Starting phenix.real_space_refine
on Fri Jun  6 14:41:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xof_38527/06_2025/8xof_38527.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xof_38527/06_2025/8xof_38527.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xof_38527/06_2025/8xof_38527.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xof_38527/06_2025/8xof_38527.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xof_38527/06_2025/8xof_38527.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xof_38527/06_2025/8xof_38527.cif"
  }
  resolution = 2.6
  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=   0.005 sd=   0.072
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: 5
    Type Number    sf(0)   Gaussians
     S      51      5.16       5
     Cl      2      4.86       5
     C    5094      2.51       5
     N    1408      2.21       5
     O    1470      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 8025
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1863
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 228, 1863
          Classifications: {'peptide': 228}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 6, 'TRANS': 221}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 2573
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2573
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 39
          Unresolved non-hydrogen dihedrals: 29
          Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "G"
      Number of atoms: 436
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 57, 436
          Classifications: {'peptide': 57}
          Link IDs: {'PTRANS': 4, 'TRANS': 52}
    Chain: "N"
      Number of atoms: 960
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 127, 960
          Classifications: {'peptide': 127}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 5, 'TRANS': 121}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "R"
      Number of atoms: 2163
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 265, 2163
          Classifications: {'peptide': 265}
          Link IDs: {'PTRANS': 8, 'TRANS': 256}
          Chain breaks: 2
    Chain: "R"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 30
          Unusual residues: {'A1LVW': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.12, per 1000 atoms: 0.64
  Number of scatterers: 8025
  At special positions: 0
  Unit cell: (83.95, 96.36, 126.29, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      2     17.00
     S      51     16.00
     O    1470      8.00
     N    1408      7.00
     C    5094      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  99 " - pdb=" SG  CYS N 107 " distance=2.37

  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: 2.39
  Conformation dependent library (CDL) restraints added in 930.4 milliseconds
  

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1916

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 10 sheets defined
      43.3% alpha, 20.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 15 through 40
      removed outlier: 3.627A  pdb=" N   GLN A  35 " --> pdb=" O   GLN A  31 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 60
      removed outlier: 3.690A  pdb=" N   MET A  60 " --> pdb=" O   ILE A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.507A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   CYS A 237 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 279
    Processing helix  chain 'A' and resid 293 through 304
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.279A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 317
    Processing helix  chain 'A' and resid 331 through 351
      removed outlier: 3.621A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 35
    Processing helix  chain 'G' and resid 7 through 24
    Processing helix  chain 'G' and resid 29 through 44
    Processing helix  chain 'G' and resid 55 through 59
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.634A  pdb=" N   TYR N  32 " --> pdb=" O   PHE N  29 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 87 through 91
    Processing helix  chain 'R' and resid 51 through 87
      removed outlier: 4.287A  pdb=" N   PHE R  70 " --> pdb=" O   THR R  66 " (cutoff:3.500A)
      Proline residue:  R  71  - end of helix
    Processing helix  chain 'R' and resid 88 through 91
    Processing helix  chain 'R' and resid 92 through 117
      removed outlier: 3.734A  pdb=" N   TYR R  97 " --> pdb=" O   ILE R  93 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   ILE R 114 " --> pdb=" O   ALA R 110 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE R 117 " --> pdb=" O   LEU R 113 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 128 through 161
    Processing helix  chain 'R' and resid 170 through 198
      Proline residue:  R 192  - end of helix
      removed outlier: 3.681A  pdb=" N   LEU R 198 " --> pdb=" O   THR R 194 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 212 through 246
      removed outlier: 5.396A  pdb=" N   VAL R 225 " --> pdb=" O   LEU R 221 " (cutoff:3.500A)
      Proline residue:  R 226  - end of helix
    Processing helix  chain 'R' and resid 250 through 283
      Proline residue:  R 274  - end of helix
      removed outlier: 3.606A  pdb=" N   HIS R 282 " --> pdb=" O   PHE R 278 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 302 through 325
      removed outlier: 3.815A  pdb=" N   SER R 317 " --> pdb=" O   ALA R 313 " (cutoff:3.500A)
      Proline residue:  R 321  - end of helix
    Processing helix  chain 'R' and resid 328 through 342
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 214
      removed outlier: 4.694A  pdb=" N   VAL A 224 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 7.845A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.317A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 8.395A  pdb=" N   ASP A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.416A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 5.906A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51
      removed outlier: 5.618A  pdb=" N   THR B  47 " --> pdb=" O   ASN B 340 " (cutoff:3.500A)
      removed outlier: 6.798A  pdb=" N   ASN B 340 " --> pdb=" O   THR B  47 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.674A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.749A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.120A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 3.588A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.193A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.085A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 3.512A  pdb=" N   GLY B 202 " --> pdb=" O   SER B 189 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.624A  pdb=" N   CYS B 250 " --> pdb=" O   THR B 263 " (cutoff:3.500A)
      removed outlier: 4.587A  pdb=" N   THR B 263 " --> pdb=" O   CYS B 250 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   LEU B 252 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   GLN B 259 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.652A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   CYS B 294 " --> pdb=" O   VAL B 307 " (cutoff:3.500A)
      removed outlier: 4.526A  pdb=" N   VAL B 307 " --> pdb=" O   CYS B 294 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   VAL B 296 " --> pdb=" O   ALA B 305 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 6
    Processing sheet with id=AB1, first strand: chain 'N' and resid 11 through 12
      removed outlier: 6.996A  pdb=" N   MET N  34 " --> pdb=" O   ASP N  50 " (cutoff:3.500A)
      removed outlier: 4.667A  pdb=" N   ASP N  50 " --> pdb=" O   MET N  34 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)

