Starting phenix.real_space_refine
on Fri Nov 15 01:25:55 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmp_16120/11_2024/8bmp_16120.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmp_16120/11_2024/8bmp_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmp_16120/11_2024/8bmp_16120.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmp_16120/11_2024/8bmp_16120.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmp_16120/11_2024/8bmp_16120.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bmp_16120/11_2024/8bmp_16120.cif"
  }
  resolution = 3.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.009 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 4.46, per 1000 atoms: 0.57
  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: 1.56
  Conformation dependent library (CDL) restraints added in 903.9 milliseconds
  

  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: 0.71
  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: 2.07

  Time building geometry restraints manager: 1.84 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:             0.690
  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:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     19.010
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.210
-------------------------------------------------------------------------------
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= 0.215
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (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
 TRP   0.021   0.001   TRP A 276 
 HIS   0.007   0.001   HIS A  41 
 PHE   0.024   0.001   PHE B 252 
 TYR   0.012   0.001   TYR D  44 
 ARG   0.007   0.001   ARG D 235 

*********************** 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  : 0.916 
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: 0.2187
  time to fit residues: 31.2138
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  : 0.898 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0020
   chunk 49 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0570
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 56 optimal weight:    0.8980
   chunk 88 optimal weight:    2.9990
   overall best weight:    0.7908

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.0786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7961  Z= 0.198
  Angle     :  0.562   6.998  10797  Z= 0.280
  Chirality :  0.043   0.148   1243
  Planarity :  0.004   0.039   1341
  Dihedral  :  9.265 161.203   1091
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  5.26 %
    Favored  : 94.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.27), residues: 979
  helix:  1.64 (0.22), residues: 573
  sheet:  0.38 (0.68), residues: 62
  loop : -0.51 (0.32), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 128 
 HIS   0.004   0.001   HIS B 242 
 PHE   0.015   0.001   PHE B 252 
 TYR   0.014   0.001   TYR D 251 
 ARG   0.003   0.000   ARG B  85 

*********************** 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
  105 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 0.855 
Fit side-chains
REVERT: A  184 ASP cc_start: 0.7892 (m-30) cc_final: 0.7424 (m-30)
REVERT: D  108 ASN cc_start: 0.8559 (m-40) cc_final: 0.8100 (m-40)
REVERT: D  155 MET cc_start: 0.8086 (mtm) cc_final: 0.7876 (mtt)
REVERT: D  203 MET cc_start: 0.8553 (ttm) cc_final: 0.8148 (ttm)
  outliers start: 4
  outliers final: 1
  residues processed: 102
  average time/residue: 0.2198
  time to fit residues: 30.3079
Evaluate side-chains
  98 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.879 
-------------------------------------------------------------------------------
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 48 optimal weight:    3.9990
   chunk 27 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   chunk 95 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9990
   chunk 87 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.1008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7961  Z= 0.196
  Angle     :  0.540   6.555  10797  Z= 0.269
  Chirality :  0.042   0.146   1243
  Planarity :  0.003   0.039   1341
  Dihedral  :  9.078 167.324   1091
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  7.05 %
    Favored  : 92.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.27), residues: 979
  helix:  1.81 (0.22), residues: 564
  sheet:  0.17 (0.67), residues: 62
  loop : -0.53 (0.32), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP C 129 
 HIS   0.004   0.001   HIS B 242 
 PHE   0.012   0.001   PHE D  86 
 TYR   0.013   0.001   TYR D 251 
 ARG   0.005   0.000   ARG A 239 

*********************** 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
  109 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 0.791 
Fit side-chains
REVERT: A  184 ASP cc_start: 0.7891 (m-30) cc_final: 0.7432 (m-30)
REVERT: A  266 ASP cc_start: 0.6897 (t0) cc_final: 0.6352 (m-30)
REVERT: C  138 PHE cc_start: 0.7862 (t80) cc_final: 0.7643 (t80)
REVERT: D  108 ASN cc_start: 0.8410 (m-40) cc_final: 0.8180 (m-40)
REVERT: D  155 MET cc_start: 0.8068 (mtm) cc_final: 0.7856 (mtt)
  outliers start: 7
  outliers final: 2
  residues processed: 104
  average time/residue: 0.2187
  time to fit residues: 30.8497
Evaluate side-chains
  102 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
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 87 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 45 optimal weight:    3.9990
   chunk 9 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0000
   overall best weight:    0.6988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8101
moved from start:          0.1171

