Starting phenix.real_space_refine
on Wed Mar  4 14:55:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9wc1_65854/03_2026/9wc1_65854.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9wc1_65854/03_2026/9wc1_65854.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9wc1_65854/03_2026/9wc1_65854.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9wc1_65854/03_2026/9wc1_65854.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9wc1_65854/03_2026/9wc1_65854.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9wc1_65854/03_2026/9wc1_65854.cif"
  }
  resolution = 3.4
  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=   0.000 sd=   0.055
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      48      5.16       5
     C    4438      2.51       5
     N    1207      2.21       5
     O    1339      1.98       5
     H    6873      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 13905
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 375, 5816
          Classifications: {'peptide': 375}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 355}
    Chain: "B"
      Number of atoms: 6537
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 428, 6537
          Classifications: {'peptide': 428}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 22, 'TRANS': 405}
    Chain: "C"
      Number of atoms: 431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 431
          Classifications: {'peptide': 27}
          Link IDs: {'PTRANS': 1, 'TRANS': 25}
    Chain: "D"
      Number of atoms: 1121
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 1121
          Classifications: {'peptide': 64}
          Link IDs: {'TRANS': 63}
  Time building chain proxies: 2.40, per 1000 atoms: 0.17
  Number of scatterers: 13905
  At special positions: 0
  Unit cell: (85.5175, 108.25, 97.425, 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      48     16.00
     O    1339      8.00
     N    1207      7.00
     C    4438      6.00
     H    6873      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.93
  Conformation dependent library (CDL) restraints added in 417.2 milliseconds
  

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1652

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 14 sheets defined
      50.3% alpha, 15.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 55 through 61
      removed outlier: 3.523A  pdb=" N   GLN A  59 " --> pdb=" O   GLY A  55 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LYS A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 78 through 92
      removed outlier: 3.899A  pdb=" N   LYS A  84 " --> pdb=" O   ASP A  80 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ILE A  85 " --> pdb=" O   ASP A  81 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   TRP A  86 " --> pdb=" O   MET A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 101
    Processing helix  chain 'A' and resid 112 through 126
      removed outlier: 3.832A  pdb=" N   ARG A 116 " --> pdb=" O   PRO A 112 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   MET A 123 " --> pdb=" O   MET A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 145
      removed outlier: 3.747A  pdb=" N   SER A 145 " --> pdb=" O   SER A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 197
    Processing helix  chain 'A' and resid 202 through 216
      removed outlier: 4.033A  pdb=" N   GLU A 207 " --> pdb=" O   THR A 203 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   ILE A 208 " --> pdb=" O   ALA A 204 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LYS A 215 " --> pdb=" O   ASP A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 233
    Processing helix  chain 'A' and resid 252 through 257
    Processing helix  chain 'A' and resid 258 through 262
    Processing helix  chain 'A' and resid 263 through 268
    Processing helix  chain 'A' and resid 273 through 284
    Processing helix  chain 'A' and resid 289 through 296
      removed outlier: 3.516A  pdb=" N   ALA A 295 " --> pdb=" O   LYS A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 306
      removed outlier: 3.518A  pdb=" N   THR A 304 " --> pdb=" O   GLY A 301 " (cutoff:3.500A)
      removed outlier: 4.031A  pdb=" N   TYR A 306 " --> pdb=" O   THR A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 321
      removed outlier: 3.621A  pdb=" N   LEU A 320 " --> pdb=" O   GLU A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 336
      No H-bonds generated for 'chain 'A' and resid 334 through 336'
    Processing helix  chain 'A' and resid 337 through 349
      removed outlier: 3.503A  pdb=" N   LEU A 349 " --> pdb=" O   ILE A 345 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 351 through 355
      removed outlier: 3.891A  pdb=" N   GLN A 354 " --> pdb=" O   THR A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 366
    Processing helix  chain 'A' and resid 368 through 374
      removed outlier: 4.230A  pdb=" N   ARG A 372 " --> pdb=" O   SER A 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 74
    Processing helix  chain 'B' and resid 93 through 108
    Processing helix  chain 'B' and resid 112 through 116
