Starting phenix.real_space_refine
on Fri Jun 13 13:24:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ouz_17206/06_2025/8ouz_17206_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ouz_17206/06_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_17206/06_2025/8ouz_17206.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ouz_17206/06_2025/8ouz_17206.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ouz_17206/06_2025/8ouz_17206_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ouz_17206/06_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.33, per 1000 atoms: 0.56
  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: 3.76
  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: 1.27
  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: 5.06

  Time building geometry restraints manager: 4.57 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:             3.650
  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:             0.310
  Extract box with map and model:          0.590
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     34.270
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:12.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.430
-------------------------------------------------------------------------------
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  : 1.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 7
  residues processed: 100
  average time/residue: 2.8971
  time to fit residues: 304.9386
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  : 1.252 
-------------------------------------------------------------------------------
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 = 39)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.116945 restraints weight = 24684.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3614 rms_B_bonded: 1.87
r_work: 0.3493 rms_B_bonded: 2.13 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  : 1.072 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  224 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6173 (ttt180)
  outliers start: 18
  outliers final: 12
  residues processed: 103
  average time/residue: 2.5904
  time to fit residues: 282.1891
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  : 1.075 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3999 r_free = 0.3999 target = 0.145982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.116990 restraints weight = 24677.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 1.88
r_work: 0.3497 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3383 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.1053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7420  Z= 0.149
  Angle     :  0.539   6.976  10033  Z= 0.281
  Chirality :  0.039   0.139   1176
  Planarity :  0.004   0.035   1256
  Dihedral  :  9.946 107.565   1074
  Min Nonbonded Distance : 1.779

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  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:  0.75 (0.28), residues: 906
  helix:  1.29 (0.25), residues: 438
  sheet:  0.20 (0.40), residues: 165
  loop : -0.37 (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   0.004   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04222 (  374)
  hydrogen bonds       : angle       4.53686 ( 1056)
  covalent geometry    : bond        0.00325 ( 7420)
  covalent geometry    : angle       0.53886 (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  : 1.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  204 ILE cc_start: 0.7685 (mt) cc_final: 0.7477 (mt)
REVERT: C  192 GLN cc_start: 0.6034 (pp30) cc_final: 0.5749 (pp30)
REVERT: D  224 ARG cc_start: 0.7397 (OUTLIER) cc_final: 0.6128 (ttt180)
REVERT: D  239 MET cc_start: 0.8275 (OUTLIER) cc_final: 0.7850 (mtt)
  outliers start: 19
  outliers final: 11
  residues processed: 112
  average time/residue: 2.5225
  time to fit residues: 299.5760
Evaluate side-chains
  101 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
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   70 SER
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=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:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   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:    0.9986

-------------------------------------------------------------------------------
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 = 0.3990 r_free = 0.3990 target = 0.145278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.116246 restraints weight = 24764.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 1.87
r_work: 0.3486 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3373 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.1211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7420  Z= 0.166
  Angle     :  0.560   6.960  10033  Z= 0.292
  Chirality :  0.040   0.139   1176
  Planarity :  0.004   0.037   1256
  Dihedral  :  9.716 105.716   1074
  Min Nonbonded Distance : 1.763

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 13.09 %
    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 : -0.46 (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  80 
 TYR   0.011   0.001   TYR D 155 
 ARG   0.004   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04336 (  374)
  hydrogen bonds       : angle       4.56142 ( 1056)
  covalent geometry    : bond        0.00366 ( 7420)
  covalent geometry    : angle       0.56048 (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
  108 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 1.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  204 ILE cc_start: 0.7711 (mt) cc_final: 0.7500 (mt)
REVERT: C  192 GLN cc_start: 0.5976 (pp30) cc_final: 0.5720 (pp30)
REVERT: D  224 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6090 (ttt180)
  outliers start: 20
  outliers final: 12
  residues processed: 104
  average time/residue: 2.5199
  time to fit residues: 278.1256
Evaluate side-chains
  99 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 1.189 
-------------------------------------------------------------------------------
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  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:    0.3980
   chunk 87 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.3992 r_free = 0.3992 target = 0.145457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.116389 restraints weight = 24758.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 1.87
r_work: 0.3487 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3375 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.1253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7420  Z= 0.161
  Angle     :  0.556   6.343  10033  Z= 0.290
  Chirality :  0.040   0.139   1176
  Planarity :  0.004   0.038   1256
  Dihedral  :  9.385 103.468   1074
  Min Nonbonded Distance : 1.756

