Starting phenix.real_space_refine
on Wed Feb 12 05:23:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wp1_37707/02_2025/8wp1_37707_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wp1_37707/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wp1_37707/02_2025/8wp1_37707.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wp1_37707/02_2025/8wp1_37707.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wp1_37707/02_2025/8wp1_37707_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wp1_37707/02_2025/8wp1_37707_trim.cif"
  }
  resolution = 3.15
  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=  -0.002 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.16, per 1000 atoms: 0.57
  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: 1.74
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.61
  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: 2.02

  Time building geometry restraints manager: 2.01 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          2.710
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     17.160
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.990
-------------------------------------------------------------------------------
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   7475  Z= 0.273
  Angle     :  0.589   8.334  10127  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 : 14.72
  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 (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:  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
 TRP   0.015   0.001   TRP D  82 
 HIS   0.003   0.001   HIS D 142 
 PHE   0.011   0.001   PHE A 115 
 TYR   0.020   0.001   TYR A  46 
 ARG   0.001   0.000   ARG A 120 

*********************** 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  : 0.800 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 97
  average time/residue: 0.2791
  time to fit residues: 34.1274
Evaluate side-chains
  92 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 90
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
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 75 optimal weight:    3.9990
   chunk 68 optimal weight:    3.9990
   chunk 37 optimal weight:    3.9990
   chunk 23 optimal weight:    0.6980
   chunk 46 optimal weight:    0.0270
   chunk 36 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 52 optimal weight:   20.0000
   chunk 81 optimal weight:    2.9990
   overall best weight:    1.1442

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.137860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2959 r_free = 0.2959 target = 0.096961 restraints weight = 8292.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 2.15
r_work: 0.2957 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2804 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.0727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   7475  Z= 0.251
  Angle     :  0.493   5.532  10127  Z= 0.271
  Chirality :  0.041   0.152   1159
  Planarity :  0.004   0.052   1278
  Dihedral  :  4.562  31.101   1003
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 13.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 18.03 %
    Favored  : 78.98 %
  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:  0.54 (0.30), residues: 909
  helix:  2.20 (0.28), residues: 379
  sheet: -0.52 (0.37), residues: 178
  loop : -1.25 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP D 332 
 HIS   0.006   0.001   HIS C 188 
 PHE   0.013   0.002   PHE A 115 
 TYR   0.019   0.001   TYR A  46 
 ARG   0.003   0.000   ARG D 251 

*********************** 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
  116 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 0.981 
Fit side-chains
REVERT: A  298 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.7890 (mp)
  outliers start: 24
  outliers final: 16
  residues processed: 102
  average time/residue: 0.2553
  time to fit residues: 33.6399
Evaluate side-chains
  107 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
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  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  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   87 THR
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.5388

-------------------------------------------------------------------------------
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 = 0.3548 r_free = 0.3548 target = 0.140334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.097237 restraints weight = 8352.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 2.34
r_work: 0.2818 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.2662 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.0975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   7475  Z= 0.323
  Angle     :  0.532   6.693  10127  Z= 0.288
  Chirality :  0.042   0.148   1159
  Planarity :  0.004   0.058   1278
  Dihedral  :  4.732  34.427   1001
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 13.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 20.40 %
    Favored  : 75.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.33 (0.29), residues: 909
  helix:  1.97 (0.28), residues: 385
  sheet: -0.57 (0.36), residues: 176
  loop : -1.36 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP D  82 
 HIS   0.006   0.001   HIS D 142 
 PHE   0.015   0.002   PHE A 112 
 TYR   0.021   0.002   TYR A  46 
 ARG   0.002   0.000   ARG A 120 

*********************** 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
  121 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 90
  time to evaluate  : 0.770 
Fit side-chains
REVERT: A  152 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7351 (mp)
REVERT: A  298 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.7884 (mp)
REVERT: C  276 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8289 (pp20)
  outliers start: 31
  outliers final: 21
  residues processed: 105
  average time/residue: 0.2911
  time to fit residues: 40.1136
Evaluate side-chains
  112 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 0.914 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 14 optimal weight:    0.0970
   chunk 37 optimal weight:    2.9990
   chunk 28 optimal weight:    0.0870
   chunk 65 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 20 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 34 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   overall best weight:    0.7958