      removed outlier: 3.764A  pdb=" N   HIS B 116 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 127 through 142
    Processing helix  chain 'B' and resid 152 through 160
    Processing helix  chain 'B' and resid 187 through 190
    Processing helix  chain 'B' and resid 196 through 212
    Processing helix  chain 'B' and resid 217 through 219
      No H-bonds generated for 'chain 'B' and resid 217 through 219'
    Processing helix  chain 'B' and resid 245 through 265
      removed outlier: 3.581A  pdb=" N   LEU B 265 " --> pdb=" O   GLN B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 273 through 278
    Processing helix  chain 'B' and resid 297 through 302
    Processing helix  chain 'B' and resid 303 through 308
      removed outlier: 4.202A  pdb=" N   PHE B 307 " --> pdb=" O   PRO B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 312
    Processing helix  chain 'B' and resid 322 through 334
      removed outlier: 3.692A  pdb=" N   VAL B 327 " --> pdb=" O   VAL B 323 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   THR B 328 " --> pdb=" O   SER B 324 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   CYS B 334 " --> pdb=" O   SER B 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 338 through 344
    Processing helix  chain 'B' and resid 350 through 355
      removed outlier: 3.761A  pdb=" N   ILE B 355 " --> pdb=" O   ASN B 352 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 370
    Processing helix  chain 'B' and resid 384 through 389
    Processing helix  chain 'B' and resid 389 through 400
      removed outlier: 3.568A  pdb=" N   GLY B 395 " --> pdb=" O   SER B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 401 through 408
      removed outlier: 3.596A  pdb=" N   GLN B 405 " --> pdb=" O   GLY B 402 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   GLN B 406 " --> pdb=" O   THR B 403 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   TRP B 408 " --> pdb=" O   GLN B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 418
    Processing helix  chain 'B' and resid 420 through 426
      removed outlier: 3.646A  pdb=" N   ARG B 424 " --> pdb=" O   GLN B 420 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 2 through 63
      removed outlier: 3.698A  pdb=" N   LYS D  49 " --> pdb=" O   GLN D  45 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ARG D  60 " --> pdb=" O   ALA D  56 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LYS D  63 " --> pdb=" O   GLU D  59 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31
      removed outlier: 6.989A  pdb=" N   LEU A   8 " --> pdb=" O   LEU A 104 " (cutoff:3.500A)
      removed outlier: 8.406A  pdb=" N   THR A 106 " --> pdb=" O   LEU A   8 " (cutoff:3.500A)
      removed outlier: 8.008A  pdb=" N   VAL A  10 " --> pdb=" O   THR A 106 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54
      removed outlier: 3.778A  pdb=" N   VAL A  35 " --> pdb=" O   LYS A  68 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 71 through 72
    Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170
      removed outlier: 3.525A  pdb=" N   TYR A 166 " --> pdb=" O   TYR A 169 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 169 through 170
      removed outlier: 3.525A  pdb=" N   TYR A 166 " --> pdb=" O   TYR A 169 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   ILE A 151 " --> pdb=" O   VAL A 298 " (cutoff:3.500A)
      removed outlier: 7.680A  pdb=" N   SER A 300 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 6.471A  pdb=" N   MET A 153 " --> pdb=" O   SER A 300 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   THR A 297 " --> pdb=" O   ILE A 330 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241
    Processing sheet with id=AA7, first strand: chain 'B' and resid 33 through 36
      removed outlier: 3.583A  pdb=" N   PHE B  35 " --> pdb=" O   VAL B  21 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   LEU B  12 " --> pdb=" O   LEU B 119 " (cutoff:3.500A)
      removed outlier: 8.032A  pdb=" N   SER B 121 " --> pdb=" O   LEU B  12 " (cutoff:3.500A)
      removed outlier: 7.514A  pdb=" N   PHE B  14 " --> pdb=" O   SER B 121 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   VAL B 118 " --> pdb=" O   PHE B 148 " (cutoff:3.500A)
      removed outlier: 7.993A  pdb=" N   CYS B 150 " --> pdb=" O   VAL B 118 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   MET B 120 " --> pdb=" O   CYS B 150 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 67
    Processing sheet with id=AA9, first strand: chain 'B' and resid 86 through 87
    Processing sheet with id=AB1, first strand: chain 'B' and resid 184 through 185
    Processing sheet with id=AB2, first strand: chain 'B' and resid 184 through 185
      removed outlier: 3.565A  pdb=" N   SER B 170 " --> pdb=" O   ALA B 349 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   VAL B 346 " --> pdb=" O   ILE B 379 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 221 through 224
      removed outlier: 6.700A  pdb=" N   LYS B 236 " --> pdb=" O   ALA B 222 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 283 through 286
    Processing sheet with id=AB5, first strand: chain 'C' and resid 31 through 37

    342 hydrogen bonds defined for protein.