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  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:  0.63 (0.28), residues: 906
  helix:  1.21 (0.25), residues: 437
  sheet:  0.13 (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   0.011   0.001   TYR D 155 
 ARG   0.005   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04215 (  374)
  hydrogen bonds       : angle       4.53520 ( 1056)
  covalent geometry    : bond        0.00355 ( 7420)
  covalent geometry    : angle       0.55626 (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
  114 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  204 ILE cc_start: 0.7748 (mt) cc_final: 0.7541 (mt)
REVERT: C  184 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7873 (mt-10)
REVERT: C  192 GLN cc_start: 0.6047 (pp30) cc_final: 0.5821 (pp30)
REVERT: D  224 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6058 (ttt180)
REVERT: D  239 MET cc_start: 0.8284 (OUTLIER) cc_final: 0.7893 (mtt)
  outliers start: 20
  outliers final: 14
  residues processed: 109
  average time/residue: 2.5268
  time to fit residues: 291.9927
Evaluate side-chains
  106 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 86 optimal weight:    0.3980
   chunk 90 optimal weight:    0.9990
   chunk 15 optimal weight:    0.0870
   chunk 75 optimal weight:    0.5980
   chunk 63 optimal weight:    0.5980
   chunk 43 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.4558

-------------------------------------------------------------------------------
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 = 0.4013 r_free = 0.4013 target = 0.147262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.118204 restraints weight = 24859.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3636 rms_B_bonded: 1.89
r_work: 0.3516 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3403 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.1343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   7420  Z= 0.108
  Angle     :  0.510   6.253  10033  Z= 0.262
  Chirality :  0.038   0.141   1176
  Planarity :  0.003   0.035   1256
  Dihedral  :  8.872  95.280   1074
  Min Nonbonded Distance : 1.792

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 15.09 %
    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:  0.89 (0.28), residues: 906
  helix:  1.47 (0.25), residues: 440
  sheet:  0.19 (0.40), residues: 162
  loop : -0.38 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 268 
 HIS   0.003   0.001   HIS D  47 
 PHE   0.009   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        0.03363 (  374)
  hydrogen bonds       : angle       4.30330 ( 1056)
  covalent geometry    : bond        0.00231 ( 7420)
  covalent geometry    : angle       0.50983 (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
  103 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 1.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  224 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6084 (ttt180)
REVERT: D  239 MET cc_start: 0.8273 (OUTLIER) cc_final: 0.7760 (mtt)
  outliers start: 15
  outliers final: 8
  residues processed: 99
  average time/residue: 2.7750
  time to fit residues: 290.0199
Evaluate side-chains
  96 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 86
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
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  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:    0.0870
   chunk 69 optimal weight:    0.4980
   chunk 46 optimal weight:    0.9990
   chunk 85 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0670
   chunk 29 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9990
   chunk 86 optimal weight:    0.0470
   chunk 20 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 87 optimal weight:    0.5980
   overall best weight:    0.2594

-------------------------------------------------------------------------------
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 = 0.4009 r_free = 0.4009 target = 0.148425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.119120 restraints weight = 25158.728|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 1.96
r_work: 0.3504 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3389 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3389
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7803
moved from start:          0.1513

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   7420  Z= 0.094
  Angle     :  0.492   6.202  10033  Z= 0.252
  Chirality :  0.038   0.139   1176
  Planarity :  0.003   0.031   1256
  Dihedral  :  8.189  87.605   1071
  Min Nonbonded Distance : 1.840