-------------------------------------------------------------------------------
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 = 0.3586 r_free = 0.3586 target = 0.143502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.100190 restraints weight = 8305.145|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 2.35
r_work: 0.2887 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.2730 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
moved from start:          0.1000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7475  Z= 0.181
  Angle     :  0.440   4.741  10127  Z= 0.243
  Chirality :  0.039   0.137   1159
  Planarity :  0.003   0.052   1278
  Dihedral  :  4.409  34.147   1001
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 14.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 21.52 %
    Favored  : 75.25 %
  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:  0.67 (0.30), residues: 909
  helix:  2.39 (0.28), residues: 378
  sheet: -0.51 (0.39), residues: 165
  loop : -1.21 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  82 
 HIS   0.004   0.001   HIS C 188 
 PHE   0.011   0.001   PHE A  34 
 TYR   0.019   0.001   TYR A  46 
 ARG   0.001   0.000   ARG A 120 

*********************** 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
  120 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 0.755 
Fit side-chains
REVERT: A  190 CYS cc_start: 0.8371 (m) cc_final: 0.8116 (m)
REVERT: A  298 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7787 (mp)
REVERT: C  276 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.8327 (pp20)
  outliers start: 26
  outliers final: 19
  residues processed: 105
  average time/residue: 0.2458
  time to fit residues: 33.3986
Evaluate side-chains
  113 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.847 
-------------------------------------------------------------------------------
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  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  161 SER
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  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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0040
   chunk 38 optimal weight:    0.7980
   chunk 6 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0270
   chunk 61 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 15 optimal weight:    7.9990
   chunk 41 optimal weight:    2.9990
   chunk 76 optimal weight:    3.9990
   overall best weight:    1.3654

-------------------------------------------------------------------------------
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 = 0.3555 r_free = 0.3555 target = 0.140836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.096986 restraints weight = 8260.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.2986 rms_B_bonded: 2.39
r_work: 0.2803 rms_B_bonded: 3.18 restraints_weight: 0.5000
r_work: 0.2646 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.1079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   7475  Z= 0.287
  Angle     :  0.504   6.208  10127  Z= 0.273
  Chirality :  0.041   0.140   1159
  Planarity :  0.004   0.056   1278
  Dihedral  :  4.593  34.056   1001
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 14.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 21.14 %
    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 (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:  0.55 (0.29), residues: 909
  helix:  2.27 (0.28), residues: 379
  sheet: -0.51 (0.37), residues: 176
  loop : -1.31 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP D  82 
 HIS   0.005   0.001   HIS D 142 
 PHE   0.014   0.002   PHE C 196 
 TYR   0.020   0.001   TYR A  46 
 ARG   0.002   0.000   ARG D  49 

*********************** 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
  120 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 89
  time to evaluate  : 0.642 
Fit side-chains
REVERT: A  298 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.7941 (mp)
REVERT: C  276 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8292 (pp20)
  outliers start: 31
  outliers final: 23
  residues processed: 105
  average time/residue: 0.2428
  time to fit residues: 32.6996
Evaluate side-chains
  113 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 88
  time to evaluate  : 0.803 
-------------------------------------------------------------------------------
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  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  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 E residue   15 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 22 optimal weight:    0.0470
   chunk 49 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9990
   chunk 65 optimal weight:    0.3980
   chunk 57 optimal weight:    0.0980
   chunk 73 optimal weight:    4.9990
   chunk 77 optimal weight:    0.8980
   overall best weight:    0.4278

-------------------------------------------------------------------------------
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 = 0.3628 r_free = 0.3628 target = 0.146451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.102570 restraints weight = 8240.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 2.46
r_work: 0.2875 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2720 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2720
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8478
moved from start:          0.1139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7475  Z= 0.118
  Angle     :  0.404   4.697  10127  Z= 0.226
  Chirality :  0.039   0.133   1159
  Planarity :  0.003   0.048   1278
  Dihedral  :  4.213  31.887   1001
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 14.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 21.52 %
    Favored  : 75.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.30), residues: 909
  helix:  2.58 (0.28), residues: 383
  sheet: -0.39 (0.38), residues: 175
  loop : -1.06 (0.35), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D  82 
 HIS   0.003   0.001   HIS C 188 
 PHE   0.012   0.001   PHE A  34 
 TYR   0.018   0.001   TYR A  46 
 ARG   0.001   0.000   ARG A  99 

*********************** 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
  118 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.780 
Fit side-chains
REVERT: A  190 CYS cc_start: 0.8346 (m) cc_final: 0.8095 (m)
REVERT: C   46 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7403 (mtpp)
REVERT: C  276 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.8325 (pp20)
  outliers start: 25
  outliers final: 20
  residues processed: 105
  average time/residue: 0.2561
  time to fit residues: 34.2508
Evaluate side-chains
  111 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.834 
-------------------------------------------------------------------------------
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  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  276 GLU
Chi-restraints excluded: chain D residue   44 GLN
Chi-restraints excluded: chain D residue   86 THR
Chi-restraints excluded: chain D residue  103 CYS
Chi-restraints excluded: chain D residue  146 LEU
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  228 ASP
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 E residue   15 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0470
   chunk 50 optimal weight:    0.1980
   chunk 87 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 57 optimal weight:    0.0170
   overall best weight:    0.3516