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= 0.174
  Angle     :  0.522   6.177  10797  Z= 0.258
  Chirality :  0.042   0.144   1243
  Planarity :  0.003   0.039   1341
  Dihedral  :  8.898 171.988   1091
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.48 %
    Allowed  :  8.36 %
    Favored  : 91.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.27), residues: 979
  helix:  1.91 (0.22), residues: 564
  sheet: -0.24 (0.63), residues: 68
  loop : -0.45 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 129 
 HIS   0.004   0.001   HIS B 242 
 PHE   0.009   0.001   PHE C  61 
 TYR   0.012   0.001   TYR D 251 
 ARG   0.004   0.000   ARG A 239 

*********************** 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: 4
    poor density    : 106
  time to evaluate  : 0.905 
Fit side-chains
REVERT: A  184 ASP cc_start: 0.7887 (m-30) cc_final: 0.7439 (m-30)
REVERT: A  266 ASP cc_start: 0.6755 (t0) cc_final: 0.6270 (m-30)
REVERT: C  138 PHE cc_start: 0.7840 (t80) cc_final: 0.7622 (t80)
REVERT: D   44 TYR cc_start: 0.7864 (m-80) cc_final: 0.7394 (m-80)
REVERT: D  108 ASN cc_start: 0.8378 (m-40) cc_final: 0.8123 (m-40)
REVERT: D  155 MET cc_start: 0.8032 (mtm) cc_final: 0.7825 (mtt)
  outliers start: 4
  outliers final: 2
  residues processed: 109
  average time/residue: 0.2169
  time to fit residues: 31.9255
Evaluate side-chains
  102 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.899 
-------------------------------------------------------------------------------
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 78 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0270
   chunk 1 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 47 optimal weight:    5.9990
   chunk 84 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   overall best weight:    1.2044

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.1300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   7961  Z= 0.256
  Angle     :  0.557   6.791  10797  Z= 0.275
  Chirality :  0.043   0.148   1243
  Planarity :  0.004   0.038   1341
  Dihedral  :  9.046 179.696   1091
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  9.44 %
    Favored  : 89.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.27), residues: 979
  helix:  1.78 (0.22), residues: 570
  sheet: -0.38 (0.66), residues: 63
  loop : -0.51 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 129 
 HIS   0.003   0.001   HIS B 242 
 PHE   0.011   0.001   PHE A 246 
 TYR   0.014   0.001   TYR D 251 
 ARG   0.007   0.000   ARG A 239 

*********************** 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
  109 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.871 
Fit side-chains
REVERT: A  184 ASP cc_start: 0.7885 (m-30) cc_final: 0.7438 (m-30)
REVERT: A  266 ASP cc_start: 0.6726 (t0) cc_final: 0.6285 (m-30)
REVERT: C  138 PHE cc_start: 0.7898 (t80) cc_final: 0.7668 (t80)
REVERT: D  108 ASN cc_start: 0.8425 (m-40) cc_final: 0.8142 (m-40)
REVERT: D  155 MET cc_start: 0.8027 (mtm) cc_final: 0.7804 (mtt)
  outliers start: 8
  outliers final: 1
  residues processed: 105
  average time/residue: 0.2088
  time to fit residues: 29.6332
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  : 0.833 
-------------------------------------------------------------------------------
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 31 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 23 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9990
   overall best weight:    1.1184

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.1401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   7961  Z= 0.235
  Angle     :  0.553   6.581  10797  Z= 0.271
  Chirality :  0.043   0.143   1243
  Planarity :  0.003   0.038   1341
  Dihedral  :  8.766 169.358   1091
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 11.35 %
    Favored  : 87.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.27), residues: 979
  helix:  1.84 (0.22), residues: 564
  sheet: -0.55 (0.63), residues: 68
  loop : -0.46 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP C 129 
 HIS   0.003   0.001   HIS B 242 
 PHE   0.016   0.001   PHE B 252 
 TYR   0.013   0.001   TYR D 251 
 ARG   0.007   0.000   ARG A 239 

