Starting phenix.real_space_refine
on Sat Aug 23 22:14:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ouz_17206/08_2025/8ouz_17206_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ouz_17206/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ouz_17206/08_2025/8ouz_17206_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ouz_17206/08_2025/8ouz_17206_trim.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ouz_17206/08_2025/8ouz_17206.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ouz_17206/08_2025/8ouz_17206.map"
  }
  resolution = 2.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 3.03, per 1000 atoms: 0.20
  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: 1.39
  Conformation dependent library (CDL) restraints added in 392.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.44
  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: 3.44

  Time building geometry restraints manager: 1.89 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:             2.820
  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:             0.130
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     15.840
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:7.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.890
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (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
 ARG   0.006   0.000   ARG C  21 
 TYR   0.009   0.001   TYR D 119 
 PHE   0.010   0.001   PHE C 176 
 TRP   0.007   0.001   TRP B 305 
 HIS   0.004   0.001   HIS B 179 

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

*********************** 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  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 8
  outliers final: 7
  residues processed: 100
  average time/residue: 1.6383
  time to fit residues: 171.3848
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  : 0.417 
-------------------------------------------------------------------------------
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 49 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    1.9990
   overall best weight:    1.1586

-------------------------------------------------------------------------------
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 = 0.3989 r_free = 0.3989 target = 0.145212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.116109 restraints weight = 24774.450|
|-----------------------------------------------------------------------------|
r_work (start): 0.3603 rms_B_bonded: 1.88
r_work: 0.3482 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3369 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.0944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   7420  Z= 0.187
  Angle     :  0.581   7.914  10033  Z= 0.306
  Chirality :  0.041   0.143   1176
  Planarity :  0.004   0.044   1256
  Dihedral  : 10.483 128.739   1077
  Min Nonbonded Distance : 1.766

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 12.47 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.70 (0.28), residues: 906
  helix:  1.20 (0.25), residues: 438
  sheet:  0.30 (0.41), residues: 164
  loop : -0.38 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C  21 
 TYR   0.013   0.002   TYR D 155 
 PHE   0.012   0.002   PHE D  80 
 TRP   0.010   0.002   TRP C 268 
 HIS   0.007   0.001   HIS D  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 7420)
  covalent geometry    : angle       0.58072 (10033)
  hydrogen bonds       : bond        0.04910 (  374)
  hydrogen bonds       : angle       4.73869 ( 1056)

*********************** 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
  110 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.463 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  224 ARG cc_start: 0.7379 (OUTLIER) cc_final: 0.6159 (ttt180)
REVERT: D  229 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7993 (tmtm)
  outliers start: 19
  outliers final: 14
  residues processed: 107
  average time/residue: 1.4586
  time to fit residues: 164.4146
Evaluate side-chains
  101 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
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   31 LEU
Chi-restraints excluded: chain D residue   42 ASP
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 7 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 52 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4000 r_free = 0.4000 target = 0.146096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.117114 restraints weight = 24856.409|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 1.89
r_work: 0.3498 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3385 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.1040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7420  Z= 0.141
  Angle     :  0.533   7.149  10033  Z= 0.277
  Chirality :  0.039   0.139   1176
  Planarity :  0.004   0.036   1256
  Dihedral  : 10.040 108.540   1076
  Min Nonbonded Distance : 1.782

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 12.97 %
    Favored  : 84.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.74 (0.28), residues: 906
  helix:  1.30 (0.25), residues: 438
  sheet:  0.17 (0.40), residues: 165
  loop : -0.38 (0.36), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 259 
 TYR   0.009   0.001   TYR D 155 
 PHE   0.011   0.001   PHE D 115 
 TRP   0.007   0.001   TRP C 268 
 HIS   0.003   0.001   HIS B 276 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 7420)
  covalent geometry    : angle       0.53253 (10033)
  hydrogen bonds       : bond        0.04136 (  374)
  hydrogen bonds       : angle       4.52672 ( 1056)

*********************** 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
  116 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  192 GLN cc_start: 0.6034 (pp30) cc_final: 0.5748 (pp30)
REVERT: D  224 ARG cc_start: 0.7388 (OUTLIER) cc_final: 0.6122 (ttt180)
REVERT: D  229 LYS cc_start: 0.8221 (mmtt) cc_final: 0.8017 (tmtm)
REVERT: D  239 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.7886 (mtt)
  outliers start: 18
  outliers final: 12
  residues processed: 111
  average time/residue: 1.4272
  time to fit residues: 167.0562
Evaluate side-chains
  104 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
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  290 ARG
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 44 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 85 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 89 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0060
   overall best weight:    0.6198