-------------------------------------------------------------------------------
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 = 0.3654 r_free = 0.3654 target = 0.148665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.105200 restraints weight = 8182.567|
|-----------------------------------------------------------------------------|
r_work (start): 0.3087 rms_B_bonded: 2.37
r_work: 0.2911 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work: 0.2757 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8451
moved from start:          0.1327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7475  Z= 0.110
  Angle     :  0.386   5.060  10127  Z= 0.215
  Chirality :  0.038   0.131   1159
  Planarity :  0.003   0.049   1278
  Dihedral  :  3.894  32.518   1001
  Min Nonbonded Distance : 2.337

Molprobity Statistics.
  All-atom Clashscore : 14.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 22.26 %
    Favored  : 75.25 %
  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 (0.30), residues: 909
  helix:  2.97 (0.29), residues: 376
  sheet: -0.24 (0.38), residues: 175
  loop : -1.08 (0.35), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  82 
 HIS   0.002   0.001   HIS C 188 
 PHE   0.007   0.001   PHE A  50 
 TYR   0.021   0.001   TYR A  46 
 ARG   0.002   0.000   ARG A 255 

*********************** 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
  115 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.810 
Fit side-chains
REVERT: A   25 TYR cc_start: 0.8174 (t80) cc_final: 0.7956 (t80)
REVERT: A  190 CYS cc_start: 0.8381 (m) cc_final: 0.8125 (m)
REVERT: A  298 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7936 (mp)
REVERT: C   17 LYS cc_start: 0.7693 (mmtm) cc_final: 0.7438 (mmtm)
  outliers start: 20
  outliers final: 18
  residues processed: 108
  average time/residue: 0.2452
  time to fit residues: 34.2826
Evaluate side-chains
  110 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
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  190 THR
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain C residue  293 SER
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  232 ILE
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  270 ILE
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  336 LEU
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 40 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 51 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 88 optimal weight:    1.9990
   chunk 89 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 25 optimal weight:    0.2980
   chunk 14 optimal weight:    2.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.3511 r_free = 0.3511 target = 0.138911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.098603 restraints weight = 8294.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.2996 rms_B_bonded: 2.06
r_work: 0.2837 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2680 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.2680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8376
moved from start:          0.1201

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7475  Z= 0.220
  Angle     :  0.453   5.038  10127  Z= 0.248
  Chirality :  0.040   0.138   1159
  Planarity :  0.003   0.053   1278
  Dihedral  :  4.193  31.944   1001
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 14.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.60 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 20.77 %
    Favored  : 75.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.30), residues: 909
  helix:  2.75 (0.28), residues: 377
  sheet: -0.39 (0.37), residues: 178
  loop : -1.16 (0.34), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  82 
 HIS   0.005   0.001   HIS C 188 
 PHE   0.012   0.001   PHE C 196 
 TYR   0.020   0.001   TYR A  46 
 ARG   0.001   0.000   ARG A 120 

*********************** 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
  122 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 91
  time to evaluate  : 0.789 
Fit side-chains
REVERT: A  190 CYS cc_start: 0.8223 (m) cc_final: 0.7960 (m)
REVERT: A  287 ASN cc_start: 0.8173 (OUTLIER) cc_final: 0.7929 (m110)
REVERT: A  298 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7795 (mp)
REVERT: C   17 LYS cc_start: 0.7571 (mmtm) cc_final: 0.7313 (mmtm)
  outliers start: 31
  outliers final: 27
  residues processed: 111
  average time/residue: 0.2349
  time to fit residues: 33.7182
Evaluate side-chains
  119 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 90
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 SER
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  287 ASN
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  293 SER
Chi-restraints excluded: chain C residue  297 GLU
Chi-restraints excluded: chain D residue   31 SER
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  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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 68 optimal weight:    0.0270
   chunk 58 optimal weight:    0.5980
   chunk 4 optimal weight:    0.0770
   chunk 29 optimal weight:    0.6980
   chunk 46 optimal weight:    5.9990
   chunk 62 optimal weight:    0.4980
   chunk 40 optimal weight:    4.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.3796