*********************** 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
  108 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 102
  time to evaluate  : 0.897 
Fit side-chains
REVERT: A  184 ASP cc_start: 0.7883 (m-30) cc_final: 0.7437 (m-30)
REVERT: A  266 ASP cc_start: 0.6742 (t0) cc_final: 0.6331 (m-30)
REVERT: C  138 PHE cc_start: 0.7894 (t80) cc_final: 0.7578 (t80)
REVERT: D  108 ASN cc_start: 0.8373 (m-40) cc_final: 0.8076 (m-40)
REVERT: D  148 LEU cc_start: 0.7160 (pp) cc_final: 0.6619 (mt)
REVERT: D  155 MET cc_start: 0.8020 (mtm) cc_final: 0.7807 (mtt)
  outliers start: 6
  outliers final: 1
  residues processed: 107
  average time/residue: 0.2067
  time to fit residues: 29.9143
Evaluate side-chains
  102 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
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 10 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   chunk 79 optimal weight:    9.9990
   chunk 52 optimal weight:    1.9990
   chunk 93 optimal weight:    0.0870
   chunk 58 optimal weight:    3.9990
   chunk 56 optimal weight:    1.9990
   chunk 43 optimal weight:    0.8980
   chunk 57 optimal weight:    0.0970
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.0160

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.1469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7961  Z= 0.223
  Angle     :  0.550   6.616  10797  Z= 0.271
  Chirality :  0.043   0.143   1243
  Planarity :  0.003   0.038   1341
  Dihedral  :  8.316 151.068   1091
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 11.83 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.27), residues: 979
  helix:  1.87 (0.22), residues: 564
  sheet: -0.65 (0.63), residues: 68
  loop : -0.46 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C 129 
 HIS   0.003   0.001   HIS B 242 
 PHE   0.010   0.001   PHE A 246 
 TYR   0.013   0.001   TYR D  44 
 ARG   0.005   0.000   ARG A 239 

*********************** 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
  112 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.911 
Fit side-chains
REVERT: A  184 ASP cc_start: 0.7882 (m-30) cc_final: 0.7435 (m-30)
REVERT: A  266 ASP cc_start: 0.6524 (t0) cc_final: 0.6154 (m-30)
REVERT: D   44 TYR cc_start: 0.8122 (m-10) cc_final: 0.7759 (m-10)
REVERT: D  108 ASN cc_start: 0.8233 (m-40) cc_final: 0.7943 (m-40)
REVERT: D  155 MET cc_start: 0.8006 (mtm) cc_final: 0.7793 (mtt)
  outliers start: 10
  outliers final: 4
  residues processed: 109
  average time/residue: 0.2108
  time to fit residues: 31.1265
Evaluate side-chains
  103 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 99
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
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  258 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 59 optimal weight:    0.2980
   chunk 63 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 85 optimal weight:    0.0470
   chunk 89 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    0.6078

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.1538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7961  Z= 0.164
  Angle     :  0.538   7.211  10797  Z= 0.261
  Chirality :  0.042   0.140   1243
  Planarity :  0.003   0.038   1341
  Dihedral  :  7.623 126.779   1091
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 11.95 %
    Favored  : 87.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.27), residues: 979
  helix:  2.05 (0.22), residues: 560
  sheet: -0.58 (0.63), residues: 67
  loop : -0.44 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP C 129 
 HIS   0.003   0.001   HIS B 242 
 PHE   0.009   0.001   PHE A   8 
 TYR   0.011   0.001   TYR D 251 
 ARG   0.007   0.000   ARG A 239 

*********************** 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
  111 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.946 
Fit side-chains
REVERT: A  184 ASP cc_start: 0.7838 (m-30) cc_final: 0.7387 (m-30)
REVERT: A  266 ASP cc_start: 0.6414 (t0) cc_final: 0.6151 (m-30)
REVERT: D   44 TYR cc_start: 0.8076 (m-10) cc_final: 0.7686 (m-10)
REVERT: D  155 MET cc_start: 0.7968 (mtm) cc_final: 0.7763 (mtt)
  outliers start: 8
  outliers final: 4
  residues processed: 109
  average time/residue: 0.2080
  time to fit residues: 30.7716
Evaluate side-chains
  104 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
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  258 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 87 optimal weight:    0.9990
   chunk 89 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 37 optimal weight:    0.5980
   chunk 68 optimal weight:    0.6980
   chunk 26 optimal weight:    6.9990
   chunk 78 optimal weight:    3.9990
   chunk 82 optimal weight:    0.9990
   chunk 86 optimal weight:    0.8980
   chunk 57 optimal weight:    0.6980
   chunk 92 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B 243 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.1632