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.46 %
    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:  1.17 (0.29), residues: 906
  helix:  1.75 (0.26), residues: 440
  sheet:  0.21 (0.39), residues: 170
  loop : -0.26 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B 305 
 HIS   0.003   0.001   HIS D  47 
 PHE   0.007   0.001   PHE D 115 
 TYR   0.007   0.001   TYR B 327 
 ARG   0.005   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02877 (  374)
  hydrogen bonds       : angle       4.10906 ( 1056)
  covalent geometry    : bond        0.00203 ( 7420)
  covalent geometry    : angle       0.49204 (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
  101 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 1.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  182 LYS cc_start: 0.8566 (ttpp) cc_final: 0.8206 (ttmm)
REVERT: D  224 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.6093 (ttt180)
REVERT: D  239 MET cc_start: 0.8263 (OUTLIER) cc_final: 0.7687 (mtt)
  outliers start: 12
  outliers final: 7
  residues processed: 96
  average time/residue: 2.7039
  time to fit residues: 274.4005
Evaluate side-chains
  94 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 1.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   54 LYS
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain C residue   23 HIS
Chi-restraints excluded: chain C residue  213 SER
Chi-restraints excluded: chain D residue   31 LEU
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:    0.9990
   chunk 6 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 64 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 17 optimal weight:    0.7980
   chunk 20 optimal weight:    0.1980
   chunk 88 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 = 0.4007 r_free = 0.4007 target = 0.146840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.117658 restraints weight = 24882.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 1.89
r_work: 0.3505 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3392 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.1458

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= 0.132
  Angle     :  0.528   6.485  10033  Z= 0.273
  Chirality :  0.039   0.145   1176
  Planarity :  0.003   0.033   1256
  Dihedral  :  8.622  96.974   1069
  Min Nonbonded Distance : 1.757

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.34 %
    Favored  : 82.67 %
  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:  1.00 (0.28), residues: 906
  helix:  1.55 (0.25), residues: 440
  sheet:  0.22 (0.39), residues: 170
  loop : -0.29 (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   0.011   0.001   PHE D  80 
 TYR   0.009   0.001   TYR B 210 
 ARG   0.003   0.000   ARG B 260 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03690 (  374)
  hydrogen bonds       : angle       4.26760 ( 1056)
  covalent geometry    : bond        0.00291 ( 7420)
  covalent geometry    : angle       0.52820 (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
  103 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 1.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  182 LYS cc_start: 0.8605 (ttpp) cc_final: 0.8312 (ttmm)
REVERT: D  224 ARG cc_start: 0.7381 (OUTLIER) cc_final: 0.6133 (ttt180)
REVERT: D  239 MET cc_start: 0.8298 (OUTLIER) cc_final: 0.7823 (mtt)
  outliers start: 16
  outliers final: 9
  residues processed: 98
  average time/residue: 2.6871
  time to fit residues: 278.9372
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  : 1.282 
-------------------------------------------------------------------------------
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   23 HIS
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:    0.8980
   chunk 81 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 3 optimal weight:    0.2980
   chunk 25 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9990
   chunk 75 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   chunk 82 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.4008 r_free = 0.4008 target = 0.146858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.117699 restraints weight = 24814.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3626 rms_B_bonded: 1.90
r_work: 0.3506 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3393 rms_B_bonded: 3.54 restraints_weight: 0.2500
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.1444

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= 0.129
  Angle     :  0.526   6.378  10033  Z= 0.271
  Chirality :  0.039   0.138   1176
  Planarity :  0.003   0.033   1256
  Dihedral  :  8.709  98.114   1069
  Min Nonbonded Distance : 1.763

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.34 %
    Favored  : 82.67 %
  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:  0.93 (0.28), residues: 906
  helix:  1.49 (0.25), residues: 440
  sheet:  0.20 (0.39), residues: 170
  loop : -0.34 (0.37), residues: 296

