Starting phenix.real_space_refine
on Fri Aug 22 21:13:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bmp_16120/08_2025/8bmp_16120.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bmp_16120/08_2025/8bmp_16120.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bmp_16120/08_2025/8bmp_16120.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bmp_16120/08_2025/8bmp_16120.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bmp_16120/08_2025/8bmp_16120.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bmp_16120/08_2025/8bmp_16120.cif"
  }
  resolution = 3.2
  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=   0.009 sd=   0.103
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: 6
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     Mg      1      5.21       5
     S      36      5.16       5
     C    5052      2.51       5
     N    1283      2.21       5
     O    1417      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7794
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2130
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2130
          Classifications: {'peptide': 278}
          Link IDs: {'PTRANS': 13, 'TRANS': 264}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2183
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 281, 2183
          Classifications: {'peptide': 281}
          Link IDs: {'PTRANS': 14, 'TRANS': 266}
    Chain: "C"
      Number of atoms: 1321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 169, 1321
          Classifications: {'peptide': 169}
          Link IDs: {'PTRANS': 4, 'TRANS': 164}
    Chain: "D"
      Number of atoms: 2101
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2101
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 9, 'TRANS': 251}
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.09, per 1000 atoms: 0.27
  Number of scatterers: 7794
  At special positions: 0
  Unit cell: (83.804, 85.848, 132.86, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      36     16.00
     P       5     15.00
     Mg      1     11.99
     O    1417      8.00
     N    1283      7.00
     C    5052      6.00
    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: 0.75
  Conformation dependent library (CDL) restraints added in 503.3 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1958 Ramachandran restraints generated.
    979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1822

