.00e-02 4.00e+02   4.85e-02 3.76e+00
        pdb=" N   PRO D 236 "    0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO D 236 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO D 236 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN C 255 "    0.008 2.00e-02 2.50e+03   1.55e-02 2.39e+00
        pdb=" C   ASN C 255 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   ASN C 255 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ASN C 256 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1275 not shown)

  Histogram of nonbonded interaction distances:
        1.70 -     2.28: 8
        2.28 -     2.86: 2756
        2.86 -     3.44: 7907
        3.44 -     4.02: 13075
        4.02 -     4.60: 20367
  Nonbonded interactions: 44113
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 277 "
            pdb=" H1  HOH A 601 "
     model   vdw
     1.698 2.450
  nonbonded pdb=" O08 U9S A 401 "
            pdb=" H2  HOH A 601 "
     model   vdw
     1.889 2.450
  nonbonded pdb=" OE1 GLN C  52 "
            pdb=" ND2 ASN C 331 "
     model   vdw
     2.208 2.950
  nonbonded pdb=" OE2 GLU A  18 "
            pdb=" ND2 ASN A 274 "
     model   vdw
     2.229 2.950
  nonbonded pdb=" OD1 ASN D  16 "
            pdb=" NH2 ARG D  19 "
     model   vdw
     2.231 2.950
  ... (remaining 44108 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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 individual isotropic
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:             2.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.060
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.290
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:0.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
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      :  0.004   0.099   7477  Z= 0.245
  Angle     :  0.589   8.334  10131  Z= 0.350
  Chirality :  0.041   0.230   1159
  Planarity :  0.003   0.058   1278
  Dihedral  : 16.530  87.954   2698
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  : 18.16 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.33 (0.30), residues: 909
  helix:  1.99 (0.29), residues: 386
  sheet: -0.70 (0.38), residues: 165
  loop : -1.32 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 120 
 TYR   0.020   0.001   TYR A  46 
 PHE   0.011   0.001   PHE A 115 
 TRP   0.015   0.001   TRP D  82 
 HIS   0.003   0.001   HIS D 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 7475)
  covalent geometry    : angle       0.58905 (10127)
  SS BOND              : bond        0.00252 (    2)
  SS BOND              : angle       1.00384 (    4)
  hydrogen bonds       : bond        0.13862 (  359)
  hydrogen bonds       : angle       5.08760 ( 1026)

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

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

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 96
  time to evaluate  : 0.269 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 97
  average time/residue: 0.0977
  time to fit residues: 12.0311
Evaluate side-chains
  91 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 89
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 ASN
Chi-restraints excluded: chain E residue   59 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.1980
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.7184

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

Flipped N/Q/H residues before XYZ refinement:
** E  59 ASN ** 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 = 0.3493 r_free = 0.3493 target = 0.140631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.099539 restraints weight = 8411.468|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.18
r_work: 0.3056 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8485
moved from start:          0.0639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7477  Z= 0.116
  Angle     :  0.444   4.978  10131  Z= 0.247
  Chirality :  0.039   0.147   1159
  Planarity :  0.003   0.047   1278
  Dihedral  :  4.364  30.789   1003
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 13.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 18.66 %
    Favored  : 78.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.30), residues: 909
  helix:  2.39 (0.29), residues: 374
  sheet: -0.47 (0.38), residues: 176
  loop : -1.25 (0.34), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  99 
 TYR   0.018   0.001   TYR A  46 
 PHE   0.010   0.001   PHE A 115 
 TRP   0.014   0.001   TRP D  82 
 HIS   0.005   0.001   HIS C 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 7475)
  covalent geometry    : angle       0.44348 (10127)
  SS BOND              : bond        0.00257 (    2)
  SS BOND              : angle       0.73521 (    4)
  hydrogen bonds       : bond        0.04681 (  359)
  hydrogen bonds       : angle       4.25058 ( 1026)