    906 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: 3.10

  Time building geometry restraints manager: 1.41 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: 6858
        1.03 -     1.23: 18
        1.23 -     1.42: 2976
        1.42 -     1.62: 4122
        1.62 -     1.81: 81
  Bond restraints: 14055
  Sorted by residual:
  bond pdb=" N   GLU D   1 "
       pdb=" CA  GLU D   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.15e+00
  bond pdb=" N   GLU D   1 "
       pdb=" H   GLU D   1 "
    ideal  model  delta    sigma   weight residual
    0.860  0.891 -0.031 2.00e-02 2.50e+03 2.33e+00
  bond pdb=" C   ILE B 144 "
       pdb=" O   ILE B 144 "
    ideal  model  delta    sigma   weight residual
    1.248  1.237  0.011 1.27e-02 6.20e+03 7.39e-01
  bond pdb=" C   VAL B 216 "
       pdb=" O   VAL B 216 "
    ideal  model  delta    sigma   weight residual
    1.240  1.231  0.009 1.26e-02 6.30e+03 5.23e-01
  bond pdb=" CA  ASP B  15 "
       pdb=" C   ASP B  15 "
    ideal  model  delta    sigma   weight residual
    1.526  1.519  0.007 1.03e-02 9.43e+03 4.97e-01
  ... (remaining 14050 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.91: 23255
        0.91 -     1.82: 2000
        1.82 -     2.74: 65
        2.74 -     3.65: 39
        3.65 -     4.56: 10
  Bond angle restraints: 25369
  Sorted by residual:
  angle pdb=" N   VAL B   9 "
        pdb=" CA  VAL B   9 "
        pdb=" C   VAL B   9 "
      ideal   model   delta    sigma   weight residual
     113.71  110.79    2.92 9.50e-01 1.11e+00 9.45e+00
  angle pdb=" CA  VAL B   9 "
        pdb=" C   VAL B   9 "
        pdb=" N   GLY B  10 "
      ideal   model   delta    sigma   weight residual
     119.87  117.03    2.84 1.34e+00 5.57e-01 4.50e+00
  angle pdb=" CA  ILE B 178 "
        pdb=" C   ILE B 178 "
        pdb=" O   ILE B 178 "
      ideal   model   delta    sigma   weight residual
     120.88  119.57    1.31 6.80e-01 2.16e+00 3.73e+00
  angle pdb=" CA  ILE B 178 "
        pdb=" C   ILE B 178 "
        pdb=" N   PRO B 179 "
      ideal   model   delta    sigma   weight residual
     118.12  119.61   -1.49 8.10e-01 1.52e+00 3.38e+00
  angle pdb=" N   ILE B  54 "
        pdb=" CA  ILE B  54 "
        pdb=" C   ILE B  54 "
      ideal   model   delta    sigma   weight residual
     109.34  105.99    3.35 2.08e+00 2.31e-01 2.59e+00
  ... (remaining 25364 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 5983
       17.89 -    35.79: 483
       35.79 -    53.68: 127
       53.68 -    71.57: 32
       71.57 -    89.47: 10
  Dihedral angle restraints: 6635
    sinusoidal: 3633
      harmonic: 3002
  Sorted by residual:
  dihedral pdb=" CB  GLU B 132 "
           pdb=" CG  GLU B 132 "
           pdb=" CD  GLU B 132 "
           pdb=" OE1 GLU B 132 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.47   89.47     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CG  ARG A 177 "
           pdb=" CD  ARG A 177 "
           pdb=" NE  ARG A 177 "
           pdb=" CZ  ARG A 177 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  136.22   43.78     2      1.50e+01 4.44e-03 1.02e+01
  dihedral pdb=" CG  ARG B 364 "
           pdb=" CD  ARG B 364 "
           pdb=" NE  ARG B 364 "
           pdb=" CZ  ARG B 364 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -132.14   42.14     2      1.50e+01 4.44e-03 9.60e+00
  ... (remaining 6632 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 677
       0.031 -    0.062: 263
       0.062 -    0.093: 53
       0.093 -    0.124: 69
       0.124 -    0.155: 3
  Chirality restraints: 1065
  Sorted by residual:
  chirality pdb=" CA  ILE B  54 "
            pdb=" N   ILE B  54 "
            pdb=" C   ILE B  54 "
            pdb=" CB  ILE B  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.99e-01
  chirality pdb=" CA  ILE B 347 "
            pdb=" N   ILE B 347 "
            pdb=" C   ILE B 347 "
            pdb=" CB  ILE B 347 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.49e-01
  chirality pdb=" CA  ILE A  71 "
            pdb=" N   ILE A  71 "
            pdb=" C   ILE A  71 "
            pdb=" CB  ILE A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.84e-01
  ... (remaining 1062 not shown)

  Planarity restraints: 2096
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 280 "   -0.020 5.00e-02 4.00e+02   3.06e-02 1.49e+00
        pdb=" N   PRO B 281 "    0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO B 281 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 281 "   -0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 111 "    0.020 5.00e-02 4.00e+02   3.00e-02 1.44e+00