-------------------------------------------------------------------------------
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 = 0.4006 r_free = 0.4006 target = 0.146596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.117705 restraints weight = 24868.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3625 rms_B_bonded: 1.88
r_work: 0.3505 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3392 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
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      :  0.003   0.032   7420  Z= 0.124
  Angle     :  0.516   6.755  10033  Z= 0.267
  Chirality :  0.039   0.135   1176
  Planarity :  0.003   0.034   1256
  Dihedral  :  9.471 100.316   1074
  Min Nonbonded Distance : 1.801

Molprobity Statistics.
  All-atom Clashscore : 3.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 13.34 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.28), residues: 906
  helix:  1.43 (0.25), residues: 439
  sheet:  0.20 (0.40), residues: 163
  loop : -0.37 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 260 
 TYR   0.008   0.001   TYR B 210 
 PHE   0.010   0.001   PHE D 115 
 TRP   0.006   0.001   TRP C 268 
 HIS   0.003   0.001   HIS B 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 7420)
  covalent geometry    : angle       0.51597 (10033)
  hydrogen bonds       : bond        0.03730 (  374)
  hydrogen bonds       : angle       4.40419 ( 1056)

*********************** 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: 17
    poor density    : 92
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  224 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6145 (ttt180)
REVERT: D  229 LYS cc_start: 0.8221 (mmtt) cc_final: 0.8020 (tmtm)
REVERT: D  239 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7859 (mtt)
  outliers start: 17
  outliers final: 11
  residues processed: 104
  average time/residue: 1.4511
  time to fit residues: 158.9390
Evaluate side-chains
  105 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
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  196 LEU
Chi-restraints excluded: chain B residue  253 ASP
Chi-restraints excluded: chain C residue  200 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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 56 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 90 optimal weight:    0.2980
   chunk 38 optimal weight:    0.0670
   chunk 84 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 57 optimal weight:    0.0870
   chunk 40 optimal weight:    0.7980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.4296

-------------------------------------------------------------------------------
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 = 0.3994 r_free = 0.3994 target = 0.147100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.117604 restraints weight = 25155.911|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 1.97
r_work: 0.3480 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3363 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.1270

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= 0.106
  Angle     :  0.501   6.455  10033  Z= 0.257
  Chirality :  0.038   0.136   1176
  Planarity :  0.003   0.039   1256
  Dihedral  :  8.986  94.121   1073
  Min Nonbonded Distance : 1.832

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 13.97 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.28), residues: 906
  helix:  1.53 (0.25), residues: 440
  sheet:  0.18 (0.39), residues: 170
  loop : -0.31 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 259 
 TYR   0.007   0.001   TYR B 210 
 PHE   0.009   0.001   PHE D 115 
 TRP   0.004   0.001   TRP C 268 
 HIS   0.003   0.001   HIS D  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 7420)
  covalent geometry    : angle       0.50125 (10033)
  hydrogen bonds       : bond        0.03322 (  374)
  hydrogen bonds       : angle       4.25466 ( 1056)

*********************** 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: 18
    poor density    : 95
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  196 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7599 (mt)
REVERT: C  184 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7823 (mt-10)
REVERT: D  224 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.6080 (ttt180)
REVERT: D  229 LYS cc_start: 0.8211 (mmtt) cc_final: 0.7885 (tmtm)
REVERT: D  239 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7826 (mtt)
  outliers start: 18
  outliers final: 9
  residues processed: 108
  average time/residue: 1.4452
  time to fit residues: 164.4988
Evaluate side-chains
  98 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
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  196 LEU
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 90 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 68 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 11 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   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 = 0.4000 r_free = 0.4000 target = 0.146182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.116982 restraints weight = 24791.426|
|-----------------------------------------------------------------------------|
r_work (start): 0.3615 rms_B_bonded: 1.89
r_work: 0.3495 rms_B_bonded: 2.14 restraints_weight: 0.5000
r_work: 0.3382 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.1302

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= 0.148
  Angle     :  0.542   6.333  10033  Z= 0.282
  Chirality :  0.040   0.141   1176
  Planarity :  0.004   0.034   1256
  Dihedral  :  9.114 101.064   1073
  Min Nonbonded Distance : 1.747

Molprobity Statistics.
  All-atom Clashscore : 3.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 14.09 %
    Favored  : 83.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.78 (0.28), residues: 906
  helix:  1.35 (0.25), residues: 439
  sheet:  0.13 (0.39), residues: 172
  loop : -0.38 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 259 
 TYR   0.010   0.001   TYR B 210 
 PHE   0.013   0.001   PHE D  80 
 TRP   0.008   0.001   TRP C 268 
 HIS   0.003   0.001   HIS D  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 7420)
  covalent geometry    : angle       0.54211 (10033)
  hydrogen bonds       : bond        0.04010 (  374)
  hydrogen bonds       : angle       4.41302 ( 1056)

