Starting phenix.real_space_refine
on Sat May 17 00:26:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ouz_17206/05_2025/8ouz_17206_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ouz_17206/05_2025/8ouz_17206.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ouz_17206/05_2025/8ouz_17206.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ouz_17206/05_2025/8ouz_17206.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ouz_17206/05_2025/8ouz_17206_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ouz_17206/05_2025/8ouz_17206_trim.cif"
  }
  resolution = 2.2
  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=   0.000 sd=   0.001
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: 7
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     Mg      3      5.21       5
     S      49      5.16       5
     C    4603      2.51       5
     N    1267      2.21       5
     O    1519      1.98       5
     H    7373      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 14822
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 1132
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 1132
          Classifications: {'peptide': 70}
          Link IDs: {'PTRANS': 2, 'TRANS': 67}
    Chain: "B"
      Number of atoms: 4960
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 312, 4960
          Classifications: {'peptide': 312}
          Link IDs: {'PTRANS': 10, 'TRANS': 301}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 4722
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 4722
          Classifications: {'peptide': 308}
          Link IDs: {'PTRANS': 7, 'TRANS': 300}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 3774
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 3774
          Classifications: {'peptide': 234}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 2
    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}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
    Chain: "B"
      Number of atoms: 51
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 51
          Classifications: {'water': 51}
          Link IDs: {None: 50}
    Chain: "C"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 43
          Classifications: {'water': 43}
          Link IDs: {None: 42}
    Chain: "D"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 42, 42
          Classifications: {'water': 42}
          Link IDs: {None: 41}
  Time building chain proxies: 7.29, per 1000 atoms: 0.49
  Number of scatterers: 14822
  At special positions: 0
  Unit cell: (93.7125, 103.275, 93.7125, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      49     16.00
     P       8     15.00
     Mg      3     11.99
     O    1519      8.00
     N    1267      7.00
     C    4603      6.00
     H    7373      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.78
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1720

