Starting phenix.real_space_refine
on Wed Feb 12 03:24:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k1p_36798/02_2025/8k1p_36798.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k1p_36798/02_2025/8k1p_36798.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k1p_36798/02_2025/8k1p_36798.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k1p_36798/02_2025/8k1p_36798.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k1p_36798/02_2025/8k1p_36798.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k1p_36798/02_2025/8k1p_36798.cif"
  }
  resolution = 3.4
  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=   0.064
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
     V       1      8.30       5
     P       9      5.49       5
     Mg      2      5.21       5
     S      21      5.16       5
     C    4558      2.51       5
     N    1240      2.21       5
     O    1308      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 41 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7139
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3711
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 509, 3711
          Classifications: {'peptide': 509}
          Link IDs: {'PTRANS': 20, 'TRANS': 488}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1606
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1606
          Classifications: {'peptide': 213}
          Link IDs: {'PTRANS': 8, 'TRANS': 204}
    Chain: "C"
      Number of atoms: 1597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 212, 1597
          Classifications: {'peptide': 212}
          Link IDs: {'PTRANS': 8, 'TRANS': 203}
    Chain: "A"
      Number of atoms: 160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 160
          Unusual residues: {'CDL': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 40
          Unresolved non-hydrogen angles: 40
          Unresolved non-hydrogen dihedrals: 40
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    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}
  Time building chain proxies: 5.97, per 1000 atoms: 0.84
  Number of scatterers: 7139
  At special positions: 0
  Unit cell: (65.6, 87.74, 113.98, 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)
     V       1     22.97
     S      21     16.00
     P       9     15.00
     Mg      2     11.99
     O    1308      8.00
     N    1240      7.00
     C    4558      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.16
  Conformation dependent library (CDL) restraints added in 845.8 milliseconds
  