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

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

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.184 
Fit side-chains
  outliers start: 20
  outliers final: 16
  residues processed: 99
  average time/residue: 0.0847
  time to fit residues: 10.7726
Evaluate side-chains
  105 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  173 ASN
Chi-restraints excluded: chain A residue  216 GLN
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain D residue   44 GLN
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  161 SER
Chi-restraints excluded: chain D residue  189 SER
Chi-restraints excluded: chain D residue  228 ASP
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain E residue   59 ASN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 8 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 39 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 25 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 69 optimal weight:    0.5980
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
C 256 ASN
E  59 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.137842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.094860 restraints weight = 8355.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.2940 rms_B_bonded: 2.34
r_work: 0.2756 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.2599 rms_B_bonded: 4.97 restraints_weight: 0.2500
r_work (final): 0.2599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.1045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.042   7477  Z= 0.264
  Angle     :  0.594   7.676  10131  Z= 0.318
  Chirality :  0.044   0.165   1159
  Planarity :  0.004   0.060   1278
  Dihedral  :  4.914  34.557   1003
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 13.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.70 %
    Favored  : 92.30 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 19.65 %
    Favored  : 76.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.19 (0.29), residues: 909
  helix:  1.83 (0.28), residues: 385
  sheet: -0.65 (0.37), residues: 178
  loop : -1.41 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  49 
 TYR   0.022   0.002   TYR A  46 
 PHE   0.020   0.002   PHE A 112 
 TRP   0.016   0.002   TRP D  82 
 HIS   0.007   0.001   HIS D 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00646 ( 7475)
  covalent geometry    : angle       0.59392 (10127)
  SS BOND              : bond        0.00356 (    2)
  SS BOND              : angle       0.92789 (    4)
  hydrogen bonds       : bond        0.06177 (  359)
  hydrogen bonds       : angle       4.46911 ( 1026)

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

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

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 88
  time to evaluate  : 0.197 
Fit side-chains
REVERT: A  152 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7405 (mp)
REVERT: A  298 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8033 (mp)
REVERT: C  276 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8302 (pp20)
  outliers start: 31
  outliers final: 19
  residues processed: 103
  average time/residue: 0.0816
  time to fit residues: 10.8205
Evaluate side-chains
  108 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  152 LEU
Chi-restraints excluded: chain A residue  173 ASN
Chi-restraints excluded: chain A residue  216 GLN
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain C residue  293 SER
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain D residue   44 GLN
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  161 SER
Chi-restraints excluded: chain D residue  173 THR
Chi-restraints excluded: chain D residue  189 SER
Chi-restraints excluded: chain D residue  217 MET
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  292 PHE
Chi-restraints excluded: chain D residue  322 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 87 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 88 optimal weight:    0.6980
   chunk 82 optimal weight:    0.4980
   chunk 58 optimal weight:    0.5980
   chunk 41 optimal weight:    9.9990
   chunk 83 optimal weight:    0.1980
   chunk 65 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
A  98 ASN
D 175 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.139414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.098466 restraints weight = 8498.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3281 rms_B_bonded: 2.06
r_work: 0.3080 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.1006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7477  Z= 0.105
  Angle     :  0.425   4.640  10131  Z= 0.236
  Chirality :  0.039   0.134   1159
  Planarity :  0.003   0.049   1278
  Dihedral  :  4.366  34.498   1001
  Min Nonbonded Distance : 2.376

Molprobity Statistics.
  All-atom Clashscore : 14.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 21.64 %
    Favored  : 75.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.72 (0.30), residues: 909
  helix:  2.40 (0.28), residues: 380
  sheet: -0.52 (0.39), residues: 165
  loop : -1.15 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 120 
 TYR   0.018   0.001   TYR A  46 
 PHE   0.010   0.001   PHE A  34 
 TRP   0.014   0.001   TRP D  82 
 HIS   0.004   0.001   HIS C 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 7475)
  covalent geometry    : angle       0.42438 (10127)
  SS BOND              : bond        0.00202 (    2)
  SS BOND              : angle       0.69404 (    4)
  hydrogen bonds       : bond        0.04164 (  359)
  hydrogen bonds       : angle       4.08517 ( 1026)

