Starting phenix.real_space_refine
on Mon Apr 28 19:42:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bmp_16120/04_2025/8bmp_16120.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bmp_16120/04_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_16120/04_2025/8bmp_16120.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bmp_16120/04_2025/8bmp_16120.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bmp_16120/04_2025/8bmp_16120.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bmp_16120/04_2025/8bmp_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-5669/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: 4.93, per 1000 atoms: 0.63
  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: 1.82
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.76
  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: 2.04

  Time building geometry restraints manager: 2.17 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:             0.870
  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:             0.010
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.380
  Find NCS groups from input model:        0.110
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.720
-------------------------------------------------------------------------------
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 (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 

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

*********************** 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  : 0.929 
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: 0.2179
  time to fit residues: 31.1670
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  : 0.809 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.140232 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.109345 restraints weight = 10113.214|
|-----------------------------------------------------------------------------|
r_work (start): 0.3284 rms_B_bonded: 2.02
r_work: 0.3142 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
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= 0.132
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04325 (  425)
  hydrogen bonds       : angle       4.21240 ( 1221)
  covalent geometry    : bond        0.00305 ( 7961)
  covalent geometry    : angle       0.56189 (10797)

*********************** 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  : 0.873 
Fit side-chains
REVERT: A  184 ASP cc_start: 0.7961 (m-30) cc_final: 0.7434 (m-30)
REVERT: C  129 TRP cc_start: 0.7700 (m-10) cc_final: 0.7267 (m-10)
REVERT: D  108 ASN cc_start: 0.7933 (m-40) cc_final: 0.7494 (m-40)
REVERT: D  155 MET cc_start: 0.8017 (mtm) cc_final: 0.7738 (mtt)
REVERT: D  203 MET cc_start: 0.8380 (ttm) cc_final: 0.7985 (ttm)
  outliers start: 4
  outliers final: 1
  residues processed: 102
  average time/residue: 0.2103
  time to fit residues: 29.0891
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  : 0.894 
-------------------------------------------------------------------------------
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 12 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 74 optimal weight:    5.9990
   chunk 94 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 29 optimal weight:    0.5980
   chunk 52 optimal weight:    8.9990
   chunk 64 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 51 optimal weight:    6.9990
   overall best weight:    2.0786

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.135429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.104300 restraints weight = 10288.544|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 2.04
r_work: 0.3067 rms_B_bonded: 2.72 restraints_weight: 0.5000
r_work: 0.2916 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.1154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.083   7961  Z= 0.243
  Angle     :  0.635   7.736  10797  Z= 0.319
  Chirality :  0.046   0.158   1243
  Planarity :  0.004   0.039   1341
  Dihedral  :  9.419 172.000   1091
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  7.41 %
    Favored  : 91.52 %
  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:  0.88 (0.27), residues: 979
  helix:  1.45 (0.22), residues: 568
  sheet: -0.38 (0.66), residues: 63
  loop : -0.61 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 128 
 HIS   0.004   0.001   HIS B 242 
 PHE   0.014   0.002   PHE D  86 
 TYR   0.015   0.002   TYR D 251 
 ARG   0.005   0.001   ARG A 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04922 (  425)
  hydrogen bonds       : angle       4.26176 ( 1221)
  covalent geometry    : bond        0.00611 ( 7961)
  covalent geometry    : angle       0.63509 (10797)

*********************** 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
  117 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 108
  time to evaluate  : 0.808 
Fit side-chains
REVERT: A  184 ASP cc_start: 0.7947 (m-30) cc_final: 0.7426 (m-30)
REVERT: A  266 ASP cc_start: 0.7036 (t0) cc_final: 0.6398 (m-30)
REVERT: A  268 ASP cc_start: 0.7235 (p0) cc_final: 0.6955 (p0)
REVERT: C  129 TRP cc_start: 0.7929 (m-10) cc_final: 0.7485 (m-10)
REVERT: C  149 GLU cc_start: 0.8236 (mp0) cc_final: 0.7924 (mp0)
REVERT: D  108 ASN cc_start: 0.7930 (m-40) cc_final: 0.7687 (m-40)
  outliers start: 9
  outliers final: 2
  residues processed: 111
  average time/residue: 0.2010
  time to fit residues: 30.2160
Evaluate side-chains
  105 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.802 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 ILE
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 36 optimal weight:    0.0870
   chunk 23 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   chunk 8 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 4 optimal weight:    2.9990
   chunk 77 optimal weight:    0.0870
   chunk 33 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   overall best weight:    0.4336