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1652

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 6 sheets defined
      57.8% alpha, 6.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.71
  Creating SS restraints...
    Processing helix  chain 'A' and resid 25 through 35
    Processing helix  chain 'A' and resid 39 through 48
      removed outlier: 3.869A  pdb=" N   LEU A  43 " --> pdb=" O   VAL A  39 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU A  48 " --> pdb=" O   TRP A  44 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 61
      removed outlier: 3.835A  pdb=" N   GLU A  61 " --> pdb=" O   ALA A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 79
      removed outlier: 3.750A  pdb=" N   ALA A  72 " --> pdb=" O   SER A  68 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   MET A  78 " --> pdb=" O   ALA A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 88
      removed outlier: 3.962A  pdb=" N   LEU A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   TYR A  87 " --> pdb=" O   GLN A  83 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 100
    Processing helix  chain 'A' and resid 101 through 104
    Processing helix  chain 'A' and resid 105 through 129
      removed outlier: 3.514A  pdb=" N   LEU A 109 " --> pdb=" O   MET A 105 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ALA A 111 " --> pdb=" O   HIS A 107 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   ALA A 124 " --> pdb=" O   ARG A 120 " (cutoff:3.500A)
      removed outlier: 5.064A  pdb=" N   ASP A 125 " --> pdb=" O   HIS A 121 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   GLU A 126 " --> pdb=" O   THR A 122 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   SER A 128 " --> pdb=" O   ALA A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 136
      removed outlier: 4.181A  pdb=" N   LEU A 133 " --> pdb=" O   GLY A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 168
      removed outlier: 3.642A  pdb=" N   GLY A 160 " --> pdb=" O   SER A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 199
      removed outlier: 3.750A  pdb=" N   SER A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   VAL A 178 " --> pdb=" O   PRO A 174 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   PHE A 191 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   THR A 192 " --> pdb=" O   GLY A 188 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ALA A 193 " --> pdb=" O   MET A 189 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL A 194 " --> pdb=" O   VAL A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 228
      removed outlier: 3.519A  pdb=" N   VAL A 215 " --> pdb=" O   VAL A 211 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU A 216 " --> pdb=" O   ALA A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 236
      removed outlier: 3.909A  pdb=" N   TRP A 235 " --> pdb=" O   THR A 232 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   CYS A 236 " --> pdb=" O   LEU A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 276
      removed outlier: 3.995A  pdb=" N   LEU A 258 " --> pdb=" O   TRP A 254 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   SER A 259 " --> pdb=" O   VAL A 255 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   THR A 262 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ALA A 263 " --> pdb=" O   SER A 259 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ALA A 264 " --> pdb=" O   LEU A 260 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   VAL A 265 " --> pdb=" O   ALA A 261 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ARG A 272 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   GLY A 276 " --> pdb=" O   ARG A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 308
    Processing helix  chain 'A' and resid 308 through 327
      removed outlier: 3.598A  pdb=" N   VAL A 325 " --> pdb=" O   LEU A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 332
      removed outlier: 3.911A  pdb=" N   HIS A 331 " --> pdb=" O   SER A 328 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLY A 332 " --> pdb=" O   VAL A 329 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 328 through 332'
    Processing helix  chain 'A' and resid 356 through 362
    Processing helix  chain 'A' and resid 365 through 381
    Processing helix  chain 'A' and resid 381 through 389
    Processing helix  chain 'A' and resid 390 through 397
      removed outlier: 4.350A  pdb=" N   THR A 394 " --> pdb=" O   LEU A 390 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   LEU A 395 " --> pdb=" O   ARG A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 405 through 437
      removed outlier: 3.958A  pdb=" N   HIS A 409 " --> pdb=" O   TRP A 405 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   ALA A 411 " --> pdb=" O   ALA A 407 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   MET A 412 " --> pdb=" O   SER A 408 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   SER A 417 " --> pdb=" O   ALA A 413 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   ALA A 418 " --> pdb=" O   LEU A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 452
      removed outlier: 4.394A  pdb=" N   THR A 445 " --> pdb=" O   GLY A 441 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 468
      removed outlier: 4.547A  pdb=" N   LEU A 460 " --> pdb=" O   ALA A 456 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   SER A 461 " --> pdb=" O   VAL A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 471 through 476
      Proline residue:  A 476  - end of helix
    Processing helix  chain 'A' and resid 477 through 496
      removed outlier: 4.865A  pdb=" N   SER A 493 " --> pdb=" O   TYR A 489 " (cutoff:3.500A)
      removed outlier: 4.727A  pdb=" N   LEU A 494 " --> pdb=" O   LEU A 490 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLY A 496 " --> pdb=" O   GLY A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 540
      removed outlier: 3.808A  pdb=" N   LEU A 524 " --> pdb=" O   ALA A 520 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 47 through 56
      removed outlier: 3.515A  pdb=" N   THR B  51 " --> pdb=" O   GLY B  47 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU B  52 " --> pdb=" O   LYS B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 108
      removed outlier: 3.650A  pdb=" N   ILE B 103 " --> pdb=" O   GLY B  99 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   ASP B 104 " --> pdb=" O   GLY B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 126
      removed outlier: 3.890A  pdb=" N   ALA B 119 " --> pdb=" O   ASN B 115 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   GLU B 120 " --> pdb=" O   ALA B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 151
      removed outlier: 3.505A  pdb=" N   LYS B 143 " --> pdb=" O   GLY B 139 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   VAL B 144 " --> pdb=" O   ASN B 140 " (cutoff:3.500A)
      removed outlier: 4.239A  pdb=" N   SER B 145 " --> pdb=" O   ARG B 141 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 169 through 182
      removed outlier: 3.745A  pdb=" N   GLN B 175 " --> pdb=" O   GLU B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 185
      No H-bonds generated for 'chain 'B' and resid 183 through 185'
    Processing helix  chain 'B' and resid 196 through 202
      removed outlier: 3.717A  pdb=" N   ALA B 200 " --> pdb=" O   ALA B 196 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 47 through 56
    Processing helix  chain 'C' and resid 79 through 83
      removed outlier: 3.778A  pdb=" N   ARG C  82 " --> pdb=" O   ASP C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 98 through 111
    Processing helix  chain 'C' and resid 114 through 126
      removed outlier: 3.519A  pdb=" N   GLU C 120 " --> pdb=" O   ALA C 116 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 136
      removed outlier: 3.667A  pdb=" N   TYR C 136 " --> pdb=" O   ALA C 133 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 138 through 151
      removed outlier: 3.799A  pdb=" N   VAL C 144 " --> pdb=" O   ASN C 140 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   SER C 145 " --> pdb=" O   ARG C 141 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 169 through 184
    Processing helix  chain 'C' and resid 194 through 202
      removed outlier: 3.561A  pdb=" N   THR C 198 " --> pdb=" O   ILE C 194 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLU C 199 " --> pdb=" O   LEU C 195 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ALA C 200 " --> pdb=" O   ALA C 196 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 23 through 31
      removed outlier: 3.550A  pdb=" N   LEU B  25 " --> pdb=" O   LYS B  17 " (cutoff:3.500A)
      removed outlier: 5.044A  pdb=" N   LEU B  15 " --> pdb=" O   GLY B  27 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   ASP B  29 " --> pdb=" O   ARG B  13 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   ARG B  13 " --> pdb=" O   ASP B  29 " (cutoff:3.500A)
      removed outlier: 6.904A  pdb=" N   THR B  31 " --> pdb=" O   GLU B  11 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   GLU B  11 " --> pdb=" O   THR B  31 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 85 through 87
      removed outlier: 7.056A  pdb=" N   ALA B  85 " --> pdb=" O   LEU B 158 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   LEU B 157 " --> pdb=" O   LEU B 189 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLU B 215 " --> pdb=" O   ILE B 207 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 15 through 18
      removed outlier: 5.847A  pdb=" N   LEU C  15 " --> pdb=" O   GLY C  27 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 37 through 39
      removed outlier: 6.209A  pdb=" N   HIS C  38 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 85 through 87
      removed outlier: 6.829A  pdb=" N   ALA C  85 " --> pdb=" O   LEU C 158 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 205 through 208
      removed outlier: 6.750A  pdb=" N   VAL C 205 " --> pdb=" O   SER C 216 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   SER C 216 " --> pdb=" O   VAL C 205 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   ILE C 207 " --> pdb=" O   VAL C 214 " (cutoff:3.500A)