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 6 sheets defined
      60.2% alpha, 9.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 54
      removed outlier: 3.598A  pdb=" N   VAL A  49 " --> pdb=" O   GLY A  45 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ASN A  54 " --> pdb=" O   SER A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 113
      removed outlier: 4.635A  pdb=" N   GLY A 109 " --> pdb=" O   ASP A 105 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   LEU A 110 " --> pdb=" O   VAL A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 131
      removed outlier: 3.847A  pdb=" N   LYS A 122 " --> pdb=" O   PRO A 118 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL A 131 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 144
    Processing helix  chain 'A' and resid 145 through 160
      removed outlier: 4.037A  pdb=" N   VAL A 160 " --> pdb=" O   GLY A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 194
    Processing helix  chain 'A' and resid 203 through 208
      removed outlier: 4.430A  pdb=" N   ALA A 207 " --> pdb=" O   ASP A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 231
    Processing helix  chain 'A' and resid 233 through 240
    Processing helix  chain 'A' and resid 245 through 258
    Processing helix  chain 'A' and resid 267 through 279
      removed outlier: 3.934A  pdb=" N   LEU A 271 " --> pdb=" O   ASP A 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 45 through 52
    Processing helix  chain 'B' and resid 79 through 86
      removed outlier: 3.766A  pdb=" N   LEU B  83 " --> pdb=" O   GLY B  79 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   LYS B  86 " --> pdb=" O   ASP B  82 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 98
      removed outlier: 3.521A  pdb=" N   LEU B  98 " --> pdb=" O   GLU B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 102 through 114
      removed outlier: 4.244A  pdb=" N   GLY B 110 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
      Proline residue:  B 111  - end of helix
      removed outlier: 3.694A  pdb=" N   PHE B 114 " --> pdb=" O   GLY B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 132
    Processing helix  chain 'B' and resid 147 through 161
    Processing helix  chain 'B' and resid 177 through 194
    Processing helix  chain 'B' and resid 204 through 212
    Processing helix  chain 'B' and resid 228 through 233
    Processing helix  chain 'B' and resid 235 through 242
    Processing helix  chain 'B' and resid 247 through 259
    Processing helix  chain 'B' and resid 269 through 281
    Processing helix  chain 'C' and resid 12 through 30
    Processing helix  chain 'C' and resid 43 through 75
      removed outlier: 3.895A  pdb=" N   GLY C  47 " --> pdb=" O   LEU C  43 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   PHE C  55 " --> pdb=" O   LEU C  51 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLY C  56 " --> pdb=" O   GLY C  52 " (cutoff:3.500A)
      Proline residue:  C  57  - end of helix
      removed outlier: 3.541A  pdb=" N   ASP C  68 " --> pdb=" O   GLY C  64 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 82 through 101
      removed outlier: 4.045A  pdb=" N   THR C  86 " --> pdb=" O   PHE C  82 " (cutoff:3.500A)
      Proline residue:  C  93  - end of helix
    Processing helix  chain 'C' and resid 106 through 121
    Processing helix  chain 'C' and resid 124 through 134
    Processing helix  chain 'C' and resid 137 through 144
    Processing helix  chain 'C' and resid 145 through 152
      removed outlier: 3.633A  pdb=" N   GLU C 149 " --> pdb=" O   ARG C 145 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 152 through 172
      removed outlier: 4.159A  pdb=" N   VAL C 158 " --> pdb=" O   TRP C 154 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   LEU C 172 " --> pdb=" O   SER C 168 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 14 through 19
    Processing helix  chain 'D' and resid 20 through 36
      removed outlier: 3.894A  pdb=" N   PHE D  36 " --> pdb=" O   ILE D  32 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 40 through 57
    Processing helix  chain 'D' and resid 61 through 70
      removed outlier: 4.201A  pdb=" N   PHE D  65 " --> pdb=" O   LYS D  61 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 72 through 87
    Processing helix  chain 'D' and resid 103 through 129
    Processing helix  chain 'D' and resid 131 through 143
    Processing helix  chain 'D' and resid 144 through 150
    Processing helix  chain 'D' and resid 152 through 183
      Proline residue:  D 168  - end of helix
    Processing helix  chain 'D' and resid 191 through 199
      removed outlier: 4.191A  pdb=" N   LYS D 195 " --> pdb=" O   GLY D 191 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 199 through 225
      removed outlier: 3.964A  pdb=" N   MET D 203 " --> pdb=" O   SER D 199 " (cutoff:3.500A)
      Proline residue:  D 206  - end of helix
    Processing helix  chain 'D' and resid 245 through 263
      removed outlier: 3.701A  pdb=" N   VAL D 249 " --> pdb=" O   ASP D 245 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ILE D 260 " --> pdb=" O   THR D 256 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   THR D 262 " --> pdb=" O   LEU D 258 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30
      removed outlier: 4.345A  pdb=" N   SER A  66 " --> pdb=" O   SER A   7 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 86 through 89
      removed outlier: 6.391A  pdb=" N   ILE A 165 " --> pdb=" O   ILE A 198 " (cutoff:3.500A)
      removed outlier: 7.366A  pdb=" N   ILE A 200 " --> pdb=" O   ILE A 165 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   LEU A 167 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
      removed outlier: 6.071A  pdb=" N   ALA A  37 " --> pdb=" O   LEU A 214 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   LEU A 216 " --> pdb=" O   ALA A  37 " (cutoff:3.500A)
      removed outlier: 6.733A  pdb=" N   ILE A  39 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ASP A 223 " --> pdb=" O   VAL A 215 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   ASP A 217 " --> pdb=" O   LEU A 221 " (cutoff:3.500A)
      removed outlier: 5.220A  pdb=" N   LEU A 221 " --> pdb=" O   ASP A 217 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 30
      removed outlier: 6.311A  pdb=" N   TYR B  10 " --> pdb=" O   GLY B  22 " (cutoff:3.500A)
      removed outlier: 4.723A  pdb=" N   ASP B  24 " --> pdb=" O   VAL B   8 " (cutoff:3.500A)
      removed outlier: 5.054A  pdb=" N   VAL B   8 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
      removed outlier: 4.845A  pdb=" N   LEU B  26 " --> pdb=" O   GLU B   6 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   GLU B   6 " --> pdb=" O   LEU B  26 " (cutoff:3.500A)
      removed outlier: 6.826A  pdb=" N   PHE B  28 " --> pdb=" O   LYS B   4 " (cutoff:3.500A)
      removed outlier: 4.652A  pdb=" N   LYS B   4 " --> pdb=" O   PHE B  28 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 87 through 90
      removed outlier: 6.528A  pdb=" N   ILE B 167 " --> pdb=" O   ILE B 199 " (cutoff:3.500A)
      removed outlier: 7.755A  pdb=" N   VAL B 201 " --> pdb=" O   ILE B 167 " (cutoff:3.500A)
      removed outlier: 6.583A  pdb=" N   LEU B 169 " --> pdb=" O   VAL B 201 " (cutoff:3.500A)
      removed outlier: 6.526A  pdb=" N   PHE B  35 " --> pdb=" O   ASP B 214 " (cutoff:3.500A)
      removed outlier: 7.819A  pdb=" N   LEU B 216 " --> pdb=" O   PHE B  35 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   ALA B  37 " --> pdb=" O   LEU B 216 " (cutoff:3.500A)
      removed outlier: 7.638A  pdb=" N   LEU B 218 " --> pdb=" O   ALA B  37 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   VAL B  39 " --> pdb=" O   LEU B 218 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LYS B 225 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   GLU B 219 " --> pdb=" O   LEU B 223 " (cutoff:3.500A)
      removed outlier: 5.191A  pdb=" N   LEU B 223 " --> pdb=" O   GLU B 219 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 33 through 35
    Processing sheet with id=AA6, first strand: chain 'D' and resid 92 through 95
      removed outlier: 6.598A  pdb=" N   LEU D 101 " --> pdb=" O   TYR D  93 " (cutoff:3.500A)