-------------------------------------------------------------------------------
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 = 0.3640 r_free = 0.3640 target = 0.139043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.108286 restraints weight = 10190.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 2.05
r_work: 0.3133 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.1214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   7961  Z= 0.107
  Angle     :  0.527   6.539  10797  Z= 0.261
  Chirality :  0.041   0.144   1243
  Planarity :  0.003   0.039   1341
  Dihedral  :  9.068 177.763   1091
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.45 %
    Favored  : 97.55 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  :  9.68 %
    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:  1.23 (0.27), residues: 979
  helix:  1.79 (0.22), residues: 564
  sheet: -0.47 (0.62), residues: 68
  loop : -0.49 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 128 
 HIS   0.005   0.001   HIS B 242 
 PHE   0.011   0.001   PHE A 246 
 TYR   0.011   0.001   TYR D 251 
 ARG   0.004   0.000   ARG A 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03762 (  425)
  hydrogen bonds       : angle       3.99901 ( 1221)
  covalent geometry    : bond        0.00234 ( 7961)
  covalent geometry    : angle       0.52745 (10797)

*********************** 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: 6
    poor density    : 104
  time to evaluate  : 0.811 
Fit side-chains
REVERT: A  184 ASP cc_start: 0.7946 (m-30) cc_final: 0.7419 (m-30)
REVERT: A  266 ASP cc_start: 0.6916 (t0) cc_final: 0.6210 (m-30)
REVERT: C  129 TRP cc_start: 0.7694 (m-10) cc_final: 0.7372 (m-10)
REVERT: D   44 TYR cc_start: 0.8079 (m-80) cc_final: 0.7877 (m-80)
REVERT: D  108 ASN cc_start: 0.7797 (m-40) cc_final: 0.7521 (m-40)
  outliers start: 6
  outliers final: 2
  residues processed: 108
  average time/residue: 0.2052
  time to fit residues: 30.1734
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  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  203 MET
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 55 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 13 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 84 optimal weight:    3.9990
   chunk 28 optimal weight:    0.2980
   chunk 91 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   overall best weight:    0.9986

-------------------------------------------------------------------------------
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 = 0.3624 r_free = 0.3624 target = 0.137567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.106902 restraints weight = 10141.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 2.05
r_work: 0.3111 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2959 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.1328

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= 0.141
  Angle     :  0.549   6.534  10797  Z= 0.271
  Chirality :  0.043   0.144   1243
  Planarity :  0.003   0.039   1341
  Dihedral  :  8.837 171.813   1091
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 11.23 %
    Favored  : 87.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.23 (0.27), residues: 979
  helix:  1.80 (0.22), residues: 564
  sheet: -0.59 (0.62), residues: 68
  loop : -0.49 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 128 
 HIS   0.003   0.001   HIS B 242 
 PHE   0.009   0.001   PHE A   8 
 TYR   0.013   0.001   TYR D 251 
 ARG   0.006   0.000   ARG A 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03939 (  425)
  hydrogen bonds       : angle       3.98804 ( 1221)
  covalent geometry    : bond        0.00344 ( 7961)
  covalent geometry    : angle       0.54858 (10797)

*********************** 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
  112 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.913 
Fit side-chains
REVERT: A  184 ASP cc_start: 0.7936 (m-30) cc_final: 0.7441 (m-30)
REVERT: A  266 ASP cc_start: 0.6966 (t0) cc_final: 0.6327 (m-30)
REVERT: C  129 TRP cc_start: 0.7726 (m-10) cc_final: 0.7346 (m-10)
REVERT: D  108 ASN cc_start: 0.7824 (m-40) cc_final: 0.7542 (m-40)
  outliers start: 9
  outliers final: 3
  residues processed: 107
  average time/residue: 0.2115
  time to fit residues: 30.7350
Evaluate side-chains
  103 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 100
  time to evaluate  : 0.841 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 HIS
Chi-restraints excluded: chain D residue  203 MET
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 18 optimal weight:    0.7980
   chunk 22 optimal weight:    0.3980
   chunk 21 optimal weight:    1.9990
   chunk 87 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 54 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 80 optimal weight:    0.0370
   chunk 67 optimal weight:    1.9990
   overall best weight:    0.4858