    327 hydrogen bonds defined for protein.
    954 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: 1.91

  Time building geometry restraints manager: 2.37 seconds

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

  Histogram of bond lengths:
        1.19 -     1.33: 1805
        1.33 -     1.48: 2215
        1.48 -     1.62: 3204
        1.62 -     1.76: 0
        1.76 -     1.91: 40
  Bond restraints: 7264
  Sorted by residual:
  bond pdb=" C4  ADP B 402 "
       pdb=" C5  ADP B 402 "
    ideal  model  delta    sigma   weight residual
    1.490  1.381  0.109 2.00e-02 2.50e+03 2.96e+01
  bond pdb=" C5  ADP B 402 "
       pdb=" C6  ADP B 402 "
    ideal  model  delta    sigma   weight residual
    1.490  1.407  0.083 2.00e-02 2.50e+03 1.72e+01
  bond pdb=" CA  ALA A 281 "
       pdb=" CB  ALA A 281 "
    ideal  model  delta    sigma   weight residual
    1.531  1.478  0.053 1.48e-02 4.57e+03 1.27e+01
  bond pdb=" CA  SER B  49 "
       pdb=" CB  SER B  49 "
    ideal  model  delta    sigma   weight residual
    1.532  1.475  0.057 1.62e-02 3.81e+03 1.23e+01
  bond pdb=" OB3 CDL A 601 "
       pdb=" PB2 CDL A 601 "
    ideal  model  delta    sigma   weight residual
    1.529  1.495  0.034 1.00e-02 1.00e+04 1.14e+01
  ... (remaining 7259 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.55: 9767
        3.55 -     7.11: 81
        7.11 -    10.66: 8
       10.66 -    14.21: 2
       14.21 -    17.77: 1
  Bond angle restraints: 9859
  Sorted by residual:
  angle pdb=" PB  ATP C 402 "
        pdb=" O3B ATP C 402 "
        pdb=" PG  ATP C 402 "
      ideal   model   delta    sigma   weight residual
     139.87  122.10   17.77 1.00e+00 1.00e+00 3.16e+02
  angle pdb=" N   VAL A  60 "
        pdb=" CA  VAL A  60 "
        pdb=" C   VAL A  60 "
      ideal   model   delta    sigma   weight residual
     113.71  107.82    5.89 9.50e-01 1.11e+00 3.84e+01
  angle pdb=" C   ARG A 402 "
        pdb=" CA  ARG A 402 "
        pdb=" CB  ARG A 402 "
      ideal   model   delta    sigma   weight residual
     111.22  118.60   -7.38 1.24e+00 6.50e-01 3.54e+01
  angle pdb=" PA  ATP C 402 "
        pdb=" O3A ATP C 402 "
        pdb=" PB  ATP C 402 "
      ideal   model   delta    sigma   weight residual
     136.83  131.11    5.72 1.00e+00 1.00e+00 3.27e+01
  angle pdb=" N   ARG A 402 "
        pdb=" CA  ARG A 402 "
        pdb=" C   ARG A 402 "
      ideal   model   delta    sigma   weight residual
     113.20  106.40    6.80 1.36e+00 5.41e-01 2.50e+01
  ... (remaining 9854 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.51: 4036
       25.51 -    51.02: 244
       51.02 -    76.53: 46
       76.53 -   102.04: 5
      102.04 -   127.54: 1
  Dihedral angle restraints: 4332
    sinusoidal: 1735
      harmonic: 2597
  Sorted by residual:
  dihedral pdb=" C5' ADP B 402 "
           pdb=" O5' ADP B 402 "
           pdb=" PA  ADP B 402 "
           pdb=" O2A ADP B 402 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  172.46  127.54     1      2.00e+01 2.50e-03 3.86e+01
  dihedral pdb=" CA  CYS B 202 "
           pdb=" C   CYS B 202 "
           pdb=" N   GLU B 203 "
           pdb=" CA  GLU B 203 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.20   20.80     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" CA  SER C 191 "
           pdb=" C   SER C 191 "
           pdb=" N   SER C 192 "
           pdb=" CA  SER C 192 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.15  -19.85     0      5.00e+00 4.00e-02 1.58e+01
  ... (remaining 4329 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 983
       0.060 -    0.119: 159
       0.119 -    0.179: 17
       0.179 -    0.238: 4
       0.238 -    0.298: 1
  Chirality restraints: 1164
  Sorted by residual:
  chirality pdb=" CA  VAL C  59 "
            pdb=" N   VAL C  59 "
            pdb=" C   VAL C  59 "
            pdb=" CB  VAL C  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.74   -0.30 2.00e-01 2.50e+01 2.22e+00
  chirality pdb=" CB  VAL A 279 "
            pdb=" CA  VAL A 279 "
            pdb=" CG1 VAL A 279 "
            pdb=" CG2 VAL A 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CA4 CDL A 601 "
            pdb=" CA3 CDL A 601 "
            pdb=" CA6 CDL A 601 "
            pdb=" OA6 CDL A 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.57   -2.38   -0.19 2.00e-01 2.50e+01 9.19e-01
  ... (remaining 1161 not shown)