*********************** 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
  109 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  204 ILE cc_start: 0.7731 (mt) cc_final: 0.7490 (mt)
REVERT: D  224 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6121 (ttt180)
  outliers start: 21
  outliers final: 12
  residues processed: 105
  average time/residue: 1.4193
  time to fit residues: 157.2030
Evaluate side-chains
  102 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 30 optimal weight:    0.8980
   chunk 71 optimal weight:    0.8980
   chunk 56 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9980
   chunk 7 optimal weight:    0.2980
   chunk 25 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.146410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.117305 restraints weight = 24751.384|
|-----------------------------------------------------------------------------|
r_work (start): 0.3618 rms_B_bonded: 1.88
r_work: 0.3498 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.3385 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.1325

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7420  Z= 0.142
  Angle     :  0.536   6.593  10033  Z= 0.278
  Chirality :  0.039   0.147   1176
  Planarity :  0.003   0.034   1256
  Dihedral  :  9.015 105.133   1071
  Min Nonbonded Distance : 1.743

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.37 %
    Allowed  : 14.59 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.28), residues: 906
  helix:  1.34 (0.25), residues: 439
  sheet:  0.11 (0.39), residues: 172
  loop : -0.41 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 259 
 TYR   0.009   0.001   TYR D 155 
 PHE   0.011   0.001   PHE D 115 
 TRP   0.008   0.001   TRP C 268 
 HIS   0.003   0.001   HIS D 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 7420)
  covalent geometry    : angle       0.53574 (10033)
  hydrogen bonds       : bond        0.03882 (  374)
  hydrogen bonds       : angle       4.39505 ( 1056)

*********************** 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: 19
    poor density    : 88
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  196 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7783 (mp)
REVERT: B  204 ILE cc_start: 0.7745 (mt) cc_final: 0.7500 (mt)
REVERT: D  224 ARG cc_start: 0.7370 (OUTLIER) cc_final: 0.6081 (ttt180)
  outliers start: 19
  outliers final: 11
  residues processed: 104
  average time/residue: 1.1346
  time to fit residues: 124.5450
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  : 0.251 
-------------------------------------------------------------------------------
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  196 LEU
Chi-restraints excluded: chain B residue  253 ASP
Chi-restraints excluded: chain C residue   23 HIS
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 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 80 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 71 optimal weight:    0.0980
   chunk 29 optimal weight:    0.2980
   chunk 21 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 89 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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 = 0.146201 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.117054 restraints weight = 24977.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3616 rms_B_bonded: 1.89
r_work: 0.3495 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3382 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3382
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.1421

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= 0.141
  Angle     :  0.538   6.528  10033  Z= 0.279
  Chirality :  0.039   0.148   1176
  Planarity :  0.003   0.034   1256
  Dihedral  :  8.987 105.457   1071
  Min Nonbonded Distance : 1.741

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 15.09 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.28), residues: 906
  helix:  1.34 (0.25), residues: 439
  sheet:  0.11 (0.39), residues: 172
  loop : -0.41 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 260 
 TYR   0.009   0.001   TYR D 155 
 PHE   0.011   0.001   PHE D 115 
 TRP   0.014   0.002   TRP C 314 
 HIS   0.004   0.001   HIS D  86 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 7420)
  covalent geometry    : angle       0.53823 (10033)
  hydrogen bonds       : bond        0.03883 (  374)
  hydrogen bonds       : angle       4.38654 ( 1056)

*********************** 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
  104 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 87
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  196 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7783 (mp)
REVERT: B  204 ILE cc_start: 0.7733 (mt) cc_final: 0.7489 (mt)
REVERT: D  224 ARG cc_start: 0.7369 (OUTLIER) cc_final: 0.6079 (ttt180)
  outliers start: 17
  outliers final: 11
  residues processed: 101
  average time/residue: 1.1402
  time to fit residues: 121.8974
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  : 0.359 
-------------------------------------------------------------------------------
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  196 LEU
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
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0170
   chunk 86 optimal weight:    0.0970
   chunk 29 optimal weight:    0.4980
   chunk 90 optimal weight:    0.8980
   chunk 75 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.4416

-------------------------------------------------------------------------------
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 = 0.4019 r_free = 0.4019 target = 0.147848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.118897 restraints weight = 24906.640|
|-----------------------------------------------------------------------------|
r_work (start): 0.3641 rms_B_bonded: 1.89
r_work: 0.3521 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3407 rms_B_bonded: 3.56 restraints_weight: 0.2500
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.1474