    440 hydrogen bonds defined for protein.
    1257 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.50

  Time building geometry restraints manager: 2.77 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1725
        1.33 -     1.45: 1881
        1.45 -     1.57: 4506
        1.57 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 8186
  Sorted by residual:
  bond pdb=" C17 A1LVW R 401 "
       pdb=" N08 A1LVW R 401 "
    ideal  model  delta    sigma   weight residual
    1.343  1.449 -0.106 2.00e-02 2.50e+03 2.81e+01
  bond pdb=" C16 A1LVW R 401 "
       pdb=" N07 A1LVW R 401 "
    ideal  model  delta    sigma   weight residual
    1.359  1.451 -0.092 2.00e-02 2.50e+03 2.09e+01
  bond pdb=" C17 A1LVW R 401 "
       pdb=" C19 A1LVW R 401 "
    ideal  model  delta    sigma   weight residual
    1.439  1.355  0.084 2.00e-02 2.50e+03 1.75e+01
  bond pdb=" C16 A1LVW R 401 "
       pdb=" C18 A1LVW R 401 "
    ideal  model  delta    sigma   weight residual
    1.436  1.355  0.081 2.00e-02 2.50e+03 1.63e+01
  bond pdb=" C32 A1LVW R 401 "
       pdb="CL01 A1LVW R 401 "
    ideal  model  delta    sigma   weight residual
    1.731  1.784 -0.053 2.00e-02 2.50e+03 7.07e+00
  ... (remaining 8181 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 10807
        1.46 -     2.92: 204
        2.92 -     4.38: 51
        4.38 -     5.84: 16
        5.84 -     7.31: 7
  Bond angle restraints: 11085
  Sorted by residual:
  angle pdb=" N   ARG A 356 "
        pdb=" CA  ARG A 356 "
        pdb=" CB  ARG A 356 "
      ideal   model   delta    sigma   weight residual
     110.40  116.39   -5.99 1.63e+00 3.76e-01 1.35e+01
  angle pdb=" N   ASN N  35 "
        pdb=" CA  ASN N  35 "
        pdb=" C   ASN N  35 "
      ideal   model   delta    sigma   weight residual
     108.99  113.67   -4.68 1.57e+00 4.06e-01 8.88e+00
  angle pdb=" N   TYR B 105 "
        pdb=" CA  TYR B 105 "
        pdb=" C   TYR B 105 "
      ideal   model   delta    sigma   weight residual
     108.90  104.14    4.76 1.63e+00 3.76e-01 8.52e+00
  angle pdb=" N   ASP R 111 "
        pdb=" CA  ASP R 111 "
        pdb=" C   ASP R 111 "
      ideal   model   delta    sigma   weight residual
     112.54  109.12    3.42 1.22e+00 6.72e-01 7.86e+00
  angle pdb=" N   HIS R 302 "
        pdb=" CA  HIS R 302 "
        pdb=" C   HIS R 302 "
      ideal   model   delta    sigma   weight residual
     109.81  115.81   -6.00 2.21e+00 2.05e-01 7.37e+00
  ... (remaining 11080 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.71: 4302
       17.71 -    35.43: 415
       35.43 -    53.14: 118
       53.14 -    70.86: 24
       70.86 -    88.57: 12
  Dihedral angle restraints: 4871
    sinusoidal: 1919
      harmonic: 2952
  Sorted by residual:
  dihedral pdb=" CB  CYS N  99 "
           pdb=" SG  CYS N  99 "
           pdb=" SG  CYS N 107 "
           pdb=" CB  CYS N 107 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -125.77   39.77     1      1.00e+01 1.00e-02 2.22e+01
  dihedral pdb=" CA  PHE N 108 "
           pdb=" C   PHE N 108 "
           pdb=" N   ASP N 109 "
           pdb=" CA  ASP N 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.81  -22.19     0      5.00e+00 4.00e-02 1.97e+01
  dihedral pdb=" CA  PHE B 292 "
           pdb=" C   PHE B 292 "