-------------------------------------------------------------------------------
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 = 0.3554 r_free = 0.3554 target = 0.142457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.102107 restraints weight = 8300.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 2.06
r_work: 0.2917 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2763 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8365
moved from start:          0.1339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7475  Z= 0.112
  Angle     :  0.391   4.869  10127  Z= 0.218
  Chirality :  0.038   0.132   1159
  Planarity :  0.003   0.048   1278
  Dihedral  :  3.911  31.910   1001
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 21.64 %
    Favored  : 75.25 %
  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:  1.20 (0.30), residues: 909
  helix:  2.96 (0.28), residues: 377
  sheet: -0.26 (0.38), residues: 178
  loop : -1.10 (0.35), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  82 
 HIS   0.004   0.001   HIS C 188 
 PHE   0.013   0.001   PHE A  34 
 TYR   0.019   0.001   TYR A  46 
 ARG   0.001   0.000   ARG C  24 

*********************** 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
  120 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.921 
Fit side-chains
REVERT: A  190 CYS cc_start: 0.8251 (m) cc_final: 0.7965 (m)
REVERT: A  287 ASN cc_start: 0.8342 (OUTLIER) cc_final: 0.8066 (m110)
REVERT: A  298 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7862 (mp)
REVERT: C   17 LYS cc_start: 0.7557 (mmtm) cc_final: 0.7283 (mmtm)
  outliers start: 25
  outliers final: 23
  residues processed: 110
  average time/residue: 0.2482
  time to fit residues: 35.4894
Evaluate side-chains
  118 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 93
  time to evaluate  : 0.813 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 SER
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  287 ASN
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  297 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  234 PHE
Chi-restraints excluded: chain D residue  270 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 38 optimal weight:    0.0030
   chunk 36 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 68 optimal weight:    2.9990
   chunk 58 optimal weight:    0.5980
   chunk 55 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 6 optimal weight:    0.0040
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.3802

-------------------------------------------------------------------------------
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 = 0.3567 r_free = 0.3567 target = 0.143775 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.105077 restraints weight = 8322.424|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 1.88
r_work: 0.2941 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.2789 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.1455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   7475  Z= 0.111
  Angle     :  0.385   4.902  10127  Z= 0.215
  Chirality :  0.038   0.131   1159
  Planarity :  0.003   0.048   1278
  Dihedral  :  3.756  31.651   1001
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 16.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 21.27 %
    Favored  : 75.25 %
  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:  1.35 (0.30), residues: 909
  helix:  3.11 (0.28), residues: 377
  sheet: -0.20 (0.38), residues: 179
  loop : -1.04 (0.35), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  82 
 HIS   0.004   0.001   HIS C 188 
 PHE   0.013   0.001   PHE A  34 
 TYR   0.019   0.001   TYR A  46 
 ARG   0.002   0.000   ARG A 281 

********************** 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
  124 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 0.852 
Fit side-chains
REVERT: A  190 CYS cc_start: 0.8199 (m) cc_final: 0.7896 (m)
REVERT: A  287 ASN cc_start: 0.8264 (OUTLIER) cc_final: 0.7959 (m110)
REVERT: A  298 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7869 (mp)
REVERT: C   17 LYS cc_start: 0.7444 (mmtm) cc_final: 0.7167 (mmtm)
  outliers start: 28
  outliers final: 25
  residues processed: 114
  average time/residue: 0.2503
  time to fit residues: 37.3127
Evaluate side-chains
  121 residues out of total 804 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 0.880 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  117 SER
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  287 ASN
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  297 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  146 LEU
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 90
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 21 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9980
   chunk 69 optimal weight:    2.9990
   chunk 26 optimal weight:    0.4980
   chunk 88 optimal weight:    2.9990
   chunk 67 optimal weight:    0.0870
   chunk 43 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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 = 0.3636 r_free = 0.3636 target = 0.147142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.103576 restraints weight = 8246.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3064 rms_B_bonded: 2.44
r_work: 0.2893 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work: 0.2736 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8462
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7475  Z= 0.136
  Angle     :  0.399   4.910  10127  Z= 0.222
  Chirality :  0.038   0.132   1159
  Planarity :  0.003   0.048   1278
  Dihedral  :  3.816  30.988   1001
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 15.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 20.77 %
    Favored  : 75.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.30), residues: 909
  helix:  3.10 (0.28), residues: 377
  sheet: -0.18 (0.38), residues: 178
  loop : -1.05 (0.35), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  82 
 HIS   0.004   0.001   HIS C 188 
 PHE   0.014   0.001   PHE A  34 
 TYR   0.020   0.001   TYR A  46 
 ARG   0.001   0.000   ARG A 255 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4306.80 seconds
wall clock time: 77 minutes 18.05 seconds (4638.05 seconds total)