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   0.010   0.001   PHE C 176 
 TYR   0.008   0.001   TYR B 210 
 ARG   0.004   0.000   ARG B 260 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03635 (  374)
  hydrogen bonds       : angle       4.28262 ( 1056)
  covalent geometry    : bond        0.00282 ( 7420)
  covalent geometry    : angle       0.52555 (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
  101 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 1.115 
Fit side-chains
   revert: symmetry clash
REVERT: B  204 ILE cc_start: 0.7721 (mt) cc_final: 0.7471 (mt)
REVERT: D  224 ARG cc_start: 0.7377 (OUTLIER) cc_final: 0.6116 (ttt180)
REVERT: D  239 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7765 (mtt)
  outliers start: 16
  outliers final: 9
  residues processed: 96
  average time/residue: 2.5950
  time to fit residues: 263.5831
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  : 1.044 
-------------------------------------------------------------------------------
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 78 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 44 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 9 optimal weight:    0.3980
   chunk 11 optimal weight:    0.4980
   chunk 0 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   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 = 0.4010 r_free = 0.4010 target = 0.147110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.117933 restraints weight = 24920.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3629 rms_B_bonded: 1.90
r_work: 0.3509 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3396 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
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      :  0.003   0.042   7420  Z= 0.121
  Angle     :  0.520   6.384  10033  Z= 0.268
  Chirality :  0.039   0.136   1176
  Planarity :  0.003   0.033   1256
  Dihedral  :  8.620  95.409   1069
  Min Nonbonded Distance : 1.772

Molprobity Statistics.
  All-atom Clashscore : 4.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 15.59 %
    Favored  : 82.79 %
  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:  0.95 (0.28), residues: 906
  helix:  1.52 (0.25), residues: 440
  sheet:  0.18 (0.39), residues: 170
  loop : -0.33 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 268 
 HIS   0.003   0.001   HIS D  86 
 PHE   0.010   0.001   PHE C 176 
 TYR   0.009   0.001   TYR B 210 
 ARG   0.004   0.000   ARG B 260 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03524 (  374)
  hydrogen bonds       : angle       4.24238 ( 1056)
  covalent geometry    : bond        0.00265 ( 7420)
  covalent geometry    : angle       0.52019 (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
  98 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 1.157 
Fit side-chains
   revert: symmetry clash
REVERT: B  204 ILE cc_start: 0.7708 (mt) cc_final: 0.7454 (mt)
REVERT: D  182 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8304 (ttmm)
REVERT: D  224 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6126 (ttt180)
REVERT: D  239 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7758 (mtt)
  outliers start: 13
  outliers final: 9
  residues processed: 94
  average time/residue: 2.6952
  time to fit residues: 268.3597
Evaluate side-chains
  94 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 1.259 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 29 optimal weight:    4.9990
   chunk 75 optimal weight:    0.5980
   chunk 86 optimal weight:    0.0670
   chunk 45 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 82 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9980
   chunk 40 optimal weight:    0.6980
   chunk 3 optimal weight:    0.3980
   overall best weight:    0.4718

-------------------------------------------------------------------------------
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 = 0.4020 r_free = 0.4020 target = 0.147901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.118883 restraints weight = 24991.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 1.90
r_work: 0.3521 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3407 rms_B_bonded: 3.57 restraints_weight: 0.2500
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.1550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   7420  Z= 0.108
  Angle     :  0.505   6.281  10033  Z= 0.259
  Chirality :  0.038   0.132   1176
  Planarity :  0.003   0.032   1256
  Dihedral  :  8.408  90.054   1069
  Min Nonbonded Distance : 1.799

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 15.59 %
    Favored  : 82.79 %
  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 (0.29), residues: 906
  helix:  1.63 (0.25), residues: 440
  sheet:  0.20 (0.39), residues: 170
  loop : -0.33 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 268 
 HIS   0.003   0.001   HIS D  47 
 PHE   0.009   0.001   PHE D 115 
 TYR   0.007   0.001   TYR B 210 
 ARG   0.005   0.000   ARG C 259 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03258 (  374)
  hydrogen bonds       : angle       4.17088 ( 1056)
  covalent geometry    : bond        0.00234 ( 7420)
  covalent geometry    : angle       0.50485 (10033)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 12966.17 seconds
wall clock time: 219 minutes 43.40 seconds (13183.40 seconds total)