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

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

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 0.166 
Fit side-chains
REVERT: A  190 CYS cc_start: 0.8506 (m) cc_final: 0.8263 (m)
REVERT: A  298 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.7965 (mp)
REVERT: C  276 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8453 (pp20)
  outliers start: 23
  outliers final: 18
  residues processed: 105
  average time/residue: 0.0880
  time to fit residues: 11.8159
Evaluate side-chains
  114 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 ASN
Chi-restraints excluded: chain A residue  216 GLN
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain A residue  306 LEU
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain D residue   44 GLN
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  189 SER
Chi-restraints excluded: chain D residue  217 MET
Chi-restraints excluded: chain D residue  228 ASP
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  292 PHE
Chi-restraints excluded: chain D residue  322 ASP
Chi-restraints excluded: chain D residue  323 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 25 optimal weight:    5.9990
   chunk 22 optimal weight:    0.1980
   chunk 51 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 18 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0870
   chunk 73 optimal weight:    4.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
D 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.144916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.101154 restraints weight = 8296.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 2.44
r_work: 0.2870 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work: 0.2716 rms_B_bonded: 4.86 restraints_weight: 0.2500
r_work (final): 0.2716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.1060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7477  Z= 0.099
  Angle     :  0.416   4.761  10131  Z= 0.231
  Chirality :  0.039   0.135   1159
  Planarity :  0.003   0.048   1278
  Dihedral  :  4.207  31.695   1001
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 21.89 %
    Favored  : 75.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.30), residues: 909
  helix:  2.54 (0.28), residues: 383
  sheet: -0.37 (0.38), residues: 175
  loop : -1.04 (0.35), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  99 
 TYR   0.019   0.001   TYR A  46 
 PHE   0.010   0.001   PHE C 196 
 TRP   0.012   0.001   TRP D  82 
 HIS   0.003   0.001   HIS C 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 7475)
  covalent geometry    : angle       0.41608 (10127)
  SS BOND              : bond        0.00207 (    2)
  SS BOND              : angle       0.66332 (    4)
  hydrogen bonds       : bond        0.04056 (  359)
  hydrogen bonds       : angle       3.96910 ( 1026)

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

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

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 97
  time to evaluate  : 0.184 
Fit side-chains
REVERT: A  190 CYS cc_start: 0.8370 (m) cc_final: 0.8115 (m)
REVERT: A  298 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7954 (mp)
  outliers start: 24
  outliers final: 20
  residues processed: 107
  average time/residue: 0.0942
  time to fit residues: 12.9889
Evaluate side-chains
  116 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 95
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 ASN
Chi-restraints excluded: chain A residue  216 GLN
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain D residue   44 GLN
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  103 CYS
Chi-restraints excluded: chain D residue  161 SER
Chi-restraints excluded: chain D residue  189 SER
Chi-restraints excluded: chain D residue  228 ASP
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  292 PHE
Chi-restraints excluded: chain D residue  322 ASP
Chi-restraints excluded: chain D residue  323 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0980
   chunk 34 optimal weight:    0.9990
   chunk 46 optimal weight:    6.9990
   chunk 5 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 29 optimal weight:    5.9990
   overall best weight:    1.4188

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

Flipped N/Q/H residues before XYZ refinement:
D 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.140801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.097138 restraints weight = 8371.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 2.38
r_work: 0.2804 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work: 0.2648 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.1118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   7477  Z= 0.186
  Angle     :  0.512   6.460  10131  Z= 0.277
  Chirality :  0.042   0.158   1159
  Planarity :  0.004   0.058   1278
  Dihedral  :  4.535  32.361   1001
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 14.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 21.64 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.69 (0.30), residues: 909
  helix:  2.35 (0.28), residues: 381
  sheet: -0.52 (0.37), residues: 178
  loop : -1.16 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D  49 
 TYR   0.021   0.001   TYR A  46 
 PHE   0.015   0.002   PHE C 196 
 TRP   0.014   0.001   TRP D  82 
 HIS   0.005   0.001   HIS D 142 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 7475)
  covalent geometry    : angle       0.51171 (10127)
  SS BOND              : bond        0.00272 (    2)
  SS BOND              : angle       0.72749 (    4)
  hydrogen bonds       : bond        0.05144 (  359)
  hydrogen bonds       : angle       4.19367 ( 1026)