           pdb=" N   ASN B 293 "
           pdb=" CA  ASN B 293 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.08   19.92     0      5.00e+00 4.00e-02 1.59e+01
  ... (remaining 4868 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1071
       0.056 -    0.112: 150
       0.112 -    0.169: 31
       0.169 -    0.225: 3
       0.225 -    0.281: 1
  Chirality restraints: 1256
  Sorted by residual:
  chirality pdb=" CA  ARG A 356 "
            pdb=" N   ARG A 356 "
            pdb=" C   ARG A 356 "
            pdb=" CB  ARG A 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.97e+00
  chirality pdb=" CA  TYR B 105 "
            pdb=" N   TYR B 105 "
            pdb=" C   TYR B 105 "
            pdb=" CB  TYR B 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.22 2.00e-01 2.50e+01 1.26e+00
  chirality pdb=" CB  ILE R 308 "
            pdb=" CA  ILE R 308 "
            pdb=" CG1 ILE R 308 "
            pdb=" CG2 ILE R 308 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.17e+00
  ... (remaining 1253 not shown)

  Planarity restraints: 1411
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 197 "   -0.202 9.50e-02 1.11e+02   9.09e-02 5.63e+00
        pdb=" NE  ARG B 197 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 197 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 197 "    0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 197 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 214 "   -0.130 9.50e-02 1.11e+02   5.85e-02 2.42e+00
        pdb=" NE  ARG B 214 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 214 "   -0.008 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 214 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 214 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 282 "   -0.007 2.00e-02 2.50e+03   1.46e-02 2.12e+00
        pdb=" C   LEU A 282 "    0.025 2.00e-02 2.50e+03
        pdb=" O   LEU A 282 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ARG A 283 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1408 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 250
        2.71 -     3.26: 8166
        3.26 -     3.80: 13118
        3.80 -     4.35: 17277
        4.35 -     4.90: 29059
  Nonbonded interactions: 67870
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 195 "
            pdb=" OG1 THR B 196 "
     model   vdw
     2.160 3.040
  nonbonded pdb=" OG1 THR R  92 "
            pdb=" OD2 ASP R  95 "
     model   vdw
     2.204 3.040
  nonbonded pdb=" O   TYR B 145 "
            pdb=" N   GLY B 162 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" OE1 GLN A  59 "
            pdb=" ND2 ASN A 371 "
     model   vdw
     2.297 3.120
  ... (remaining 67865 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.410
  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:             0.000
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.820
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:15.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
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      :  0.005   0.335   8187  Z= 0.276
  Angle     :  0.622  19.691  11087  Z= 0.327
  Chirality :  0.042   0.281   1256
  Planarity :  0.004   0.091   1411
  Dihedral  : 15.971  88.571   2952
  Min Nonbonded Distance : 2.160