  Planarity restraints: 1220
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 400 "   -0.016 2.00e-02 2.50e+03   3.24e-02 1.05e+01
        pdb=" C   VAL A 400 "    0.056 2.00e-02 2.50e+03
        pdb=" O   VAL A 400 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   SER A 401 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 138 "    0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" C   LYS C 138 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   LYS C 138 "    0.021 2.00e-02 2.50e+03
        pdb=" N   GLY C 139 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C  58 "   -0.011 2.00e-02 2.50e+03   2.27e-02 5.14e+00
        pdb=" C   LEU C  58 "    0.039 2.00e-02 2.50e+03
        pdb=" O   LEU C  58 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   VAL C  59 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1217 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 59
        2.63 -     3.20: 6188
        3.20 -     3.76: 10039
        3.76 -     4.33: 14156
        4.33 -     4.90: 24804
  Nonbonded interactions: 55246
  Sorted by model distance:
  nonbonded pdb=" OG  SER C  49 "
            pdb="MG    MG C 401 "
     model   vdw
     2.062 2.170
  nonbonded pdb="MG    MG B 401 "
            pdb=" O2  VO4 B 403 "
     model   vdw
     2.127 2.170
  nonbonded pdb=" O   SER C 163 "
            pdb=" OG  SER C 163 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" OE2 GLU A 132 "
            pdb=" NH1 ARG C  53 "
     model   vdw
     2.305 3.120
  nonbonded pdb=" O   ILE B 147 "
            pdb=" OG  SER B 151 "
     model   vdw
     2.320 3.040
  ... (remaining 55241 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
Found NCS groups:
ncs_group {
  reference = (chain 'B' and (resid 8 through 219 or resid 401))
  selection = (chain 'C' and (resid 8 through 219 or resid 401))
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.950
  Find NCS groups from input model:        0.200
  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:             0.000
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8464
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      :  0.007   0.109   7264  Z= 0.445
  Angle     :  0.862  17.768   9859  Z= 0.511
  Chirality :  0.047   0.298   1164
  Planarity :  0.005   0.070   1220
  Dihedral  : 16.577 127.544   2680
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.56 %
    Favored  : 92.44 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  0.28 %
    Favored  : 99.58 %
  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: -1.68 (0.27), residues: 926
  helix: -0.11 (0.24), residues: 506
  sheet: -2.30 (1.17), residues: 23
  loop : -2.40 (0.28), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A  44 
 HIS   0.005   0.001   HIS A 384 
 PHE   0.022   0.002   PHE C  40 
 TYR   0.013   0.002   TYR A  64 
 ARG   0.008   0.001   ARG A 402 