    425 hydrogen bonds defined for protein.
    1221 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: 1.22

  Time building geometry restraints manager: 0.96 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2456
        1.34 -     1.46: 1683
        1.46 -     1.58: 3747
        1.58 -     1.70: 7
        1.70 -     1.81: 68
  Bond restraints: 7961
  Sorted by residual:
  bond pdb=" C   VAL D 167 "
       pdb=" N   PRO D 168 "
    ideal  model  delta    sigma   weight residual
    1.335  1.355 -0.019 1.36e-02 5.41e+03 1.97e+00
  bond pdb=" C4  ADP B 301 "
       pdb=" C5  ADP B 301 "
    ideal  model  delta    sigma   weight residual
    1.490  1.470  0.020 2.00e-02 2.50e+03 1.03e+00
  bond pdb=" CA  SER A  27 "
       pdb=" C   SER A  27 "
    ideal  model  delta    sigma   weight residual
    1.522  1.532 -0.010 1.08e-02 8.57e+03 9.27e-01
  bond pdb=" CA  THR C 152 "
       pdb=" C   THR C 152 "
    ideal  model  delta    sigma   weight residual
    1.522  1.533 -0.011 1.26e-02 6.30e+03 7.83e-01
  bond pdb=" CA  GLU B 171 "
       pdb=" C   GLU B 171 "
    ideal  model  delta    sigma   weight residual
    1.524  1.534 -0.010 1.26e-02 6.30e+03 6.74e-01
  ... (remaining 7956 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.45: 10416
        1.45 -     2.90: 298
        2.90 -     4.35: 58
        4.35 -     5.80: 23
        5.80 -     7.25: 2
  Bond angle restraints: 10797
  Sorted by residual:
  angle pdb=" N   ILE D  98 "
        pdb=" CA  ILE D  98 "
        pdb=" C   ILE D  98 "
      ideal   model   delta    sigma   weight residual
     113.71  110.15    3.56 9.50e-01 1.11e+00 1.40e+01
  angle pdb=" N   GLU B   6 "
        pdb=" CA  GLU B   6 "
        pdb=" C   GLU B   6 "
      ideal   model   delta    sigma   weight residual
     109.94  104.74    5.20 1.57e+00 4.06e-01 1.10e+01
  angle pdb=" C   ASP A 267 "
        pdb=" N   ASP A 268 "
        pdb=" CA  ASP A 268 "
      ideal   model   delta    sigma   weight residual
     120.63  125.93   -5.30 1.61e+00 3.86e-01 1.08e+01
  angle pdb=" N   ASP A 268 "
        pdb=" CA  ASP A 268 "
        pdb=" C   ASP A 268 "
      ideal   model   delta    sigma   weight residual
     112.34  116.45   -4.11 1.30e+00 5.92e-01 1.00e+01
  angle pdb=" N   GLY C  35 "
        pdb=" CA  GLY C  35 "
        pdb=" C   GLY C  35 "
      ideal   model   delta    sigma   weight residual
     110.38  114.71   -4.33 1.42e+00 4.96e-01 9.30e+00
  ... (remaining 10792 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.01: 4613
       31.01 -    62.02: 123
       62.02 -    93.03: 9
       93.03 -   124.04: 0
      124.04 -   155.04: 2
  Dihedral angle restraints: 4747
    sinusoidal: 1918
      harmonic: 2829
  Sorted by residual:
  dihedral pdb=" O2A ADP B 301 "
           pdb=" O3A ADP B 301 "
           pdb=" PA  ADP B 301 "
           pdb=" PB  ADP B 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   95.05 -155.04     1      2.00e+01 2.50e-03 4.58e+01
  dihedral pdb=" O1B ADP B 301 "
           pdb=" O3A ADP B 301 "
           pdb=" PB  ADP B 301 "
           pdb=" PA  ADP B 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   74.33 -134.34     1      2.00e+01 2.50e-03 4.08e+01
  dihedral pdb=" CA  ASP A 267 "
           pdb=" C   ASP A 267 "
           pdb=" N   ASP A 268 "
           pdb=" CA  ASP A 268 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.06  -21.94     0      5.00e+00 4.00e-02 1.93e+01
  ... (remaining 4744 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 692
       0.029 -    0.057: 339
       0.057 -    0.086: 127
       0.086 -    0.114: 67
       0.114 -    0.143: 18
  Chirality restraints: 1243
  Sorted by residual:
  chirality pdb=" CA  THR C 152 "
            pdb=" N   THR C 152 "
            pdb=" C   THR C 152 "
            pdb=" CB  THR C 152 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.38    0.14 2.00e-01 2.50e+01 5.11e-01
  chirality pdb=" CA  ILE C 123 "
            pdb=" N   ILE C 123 "
            pdb=" C   ILE C 123 "
            pdb=" CB  ILE C 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.09e-01
  chirality pdb=" CA  ILE A 244 "
            pdb=" N   ILE A 244 "
            pdb=" C   ILE A 244 "
            pdb=" CB  ILE A 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.85e-01
  ... (remaining 1240 not shown)