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 16.88 %
    Favored  : 82.66 %
  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:  1.62 (0.28), residues: 997
  helix:  2.91 (0.26), residues: 385
  sheet: -0.40 (0.32), residues: 221
  loop :  0.19 (0.34), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.007   0.001   HIS R 245 
 PHE   0.009   0.001   PHE A 212 
 TYR   0.019   0.001   TYR R  55 
 ARG   0.013   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13664 (  440)
  hydrogen bonds       : angle       5.46106 ( 1257)
  SS BOND              : bond        0.33470 (    1)
  SS BOND              : angle      17.13625 (    2)
  covalent geometry    : bond        0.00391 ( 8186)
  covalent geometry    : angle       0.57799 (11085)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 145
  time to evaluate  : 0.838 
Fit side-chains
   revert: symmetry clash
REVERT: A  358 ILE cc_start: 0.9182 (mm) cc_final: 0.8957 (mm)
REVERT: B   16 ASN cc_start: 0.8032 (m-40) cc_final: 0.7756 (m-40)
REVERT: B   17 GLN cc_start: 0.7900 (tt0) cc_final: 0.7431 (mt0)
REVERT: B   44 GLN cc_start: 0.8162 (tt0) cc_final: 0.7813 (tt0)
REVERT: B  262 MET cc_start: 0.8897 (tpt) cc_final: 0.8658 (tpp)
  outliers start: 4
  outliers final: 2
  residues processed: 146
  average time/residue: 1.2705
  time to fit residues: 195.9928
Evaluate side-chains
  135 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 133
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain N residue   99 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.5980
   chunk 74 optimal weight:    7.9990
   chunk 41 optimal weight:    0.8980
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   chunk 57 optimal weight:    5.9990
   chunk 88 optimal weight:    0.0170
   overall best weight:    1.1022

-------------------------------------------------------------------------------
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 = 0.3948 r_free = 0.3948 target = 0.156646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.115382 restraints weight = 10083.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 2.46
r_work: 0.3367 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.1191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8187  Z= 0.139
  Angle     :  0.554  10.293  11087  Z= 0.293
  Chirality :  0.043   0.159   1256
  Planarity :  0.004   0.040   1411
  Dihedral  :  5.891  75.439   1114
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 2.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 15.72 %
    Favored  : 80.46 %
  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:  1.61 (0.27), residues: 997
  helix:  2.82 (0.25), residues: 390
  sheet: -0.41 (0.33), residues: 208
  loop :  0.20 (0.33), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.009   0.001   HIS R 245 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.017   0.001   TYR R  55 
 ARG   0.011   0.001   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04330 (  440)
  hydrogen bonds       : angle       4.64075 ( 1257)
  SS BOND              : bond        0.00204 (    1)
  SS BOND              : angle       2.03899 (    2)
  covalent geometry    : bond        0.00310 ( 8186)
  covalent geometry    : angle       0.55293 (11085)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 145
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7946 (mm-30)
REVERT: A  358 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8851 (mm)
REVERT: B   16 ASN cc_start: 0.7978 (m-40) cc_final: 0.7671 (m-40)
REVERT: B   46 ARG cc_start: 0.7681 (mtt180) cc_final: 0.7156 (mtm-85)
REVERT: B  153 ASP cc_start: 0.8108 (m-30) cc_final: 0.7759 (p0)
REVERT: B  214 ARG cc_start: 0.8645 (mmm160) cc_final: 0.8373 (mmm-85)
REVERT: B  261 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8500 (mp)
REVERT: B  262 MET cc_start: 0.9026 (tpt) cc_final: 0.8693 (tpp)
REVERT: N  120 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.8433 (mp10)
REVERT: R   95 ASP cc_start: 0.8769 (m-30) cc_final: 0.8529 (m-30)
  outliers start: 33
  outliers final: 10
  residues processed: 161
  average time/residue: 1.1488
  time to fit residues: 196.8102
Evaluate side-chains
  144 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 131
  time to evaluate  : 0.974 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  108 LEU
Chi-restraints excluded: chain R residue  170 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 68 optimal weight:    6.9990
   chunk 73 optimal weight:    5.9990
   chunk 60 optimal weight:   10.0000
   chunk 82 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 71 optimal weight:    0.5980
   chunk 37 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 84 optimal weight:    6.9990
   chunk 63 optimal weight:    2.9990
   chunk 93 optimal weight:    5.9990
   overall best weight:    2.5186