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

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

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 93
  time to evaluate  : 0.233 
Fit side-chains
REVERT: A  298 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8014 (mp)
REVERT: C  276 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8324 (pp20)
  outliers start: 28
  outliers final: 23
  residues processed: 107
  average time/residue: 0.0847
  time to fit residues: 11.7076
Evaluate side-chains
  117 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  173 ASN
Chi-restraints excluded: chain A residue  216 GLN
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain D residue   44 GLN
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  103 CYS
Chi-restraints excluded: chain D residue  161 SER
Chi-restraints excluded: chain D residue  189 SER
Chi-restraints excluded: chain D residue  217 MET
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  292 PHE
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  322 ASP
Chi-restraints excluded: chain D residue  323 ASP
Chi-restraints excluded: chain E residue   15 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 72 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 49 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0050
   chunk 11 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9990
   overall best weight:    0.5994

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

Flipped N/Q/H residues before XYZ refinement:
D 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.144405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.100984 restraints weight = 8342.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 2.38
r_work: 0.2874 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2719 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8460
moved from start:          0.1130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7477  Z= 0.098
  Angle     :  0.419   4.730  10131  Z= 0.233
  Chirality :  0.039   0.134   1159
  Planarity :  0.003   0.051   1278
  Dihedral  :  4.230  32.282   1001
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 14.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 21.89 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.93 (0.30), residues: 909
  helix:  2.60 (0.28), residues: 383
  sheet: -0.47 (0.38), residues: 178
  loop : -1.08 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  99 
 TYR   0.018   0.001   TYR A  46 
 PHE   0.009   0.001   PHE C 196 
 TRP   0.014   0.001   TRP D  82 
 HIS   0.004   0.001   HIS C 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 7475)
  covalent geometry    : angle       0.41896 (10127)
  SS BOND              : bond        0.00188 (    2)
  SS BOND              : angle       0.58722 (    4)
  hydrogen bonds       : bond        0.04054 (  359)
  hydrogen bonds       : angle       3.98374 ( 1026)

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

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

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A  190 CYS cc_start: 0.8315 (m) cc_final: 0.8059 (m)
REVERT: A  255 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.6413 (ttt90)
REVERT: A  298 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7893 (mp)
REVERT: D  262 MET cc_start: 0.8786 (ttm) cc_final: 0.8550 (mtp)
  outliers start: 26
  outliers final: 22
  residues processed: 106
  average time/residue: 0.0791
  time to fit residues: 10.9082
Evaluate side-chains
  117 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 ASN
Chi-restraints excluded: chain A residue  216 GLN
Chi-restraints excluded: chain A residue  255 ARG
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  256 ASN
Chi-restraints excluded: chain D residue   44 GLN
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  103 CYS
Chi-restraints excluded: chain D residue  161 SER
Chi-restraints excluded: chain D residue  189 SER
Chi-restraints excluded: chain D residue  228 ASP
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  292 PHE
Chi-restraints excluded: chain D residue  322 ASP
Chi-restraints excluded: chain D residue  323 ASP
Chi-restraints excluded: chain E residue   15 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9980
   chunk 72 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9990
   chunk 61 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 18 optimal weight:    0.7980
   chunk 55 optimal weight:    0.3980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
D 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.143575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.100001 restraints weight = 8409.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 2.44
r_work: 0.2864 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2710 rms_B_bonded: 4.75 restraints_weight: 0.2500
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.1155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7477  Z= 0.115
  Angle     :  0.432   4.771  10131  Z= 0.238
  Chirality :  0.039   0.133   1159
  Planarity :  0.003   0.051   1278
  Dihedral  :  4.216  32.624   1001
  Min Nonbonded Distance : 2.335