  Planarity restraints: 1341
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B 270 "    0.033 5.00e-02 4.00e+02   4.98e-02 3.97e+00
        pdb=" N   PRO B 271 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO B 271 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO B 271 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY C  92 "    0.025 5.00e-02 4.00e+02   3.75e-02 2.25e+00
        pdb=" N   PRO C  93 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO C  93 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO C  93 "    0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 252 "    0.007 2.00e-02 2.50e+03   1.08e-02 2.03e+00
        pdb=" CG  PHE B 252 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 252 "    0.008 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 252 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 252 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 252 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 252 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1338 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1572
        2.78 -     3.31: 7626
        3.31 -     3.84: 12653
        3.84 -     4.37: 15098
        4.37 -     4.90: 26060
  Nonbonded interactions: 63009
  Sorted by model distance:
  nonbonded pdb=" O   GLU D 104 "
            pdb=" ND2 ASN D 108 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" OD2 ASP A  61 "
            pdb=" NZ  LYS A  64 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" OG1 THR A 101 "
            pdb=" OD1 ASP A 104 "
     model   vdw
     2.327 3.040
  nonbonded pdb=" OD2 ASP D 172 "
            pdb=" NZ  LYS D 176 "
     model   vdw
     2.351 3.120
  nonbonded pdb=" OD1 ASP A 266 "
            pdb=" N   ASP A 267 "
     model   vdw
     2.378 3.120
  ... (remaining 63004 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:             1.360
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.440
  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:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
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   0.035   7961  Z= 0.151
  Angle     :  0.636   7.246  10797  Z= 0.351
  Chirality :  0.043   0.143   1243
  Planarity :  0.004   0.050   1341
  Dihedral  : 14.233 155.045   2925
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 6.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.27), residues: 979
  helix:  1.09 (0.22), residues: 571
  sheet:  0.87 (0.71), residues: 62
  loop : -0.65 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 235 
 TYR   0.012   0.001   TYR D  44 
 PHE   0.024   0.001   PHE B 252 
 TRP   0.021   0.001   TRP A 276 
 HIS   0.007   0.001   HIS A  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 7961)
  covalent geometry    : angle       0.63606 (10797)
  hydrogen bonds       : bond        0.14881 (  425)
  hydrogen bonds       : angle       5.60249 ( 1221)

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

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

  1958 Ramachandran restraints generated.
    979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1958 Ramachandran restraints generated.
    979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.386 
Fit side-chains
REVERT: A  184 ASP cc_start: 0.7837 (m-30) cc_final: 0.7391 (m-30)
REVERT: C  129 TRP cc_start: 0.8101 (m-10) cc_final: 0.7843 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 106
  average time/residue: 0.1187
  time to fit residues: 16.8684
Evaluate side-chains
  96 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0870
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0980
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
B 101 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.141591 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.110367 restraints weight = 10262.490|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 2.08
r_work: 0.3151 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2999 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.0794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   7961  Z= 0.115
  Angle     :  0.546   6.728  10797  Z= 0.272
  Chirality :  0.042   0.144   1243
  Planarity :  0.004   0.039   1341
  Dihedral  :  9.222 159.861   1091
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  5.50 %
    Favored  : 94.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.27), residues: 979
  helix:  1.68 (0.22), residues: 573
  sheet:  0.52 (0.68), residues: 62
  loop : -0.50 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 249 
 TYR   0.011   0.001   TYR D  44 
 PHE   0.015   0.001   PHE B 252 
 TRP   0.011   0.001   TRP B 128 
 HIS   0.004   0.001   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 7961)
  covalent geometry    : angle       0.54558 (10797)
  hydrogen bonds       : bond        0.04404 (  425)
  hydrogen bonds       : angle       4.20370 ( 1221)