        pdb=" N   PRO A 112 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 112 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 112 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 116 "    0.016 5.00e-02 4.00e+02   2.37e-02 8.97e-01
        pdb=" N   PRO B 117 "   -0.041 5.00e-02 4.00e+02
        pdb=" CA  PRO B 117 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO B 117 "    0.013 5.00e-02 4.00e+02
  ... (remaining 2093 not shown)

  Histogram of nonbonded interaction distances:
        1.61 -     2.21: 970
        2.21 -     2.81: 28787
        2.81 -     3.41: 36206
        3.41 -     4.00: 48274
        4.00 -     4.60: 74663
  Nonbonded interactions: 188900
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 335 "
            pdb=" H   ASP B 337 "
     model   vdw
     1.614 2.450
  nonbonded pdb=" O   GLN A 314 "
            pdb=" HG1 THR A 318 "
     model   vdw
     1.617 2.450
  nonbonded pdb=" OD1 ASP B  15 "
            pdb=" HG  SER B 121 "
     model   vdw
     1.660 2.450
  nonbonded pdb=" O   THR A 304 "
            pdb="HH11 ARG A 335 "
     model   vdw
     1.664 2.450
  nonbonded pdb=" OD1 ASP B 102 "
            pdb=" HH  TYR B 142 "
     model   vdw
     1.670 2.450
  ... (remaining 188895 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:             3.840
  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:             0.090
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     13.430
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  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:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.110
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
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      :  0.003   0.034   7182  Z= 0.140
  Angle     :  0.454   4.012   9713  Z= 0.243
  Chirality :  0.041   0.155   1065
  Planarity :  0.003   0.031   1256
  Dihedral  : 13.817  89.466   2687
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  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 are not related in a simple way.
  whole:  0.99 (0.29), residues: 886
  helix:  1.13 (0.28), residues: 374
  sheet:  0.31 (0.43), residues: 138
  loop :  0.50 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  62 
 TYR   0.007   0.001   TYR C  46 
 PHE   0.009   0.001   PHE A 255 
 TRP   0.007   0.001   TRP B 408 
 HIS   0.006   0.001   HIS A  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 7182)
  covalent geometry    : angle       0.45383 ( 9713)
  hydrogen bonds       : bond        0.23438 (  339)
  hydrogen bonds       : angle       7.74839 (  906)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.1097 (mmt) cc_final: 0.0611 (tpp)
REVERT: B  209 GLN cc_start: 0.8232 (tm-30) cc_final: 0.7937 (tm-30)
REVERT: D   21 GLU cc_start: 0.8542 (tp30) cc_final: 0.8257 (tp30)
REVERT: D   45 GLN cc_start: 0.8291 (tm130) cc_final: 0.7908 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 121
  average time/residue: 0.2124
  time to fit residues: 33.1944
Evaluate side-chains
  97 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  12 ASN
A 161 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.124465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.096158 restraints weight = 32199.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 3.09
r_work: 0.3040 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.1145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7182  Z= 0.136
  Angle     :  0.510   4.134   9713  Z= 0.276
  Chirality :  0.043   0.149   1065
  Planarity :  0.004   0.039   1256
  Dihedral  :  3.844  15.315    970
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 3.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  4.83 %
    Favored  : 94.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.94 (0.29), residues: 886
  helix:  1.30 (0.28), residues: 365
  sheet:  0.10 (0.42), residues: 146
  loop :  0.32 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 335 
 TYR   0.012   0.001   TYR D  22 
 PHE   0.020   0.001   PHE D  33 
 TRP   0.006   0.001   TRP B 392 
 HIS   0.005   0.001   HIS A  73 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 7182)
  covalent geometry    : angle       0.50988 ( 9713)
  hydrogen bonds       : bond        0.05209 (  339)
  hydrogen bonds       : angle       5.40520 (  906)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 105
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  386 GLU cc_start: 0.8337 (pt0) cc_final: 0.8100 (pm20)
REVERT: D   45 GLN cc_start: 0.8355 (tm130) cc_final: 0.7845 (tm-30)