Molprobity Statistics.
  All-atom Clashscore : 14.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 21.52 %
    Favored  : 74.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.30), residues: 909
  helix:  2.62 (0.28), residues: 383
  sheet: -0.45 (0.38), residues: 178
  loop : -1.11 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 120 
 TYR   0.019   0.001   TYR A  46 
 PHE   0.014   0.001   PHE A  34 
 TRP   0.014   0.001   TRP D  82 
 HIS   0.004   0.001   HIS C 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 7475)
  covalent geometry    : angle       0.43225 (10127)
  SS BOND              : bond        0.00212 (    2)
  SS BOND              : angle       0.59708 (    4)
  hydrogen bonds       : bond        0.04212 (  359)
  hydrogen bonds       : angle       3.97849 ( 1026)

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

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

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 96
  time to evaluate  : 0.176 
Fit side-chains
REVERT: A  190 CYS cc_start: 0.8362 (m) cc_final: 0.8113 (m)
REVERT: A  255 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6489 (ttt90)
REVERT: A  298 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7983 (mp)
REVERT: C   46 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7427 (mtpp)
REVERT: C  276 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.8362 (pp20)
REVERT: D  262 MET cc_start: 0.8787 (ttm) cc_final: 0.8586 (mtp)
  outliers start: 29
  outliers final: 24
  residues processed: 111
  average time/residue: 0.0933
  time to fit residues: 13.3002
Evaluate side-chains
  121 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 93
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  173 ASN
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  216 GLN
Chi-restraints excluded: chain A residue  255 ARG
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  256 ASN
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain D residue   44 GLN
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  103 CYS
Chi-restraints excluded: chain D residue  161 SER
Chi-restraints excluded: chain D residue  189 SER
Chi-restraints excluded: chain D residue  228 ASP
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  292 PHE
Chi-restraints excluded: chain D residue  322 ASP
Chi-restraints excluded: chain D residue  323 ASP
Chi-restraints excluded: chain E residue   15 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 86 optimal weight:    0.7980
   chunk 78 optimal weight:    0.0980
   chunk 63 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 1 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 72 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
D 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.144357 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.100345 restraints weight = 8273.940|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 2.46
r_work: 0.2864 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2709 rms_B_bonded: 4.93 restraints_weight: 0.2500
r_work (final): 0.2709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.1204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7477  Z= 0.104
  Angle     :  0.420   4.766  10131  Z= 0.232
  Chirality :  0.039   0.133   1159
  Planarity :  0.003   0.050   1278
  Dihedral  :  4.132  32.766   1001
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 21.64 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.02 (0.30), residues: 909
  helix:  2.70 (0.28), residues: 383
  sheet: -0.43 (0.37), residues: 178
  loop : -1.06 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 120 
 TYR   0.018   0.001   TYR A  46 
 PHE   0.009   0.001   PHE C 196 
 TRP   0.014   0.001   TRP D  82 
 HIS   0.003   0.001   HIS C 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 7475)
  covalent geometry    : angle       0.41972 (10127)
  SS BOND              : bond        0.00193 (    2)
  SS BOND              : angle       0.55558 (    4)
  hydrogen bonds       : bond        0.04005 (  359)
  hydrogen bonds       : angle       3.93401 ( 1026)

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

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

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 96
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A  190 CYS cc_start: 0.8362 (m) cc_final: 0.8131 (m)
REVERT: A  287 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.8123 (m110)
REVERT: A  298 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7961 (mp)
REVERT: C   46 LYS cc_start: 0.7875 (OUTLIER) cc_final: 0.7431 (mtpp)
REVERT: C  276 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8346 (pp20)
  outliers start: 29
  outliers final: 24
  residues processed: 111
  average time/residue: 0.0792
  time to fit residues: 11.2465
Evaluate side-chains
  122 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 94
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  173 ASN
Chi-restraints excluded: chain A residue  203 MET
Chi-restraints excluded: chain A residue  216 GLN
Chi-restraints excluded: chain A residue  287 ASN
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  256 ASN
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain D residue   44 GLN
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  103 CYS
Chi-restraints excluded: chain D residue  161 SER
Chi-restraints excluded: chain D residue  189 SER
Chi-restraints excluded: chain D residue  228 ASP
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  292 PHE
Chi-restraints excluded: chain D residue  322 ASP
Chi-restraints excluded: chain D residue  323 ASP
Chi-restraints excluded: chain E residue   15 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 55 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
D 175 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.136450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.096033 restraints weight = 8361.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.2968 rms_B_bonded: 2.05
r_work: 0.2808 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2653 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8432
moved from start:          0.1245