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 6 sheets defined
      52.6% alpha, 15.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 10
      removed outlier: 3.639A  pdb=" N   VAL A   9 " --> pdb=" O   LYS A   5 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLY A  10 " --> pdb=" O   LEU A   6 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 5 through 10'
    Processing helix  chain 'A' and resid 12 through 21
    Processing helix  chain 'A' and resid 26 through 32
    Processing helix  chain 'A' and resid 34 through 43
    Processing helix  chain 'A' and resid 45 through 59
      removed outlier: 3.664A  pdb=" N   ALA A  59 " --> pdb=" O   MET A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 67 through 72
    Processing helix  chain 'B' and resid 13 through 17
    Processing helix  chain 'B' and resid 20 through 30
    Processing helix  chain 'B' and resid 34 through 39
      removed outlier: 3.826A  pdb=" N   LEU B  39 " --> pdb=" O   GLU B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 50
    Processing helix  chain 'B' and resid 53 through 66
    Processing helix  chain 'B' and resid 87 through 97
    Processing helix  chain 'B' and resid 104 through 112
    Processing helix  chain 'B' and resid 130 through 142
    Processing helix  chain 'B' and resid 143 through 144
      No H-bonds generated for 'chain 'B' and resid 143 through 144'
    Processing helix  chain 'B' and resid 145 through 149
    Processing helix  chain 'B' and resid 165 through 185
      removed outlier: 3.807A  pdb=" N   VAL B 169 " --> pdb=" O   MET B 165 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   GLU B 185 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 190 through 199
      removed outlier: 4.141A  pdb=" N   LYS B 194 " --> pdb=" O   GLU B 190 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   ASP B 198 " --> pdb=" O   LYS B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 206
    Processing helix  chain 'B' and resid 215 through 232
      Proline residue:  B 227  - end of helix
      removed outlier: 3.811A  pdb=" N   GLU B 232 " --> pdb=" O   ASP B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 262
    Processing helix  chain 'B' and resid 266 through 276
    Processing helix  chain 'B' and resid 304 through 308
    Processing helix  chain 'C' and resid 13 through 23
    Processing helix  chain 'C' and resid 27 through 33
    Processing helix  chain 'C' and resid 35 through 42
    Processing helix  chain 'C' and resid 46 through 62
    Processing helix  chain 'C' and resid 68 through 79
      removed outlier: 3.715A  pdb=" N   THR C  77 " --> pdb=" O   GLU C  73 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 94
    Processing helix  chain 'C' and resid 112 through 127
    Processing helix  chain 'C' and resid 142 through 152
    Processing helix  chain 'C' and resid 156 through 166
    Processing helix  chain 'C' and resid 174 through 192
    Processing helix  chain 'C' and resid 207 through 213
      removed outlier: 3.816A  pdb=" N   VAL C 211 " --> pdb=" O   SER C 207 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 214 through 216
      No H-bonds generated for 'chain 'C' and resid 214 through 216'
    Processing helix  chain 'C' and resid 221 through 240
    Processing helix  chain 'C' and resid 265 through 270
      removed outlier: 3.804A  pdb=" N   PHE C 270 " --> pdb=" O   ARG C 266 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 23 through 28
    Processing helix  chain 'D' and resid 53 through 67
    Processing helix  chain 'D' and resid 68 through 72
    Processing helix  chain 'D' and resid 88 through 100
    Processing helix  chain 'D' and resid 104 through 113
    Processing helix  chain 'D' and resid 122 through 140
      removed outlier: 3.985A  pdb=" N   GLU D 134 " --> pdb=" O   LEU D 130 " (cutoff:3.500A)
      removed outlier: 5.346A  pdb=" N   SER D 135 " --> pdb=" O   TYR D 131 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   MET D 136 " --> pdb=" O   SER D 132 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 154 through 163
      removed outlier: 3.768A  pdb=" N   GLY D 163 " --> pdb=" O   ARG D 159 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 165 through 170
    Processing helix  chain 'D' and resid 170 through 187
    Processing helix  chain 'D' and resid 228 through 233
    Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66
      removed outlier: 5.636A  pdb=" N   GLU B 154 " --> pdb=" O   VAL B 236 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   THR B 121 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 7.587A  pdb=" N   ASN B 284 " --> pdb=" O   THR B 121 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   ILE B 123 " --> pdb=" O   ASN B 284 " (cutoff:3.500A)
      removed outlier: 6.644A  pdb=" N   ARG B 312 " --> pdb=" O   TYR B 327 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 85 through 86
      removed outlier: 3.916A  pdb=" N   CYS B  85 " --> pdb=" O   VAL C 169 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   VAL C 132 " --> pdb=" O   GLN C 168 " (cutoff:3.500A)
      removed outlier: 7.778A  pdb=" N   VAL C 170 " --> pdb=" O   VAL C 132 " (cutoff:3.500A)
      removed outlier: 6.375A  pdb=" N   TYR C 134 " --> pdb=" O   VAL C 170 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   VAL C 203 " --> pdb=" O   VAL C 246 " (cutoff:3.500A)
      removed outlier: 7.921A  pdb=" N   THR C 248 " --> pdb=" O   VAL C 203 " (cutoff:3.500A)
      removed outlier: 7.267A  pdb=" N   VAL C 205 " --> pdb=" O   THR C 248 " (cutoff:3.500A)
      removed outlier: 6.230A  pdb=" N   ARG C 275 " --> pdb=" O   ALA C 296 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 340 through 342
    Processing sheet with id=AA4, first strand: chain 'C' and resid 66 through 67
      removed outlier: 6.972A  pdb=" N   GLU D  77 " --> pdb=" O   LEU D 145 " (cutoff:3.500A)
      removed outlier: 8.220A  pdb=" N   ILE D 147 " --> pdb=" O   GLU D  77 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   LEU D  79 " --> pdb=" O   ILE D 147 " (cutoff:3.500A)
      removed outlier: 7.472A  pdb=" N   ASP D 149 " --> pdb=" O   LEU D  79 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   ILE D  81 " --> pdb=" O   ASP D 149 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   CYS D 144 " --> pdb=" O   VAL D 190 " (cutoff:3.500A)
      removed outlier: 7.645A  pdb=" N   PHE D 192 " --> pdb=" O   CYS D 144 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   LEU D 146 " --> pdb=" O   PHE D 192 " (cutoff:3.500A)
      removed outlier: 7.768A  pdb=" N   THR D 194 " --> pdb=" O   LEU D 146 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   LEU D 148 " --> pdb=" O   THR D 194 " (cutoff:3.500A)
      removed outlier: 8.609A  pdb=" N   GLN D 196 " --> pdb=" O   LEU D 148 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   ASP D  42 " --> pdb=" O   LEU D 191 " (cutoff:3.500A)
      removed outlier: 7.899A  pdb=" N   ALA D 193 " --> pdb=" O   ASP D  42 " (cutoff:3.500A)
      removed outlier: 6.490A  pdb=" N   LEU D  44 " --> pdb=" O   ALA D 193 " (cutoff:3.500A)
      removed outlier: 7.617A  pdb=" N   THR D 195 " --> pdb=" O   LEU D  44 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   PHE D  46 " --> pdb=" O   THR D 195 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   HIS D 237 " --> pdb=" O   ILE D  43 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 81 through 82
    Processing sheet with id=AA6, first strand: chain 'C' and resid 251 through 253