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= 0.189
  Angle     :  0.548   7.455  10797  Z= 0.267
  Chirality :  0.042   0.142   1243
  Planarity :  0.003   0.038   1341
  Dihedral  :  7.282 107.978   1091
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 11.95 %
    Favored  : 87.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.44 (0.27), residues: 979
  helix:  2.03 (0.22), residues: 559
  sheet: -0.74 (0.62), residues: 68
  loop : -0.42 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP C 129 
 HIS   0.004   0.001   HIS B 243 
 PHE   0.012   0.001   PHE A 246 
 TYR   0.012   0.001   TYR D 251 
 ARG   0.006   0.000   ARG A 239 

*********************** 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
  111 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 103
  time to evaluate  : 0.851 
Fit side-chains
REVERT: A  184 ASP cc_start: 0.7814 (m-30) cc_final: 0.7364 (m-30)
REVERT: A  266 ASP cc_start: 0.6383 (t0) cc_final: 0.6147 (m-30)
REVERT: D  155 MET cc_start: 0.8012 (mtm) cc_final: 0.7791 (mtt)
  outliers start: 8
  outliers final: 5
  residues processed: 107
  average time/residue: 0.2104
  time to fit residues: 30.5451
Evaluate side-chains
  106 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 101
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
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  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 64 optimal weight:    0.9980
   chunk 96 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   chunk 7 optimal weight:    4.9990
   chunk 59 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0570
   chunk 61 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   overall best weight:    1.4104

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

Flipped N/Q/H residues before XYZ refinement:
B 101 ASN
B 243 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.1651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064   7961  Z= 0.290
  Angle     :  0.596   8.671  10797  Z= 0.292
  Chirality :  0.044   0.147   1243
  Planarity :  0.004   0.038   1341
  Dihedral  :  7.352  95.491   1091
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.14
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.21 (0.27), residues: 979
  helix:  1.81 (0.22), residues: 562
  sheet: -0.86 (0.61), residues: 68
  loop : -0.48 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP C 129 
 HIS   0.004   0.001   HIS B 243 
 PHE   0.017   0.001   PHE B 252 
 TYR   0.014   0.002   TYR A 248 
 ARG   0.006   0.000   ARG A 239 

********************** 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
  108 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 102
  time to evaluate  : 0.945 
Fit side-chains
REVERT: A  184 ASP cc_start: 0.7864 (m-30) cc_final: 0.7404 (m-30)
REVERT: A  266 ASP cc_start: 0.6532 (t0) cc_final: 0.6298 (m-30)
  outliers start: 6
  outliers final: 5
  residues processed: 105
  average time/residue: 0.2278
  time to fit residues: 32.4906
Evaluate side-chains
  104 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
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  258 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 23 optimal weight:    0.0050
   chunk 70 optimal weight:    0.6980
   chunk 11 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 77 optimal weight:    0.6980
   chunk 32 optimal weight:    0.7980
   chunk 79 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 67 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
B 243 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.139931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.109120 restraints weight = 10087.842|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 2.06
r_work: 0.3141 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2989 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7961  Z= 0.164
  Angle     :  0.550   9.390  10797  Z= 0.266
  Chirality :  0.042   0.193   1243
  Planarity :  0.003   0.038   1341
  Dihedral  :  6.863  86.394   1091
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.60 %
    Allowed  : 12.43 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.41 (0.27), residues: 979
  helix:  2.03 (0.22), residues: 560
  sheet: -0.86 (0.62), residues: 68
  loop : -0.44 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.002   TRP A 276 
 HIS   0.004   0.001   HIS B 242 
 PHE   0.013   0.001   PHE D 149 
 TYR   0.011   0.001   TYR D 251 
 ARG   0.006   0.000   ARG A 239 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1820.83 seconds
wall clock time: 33 minutes 59.70 seconds (2039.70 seconds total)