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.708 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 88
  average time/residue: 0.1964
  time to fit residues: 23.5804
Evaluate side-chains
  75 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 77 optimal weight:    1.9990
   chunk 69 optimal weight:    0.3980
   chunk 38 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 72 optimal weight:    0.4980
   chunk 27 optimal weight:    0.0470
   chunk 43 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.5278

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

Flipped N/Q/H residues before XYZ refinement:
C 193 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.114909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.095909 restraints weight = 8758.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.2928 rms_B_bonded: 1.51
r_work: 0.2819 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2683 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.1022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7264  Z= 0.196
  Angle     :  0.583   7.123   9859  Z= 0.291
  Chirality :  0.041   0.132   1164
  Planarity :  0.004   0.050   1220
  Dihedral  : 13.792  94.933   1202
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  5.24 %
    Favored  : 94.33 %
  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 (0.28), residues: 926
  helix:  0.37 (0.24), residues: 520
  sheet: -2.12 (1.11), residues: 23
  loop : -2.34 (0.29), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  44 
 HIS   0.003   0.001   HIS A 404 
 PHE   0.011   0.001   PHE C  40 
 TYR   0.015   0.001   TYR A 489 
 ARG   0.004   0.000   ARG A 402 

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 70
  time to evaluate  : 0.736 
Fit side-chains
REVERT: A  430 LEU cc_start: 0.8094 (tt) cc_final: 0.7853 (tp)
REVERT: C   26 ASP cc_start: 0.7852 (t0) cc_final: 0.7596 (t0)
  outliers start: 3
  outliers final: 1
  residues processed: 73
  average time/residue: 0.2000
  time to fit residues: 20.9169
Evaluate side-chains
  58 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  216 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 46 optimal weight:    0.0070
   chunk 81 optimal weight:    0.7980
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.6998

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

Flipped N/Q/H residues before XYZ refinement:
A 308 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.114293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.095405 restraints weight = 8933.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.2919 rms_B_bonded: 1.49
r_work: 0.2808 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.2674 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8532
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7264  Z= 0.222
  Angle     :  0.561   6.534   9859  Z= 0.278
  Chirality :  0.041   0.130   1164
  Planarity :  0.004   0.047   1220
  Dihedral  : 12.614  74.581   1202
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  :  8.07 %
    Favored  : 91.22 %
  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: -0.94 (0.28), residues: 926
  helix:  0.57 (0.24), residues: 520
  sheet: -1.94 (1.07), residues: 23
  loop : -2.27 (0.28), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  44 
 HIS   0.003   0.001   HIS A 384 
 PHE   0.012   0.001   PHE C  40 
 TYR   0.008   0.001   TYR A 489 
 ARG   0.003   0.000   ARG A  35 

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.716 
Fit side-chains
REVERT: B   33 ARG cc_start: 0.8278 (mtp-110) cc_final: 0.7854 (ttm-80)
REVERT: C   26 ASP cc_start: 0.7890 (t0) cc_final: 0.7612 (t0)
  outliers start: 5
  outliers final: 2
  residues processed: 73
  average time/residue: 0.2090
  time to fit residues: 20.7081
Evaluate side-chains
  64 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 62
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  272 ARG
Chi-restraints excluded: chain B residue  216 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   chunk 26 optimal weight:    0.3980
   chunk 1 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 73 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 = 0.3170 r_free = 0.3170 target = 0.113990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2913 r_free = 0.2913 target = 0.094650 restraints weight = 8949.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 1.53
r_work: 0.2796 rms_B_bonded: 2.16 restraints_weight: 0.5000
r_work: 0.2661 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.1455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7264  Z= 0.235
  Angle     :  0.560   6.968   9859  Z= 0.277
  Chirality :  0.041   0.125   1164
  Planarity :  0.004   0.044   1220
  Dihedral  : 12.170  73.794   1202
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 3.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 10.34 %
    Favored  : 88.67 %
  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: -0.81 (0.28), residues: 926
  helix:  0.66 (0.24), residues: 521
  sheet: -2.02 (1.02), residues: 23
  loop : -2.18 (0.28), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  44 
 HIS   0.003   0.001   HIS B  81 
 PHE   0.010   0.001   PHE C  40 
 TYR   0.007   0.001   TYR A 489 
 ARG   0.004   0.000   ARG A  35 