  outliers start: 2
  outliers final: 2
  residues processed: 106
  average time/residue: 0.1597
  time to fit residues: 23.5846
Evaluate side-chains
  101 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue   70 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 43 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.122660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.094193 restraints weight = 32634.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.3133 rms_B_bonded: 3.10
r_work: 0.3006 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.1408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   7182  Z= 0.212
  Angle     :  0.509   4.177   9713  Z= 0.272
  Chirality :  0.043   0.146   1065
  Planarity :  0.004   0.032   1256
  Dihedral  :  3.920  17.501    970
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 3.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  6.66 %
    Favored  : 92.69 %
  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 are not related in a simple way.
  whole:  0.89 (0.29), residues: 886
  helix:  1.33 (0.28), residues: 364
  sheet:  0.00 (0.42), residues: 147
  loop :  0.26 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 335 
 TYR   0.012   0.001   TYR D  22 
 PHE   0.019   0.001   PHE D  33 
 TRP   0.009   0.001   TRP B 408 
 HIS   0.005   0.001   HIS D  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 ( 7182)
  covalent geometry    : angle       0.50939 ( 9713)
  hydrogen bonds       : bond        0.05010 (  339)
  hydrogen bonds       : angle       5.27182 (  906)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.0696 (mmt) cc_final: 0.0221 (tpp)
REVERT: D   45 GLN cc_start: 0.8315 (tm130) cc_final: 0.7720 (tm-30)
  outliers start: 5
  outliers final: 5
  residues processed: 104
  average time/residue: 0.1672
  time to fit residues: 23.8124
Evaluate side-chains
  101 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  257 CYS
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue  410 SER
Chi-restraints excluded: chain D residue   10 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 82 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 81 optimal weight:   10.0000
   chunk 25 optimal weight:    1.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.123294 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.094868 restraints weight = 32257.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3138 rms_B_bonded: 3.08
r_work: 0.3014 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7182  Z= 0.164
  Angle     :  0.499   6.635   9713  Z= 0.263
  Chirality :  0.043   0.144   1065
  Planarity :  0.003   0.028   1256
  Dihedral  :  3.928  18.840    970
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 3.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  8.22 %
    Favored  : 91.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.29), residues: 886
  helix:  1.36 (0.28), residues: 367
  sheet:  0.05 (0.42), residues: 147
  loop :  0.20 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  16 
 TYR   0.013   0.001   TYR D  22 
 PHE   0.018   0.001   PHE D  33 
 TRP   0.008   0.001   TRP B 408 
 HIS   0.005   0.001   HIS D  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 7182)
  covalent geometry    : angle       0.49938 ( 9713)
  hydrogen bonds       : bond        0.04314 (  339)
  hydrogen bonds       : angle       5.02500 (  906)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.313 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.0753 (mmt) cc_final: 0.0312 (tpp)
REVERT: B  333 MET cc_start: 0.8673 (mtm) cc_final: 0.8370 (mtp)
  outliers start: 4
  outliers final: 4
  residues processed: 101
  average time/residue: 0.1716
  time to fit residues: 24.0290
Evaluate side-chains
  99 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 95
  time to evaluate  : 0.448 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  257 CYS
Chi-restraints excluded: chain B residue   33 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 51 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 40 optimal weight:    0.5980
   chunk 73 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
D  45 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.123863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.095473 restraints weight = 32215.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 3.08
r_work: 0.3032 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3032
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7182  Z= 0.134
  Angle     :  0.479   4.918   9713  Z= 0.250