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

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

  1958 Ramachandran restraints generated.
    979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1958 Ramachandran restraints generated.
    979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 0.339 
Fit side-chains
REVERT: A  184 ASP cc_start: 0.7913 (m-30) cc_final: 0.7385 (m-30)
REVERT: C  129 TRP cc_start: 0.7631 (m-10) cc_final: 0.7235 (m-10)
REVERT: C  138 PHE cc_start: 0.7621 (t80) cc_final: 0.7357 (t80)
REVERT: D  108 ASN cc_start: 0.7959 (m-40) cc_final: 0.7526 (m-40)
REVERT: D  155 MET cc_start: 0.8017 (mtm) cc_final: 0.7730 (mtt)
REVERT: D  203 MET cc_start: 0.8210 (ttm) cc_final: 0.7780 (ttm)
  outliers start: 4
  outliers final: 1
  residues processed: 104
  average time/residue: 0.0940
  time to fit residues: 13.3487
Evaluate side-chains
  99 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 98
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 31 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0170
   chunk 29 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 40 optimal weight:    5.9990
   chunk 92 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   overall best weight:    1.1222

-------------------------------------------------------------------------------
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 = 0.3633 r_free = 0.3633 target = 0.138238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.107460 restraints weight = 10125.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 2.06
r_work: 0.3121 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2970 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2970
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.1029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7961  Z= 0.152
  Angle     :  0.557   6.737  10797  Z= 0.278
  Chirality :  0.043   0.148   1243
  Planarity :  0.004   0.039   1341
  Dihedral  :  9.092 168.427   1091
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  6.33 %
    Favored  : 92.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.27), residues: 979
  helix:  1.74 (0.22), residues: 570
  sheet:  0.14 (0.67), residues: 62
  loop : -0.51 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 239 
 TYR   0.013   0.001   TYR D 251 
 PHE   0.012   0.001   PHE A 246 
 TRP   0.012   0.001   TRP B 128 
 HIS   0.004   0.001   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00371 ( 7961)
  covalent geometry    : angle       0.55749 (10797)
  hydrogen bonds       : bond        0.04210 (  425)
  hydrogen bonds       : angle       4.06707 ( 1221)

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

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

  1958 Ramachandran restraints generated.
    979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1958 Ramachandran restraints generated.
    979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.369 
Fit side-chains
REVERT: A  184 ASP cc_start: 0.7951 (m-30) cc_final: 0.7434 (m-30)
REVERT: A  266 ASP cc_start: 0.7034 (t0) cc_final: 0.6410 (m-30)
REVERT: C  129 TRP cc_start: 0.7764 (m-10) cc_final: 0.7348 (m-10)
REVERT: C  138 PHE cc_start: 0.7643 (t80) cc_final: 0.7388 (t80)
REVERT: D  108 ASN cc_start: 0.7797 (m-40) cc_final: 0.7569 (m-40)
REVERT: D  155 MET cc_start: 0.7932 (mtm) cc_final: 0.7644 (mtt)
  outliers start: 7
  outliers final: 2
  residues processed: 102
  average time/residue: 0.1083
  time to fit residues: 14.9219
Evaluate side-chains
  100 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 98
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 HIS
Chi-restraints excluded: chain D residue  258 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 51 optimal weight:    8.9990
   chunk 89 optimal weight:    3.9990
   chunk 93 optimal weight:    0.2980
   chunk 57 optimal weight:    0.0000
   chunk 67 optimal weight:    2.9990
   chunk 27 optimal weight:    0.4980
   chunk 84 optimal weight:    3.9990
   chunk 46 optimal weight:    4.9990
   chunk 85 optimal weight:    0.5980
   chunk 3 optimal weight:    6.9990
   overall best weight:    0.6786

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
B 101 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.139874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.108974 restraints weight = 10281.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 2.08
r_work: 0.3140 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2990 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.1190

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7961  Z= 0.115
  Angle     :  0.521   6.315  10797  Z= 0.258
  Chirality :  0.042   0.143   1243
  Planarity :  0.003   0.038   1341
  Dihedral  :  8.924 173.004   1091
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  :  8.60 %
    Favored  : 90.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.27), residues: 979
  helix:  1.89 (0.22), residues: 564
  sheet: -0.25 (0.63), residues: 68
  loop : -0.46 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 239 
 TYR   0.012   0.001   TYR D 251 
 PHE   0.018   0.001   PHE B 252 
 TRP   0.011   0.001   TRP B 128 
 HIS   0.004   0.001   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 7961)
  covalent geometry    : angle       0.52145 (10797)
  hydrogen bonds       : bond        0.03739 (  425)
  hydrogen bonds       : angle       3.95776 ( 1221)

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

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

  1958 Ramachandran restraints generated.
    979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1958 Ramachandran restraints generated.
    979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A  184 ASP cc_start: 0.7975 (m-30) cc_final: 0.7479 (m-30)
REVERT: A  266 ASP cc_start: 0.6882 (t0) cc_final: 0.6249 (m-30)
REVERT: C  129 TRP cc_start: 0.7676 (m-10) cc_final: 0.7412 (m-10)
REVERT: C  138 PHE cc_start: 0.7636 (t80) cc_final: 0.7383 (t80)
REVERT: D  108 ASN cc_start: 0.7805 (m-40) cc_final: 0.7540 (m-40)
REVERT: D  155 MET cc_start: 0.7930 (mtm) cc_final: 0.7668 (mtt)
  outliers start: 5
  outliers final: 2
  residues processed: 108
  average time/residue: 0.1016
  time to fit residues: 14.9234
Evaluate side-chains
  101 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 HIS
Chi-restraints excluded: chain D residue  258 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 69 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0020
   chunk 47 optimal weight:    6.9990
   chunk 30 optimal weight:    0.6980
   chunk 11 optimal weight:    0.7980
   overall best weight:    1.6992