    374 hydrogen bonds defined for protein.
    1056 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: 4.92

  Time building geometry restraints manager: 4.51 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 7345
        1.03 -     1.23: 31
        1.23 -     1.42: 2984
        1.42 -     1.62: 4363
        1.62 -     1.81: 70
  Bond restraints: 14793
  Sorted by residual:
  bond pdb=" N   GLY D  20 "
       pdb=" CA  GLY D  20 "
    ideal  model  delta    sigma   weight residual
    1.451  1.492 -0.041 1.60e-02 3.91e+03 6.43e+00
  bond pdb=" N   GLY C   2 "
       pdb=" CA  GLY C   2 "
    ideal  model  delta    sigma   weight residual
    1.451  1.490 -0.039 1.60e-02 3.91e+03 5.96e+00
  bond pdb=" N   GLN B  11 "
       pdb=" CA  GLN B  11 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.10e+00
  bond pdb=" N   LYS A   4 "
       pdb=" CA  LYS A   4 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.79e+00
  bond pdb=" N   GLY D  20 "
       pdb=" H   GLY D  20 "
    ideal  model  delta    sigma   weight residual
    0.860  0.891 -0.031 2.00e-02 2.50e+03 2.40e+00
  ... (remaining 14788 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.43: 26191
        1.43 -     2.86: 493
        2.86 -     4.30: 46
        4.30 -     5.73: 16
        5.73 -     7.16: 8
  Bond angle restraints: 26754
  Sorted by residual:
  angle pdb=" C3' ATP D 301 "
        pdb=" C2' ATP D 301 "
        pdb=" O2' ATP D 301 "
      ideal   model   delta    sigma   weight residual
     111.83  104.67    7.16 2.67e+00 1.40e-01 7.20e+00
  angle pdb=" C3' ATP C 401 "
        pdb=" C4' ATP C 401 "
        pdb=" C5' ATP C 401 "
      ideal   model   delta    sigma   weight residual
     115.19  110.70    4.49 1.76e+00 3.23e-01 6.50e+00
  angle pdb=" C3' ATP D 301 "
        pdb=" C4' ATP D 301 "
        pdb=" C5' ATP D 301 "
      ideal   model   delta    sigma   weight residual
     115.19  110.75    4.44 1.76e+00 3.23e-01 6.37e+00
  angle pdb=" C2' ATP D 301 "
        pdb=" C3' ATP D 301 "
        pdb=" O3' ATP D 301 "
      ideal   model   delta    sigma   weight residual
     111.83  105.24    6.59 2.67e+00 1.40e-01 6.10e+00
  angle pdb=" C3' ATP D 301 "
        pdb=" C4' ATP D 301 "
        pdb=" O4' ATP D 301 "
      ideal   model   delta    sigma   weight residual
     105.22  102.02    3.20 1.30e+00 5.94e-01 6.09e+00
  ... (remaining 26749 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.10: 6562
       29.10 -    58.20: 311
       58.20 -    87.29: 34
       87.29 -   116.39: 3
      116.39 -   145.49: 1
  Dihedral angle restraints: 6911
    sinusoidal: 3876
      harmonic: 3035
  Sorted by residual:
  dihedral pdb=" O2A ADP B 401 "
           pdb=" O3A ADP B 401 "
           pdb=" PA  ADP B 401 "
           pdb=" PB  ADP B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   85.49 -145.49     1      2.00e+01 2.50e-03 4.38e+01
  dihedral pdb=" O1B ADP B 401 "
           pdb=" O3A ADP B 401 "
           pdb=" PB  ADP B 401 "
           pdb=" PA  ADP B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -171.86  111.86     1      2.00e+01 2.50e-03 3.29e+01
  dihedral pdb=" C5' ADP B 401 "
           pdb=" O5' ADP B 401 "
           pdb=" PA  ADP B 401 "
           pdb=" O2A ADP B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   36.74  -96.74     1      2.00e+01 2.50e-03 2.68e+01
  ... (remaining 6908 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1042
       0.060 -    0.119: 111
       0.119 -    0.179: 17
       0.179 -    0.239: 0
       0.239 -    0.298: 6
  Chirality restraints: 1176
  Sorted by residual:
  chirality pdb=" C2' ATP D 301 "
            pdb=" C1' ATP D 301 "
            pdb=" C3' ATP D 301 "
            pdb=" O2' ATP D 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.98    0.30 2.00e-01 2.50e+01 2.23e+00
  chirality pdb=" C3' ATP D 301 "
            pdb=" C2' ATP D 301 "
            pdb=" C4' ATP D 301 "
            pdb=" O3' ATP D 301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.93    0.30 2.00e-01 2.50e+01 2.20e+00
  chirality pdb=" C2' ATP C 401 "
            pdb=" C1' ATP C 401 "
            pdb=" C3' ATP C 401 "
            pdb=" O2' ATP C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.96    0.28 2.00e-01 2.50e+01 2.01e+00
  ... (remaining 1173 not shown)