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.139985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.109229 restraints weight = 10074.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3280 rms_B_bonded: 2.06
r_work: 0.3145 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2993 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2993
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.1475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   7961  Z= 0.104
  Angle     :  0.517   6.214  10797  Z= 0.254
  Chirality :  0.041   0.141   1243
  Planarity :  0.003   0.038   1341
  Dihedral  :  8.214 155.071   1091
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 12.07 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.49 (0.27), residues: 979
  helix:  2.03 (0.22), residues: 560
  sheet: -0.49 (0.63), residues: 68
  loop : -0.38 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 128 
 HIS   0.004   0.000   HIS B 242 
 PHE   0.018   0.001   PHE B 252 
 TYR   0.011   0.001   TYR D  44 
 ARG   0.006   0.000   ARG A 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03514 (  425)
  hydrogen bonds       : angle       3.89313 ( 1221)
  covalent geometry    : bond        0.00229 ( 7961)
  covalent geometry    : angle       0.51665 (10797)

*********************** 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
  115 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.793 
Fit side-chains
REVERT: A  184 ASP cc_start: 0.7888 (m-30) cc_final: 0.7394 (m-30)
REVERT: A  266 ASP cc_start: 0.6751 (t0) cc_final: 0.6136 (m-30)
REVERT: C  129 TRP cc_start: 0.7644 (m-10) cc_final: 0.7371 (m-10)
  outliers start: 9
  outliers final: 4
  residues processed: 113
  average time/residue: 0.2004
  time to fit residues: 30.8647
Evaluate side-chains
  106 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 102
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 HIS
Chi-restraints excluded: chain D residue   14 THR
Chi-restraints excluded: chain D residue  203 MET
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 30 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 96 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0170
   chunk 13 optimal weight:    4.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.6026

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.136412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.105361 restraints weight = 10178.535|
|-----------------------------------------------------------------------------|
r_work (start): 0.3223 rms_B_bonded: 2.06
r_work: 0.3083 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2934 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.1494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071   7961  Z= 0.199
  Angle     :  0.592   6.965  10797  Z= 0.292
  Chirality :  0.045   0.148   1243
  Planarity :  0.004   0.039   1341
  Dihedral  :  8.065 133.717   1091
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 12.31 %
    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 (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:  1.18 (0.27), residues: 979
  helix:  1.75 (0.22), residues: 567
  sheet: -0.67 (0.65), residues: 63
  loop : -0.50 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 128 
 HIS   0.002   0.001   HIS B 242 
 PHE   0.013   0.001   PHE A   8 
 TYR   0.023   0.002   TYR D  44 
 ARG   0.007   0.000   ARG A 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04282 (  425)
  hydrogen bonds       : angle       4.05400 ( 1221)
  covalent geometry    : bond        0.00498 ( 7961)
  covalent geometry    : angle       0.59248 (10797)

*********************** 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
  115 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.880 
Fit side-chains
REVERT: A   25 ASP cc_start: 0.7832 (m-30) cc_final: 0.7377 (t0)
REVERT: A  184 ASP cc_start: 0.7879 (m-30) cc_final: 0.7387 (m-30)
REVERT: A  266 ASP cc_start: 0.6908 (t0) cc_final: 0.6309 (m-30)
REVERT: C  129 TRP cc_start: 0.7802 (m-10) cc_final: 0.7429 (m-10)
REVERT: C  149 GLU cc_start: 0.8126 (mp0) cc_final: 0.7485 (mp0)
REVERT: D  108 ASN cc_start: 0.7793 (m-40) cc_final: 0.7506 (m-40)
  outliers start: 12
  outliers final: 5
  residues processed: 111
  average time/residue: 0.2026
  time to fit residues: 30.6849
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  : 0.863 
-------------------------------------------------------------------------------
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 D residue  203 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 37 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0770
   chunk 66 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 79 optimal weight:    9.9990
   chunk 31 optimal weight:    0.8980
   chunk 64 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.7338