  Chirality :  0.042   0.141   1065
  Planarity :  0.003   0.032   1256
  Dihedral  :  3.844  18.513    970
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  9.01 %
    Favored  : 90.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.01 (0.29), residues: 886
  helix:  1.45 (0.28), residues: 374
  sheet:  0.09 (0.42), residues: 147
  loop :  0.25 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 196 
 TYR   0.014   0.001   TYR D  22 
 PHE   0.017   0.001   PHE D  33 
 TRP   0.007   0.001   TRP B 408 
 HIS   0.005   0.001   HIS D  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 7182)
  covalent geometry    : angle       0.47886 ( 9713)
  hydrogen bonds       : bond        0.03922 (  339)
  hydrogen bonds       : angle       4.83519 (  906)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 0.384 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.0764 (mmt) cc_final: 0.0312 (tpp)
REVERT: B  333 MET cc_start: 0.8664 (mtm) cc_final: 0.8370 (mtp)
  outliers start: 4
  outliers final: 4
  residues processed: 103
  average time/residue: 0.1729
  time to fit residues: 24.7585
Evaluate side-chains
  102 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  257 CYS
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain D residue   10 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 19 optimal weight:    1.9990
   chunk 69 optimal weight:    0.4980
   chunk 29 optimal weight:    0.9990
   chunk 31 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 85 optimal weight:    0.6980
   chunk 33 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
D  45 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.124390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.095945 restraints weight = 32082.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 3.07
r_work: 0.3027 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.1884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   7182  Z= 0.116
  Angle     :  0.471   5.618   9713  Z= 0.243
  Chirality :  0.041   0.138   1065
  Planarity :  0.003   0.035   1256
  Dihedral  :  3.779  17.690    970
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 3.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  9.66 %
    Favored  : 89.56 %
  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 are not related in a simple way.
  whole:  1.11 (0.29), residues: 886
  helix:  1.53 (0.28), residues: 380
  sheet:  0.11 (0.42), residues: 147
  loop :  0.30 (0.34), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  16 
 TYR   0.012   0.001   TYR D  22 
 PHE   0.016   0.001   PHE D  33 
 TRP   0.007   0.001   TRP B 408 
 HIS   0.005   0.001   HIS D  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 7182)
  covalent geometry    : angle       0.47061 ( 9713)
  hydrogen bonds       : bond        0.03663 (  339)
  hydrogen bonds       : angle       4.68706 (  906)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 0.447 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.0727 (mmt) cc_final: 0.0280 (tpp)
REVERT: B  333 MET cc_start: 0.8658 (mtm) cc_final: 0.8371 (mtp)
REVERT: D   35 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7982 (tm-30)
  outliers start: 6
  outliers final: 5
  residues processed: 102
  average time/residue: 0.1656
  time to fit residues: 23.3741
Evaluate side-chains
  102 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 97
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  119 MET
Chi-restraints excluded: chain A residue  227 MET
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain D residue   10 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 76 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    1.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 115 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 = 0.3529 r_free = 0.3529 target = 0.121140 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.092763 restraints weight = 32633.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3101 rms_B_bonded: 3.06
r_work: 0.2975 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.2975
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.1954

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.039   7182  Z= 0.268
  Angle     :  0.543   4.741   9713  Z= 0.291
  Chirality :  0.044   0.148   1065
  Planarity :  0.004   0.037   1256
  Dihedral  :  4.034  23.047    970
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  1.17 %
    Allowed  : 10.97 %
    Favored  : 87.86 %
  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 are not related in a simple way.