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7477  Z= 0.176
  Angle     :  0.497   6.068  10131  Z= 0.269
  Chirality :  0.041   0.147   1159
  Planarity :  0.003   0.054   1278
  Dihedral  :  4.445  33.426   1001
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 21.39 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.30), residues: 909
  helix:  2.49 (0.28), residues: 382
  sheet: -0.52 (0.37), residues: 178
  loop : -1.12 (0.35), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 255 
 TYR   0.020   0.001   TYR A  46 
 PHE   0.015   0.002   PHE A  34 
 TRP   0.014   0.001   TRP D  82 
 HIS   0.007   0.001   HIS C 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 ( 7475)
  covalent geometry    : angle       0.49727 (10127)
  SS BOND              : bond        0.00300 (    2)
  SS BOND              : angle       0.61372 (    4)
  hydrogen bonds       : bond        0.04977 (  359)
  hydrogen bonds       : angle       4.13588 ( 1026)

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

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

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1818 Ramachandran restraints generated.
    909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 89
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A  287 ASN cc_start: 0.8213 (OUTLIER) cc_final: 0.7984 (m110)
REVERT: A  298 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7966 (mp)
REVERT: C   46 LYS cc_start: 0.7852 (OUTLIER) cc_final: 0.7395 (mtpp)
REVERT: C  276 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8287 (pp20)
  outliers start: 29
  outliers final: 22
  residues processed: 104
  average time/residue: 0.0869
  time to fit residues: 11.4891
Evaluate side-chains
  115 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 89
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 SER
Chi-restraints excluded: chain A residue  173 ASN
Chi-restraints excluded: chain A residue  216 GLN
Chi-restraints excluded: chain A residue  287 ASN
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain C residue   46 LYS
Chi-restraints excluded: chain C residue   53 MET
Chi-restraints excluded: chain C residue  184 ILE
Chi-restraints excluded: chain C residue  190 THR
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  256 ASN
Chi-restraints excluded: chain C residue  276 GLU
Chi-restraints excluded: chain D residue   44 GLN
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  103 CYS
Chi-restraints excluded: chain D residue  161 SER
Chi-restraints excluded: chain D residue  189 SER
Chi-restraints excluded: chain D residue  232 ILE
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  292 PHE
Chi-restraints excluded: chain D residue  322 ASP
Chi-restraints excluded: chain D residue  323 ASP
Chi-restraints excluded: chain E residue   15 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 59 optimal weight:    0.9980
   chunk 77 optimal weight:    3.9990
   chunk 60 optimal weight:    0.6980
   chunk 19 optimal weight:    0.1980
   chunk 20 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 11 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 86 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.143680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.100464 restraints weight = 8278.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 2.34
r_work: 0.2866 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2712 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.1244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   7477  Z= 0.105
  Angle     :  0.423   4.794  10131  Z= 0.234
  Chirality :  0.039   0.135   1159
  Planarity :  0.003   0.050   1278
  Dihedral  :  4.185  33.506   1001
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 14.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 21.52 %
    Favored  : 75.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.99 (0.30), residues: 909
  helix:  2.68 (0.28), residues: 383
  sheet: -0.46 (0.38), residues: 178
  loop : -1.08 (0.35), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 255 
 TYR   0.018   0.001   TYR A  46 
 PHE   0.009   0.001   PHE C 196 
 TRP   0.012   0.001   TRP D  82 
 HIS   0.005   0.001   HIS C 188 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 ( 7475)
  covalent geometry    : angle       0.42337 (10127)
  SS BOND              : bond        0.00216 (    2)
  SS BOND              : angle       0.52734 (    4)
  hydrogen bonds       : bond        0.04073 (  359)
  hydrogen bonds       : angle       3.97924 ( 1026)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1613.47 seconds
wall clock time: 28 minutes 19.86 seconds (1699.86 seconds total)