  Planarity restraints: 2146
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A  34 "    0.021 5.00e-02 4.00e+02   3.14e-02 1.58e+00
        pdb=" N   PRO A  35 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO A  35 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A  35 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU C 307 "   -0.006 2.00e-02 2.50e+03   1.23e-02 1.51e+00
        pdb=" CD  GLU C 307 "    0.021 2.00e-02 2.50e+03
        pdb=" OE1 GLU C 307 "   -0.008 2.00e-02 2.50e+03
        pdb=" OE2 GLU C 307 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 263 "   -0.005 2.00e-02 2.50e+03   9.70e-03 9.41e-01
        pdb=" C   ASN B 263 "    0.017 2.00e-02 2.50e+03
        pdb=" O   ASN B 263 "   -0.006 2.00e-02 2.50e+03
        pdb=" N   GLY B 264 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 2143 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.13: 385
        2.13 -     2.75: 27064
        2.75 -     3.37: 42365
        3.37 -     3.98: 55218
        3.98 -     4.60: 86854
  Nonbonded interactions: 211886
  Sorted by model distance:
  nonbonded pdb=" HG1 THR B 132 "
            pdb="MG    MG B 402 "
     model   vdw
     1.513 1.700
  nonbonded pdb=" OE1 GLN D 200 "
            pdb=" H   GLN D 200 "
     model   vdw
     1.534 2.450
  nonbonded pdb=" HG1 THR D  55 "
            pdb="MG    MG D 302 "
     model   vdw
     1.548 1.700
  nonbonded pdb=" O   ILE D  66 "
            pdb="HH21 ARG D 114 "
     model   vdw
     1.652 2.450
  nonbonded pdb=" OE1 GLU C 104 "
            pdb="HH11 ARG C 275 "
     model   vdw
     1.652 2.450
  ... (remaining 211881 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.660
  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:             0.280
  Extract box with map and model:          0.550
  Check model and map are aligned:         0.120
  Set scattering table:                    0.150
  Process input model:                     32.470
  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:10.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
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   0.041   7420  Z= 0.130
  Angle     :  0.561   7.161  10033  Z= 0.290
  Chirality :  0.044   0.298   1176
  Planarity :  0.003   0.031   1256
  Dihedral  : 16.592 145.487   2805
  Min Nonbonded Distance : 1.833

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 12.84 %
    Favored  : 86.16 %
  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:  1.04 (0.28), residues: 906
  helix:  1.66 (0.26), residues: 423
  sheet:  0.45 (0.41), residues: 163
  loop : -0.43 (0.33), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 305 
 HIS   0.004   0.001   HIS B 179 
 PHE   0.010   0.001   PHE C 176 
 TYR   0.009   0.001   TYR D 119 
 ARG   0.006   0.000   ARG C  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13940 (  374)
  hydrogen bonds       : angle       5.32091 ( 1056)
  covalent geometry    : bond        0.00266 ( 7420)
  covalent geometry    : angle       0.56058 (10033)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 93
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 7
  residues processed: 100
  average time/residue: 2.9563
  time to fit residues: 310.5435
Evaluate side-chains
  88 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 81
  time to evaluate  : 1.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  234 SER
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue  160 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
B 178 GLN
** C 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.145846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.116945 restraints weight = 24684.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 1.87
r_work: 0.3493 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3379 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.0897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7420  Z= 0.163
  Angle     :  0.558   7.397  10033  Z= 0.293
  Chirality :  0.040   0.141   1176
  Planarity :  0.004   0.044   1256
  Dihedral  : 10.303 126.533   1077
  Min Nonbonded Distance : 1.785