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.756 
Fit side-chains
REVERT: A   35 ARG cc_start: 0.8566 (ttt90) cc_final: 0.7701 (ttp-170)
REVERT: B   33 ARG cc_start: 0.8320 (mtp-110) cc_final: 0.7952 (tpp-160)
REVERT: C   26 ASP cc_start: 0.7877 (t0) cc_final: 0.7609 (t0)
REVERT: C   67 ARG cc_start: 0.7971 (ttp80) cc_final: 0.7557 (ttm-80)
  outliers start: 7
  outliers final: 2
  residues processed: 80
  average time/residue: 0.1876
  time to fit residues: 20.4989
Evaluate side-chains
  67 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 65
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain C residue  193 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   chunk 25 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 83 optimal weight:    2.9990
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3170 r_free = 0.3170 target = 0.113968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.094493 restraints weight = 8903.003|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 1.54
r_work: 0.2789 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.2652 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8537
moved from start:          0.1530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7264  Z= 0.238
  Angle     :  0.552   6.116   9859  Z= 0.275
  Chirality :  0.041   0.130   1164
  Planarity :  0.004   0.043   1220
  Dihedral  : 11.927  73.607   1202
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 3.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  0.71 %
    Allowed  : 12.04 %
    Favored  : 87.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.28), residues: 926
  helix:  0.80 (0.24), residues: 516
  sheet: -1.98 (1.01), residues: 23
  loop : -2.12 (0.28), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  44 
 HIS   0.003   0.001   HIS B  81 
 PHE   0.009   0.001   PHE A 191 
 TYR   0.007   0.001   TYR B  86 
 ARG   0.003   0.000   ARG A  35 

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.811 
Fit side-chains
REVERT: A   35 ARG cc_start: 0.8571 (ttt90) cc_final: 0.7706 (ttp-170)
REVERT: B   33 ARG cc_start: 0.8377 (mtp-110) cc_final: 0.7944 (tpp-160)
REVERT: C   26 ASP cc_start: 0.7914 (t0) cc_final: 0.7679 (t0)
REVERT: C   67 ARG cc_start: 0.7970 (ttp80) cc_final: 0.7556 (ttm-80)
  outliers start: 5
  outliers final: 2
  residues processed: 76
  average time/residue: 0.2066
  time to fit residues: 21.3048
Evaluate side-chains
  66 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain C residue  193 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 8 optimal weight:    3.9990
   chunk 80 optimal weight:    1.9990
   chunk 47 optimal weight:    4.9990
   chunk 86 optimal weight:    0.0040
   chunk 31 optimal weight:    5.9990
   chunk 15 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0030
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.5002

-------------------------------------------------------------------------------
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 = 0.3190 r_free = 0.3190 target = 0.115679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.096376 restraints weight = 8863.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.2931 rms_B_bonded: 1.53
r_work: 0.2822 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2687 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.2687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.1716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7264  Z= 0.177
  Angle     :  0.527   6.563   9859  Z= 0.260
  Chirality :  0.040   0.123   1164
  Planarity :  0.004   0.044   1220
  Dihedral  : 11.617  85.749   1202
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 11.90 %
    Favored  : 86.97 %
  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: -0.46 (0.28), residues: 926
  helix:  0.99 (0.24), residues: 517
  sheet: -2.01 (0.81), residues: 32
  loop : -2.05 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  44 
 HIS   0.002   0.001   HIS A 404 
 PHE   0.008   0.001   PHE A 191 
 TYR   0.012   0.001   TYR A  64 
 ARG   0.002   0.000   ARG A  35 

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.784 
Fit side-chains
REVERT: A   35 ARG cc_start: 0.8512 (ttt90) cc_final: 0.7678 (ttp-170)
REVERT: B   33 ARG cc_start: 0.8333 (mtp-110) cc_final: 0.7937 (tpp-160)
REVERT: C   67 ARG cc_start: 0.7956 (ttp80) cc_final: 0.7551 (ttm-80)
REVERT: C  170 MET cc_start: 0.7612 (mmp) cc_final: 0.7319 (mmt)
  outliers start: 8
  outliers final: 5
  residues processed: 81
  average time/residue: 0.1965
  time to fit residues: 21.7178
Evaluate side-chains
  74 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue  193 HIS
Chi-restraints excluded: chain C residue  204 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 8 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 6 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0870
   chunk 80 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0270
   chunk 74 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.4816