  whole:  0.71 (0.29), residues: 886
  helix:  1.32 (0.28), residues: 373
  sheet: -0.01 (0.42), residues: 147
  loop : -0.09 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 128 
 TYR   0.013   0.001   TYR C  46 
 PHE   0.020   0.002   PHE D  33 
 TRP   0.010   0.002   TRP B 408 
 HIS   0.004   0.001   HIS D  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00619 ( 7182)
  covalent geometry    : angle       0.54334 ( 9713)
  hydrogen bonds       : bond        0.04500 (  339)
  hydrogen bonds       : angle       4.99860 (  906)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 96
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.0759 (mmt) cc_final: 0.0309 (tpp)
REVERT: A   83 GLU cc_start: 0.8355 (tm-30) cc_final: 0.8136 (tm-30)
REVERT: A  286 ASP cc_start: 0.7650 (t0) cc_final: 0.7388 (t0)
REVERT: B  333 MET cc_start: 0.8725 (mtm) cc_final: 0.8440 (mtp)
REVERT: D   35 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7919 (tm-30)
REVERT: D   45 GLN cc_start: 0.8529 (tm130) cc_final: 0.7978 (tm130)
  outliers start: 9
  outliers final: 8
  residues processed: 101
  average time/residue: 0.1697
  time to fit residues: 23.4853
Evaluate side-chains
  102 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  119 MET
Chi-restraints excluded: chain A residue  120 THR
Chi-restraints excluded: chain A residue  227 MET
Chi-restraints excluded: chain A residue  257 CYS
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain B residue  410 SER
Chi-restraints excluded: chain D residue   10 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 76 optimal weight:    0.3980
   chunk 17 optimal weight:    0.3980
   chunk 9 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3561 r_free = 0.3561 target = 0.123465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.094738 restraints weight = 32184.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3139 rms_B_bonded: 3.09
r_work: 0.3014 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7182  Z= 0.124
  Angle     :  0.479   4.722   9713  Z= 0.250
  Chirality :  0.042   0.143   1065
  Planarity :  0.003   0.033   1256
  Dihedral  :  3.878  21.805    970
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 11.36 %
    Favored  : 87.99 %
  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 are not related in a simple way.
  whole:  0.94 (0.29), residues: 886
  helix:  1.54 (0.29), residues: 374
  sheet:  0.01 (0.42), residues: 147
  loop :  0.05 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  16 
 TYR   0.011   0.001   TYR D  22 
 PHE   0.016   0.001   PHE D  33 
 TRP   0.007   0.001   TRP B 408 
 HIS   0.004   0.001   HIS D  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 7182)
  covalent geometry    : angle       0.47868 ( 9713)
  hydrogen bonds       : bond        0.03758 (  339)
  hydrogen bonds       : angle       4.70534 (  906)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.0765 (mmt) cc_final: 0.0306 (tpp)
REVERT: A   83 GLU cc_start: 0.8282 (tm-30) cc_final: 0.8055 (tm-30)
REVERT: A  286 ASP cc_start: 0.7576 (t0) cc_final: 0.7301 (t0)
REVERT: B  333 MET cc_start: 0.8648 (mtm) cc_final: 0.8348 (mtp)
REVERT: D   45 GLN cc_start: 0.8518 (tm130) cc_final: 0.7994 (tm130)
  outliers start: 5
  outliers final: 5
  residues processed: 97
  average time/residue: 0.1770
  time to fit residues: 23.5631
Evaluate side-chains
  101 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  119 MET
Chi-restraints excluded: chain A residue  227 MET
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain D residue   10 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0270
   chunk 54 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.7040

-------------------------------------------------------------------------------
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 = 0.3569 r_free = 0.3569 target = 0.124126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.095351 restraints weight = 32426.146|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 3.10
r_work: 0.3020 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.2144

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7182  Z= 0.118
  Angle     :  0.477   8.081   9713  Z= 0.246
  Chirality :  0.041   0.137   1065
  Planarity :  0.003   0.034   1256
  Dihedral  :  3.768  19.890    970
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 11.49 %
    Favored  : 87.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.11 (0.29), residues: 886
  helix:  1.70 (0.29), residues: 374
  sheet:  0.07 (0.42), residues: 147
  loop :  0.12 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  16 
 TYR   0.012   0.001   TYR D  22 
 PHE   0.015   0.001   PHE D  33 
 TRP   0.008   0.001   TRP B 408 
 HIS   0.005   0.001   HIS D  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 7182)
  covalent geometry    : angle       0.47689 ( 9713)
  hydrogen bonds       : bond        0.03537 (  339)
  hydrogen bonds       : angle       4.57252 (  906)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 101