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= 0.105
  Angle     :  0.506   6.340  10033  Z= 0.259
  Chirality :  0.038   0.145   1176
  Planarity :  0.003   0.033   1256
  Dihedral  :  8.572  93.615   1071
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 3.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 15.84 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.97 (0.28), residues: 906
  helix:  1.56 (0.25), residues: 440
  sheet:  0.15 (0.39), residues: 170
  loop : -0.35 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 260 
 TYR   0.007   0.001   TYR D 119 
 PHE   0.009   0.001   PHE D 115 
 TRP   0.005   0.001   TRP C 268 
 HIS   0.004   0.001   HIS B 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00227 ( 7420)
  covalent geometry    : angle       0.50582 (10033)
  hydrogen bonds       : bond        0.03252 (  374)
  hydrogen bonds       : angle       4.21007 ( 1056)

*********************** 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: 13
    poor density    : 88
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
REVERT: B  204 ILE cc_start: 0.7697 (mt) cc_final: 0.7463 (mt)
REVERT: D  224 ARG cc_start: 0.7396 (OUTLIER) cc_final: 0.6127 (ttt180)
  outliers start: 13
  outliers final: 9
  residues processed: 97
  average time/residue: 1.3623
  time to fit residues: 139.0378
Evaluate side-chains
  98 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
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  208 VAL
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  160 VAL
Chi-restraints excluded: chain D residue  224 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 76 optimal weight:    1.9990
   chunk 23 optimal weight:    0.3980
   chunk 80 optimal weight:    0.9990
   chunk 86 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0050
   chunk 22 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 39 optimal weight:    0.5980
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.4794

-------------------------------------------------------------------------------
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 = 0.3990 r_free = 0.3990 target = 0.146841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.117298 restraints weight = 24914.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3599 rms_B_bonded: 1.96
r_work: 0.3477 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.3361 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.1539

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= 0.109
  Angle     :  0.509   6.305  10033  Z= 0.262
  Chirality :  0.038   0.133   1176
  Planarity :  0.003   0.033   1256
  Dihedral  :  8.458  91.132   1071
  Min Nonbonded Distance : 1.788

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 16.08 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.28), residues: 906
  helix:  1.61 (0.25), residues: 440
  sheet:  0.19 (0.39), residues: 170
  loop : -0.31 (0.37), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 259 
 TYR   0.008   0.001   TYR B 210 
 PHE   0.010   0.001   PHE C 176 
 TRP   0.005   0.001   TRP C 268 
 HIS   0.004   0.001   HIS B 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 7420)
  covalent geometry    : angle       0.50943 (10033)
  hydrogen bonds       : bond        0.03333 (  374)
  hydrogen bonds       : angle       4.19032 ( 1056)

********************** 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: 11
    poor density    : 88
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: B  196 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7692 (mp)
REVERT: B  204 ILE cc_start: 0.7663 (mt) cc_final: 0.7437 (mt)
REVERT: D  182 LYS cc_start: 0.8562 (ttpp) cc_final: 0.8204 (ttmm)
REVERT: D  224 ARG cc_start: 0.7326 (OUTLIER) cc_final: 0.6060 (ttt180)
  outliers start: 11
  outliers final: 6
  residues processed: 97
  average time/residue: 1.2421
  time to fit residues: 126.7971
Evaluate side-chains
  92 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   54 LYS
Chi-restraints excluded: chain B residue  160 THR
Chi-restraints excluded: chain B residue  196 LEU
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  160 VAL
Chi-restraints excluded: chain D residue  224 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 1 optimal weight:    0.8980
   chunk 42 optimal weight:    1.9990
   chunk 80 optimal weight:    0.5980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.4000 r_free = 0.4000 target = 0.146242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.117093 restraints weight = 24831.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 1.89
r_work: 0.3496 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.3383 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3383
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.1462

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= 0.143
  Angle     :  0.546   6.552  10033  Z= 0.283
  Chirality :  0.039   0.134   1176
  Planarity :  0.003   0.034   1256
  Dihedral  :  8.814 101.062   1069
  Min Nonbonded Distance : 1.750

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.96 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.28), residues: 906
  helix:  1.43 (0.25), residues: 439
  sheet:  0.13 (0.38), residues: 172
  loop : -0.40 (0.37), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 260 
 TYR   0.010   0.001   TYR D 155 
 PHE   0.012   0.001   PHE D  80 
 TRP   0.008   0.001   TRP C 268 
 HIS   0.004   0.001   HIS B 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7420)
  covalent geometry    : angle       0.54648 (10033)
  hydrogen bonds       : bond        0.03892 (  374)
  hydrogen bonds       : angle       4.34225 ( 1056)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6479.18 seconds
wall clock time: 110 minutes 16.50 seconds (6616.50 seconds total)