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 12.59 %
    Favored  : 85.16 %
  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:  0.82 (0.28), residues: 906
  helix:  1.32 (0.25), residues: 438
  sheet:  0.31 (0.41), residues: 164
  loop : -0.33 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C 268 
 HIS   0.006   0.001   HIS D  60 
 PHE   0.011   0.001   PHE D 115 
 TYR   0.011   0.002   TYR D 155 
 ARG   0.007   0.000   ARG C  21 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04605 (  374)
  hydrogen bonds       : angle       4.66676 ( 1056)
  covalent geometry    : bond        0.00355 ( 7420)
  covalent geometry    : angle       0.55806 (10033)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 1.193 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  224 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6171 (ttt180)
  outliers start: 18
  outliers final: 12
  residues processed: 103
  average time/residue: 2.6147
  time to fit residues: 284.8616
Evaluate side-chains
  98 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 1.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   54 LYS
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  253 ASP
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  290 ARG
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  173 LEU
Chi-restraints excluded: chain D residue  224 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 90 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 = 0.3997 r_free = 0.3997 target = 0.145814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.116811 restraints weight = 24670.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 1.88
r_work: 0.3495 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3381 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.1058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7420  Z= 0.153
  Angle     :  0.543   7.058  10033  Z= 0.284
  Chirality :  0.040   0.139   1176
  Planarity :  0.004   0.036   1256
  Dihedral  :  9.977 108.459   1074
  Min Nonbonded Distance : 1.774

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 12.59 %
    Favored  : 85.04 %
  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:  0.72 (0.28), residues: 906
  helix:  1.26 (0.25), residues: 438
  sheet:  0.19 (0.40), residues: 165
  loop : -0.39 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP C 268 
 HIS   0.003   0.001   HIS B 276 
 PHE   0.011   0.001   PHE D 115 
 TYR   0.010   0.001   TYR D 155 
 ARG   0.005   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04285 (  374)
  hydrogen bonds       : angle       4.55151 ( 1056)
  covalent geometry    : bond        0.00335 ( 7420)
  covalent geometry    : angle       0.54328 (10033)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 98
  time to evaluate  : 1.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  204 ILE cc_start: 0.7673 (mt) cc_final: 0.7464 (mt)
REVERT: C  192 GLN cc_start: 0.6048 (pp30) cc_final: 0.5763 (pp30)
REVERT: D  224 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6122 (ttt180)
REVERT: D  239 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7879 (mtt)
  outliers start: 19
  outliers final: 13
  residues processed: 112
  average time/residue: 2.5234
  time to fit residues: 299.5412
Evaluate side-chains
  103 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   54 LYS
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  253 ASP
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   42 ASP
Chi-restraints excluded: chain D residue   70 SER
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  173 LEU
Chi-restraints excluded: chain D residue  224 ARG
Chi-restraints excluded: chain D residue  239 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 64 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.9988

-------------------------------------------------------------------------------
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 = 0.3990 r_free = 0.3990 target = 0.145260 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.115980 restraints weight = 24687.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 1.89
r_work: 0.3486 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3372 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7954
moved from start:          0.1187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7420  Z= 0.166
  Angle     :  0.559   6.962  10033  Z= 0.292
  Chirality :  0.040   0.139   1176
  Planarity :  0.004   0.037   1256
  Dihedral  :  9.697 105.735   1074
  Min Nonbonded Distance : 1.763

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 12.97 %
    Favored  : 84.41 %
  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:  0.65 (0.28), residues: 906
  helix:  1.23 (0.25), residues: 437
  sheet:  0.17 (0.40), residues: 165
  loop : -0.47 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP C 268 
 HIS   0.004   0.001   HIS D  60 
 PHE   0.012   0.001   PHE D 115 
 TYR   0.011   0.002   TYR D 155 
 ARG   0.004   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04324 (  374)
  hydrogen bonds       : angle       4.56475 ( 1056)
  covalent geometry    : bond        0.00366 ( 7420)
  covalent geometry    : angle       0.55871 (10033)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 1.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  204 ILE cc_start: 0.7713 (mt) cc_final: 0.7501 (mt)
REVERT: C  192 GLN cc_start: 0.5982 (pp30) cc_final: 0.5726 (pp30)
REVERT: D  224 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6085 (ttt180)
  outliers start: 21
  outliers final: 13
  residues processed: 105
  average time/residue: 2.5129
  time to fit residues: 279.7951
Evaluate side-chains
  100 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   54 LYS
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  253 ASP
Chi-restraints excluded: chain C residue  200 VAL
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   70 SER
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  173 LEU
Chi-restraints excluded: chain D residue  224 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 86 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0870
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.9364