-------------------------------------------------------------------------------
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 = 0.3922 r_free = 0.3922 target = 0.154074 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.112061 restraints weight = 10251.420|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 2.48
r_work: 0.3309 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3193 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.3193
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062   8187  Z= 0.216
  Angle     :  0.594  11.455  11087  Z= 0.312
  Chirality :  0.045   0.248   1256
  Planarity :  0.004   0.043   1411
  Dihedral  :  5.995  72.419   1114
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  4.86 %
    Allowed  : 15.03 %
    Favored  : 80.12 %
  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:  1.39 (0.27), residues: 997
  helix:  2.63 (0.26), residues: 390
  sheet: -0.47 (0.32), residues: 225
  loop :  0.09 (0.34), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  82 
 HIS   0.008   0.001   HIS R 245 
 PHE   0.017   0.002   PHE B 292 
 TYR   0.019   0.002   TYR R  55 
 ARG   0.008   0.000   ARG B  96 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04659 (  440)
  hydrogen bonds       : angle       4.65776 ( 1257)
  SS BOND              : bond        0.00103 (    1)
  SS BOND              : angle       2.09993 (    2)
  covalent geometry    : bond        0.00507 ( 8186)
  covalent geometry    : angle       0.59349 (11085)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 130
  time to evaluate  : 0.915 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  358 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8973 (mm)
REVERT: A  391 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.7979 (t80)
REVERT: B   46 ARG cc_start: 0.7856 (mtt180) cc_final: 0.7360 (mtm-85)
REVERT: B  153 ASP cc_start: 0.8173 (m-30) cc_final: 0.7814 (p0)
REVERT: B  214 ARG cc_start: 0.8630 (mmm160) cc_final: 0.8345 (mmm-85)
REVERT: B  261 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8602 (mp)
REVERT: B  262 MET cc_start: 0.9010 (tpt) cc_final: 0.8695 (tpp)
REVERT: B  292 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8118 (p90)
REVERT: N  120 GLN cc_start: 0.8882 (OUTLIER) cc_final: 0.8452 (mp10)
REVERT: R   99 ILE cc_start: 0.8426 (pt) cc_final: 0.8205 (pp)
  outliers start: 42
  outliers final: 16
  residues processed: 152
  average time/residue: 1.1134
  time to fit residues: 180.2057
Evaluate side-chains
  143 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  215 GLU
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  170 THR
Chi-restraints excluded: chain R residue  198 LEU
Chi-restraints excluded: chain R residue  277 VAL
Chi-restraints excluded: chain R residue  329 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 92 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9990
   chunk 95 optimal weight:   10.0000
   chunk 79 optimal weight:    3.9990
   chunk 61 optimal weight:    8.9990
   chunk 43 optimal weight:    5.9990
   chunk 9 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   chunk 25 optimal weight:    8.9990
   chunk 36 optimal weight:    5.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    1.7388