-------------------------------------------------------------------------------
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 = 0.3195 r_free = 0.3195 target = 0.116075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2941 r_free = 0.2941 target = 0.096820 restraints weight = 8788.570|
|-----------------------------------------------------------------------------|
r_work (start): 0.2938 rms_B_bonded: 1.52
r_work: 0.2829 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2694 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.2694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7264  Z= 0.174
  Angle     :  0.521   5.896   9859  Z= 0.258
  Chirality :  0.039   0.123   1164
  Planarity :  0.004   0.052   1220
  Dihedral  : 11.437  88.613   1202
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 12.61 %
    Favored  : 86.12 %
  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: -0.32 (0.28), residues: 926
  helix:  1.10 (0.24), residues: 522
  sheet: -1.83 (0.83), residues: 32
  loop : -2.05 (0.29), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  44 
 HIS   0.002   0.001   HIS C  38 
 PHE   0.008   0.001   PHE A 191 
 TYR   0.008   0.001   TYR A 432 
 ARG   0.002   0.000   ARG A  35 

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.744 
Fit side-chains
REVERT: A   35 ARG cc_start: 0.8482 (ttt90) cc_final: 0.7596 (ttp-170)
REVERT: B   33 ARG cc_start: 0.8266 (mtp-110) cc_final: 0.7914 (tpp-160)
REVERT: C   67 ARG cc_start: 0.7935 (ttp80) cc_final: 0.7526 (ttm-80)
  outliers start: 9
  outliers final: 7
  residues processed: 82
  average time/residue: 0.2056
  time to fit residues: 23.1045
Evaluate side-chains
  73 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue  193 HIS
Chi-restraints excluded: chain C residue  198 THR
Chi-restraints excluded: chain C residue  204 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 70 optimal weight:    0.0000
   chunk 65 optimal weight:    0.0270
   chunk 86 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9980
   chunk 77 optimal weight:    0.0170
   overall best weight:    0.3480

-------------------------------------------------------------------------------
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 = 0.3211 r_free = 0.3211 target = 0.117453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.098210 restraints weight = 8855.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 1.53
r_work: 0.2851 rms_B_bonded: 2.18 restraints_weight: 0.5000
r_work: 0.2717 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   7264  Z= 0.151
  Angle     :  0.511   5.822   9859  Z= 0.254
  Chirality :  0.039   0.122   1164
  Planarity :  0.004   0.047   1220
  Dihedral  : 11.182  83.285   1202
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 12.61 %
    Favored  : 86.12 %
  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: -0.17 (0.28), residues: 926
  helix:  1.26 (0.24), residues: 520
  sheet: -1.70 (0.84), residues: 32
  loop : -2.02 (0.29), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  44 
 HIS   0.002   0.001   HIS C  38 
 PHE   0.008   0.001   PHE A 191 
 TYR   0.014   0.001   TYR A  64 
 ARG   0.002   0.000   ARG A  35 

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.771 
Fit side-chains
REVERT: A   35 ARG cc_start: 0.8467 (ttt90) cc_final: 0.7575 (ttp-170)
REVERT: B   33 ARG cc_start: 0.8245 (mtp-110) cc_final: 0.7953 (tpp-160)
REVERT: C   67 ARG cc_start: 0.7921 (ttp80) cc_final: 0.7513 (ttm-80)
  outliers start: 9
  outliers final: 8
  residues processed: 76
  average time/residue: 0.2070
  time to fit residues: 21.3233
Evaluate side-chains
  75 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 67
  time to evaluate  : 0.779 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain C residue   28 LEU
Chi-restraints excluded: chain C residue  193 HIS
Chi-restraints excluded: chain C residue  198 THR
Chi-restraints excluded: chain C residue  204 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 1 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0010
   chunk 57 optimal weight:    0.0770
   chunk 69 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.4544

-------------------------------------------------------------------------------
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 = 0.3202 r_free = 0.3202 target = 0.116774 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.098289 restraints weight = 8940.406|
|-----------------------------------------------------------------------------|
r_work (start): 0.2958 rms_B_bonded: 1.44
r_work: 0.2851 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2722 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.2722
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.1979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7264  Z= 0.170
  Angle     :  0.531   8.512   9859  Z= 0.261
  Chirality :  0.039   0.122   1164
  Planarity :  0.004   0.049   1220
  Dihedral  : 11.134  84.569   1202
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 13.03 %
    Favored  : 85.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.28), residues: 926
  helix:  1.32 (0.24), residues: 520
  sheet: -1.55 (1.02), residues: 23
  loop : -2.00 (0.29), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  44 
 HIS   0.002   0.001   HIS C  38 
 PHE   0.008   0.001   PHE A 191 
 TYR   0.005   0.001   TYR A 489 
 ARG   0.002   0.000   ARG A  70 