-------------------------------------------------------------------------------
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 = 0.3993 r_free = 0.3993 target = 0.145528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.116523 restraints weight = 24772.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3610 rms_B_bonded: 1.87
r_work: 0.3490 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3376 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.1266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7420  Z= 0.157
  Angle     :  0.552   6.298  10033  Z= 0.288
  Chirality :  0.040   0.139   1176
  Planarity :  0.004   0.038   1256
  Dihedral  :  9.368 102.467   1074
  Min Nonbonded Distance : 1.759

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 13.84 %
    Favored  : 83.67 %
  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:  0.65 (0.28), residues: 906
  helix:  1.23 (0.25), residues: 437
  sheet:  0.12 (0.39), residues: 165
  loop : -0.45 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP C 314 
 HIS   0.003   0.001   HIS D  60 
 PHE   0.012   0.001   PHE D 115 
 TYR   0.010   0.001   TYR D 155 
 ARG   0.005   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04159 (  374)
  hydrogen bonds       : angle       4.52374 ( 1056)
  covalent geometry    : bond        0.00343 ( 7420)
  covalent geometry    : angle       0.55232 (10033)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 1.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  204 ILE cc_start: 0.7746 (mt) cc_final: 0.7540 (mt)
REVERT: C  184 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7882 (mt-10)
REVERT: C  192 GLN cc_start: 0.6035 (pp30) cc_final: 0.5812 (pp30)
REVERT: D  224 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6062 (ttt180)
REVERT: D  239 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7886 (mtt)
  outliers start: 20
  outliers final: 14
  residues processed: 108
  average time/residue: 2.5100
  time to fit residues: 287.2000
Evaluate side-chains
  105 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 89
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   54 LYS
Chi-restraints excluded: chain B residue   64 ILE
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  253 ASP
Chi-restraints excluded: chain C residue  208 VAL
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  213 SER
Chi-restraints excluded: chain C residue  290 ARG
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   70 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  224 ARG
Chi-restraints excluded: chain D residue  239 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 86 optimal weight:    0.6980
   chunk 90 optimal weight:    0.9980
   chunk 15 optimal weight:    0.0670
   chunk 75 optimal weight:    0.4980
   chunk 63 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.5318

-------------------------------------------------------------------------------
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 = 0.4010 r_free = 0.4010 target = 0.146999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.118031 restraints weight = 24942.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3631 rms_B_bonded: 1.89
r_work: 0.3510 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3397 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.1307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7420  Z= 0.115
  Angle     :  0.516   6.285  10033  Z= 0.266
  Chirality :  0.039   0.142   1176
  Planarity :  0.003   0.035   1256
  Dihedral  :  8.954  96.541   1074
  Min Nonbonded Distance : 1.780

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 14.84 %
    Favored  : 83.04 %
  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:  0.86 (0.28), residues: 906
  helix:  1.43 (0.25), residues: 440
  sheet:  0.23 (0.40), residues: 156
  loop : -0.39 (0.36), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 268 
 HIS   0.003   0.001   HIS B 179 
 PHE   0.010   0.001   PHE D 115 
 TYR   0.007   0.001   TYR D 119 
 ARG   0.005   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03500 (  374)
  hydrogen bonds       : angle       4.34196 ( 1056)
  covalent geometry    : bond        0.00247 ( 7420)
  covalent geometry    : angle       0.51608 (10033)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  196 LEU cc_start: 0.8024 (mp) cc_final: 0.7822 (mt)
REVERT: D  224 ARG cc_start: 0.7376 (OUTLIER) cc_final: 0.6086 (ttt180)
REVERT: D  239 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7795 (mtt)
  outliers start: 17
  outliers final: 10
  residues processed: 100
  average time/residue: 2.6342
  time to fit residues: 278.5613
Evaluate side-chains
  100 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   54 LYS
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  253 ASP
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  213 SER
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   70 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  224 ARG
Chi-restraints excluded: chain D residue  239 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 58 optimal weight:    0.9980
   chunk 69 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0870
   chunk 20 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 87 optimal weight:    0.7980
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
B 178 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.145752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.116049 restraints weight = 25062.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.3583 rms_B_bonded: 1.95
r_work: 0.3458 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3343 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7846
moved from start:          0.1391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7420  Z= 0.133
  Angle     :  0.533   6.577  10033  Z= 0.276
  Chirality :  0.039   0.147   1176
  Planarity :  0.003   0.034   1256
  Dihedral  :  8.881  99.890   1071
  Min Nonbonded Distance : 1.758