-------------------------------------------------------------------------------
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 = 0.3609 r_free = 0.3609 target = 0.136765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.105278 restraints weight = 10286.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 2.06
r_work: 0.3078 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.1343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073   7961  Z= 0.207
  Angle     :  0.600   7.295  10797  Z= 0.298
  Chirality :  0.045   0.154   1243
  Planarity :  0.004   0.038   1341
  Dihedral  :  9.158 177.890   1091
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  9.92 %
    Favored  : 89.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.27), residues: 979
  helix:  1.63 (0.22), residues: 571
  sheet: -0.42 (0.66), residues: 63
  loop : -0.50 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 239 
 TYR   0.015   0.002   TYR D 251 
 PHE   0.011   0.002   PHE A   8 
 TRP   0.011   0.001   TRP B 128 
 HIS   0.003   0.001   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00516 ( 7961)
  covalent geometry    : angle       0.59988 (10797)
  hydrogen bonds       : bond        0.04476 (  425)
  hydrogen bonds       : angle       4.10287 ( 1221)

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

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

  1958 Ramachandran restraints generated.
    979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1958 Ramachandran restraints generated.
    979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A  184 ASP cc_start: 0.7942 (m-30) cc_final: 0.7443 (m-30)
REVERT: A  266 ASP cc_start: 0.6969 (t0) cc_final: 0.6350 (m-30)
REVERT: A  268 ASP cc_start: 0.7220 (p0) cc_final: 0.6927 (p0)
REVERT: C  129 TRP cc_start: 0.7903 (m-10) cc_final: 0.7525 (m-10)
REVERT: C  149 GLU cc_start: 0.8208 (mp0) cc_final: 0.7842 (mp0)
REVERT: D  108 ASN cc_start: 0.7956 (m-40) cc_final: 0.7663 (m-40)
  outliers start: 8
  outliers final: 1
  residues processed: 111
  average time/residue: 0.0960
  time to fit residues: 14.5254
Evaluate side-chains
  107 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  258 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 4 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 0 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 63 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A  42 ASN
B 101 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.138173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.107056 restraints weight = 10193.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.10
r_work: 0.3108 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.1424

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7961  Z= 0.132
  Angle     :  0.543   6.376  10797  Z= 0.267
  Chirality :  0.042   0.141   1243
  Planarity :  0.003   0.038   1341
  Dihedral  :  8.720 166.697   1091
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 12.31 %
    Favored  : 86.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.27), residues: 979
  helix:  1.80 (0.22), residues: 564
  sheet: -0.56 (0.63), residues: 68
  loop : -0.45 (0.34), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 239 
 TYR   0.013   0.001   TYR D  44 
 PHE   0.019   0.001   PHE B 252 
 TRP   0.012   0.001   TRP B 128 
 HIS   0.004   0.001   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7961)
  covalent geometry    : angle       0.54290 (10797)
  hydrogen bonds       : bond        0.03861 (  425)
  hydrogen bonds       : angle       3.99851 ( 1221)

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

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

  1958 Ramachandran restraints generated.
    979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1958 Ramachandran restraints generated.
    979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 103
  time to evaluate  : 0.321 
Fit side-chains
REVERT: A  184 ASP cc_start: 0.7948 (m-30) cc_final: 0.7445 (m-30)
REVERT: A  266 ASP cc_start: 0.6925 (t0) cc_final: 0.6296 (m-30)
REVERT: B  270 MET cc_start: 0.8567 (tpp) cc_final: 0.8330 (tpp)
REVERT: C  129 TRP cc_start: 0.7770 (m-10) cc_final: 0.7439 (m-10)
REVERT: D   44 TYR cc_start: 0.7922 (m-10) cc_final: 0.7523 (m-10)
REVERT: D  108 ASN cc_start: 0.7692 (m-40) cc_final: 0.7376 (m-40)
REVERT: D  148 LEU cc_start: 0.7253 (pp) cc_final: 0.6760 (mt)
REVERT: D  203 MET cc_start: 0.8145 (ttm) cc_final: 0.7916 (ttp)
  outliers start: 6
  outliers final: 1
  residues processed: 108
  average time/residue: 0.0965
  time to fit residues: 14.1780
Evaluate side-chains
  100 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  258 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 32 optimal weight:    0.0470
   chunk 4 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 2 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 90 optimal weight:    0.1980
   chunk 63 optimal weight:    0.5980
   chunk 3 optimal weight:    5.9990
   chunk 91 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9990
   overall best weight:    0.5080