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.793 
Fit side-chains
REVERT: A   35 ARG cc_start: 0.8461 (ttt90) cc_final: 0.7596 (ttp-170)
REVERT: B   33 ARG cc_start: 0.8196 (mtp-110) cc_final: 0.7947 (tpp-160)
REVERT: C   67 ARG cc_start: 0.7883 (ttp80) cc_final: 0.7478 (ttm-80)
REVERT: C  170 MET cc_start: 0.7487 (mmp) cc_final: 0.7124 (mmt)
  outliers start: 9
  outliers final: 8
  residues processed: 73
  average time/residue: 0.2090
  time to fit residues: 20.8672
Evaluate side-chains
  73 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 65
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain B residue  201 LEU
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  193 HIS
Chi-restraints excluded: chain C residue  198 THR
Chi-restraints excluded: chain C residue  204 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0570
   chunk 13 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 66 optimal weight:    0.9990
   chunk 91 optimal weight:    0.7980
   chunk 65 optimal weight:    2.9990
   chunk 51 optimal weight:    0.3980
   chunk 58 optimal weight:    0.9990
   chunk 39 optimal weight:    5.9990
   chunk 41 optimal weight:    0.2980
   overall best weight:    0.5098

-------------------------------------------------------------------------------
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 = 0.3199 r_free = 0.3199 target = 0.116534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.097462 restraints weight = 9082.491|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 1.51
r_work: 0.2838 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2706 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.2001

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7264  Z= 0.182
  Angle     :  0.541   8.683   9859  Z= 0.265
  Chirality :  0.039   0.122   1164
  Planarity :  0.004   0.047   1220
  Dihedral  : 11.126  86.584   1202
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.62 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  : 13.31 %
    Favored  : 85.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.28), residues: 926
  helix:  1.31 (0.24), residues: 522
  sheet: -1.43 (1.02), residues: 23
  loop : -1.99 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  44 
 HIS   0.003   0.001   HIS C  38 
 PHE   0.008   0.001   PHE A 191 
 TYR   0.013   0.001   TYR A  64 
 ARG   0.002   0.000   ARG A  35 

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

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

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1852 Ramachandran restraints generated.
    926 Oldfield, 0 Emsley, 926 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.766 
Fit side-chains
REVERT: A   35 ARG cc_start: 0.8456 (ttt90) cc_final: 0.7531 (ttp-170)
REVERT: B   33 ARG cc_start: 0.8217 (mtp-110) cc_final: 0.7929 (tpp-160)
REVERT: C   67 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7449 (ttm-80)
REVERT: C  170 MET cc_start: 0.7484 (mmp) cc_final: 0.7219 (mmt)
  outliers start: 7
  outliers final: 7
  residues processed: 70
  average time/residue: 0.2164
  time to fit residues: 20.5130
Evaluate side-chains
  71 residues out of total 706 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.720 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain B residue  216 SER
Chi-restraints excluded: chain B residue  218 SER
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain C residue  193 HIS
Chi-restraints excluded: chain C residue  198 THR
Chi-restraints excluded: chain C residue  204 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 92
   random chunks:
   chunk 87 optimal weight:    0.8980
   chunk 56 optimal weight:    0.4980
   chunk 15 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 26 optimal weight:    5.9990
   chunk 81 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 86 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 = 0.3174 r_free = 0.3174 target = 0.114371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2915 r_free = 0.2915 target = 0.094940 restraints weight = 8904.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.2911 rms_B_bonded: 1.52
r_work: 0.2801 rms_B_bonded: 2.15 restraints_weight: 0.5000
r_work: 0.2666 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7264  Z= 0.244
  Angle     :  0.571   9.047   9859  Z= 0.280
  Chirality :  0.041   0.129   1164
  Planarity :  0.004   0.049   1220
  Dihedral  : 11.383  84.122   1202
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  1.27 %
    Allowed  : 13.03 %
    Favored  : 85.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.28), residues: 926
  helix:  1.19 (0.24), residues: 522
  sheet: -1.43 (1.02), residues: 23
  loop : -2.04 (0.29), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  44 
 HIS   0.003   0.001   HIS C  38 
 PHE   0.009   0.001   PHE A 191 
 TYR   0.008   0.001   TYR A  64 
 ARG   0.002   0.000   ARG A  35 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3498.85 seconds
wall clock time: 62 minutes 45.38 seconds (3765.38 seconds total)