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 14.59 %
    Favored  : 83.17 %
  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:  0.77 (0.28), residues: 906
  helix:  1.36 (0.25), residues: 439
  sheet:  0.11 (0.38), residues: 172
  loop : -0.40 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 268 
 HIS   0.003   0.001   HIS B 179 
 PHE   0.011   0.001   PHE D 115 
 TYR   0.009   0.001   TYR D 155 
 ARG   0.004   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03759 (  374)
  hydrogen bonds       : angle       4.38052 ( 1056)
  covalent geometry    : bond        0.00292 ( 7420)
  covalent geometry    : angle       0.53288 (10033)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 89
  time to evaluate  : 1.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  184 GLU cc_start: 0.8065 (mt-10) cc_final: 0.7797 (mt-10)
REVERT: D  224 ARG cc_start: 0.7318 (OUTLIER) cc_final: 0.6009 (ttt180)
REVERT: D  239 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7812 (mtt)
  outliers start: 18
  outliers final: 11
  residues processed: 101
  average time/residue: 2.5779
  time to fit residues: 275.8356
Evaluate side-chains
  97 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 1.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   54 LYS
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  253 ASP
Chi-restraints excluded: chain C residue   23 HIS
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  213 SER
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   70 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  224 ARG
Chi-restraints excluded: chain D residue  239 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 54 optimal weight:    1.9990
   chunk 8 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 14 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 64 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0980
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3983 r_free = 0.3983 target = 0.146219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.116564 restraints weight = 25019.012|
|-----------------------------------------------------------------------------|
r_work (start): 0.3589 rms_B_bonded: 1.95
r_work: 0.3466 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3350 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7420  Z= 0.122
  Angle     :  0.521   6.425  10033  Z= 0.269
  Chirality :  0.039   0.142   1176
  Planarity :  0.003   0.034   1256
  Dihedral  :  8.764  97.684   1071
  Min Nonbonded Distance : 1.770

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.34 %
    Favored  : 82.54 %
  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:  0.82 (0.28), residues: 906
  helix:  1.41 (0.25), residues: 440
  sheet:  0.15 (0.39), residues: 170
  loop : -0.41 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 268 
 HIS   0.004   0.001   HIS B 179 
 PHE   0.010   0.001   PHE D 115 
 TYR   0.008   0.001   TYR B 210 
 ARG   0.004   0.000   ARG B 260 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03564 (  374)
  hydrogen bonds       : angle       4.30744 ( 1056)
  covalent geometry    : bond        0.00264 ( 7420)
  covalent geometry    : angle       0.52142 (10033)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 1.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  224 ARG cc_start: 0.7328 (OUTLIER) cc_final: 0.6025 (ttt180)
REVERT: D  239 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7759 (mtt)
  outliers start: 17
  outliers final: 11
  residues processed: 97
  average time/residue: 2.7140
  time to fit residues: 279.1335
Evaluate side-chains
  100 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   54 LYS
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  253 ASP
Chi-restraints excluded: chain C residue   23 HIS
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  213 SER
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   70 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  224 ARG
Chi-restraints excluded: chain D residue  239 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 3 optimal weight:    0.2980
   chunk 25 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9990
   chunk 75 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 82 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3977 r_free = 0.3977 target = 0.145683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.115979 restraints weight = 24959.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3582 rms_B_bonded: 1.96
r_work: 0.3458 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.3342 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.1427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7420  Z= 0.133
  Angle     :  0.534   6.464  10033  Z= 0.276
  Chirality :  0.039   0.141   1176
  Planarity :  0.003   0.034   1256
  Dihedral  :  8.827  99.614   1071
  Min Nonbonded Distance : 1.756

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.59 %
    Favored  : 82.42 %
  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:  0.76 (0.28), residues: 906
  helix:  1.36 (0.25), residues: 439
  sheet:  0.15 (0.39), residues: 170
  loop : -0.45 (0.37), residues: 297