-------------------------------------------------------------------------------
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 = 0.3660 r_free = 0.3660 target = 0.140982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.109598 restraints weight = 10221.916|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 2.08
r_work: 0.3138 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7760
moved from start:          0.1548

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   7961  Z= 0.105
  Angle     :  0.524   6.546  10797  Z= 0.257
  Chirality :  0.041   0.137   1243
  Planarity :  0.003   0.038   1341
  Dihedral  :  7.942 144.111   1091
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 12.43 %
    Favored  : 86.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.27), residues: 979
  helix:  2.04 (0.22), residues: 559
  sheet: -0.65 (0.63), residues: 68
  loop : -0.41 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 239 
 TYR   0.011   0.001   TYR D 251 
 PHE   0.010   0.001   PHE A   8 
 TRP   0.012   0.001   TRP B 128 
 HIS   0.004   0.000   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 7961)
  covalent geometry    : angle       0.52364 (10797)
  hydrogen bonds       : bond        0.03537 (  425)
  hydrogen bonds       : angle       3.90254 ( 1221)

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

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

  1958 Ramachandran restraints generated.
    979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1958 Ramachandran restraints generated.
    979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A  184 ASP cc_start: 0.7907 (m-30) cc_final: 0.7393 (m-30)
REVERT: A  266 ASP cc_start: 0.6651 (t0) cc_final: 0.6127 (m-30)
REVERT: C  129 TRP cc_start: 0.7697 (m-10) cc_final: 0.7459 (m-10)
  outliers start: 8
  outliers final: 5
  residues processed: 109
  average time/residue: 0.1031
  time to fit residues: 15.2139
Evaluate side-chains
  105 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 HIS
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain D residue   14 THR
Chi-restraints excluded: chain D residue  258 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 10 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 40 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 27 optimal weight:    0.5980
   chunk 88 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   overall best weight:    1.4986

-------------------------------------------------------------------------------
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 = 0.3612 r_free = 0.3612 target = 0.136649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.105652 restraints weight = 10225.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3219 rms_B_bonded: 2.06
r_work: 0.3079 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2928 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2928
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.1559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   7961  Z= 0.184
  Angle     :  0.594   6.955  10797  Z= 0.291
  Chirality :  0.044   0.148   1243
  Planarity :  0.004   0.038   1341
  Dihedral  :  7.833 122.387   1091
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 12.66 %
    Favored  : 86.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.27), residues: 979
  helix:  1.77 (0.22), residues: 567
  sheet: -0.70 (0.66), residues: 63
  loop : -0.52 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 239 
 TYR   0.015   0.002   TYR D  44 
 PHE   0.017   0.001   PHE B 252 
 TRP   0.010   0.001   TRP B 128 
 HIS   0.002   0.001   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 7961)
  covalent geometry    : angle       0.59384 (10797)
  hydrogen bonds       : bond        0.04217 (  425)
  hydrogen bonds       : angle       4.03829 ( 1221)

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

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

  1958 Ramachandran restraints generated.
    979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1958 Ramachandran restraints generated.
    979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.335 
Fit side-chains
REVERT: A   25 ASP cc_start: 0.7883 (m-30) cc_final: 0.7398 (t0)
REVERT: A  184 ASP cc_start: 0.7901 (m-30) cc_final: 0.7386 (m-30)
REVERT: A  266 ASP cc_start: 0.6811 (t0) cc_final: 0.6305 (m-30)
REVERT: C  129 TRP cc_start: 0.7781 (m-10) cc_final: 0.7411 (m-10)
  outliers start: 9
  outliers final: 4
  residues processed: 106
  average time/residue: 0.1042
  time to fit residues: 15.0216
Evaluate side-chains
  101 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 HIS
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain D residue  258 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 84 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 77 optimal weight:    0.6980
   chunk 67 optimal weight:    0.6980
   chunk 20 optimal weight:    7.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3641 r_free = 0.3641 target = 0.139416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.108208 restraints weight = 10253.912|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 2.05
r_work: 0.3124 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   7961  Z= 0.128
  Angle     :  0.556   7.932  10797  Z= 0.271
  Chirality :  0.042   0.142   1243
  Planarity :  0.003   0.038   1341
  Dihedral  :  7.419 106.932   1091
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 12.90 %
    Favored  : 86.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.27), residues: 979
  helix:  1.94 (0.22), residues: 558
  sheet: -0.81 (0.62), residues: 68
  loop : -0.40 (0.33), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 239 
 TYR   0.012   0.001   TYR D 251 
 PHE   0.011   0.001   PHE D 149 
 TRP   0.011   0.001   TRP B 128 
 HIS   0.003   0.001   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 7961)
  covalent geometry    : angle       0.55641 (10797)
  hydrogen bonds       : bond        0.03764 (  425)
  hydrogen bonds       : angle       3.95141 ( 1221)