-------------------------------------------------------------------------------
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 = 0.3635 r_free = 0.3635 target = 0.138593 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.107750 restraints weight = 10212.448|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 2.06
r_work: 0.3122 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.1588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7961  Z= 0.120
  Angle     :  0.547   7.283  10797  Z= 0.267
  Chirality :  0.042   0.140   1243
  Planarity :  0.003   0.037   1341
  Dihedral  :  7.567 116.031   1091
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 13.14 %
    Favored  : 85.78 %
  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:  1.38 (0.27), residues: 979
  helix:  1.95 (0.22), residues: 558
  sheet: -0.75 (0.62), residues: 68
  loop : -0.39 (0.34), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 128 
 HIS   0.003   0.001   HIS B 242 
 PHE   0.017   0.001   PHE B 252 
 TYR   0.024   0.001   TYR D  44 
 ARG   0.006   0.000   ARG A 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03727 (  425)
  hydrogen bonds       : angle       3.95716 ( 1221)
  covalent geometry    : bond        0.00279 ( 7961)
  covalent geometry    : angle       0.54717 (10797)

*********************** 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: 9
    poor density    : 102
  time to evaluate  : 0.815 
Fit side-chains
REVERT: A   25 ASP cc_start: 0.7858 (m-30) cc_final: 0.7403 (t0)
REVERT: A  184 ASP cc_start: 0.7887 (m-30) cc_final: 0.7375 (m-30)
REVERT: A  266 ASP cc_start: 0.6808 (t0) cc_final: 0.6298 (m-30)
REVERT: C  129 TRP cc_start: 0.7723 (m-10) cc_final: 0.7402 (m-10)
REVERT: D   44 TYR cc_start: 0.7904 (m-10) cc_final: 0.7485 (m-10)
  outliers start: 9
  outliers final: 5
  residues processed: 106
  average time/residue: 0.2065
  time to fit residues: 29.6640
Evaluate side-chains
  101 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 HIS
Chi-restraints excluded: chain A residue   41 HIS
Chi-restraints excluded: chain A residue  214 LEU
Chi-restraints excluded: chain D residue  203 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 77 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   chunk 8 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 55 optimal weight:    2.9990
   chunk 66 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 92 optimal weight:    0.9980
   chunk 14 optimal weight:    0.6980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.139203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.108213 restraints weight = 10297.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3272 rms_B_bonded: 2.08
r_work: 0.3128 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.2976 rms_B_bonded: 4.58 restraints_weight: 0.2500
r_work (final): 0.2976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7961  Z= 0.121
  Angle     :  0.546   7.149  10797  Z= 0.266
  Chirality :  0.042   0.141   1243
  Planarity :  0.003   0.038   1341
  Dihedral  :  7.080  95.280   1091
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 12.78 %
    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 (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:  2.00 (0.22), residues: 559
  sheet: -0.78 (0.62), residues: 68
  loop : -0.41 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  94 
 HIS   0.003   0.000   HIS B 242 
 PHE   0.011   0.001   PHE D 149 
 TYR   0.021   0.001   TYR D  44 
 ARG   0.006   0.000   ARG A 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03676 (  425)
  hydrogen bonds       : angle       3.92038 ( 1221)
  covalent geometry    : bond        0.00284 ( 7961)
  covalent geometry    : angle       0.54619 (10797)

*********************** 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
  116 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.823 
Fit side-chains
REVERT: A   25 ASP cc_start: 0.7818 (m-30) cc_final: 0.7427 (t0)
REVERT: A  184 ASP cc_start: 0.7868 (m-30) cc_final: 0.7381 (m-30)
REVERT: A  266 ASP cc_start: 0.6553 (t0) cc_final: 0.6103 (m-30)
REVERT: C  129 TRP cc_start: 0.7680 (m-10) cc_final: 0.7372 (m-10)
  outliers start: 11
  outliers final: 9
  residues processed: 111
  average time/residue: 0.1975
  time to fit residues: 30.0433
Evaluate side-chains
  111 residues out of total 837 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 102
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
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   41 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   14 THR
Chi-restraints excluded: chain D residue  203 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 50 optimal weight:    5.9990
   chunk 54 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 91 optimal weight:    0.6980
   chunk 40 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 24 optimal weight:    7.9990
   chunk 7 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9980
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 = 0.3631 r_free = 0.3631 target = 0.138236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.107250 restraints weight = 10309.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 2.08
r_work: 0.3112 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.1652