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.0796 (mmt) cc_final: 0.0329 (tpp)
REVERT: A   83 GLU cc_start: 0.8285 (tm-30) cc_final: 0.8056 (tm-30)
REVERT: B  206 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7519 (tm-30)
REVERT: B  333 MET cc_start: 0.8632 (mtm) cc_final: 0.8306 (mtp)
REVERT: D   35 GLU cc_start: 0.8235 (tm-30) cc_final: 0.8034 (tm-30)
REVERT: D   45 GLN cc_start: 0.8449 (tm130) cc_final: 0.7903 (tm130)
  outliers start: 6
  outliers final: 6
  residues processed: 103
  average time/residue: 0.1694
  time to fit residues: 23.8577
Evaluate side-chains
  102 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 96
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  119 MET
Chi-restraints excluded: chain A residue  227 MET
Chi-restraints excluded: chain A residue  257 CYS
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain D residue   10 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9990
   chunk 0 optimal weight:    1.9990
   chunk 75 optimal weight:    0.2980
   chunk 82 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.124153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.095428 restraints weight = 32139.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3155 rms_B_bonded: 3.09
r_work: 0.3033 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.2194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7182  Z= 0.119
  Angle     :  0.475   7.518   9713  Z= 0.245
  Chirality :  0.041   0.138   1065
  Planarity :  0.003   0.034   1256
  Dihedral  :  3.742  19.400    970
  Min Nonbonded Distance : 2.409

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 11.49 %
    Favored  : 87.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.15 (0.29), residues: 886
  helix:  1.76 (0.29), residues: 374
  sheet:  0.06 (0.42), residues: 147
  loop :  0.13 (0.33), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 128 
 TYR   0.011   0.001   TYR D  22 
 PHE   0.016   0.001   PHE D  33 
 TRP   0.008   0.001   TRP B 408 
 HIS   0.005   0.001   HIS D  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 7182)
  covalent geometry    : angle       0.47484 ( 9713)
  hydrogen bonds       : bond        0.03505 (  339)
  hydrogen bonds       : angle       4.55628 (  906)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: A   47 MET cc_start: 0.0841 (mmt) cc_final: 0.0368 (tpp)
REVERT: A   83 GLU cc_start: 0.8296 (tm-30) cc_final: 0.8069 (tm-30)
REVERT: B  206 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7501 (tm-30)
REVERT: B  333 MET cc_start: 0.8636 (mtm) cc_final: 0.8336 (mtp)
REVERT: D   45 GLN cc_start: 0.8426 (tm130) cc_final: 0.7908 (tm130)
  outliers start: 6
  outliers final: 6
  residues processed: 99
  average time/residue: 0.1737
  time to fit residues: 23.5623
Evaluate side-chains
  103 residues out of total 766 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 THR
Chi-restraints excluded: chain A residue  119 MET
Chi-restraints excluded: chain A residue  227 MET
Chi-restraints excluded: chain A residue  257 CYS
Chi-restraints excluded: chain B residue   33 VAL
Chi-restraints excluded: chain D residue   10 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 40 optimal weight:    0.0870
   chunk 59 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   chunk 42 optimal weight:    7.9990
   chunk 13 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 47 optimal weight:    0.5980
   chunk 85 optimal weight:    0.0970
   chunk 10 optimal weight:    0.5980
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.4156

-------------------------------------------------------------------------------
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 = 0.3585 r_free = 0.3585 target = 0.125267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.096580 restraints weight = 31994.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 3.10
r_work: 0.3050 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7899
moved from start:          0.2309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7182  Z= 0.092
  Angle     :  0.470   7.803   9713  Z= 0.241
  Chirality :  0.041   0.151   1065
  Planarity :  0.003   0.034   1256
  Dihedral  :  3.649  17.058    970
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 11.49 %
    Favored  : 87.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.32 (0.30), residues: 886
  helix:  1.90 (0.29), residues: 374
  sheet:  0.06 (0.43), residues: 147
  loop :  0.26 (0.34), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 128 
 TYR   0.012   0.001   TYR D  22 
 PHE   0.015   0.001   PHE D  33 
 TRP   0.007   0.001   TRP B 408 
 HIS   0.006   0.001   HIS D  37 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 ( 7182)
  covalent geometry    : angle       0.47003 ( 9713)
  hydrogen bonds       : bond        0.03264 (  339)
  hydrogen bonds       : angle       4.44953 (  906)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2835.33 seconds
wall clock time: 48 minutes 45.62 seconds (2925.62 seconds total)