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

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

  1958 Ramachandran restraints generated.
    979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1958 Ramachandran restraints generated.
    979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A   25 ASP cc_start: 0.7897 (m-30) cc_final: 0.7440 (t0)
REVERT: A  184 ASP cc_start: 0.7868 (m-30) cc_final: 0.7380 (m-30)
REVERT: A  266 ASP cc_start: 0.6578 (t0) cc_final: 0.6102 (m-30)
REVERT: C  129 TRP cc_start: 0.7715 (m-10) cc_final: 0.7384 (m-10)
  outliers start: 7
  outliers final: 6
  residues processed: 103
  average time/residue: 0.1035
  time to fit residues: 14.4654
Evaluate side-chains
  103 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 97
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 HIS
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain D residue  258 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 64 optimal weight:    0.6980
   overall best weight:    1.5386

-------------------------------------------------------------------------------
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 = 0.3611 r_free = 0.3611 target = 0.136683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.105679 restraints weight = 10179.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 2.08
r_work: 0.3092 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7790
moved from start:          0.1629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   7961  Z= 0.189
  Angle     :  0.607   7.922  10797  Z= 0.297
  Chirality :  0.045   0.156   1243
  Planarity :  0.004   0.038   1341
  Dihedral  :  7.476  96.399   1091
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 13.02 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.08 (0.27), residues: 979
  helix:  1.69 (0.22), residues: 566
  sheet: -0.83 (0.66), residues: 63
  loop : -0.56 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 239 
 TYR   0.014   0.002   TYR D 251 
 PHE   0.010   0.001   PHE A 246 
 TRP   0.010   0.001   TRP D  94 
 HIS   0.002   0.001   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00468 ( 7961)
  covalent geometry    : angle       0.60709 (10797)
  hydrogen bonds       : bond        0.04273 (  425)
  hydrogen bonds       : angle       4.07240 ( 1221)

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

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

  1958 Ramachandran restraints generated.
    979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1958 Ramachandran restraints generated.
    979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A   25 ASP cc_start: 0.7926 (m-30) cc_final: 0.7485 (t0)
REVERT: A  184 ASP cc_start: 0.7908 (m-30) cc_final: 0.7394 (m-30)
REVERT: A  266 ASP cc_start: 0.6869 (t0) cc_final: 0.6353 (m-30)
REVERT: C  129 TRP cc_start: 0.7810 (m-10) cc_final: 0.7489 (m-10)
REVERT: D  108 ASN cc_start: 0.7696 (m-40) cc_final: 0.7391 (m-40)
  outliers start: 9
  outliers final: 6
  residues processed: 109
  average time/residue: 0.1020
  time to fit residues: 15.1997
Evaluate side-chains
  105 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 99
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    8 PHE
Chi-restraints excluded: chain A residue   10 HIS
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain C residue  133 MET
Chi-restraints excluded: chain D residue  130 THR
Chi-restraints excluded: chain D residue  258 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 49 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0670
   chunk 30 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9990
   chunk 64 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 77 optimal weight:    0.0170
   overall best weight:    0.4556

-------------------------------------------------------------------------------
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 = 0.3659 r_free = 0.3659 target = 0.140999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.109829 restraints weight = 10173.039|
|-----------------------------------------------------------------------------|
r_work (start): 0.3286 rms_B_bonded: 2.05
r_work: 0.3145 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.2994 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2994
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7727
moved from start:          0.1713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7961  Z= 0.109
  Angle     :  0.553  10.316  10797  Z= 0.267
  Chirality :  0.042   0.194   1243
  Planarity :  0.003   0.037   1341
  Dihedral  :  6.881  85.389   1091
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 13.74 %
    Favored  : 85.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.27), residues: 979
  helix:  2.00 (0.22), residues: 560
  sheet: -0.86 (0.63), residues: 68
  loop : -0.38 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 239 
 TYR   0.010   0.001   TYR D 251 
 PHE   0.013   0.001   PHE D 149 
 TRP   0.012   0.001   TRP D  94 
 HIS   0.003   0.001   HIS B 242 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 7961)
  covalent geometry    : angle       0.55297 (10797)
  hydrogen bonds       : bond        0.03591 (  425)
  hydrogen bonds       : angle       3.93067 ( 1221)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2064.53 seconds
wall clock time: 36 minutes 8.96 seconds (2168.96 seconds total)