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 268 
 HIS   0.004   0.001   HIS B 179 
 PHE   0.011   0.001   PHE D 115 
 TYR   0.009   0.001   TYR B 210 
 ARG   0.004   0.000   ARG B 260 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03755 (  374)
  hydrogen bonds       : angle       4.34898 ( 1056)
  covalent geometry    : bond        0.00290 ( 7420)
  covalent geometry    : angle       0.53361 (10033)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 1.275 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  204 ILE cc_start: 0.7674 (mt) cc_final: 0.7430 (mt)
REVERT: C  184 GLU cc_start: 0.8053 (mt-10) cc_final: 0.7795 (mt-10)
REVERT: D  224 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6011 (ttt180)
REVERT: D  239 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7816 (mtt)
  outliers start: 16
  outliers final: 11
  residues processed: 98
  average time/residue: 2.6192
  time to fit residues: 271.9728
Evaluate side-chains
  98 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 1.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   54 LYS
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  253 ASP
Chi-restraints excluded: chain C residue   23 HIS
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  213 SER
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   70 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  224 ARG
Chi-restraints excluded: chain D residue  239 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 78 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9980
   chunk 1 optimal weight:    0.6980
   chunk 44 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 0 optimal weight:    0.9980
   chunk 55 optimal weight:    0.0170
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.5418

-------------------------------------------------------------------------------
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 = 0.3987 r_free = 0.3987 target = 0.146627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.117035 restraints weight = 25083.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 1.96
r_work: 0.3473 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3357 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   7420  Z= 0.114
  Angle     :  0.515   6.368  10033  Z= 0.265
  Chirality :  0.038   0.134   1176
  Planarity :  0.003   0.034   1256
  Dihedral  :  8.615  93.661   1071
  Min Nonbonded Distance : 1.785

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 15.84 %
    Favored  : 82.42 %
  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:  0.87 (0.28), residues: 906
  helix:  1.47 (0.25), residues: 440
  sheet:  0.15 (0.39), residues: 170
  loop : -0.41 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 268 
 HIS   0.004   0.001   HIS B 179 
 PHE   0.010   0.001   PHE D 115 
 TYR   0.008   0.001   TYR B 210 
 ARG   0.004   0.000   ARG B 260 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03415 (  374)
  hydrogen bonds       : angle       4.25592 ( 1056)
  covalent geometry    : bond        0.00249 ( 7420)
  covalent geometry    : angle       0.51460 (10033)

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

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

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1812 Ramachandran restraints generated.
    906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 1.142 
Fit side-chains
   revert: symmetry clash
REVERT: D  224 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6046 (ttt180)
REVERT: D  239 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7731 (mtt)
  outliers start: 14
  outliers final: 9
  residues processed: 94
  average time/residue: 2.7617
  time to fit residues: 274.1862
Evaluate side-chains
  95 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   50 VAL
Chi-restraints excluded: chain B residue   54 LYS
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain C residue  209 THR
Chi-restraints excluded: chain C residue  213 SER
Chi-restraints excluded: chain D residue   31 LEU
Chi-restraints excluded: chain D residue   70 SER
Chi-restraints excluded: chain D residue  118 VAL
Chi-restraints excluded: chain D residue  160 VAL
Chi-restraints excluded: chain D residue  224 ARG
Chi-restraints excluded: chain D residue  239 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 75 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 82 optimal weight:    0.4980
   chunk 60 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
B 178 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.146249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.116874 restraints weight = 24934.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 1.90
r_work: 0.3494 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3381 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.1477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   7420  Z= 0.144
  Angle     :  0.546   6.576  10033  Z= 0.283
  Chirality :  0.039   0.135   1176
  Planarity :  0.003   0.034   1256
  Dihedral  :  8.860 100.833   1071
  Min Nonbonded Distance : 1.748

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 16.08 %
    Favored  : 82.29 %
  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:  0.73 (0.28), residues: 906
  helix:  1.34 (0.25), residues: 439
  sheet:  0.12 (0.39), residues: 172
  loop : -0.46 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 268 
 HIS   0.003   0.001   HIS B 276 
 PHE   0.012   0.001   PHE D  80 
 TYR   0.010   0.001   TYR D 155 
 ARG   0.005   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03912 (  374)
  hydrogen bonds       : angle       4.37983 ( 1056)
  covalent geometry    : bond        0.00316 ( 7420)
  covalent geometry    : angle       0.54572 (10033)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12372.15 seconds
wall clock time: 211 minutes 31.42 seconds (12691.42 seconds total)