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7961  Z= 0.145
  Angle     :  0.567   8.468  10797  Z= 0.276
  Chirality :  0.043   0.142   1243
  Planarity :  0.003   0.038   1341
  Dihedral  :  6.990  89.055   1091
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 12.78 %
    Favored  : 86.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.27), residues: 979
  helix:  1.93 (0.22), residues: 559
  sheet: -0.84 (0.61), residues: 68
  loop : -0.41 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  94 
 HIS   0.002   0.000   HIS B 242 
 PHE   0.009   0.001   PHE D 149 
 TYR   0.013   0.001   TYR A 248 
 ARG   0.007   0.000   ARG A 239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03867 (  425)
  hydrogen bonds       : angle       3.97862 ( 1221)
  covalent geometry    : bond        0.00351 ( 7961)
  covalent geometry    : angle       0.56742 (10797)

********************** 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: 10
    poor density    : 102
  time to evaluate  : 0.863 
Fit side-chains
REVERT: A   25 ASP cc_start: 0.7816 (m-30) cc_final: 0.7433 (t0)
REVERT: A  184 ASP cc_start: 0.7847 (m-30) cc_final: 0.7358 (m-30)
REVERT: A  266 ASP cc_start: 0.6566 (t0) cc_final: 0.6110 (m-30)
REVERT: C  129 TRP cc_start: 0.7723 (m-10) cc_final: 0.7447 (m-10)
  outliers start: 10
  outliers final: 8
  residues processed: 106
  average time/residue: 0.2136
  time to fit residues: 30.9515
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  : 0.814 
-------------------------------------------------------------------------------
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   41 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  203 MET
Chi-restraints excluded: chain D residue  258 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 71.3669 > 50:
  distance: 37 - 60:  35.949
  distance: 43 - 69:  35.688
  distance: 55 - 60:  34.458
  distance: 60 - 61:  31.696
  distance: 61 - 62:   6.677
  distance: 61 - 64:   8.604
  distance: 62 - 63:  56.252
  distance: 64 - 65:  26.230
  distance: 66 - 67:  40.176
  distance: 66 - 68:  56.886
  distance: 70 - 71:  40.043
  distance: 71 - 79:  22.270
  distance: 74 - 75:  40.583
  distance: 74 - 76:  38.731
  distance: 76 - 78:  37.473
  distance: 77 - 78:  40.256
  distance: 79 - 80:  40.172
  distance: 80 - 81:  12.320
  distance: 80 - 83:  26.135
  distance: 81 - 82:  57.124
  distance: 81 - 90:  34.963
  distance: 84 - 85:  39.584
  distance: 86 - 88:  35.738
  distance: 87 - 89:  17.147
  distance: 88 - 89:  15.966
  distance: 90 - 91:  39.830
  distance: 91 - 92:  18.852
  distance: 91 - 94:  45.172
  distance: 92 - 98:  40.431
  distance: 98 - 99:  40.506
  distance: 99 - 102:  39.133
  distance: 100 - 103:  69.552
  distance: 104 - 105:  39.249
  distance: 104 - 107:  39.246
  distance: 105 - 111:  40.785
  distance: 107 - 108:  39.486
  distance: 108 - 110:  38.906
  distance: 111 - 112:  31.760
  distance: 112 - 113:  64.654
  distance: 112 - 115:   8.193
  distance: 113 - 114:  41.217
  distance: 113 - 119:  56.824
  distance: 115 - 116:  38.906
  distance: 116 - 117:  57.156
  distance: 116 - 118:  40.342
  distance: 120 - 121:  39.117
  distance: 120 - 123:  40.643
  distance: 121 - 128:  40.340
  distance: 123 - 124:  55.551
  distance: 124 - 125:  40.271
  distance: 125 - 126:  39.644
  distance: 126 - 127:  69.080
  distance: 128 - 129:  39.834
  distance: 128 - 134:  39.248
  distance: 135 - 136:  38.009
  distance: 136 - 137:  23.923
  distance: 136 - 139:   3.357
  distance: 137 - 138:  11.507
  distance: 137 - 142:  29.866
  distance: 139 - 141:  47.772