-------------------------------------------------------------------------------
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 = 0.3935 r_free = 0.3935 target = 0.155152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.113413 restraints weight = 10191.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 2.48
r_work: 0.3329 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8187  Z= 0.166
  Angle     :  0.554  11.029  11087  Z= 0.291
  Chirality :  0.043   0.209   1256
  Planarity :  0.004   0.045   1411
  Dihedral  :  5.883  74.032   1114
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.31 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 16.30 %
    Favored  : 79.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.38 (0.27), residues: 997
  helix:  2.60 (0.26), residues: 390
  sheet: -0.39 (0.32), residues: 234
  loop :  0.06 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP B  82 
 HIS   0.008   0.001   HIS R 245 
 PHE   0.014   0.001   PHE A 212 
 TYR   0.018   0.001   TYR R  55 
 ARG   0.007   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04275 (  440)
  hydrogen bonds       : angle       4.53336 ( 1257)
  SS BOND              : bond        0.00113 (    1)
  SS BOND              : angle       1.82414 (    2)
  covalent geometry    : bond        0.00383 ( 8186)
  covalent geometry    : angle       0.55399 (11085)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 126
  time to evaluate  : 0.942 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 GLU cc_start: 0.8249 (mm-30) cc_final: 0.8021 (mm-30)
REVERT: A  358 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8911 (mm)
REVERT: B   16 ASN cc_start: 0.8076 (m-40) cc_final: 0.7623 (m-40)
REVERT: B   46 ARG cc_start: 0.7916 (mtt180) cc_final: 0.7402 (mtm-85)
REVERT: B  153 ASP cc_start: 0.8186 (m-30) cc_final: 0.7842 (p0)
REVERT: B  214 ARG cc_start: 0.8630 (mmm160) cc_final: 0.8349 (mmm-85)
REVERT: B  261 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8632 (mp)
REVERT: N  120 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.8424 (mp10)
REVERT: R   99 ILE cc_start: 0.8427 (pt) cc_final: 0.8205 (pp)
  outliers start: 34
  outliers final: 18
  residues processed: 144
  average time/residue: 1.1732
  time to fit residues: 179.3559
Evaluate side-chains
  141 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  358 ILE
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   92 THR
Chi-restraints excluded: chain R residue  170 THR
Chi-restraints excluded: chain R residue  277 VAL
Chi-restraints excluded: chain R residue  329 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 3 optimal weight:    2.9990
   chunk 86 optimal weight:    0.0060
   chunk 4 optimal weight:    0.7980
   chunk 43 optimal weight:    8.9990
   chunk 44 optimal weight:    4.9990
   chunk 13 optimal weight:    0.0980
   chunk 70 optimal weight:    3.9990
   chunk 73 optimal weight:    6.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.9800

-------------------------------------------------------------------------------
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 = 0.3957 r_free = 0.3957 target = 0.157187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.115808 restraints weight = 10060.166|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 2.47
r_work: 0.3369 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3252 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.1760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8187  Z= 0.123
  Angle     :  0.522  10.891  11087  Z= 0.271
  Chirality :  0.042   0.214   1256
  Planarity :  0.004   0.046   1411
  Dihedral  :  5.676  75.656   1114
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 18.15 %
    Favored  : 78.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.27), residues: 997
  helix:  2.67 (0.26), residues: 391
  sheet: -0.24 (0.32), residues: 230
  loop :  0.01 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  82 
 HIS   0.008   0.001   HIS R 245 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.023   0.001   TYR N  60 
 ARG   0.009   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03871 (  440)
  hydrogen bonds       : angle       4.34296 ( 1257)
  SS BOND              : bond        0.00048 (    1)
  SS BOND              : angle       1.65627 (    2)
  covalent geometry    : bond        0.00273 ( 8186)
  covalent geometry    : angle       0.52193 (11085)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 128
  time to evaluate  : 0.854 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  391 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.7832 (t80)
REVERT: B   16 ASN cc_start: 0.8110 (m-40) cc_final: 0.7718 (m-40)
REVERT: B   46 ARG cc_start: 0.7946 (mtt180) cc_final: 0.7411 (mtm-85)
REVERT: B  153 ASP cc_start: 0.8174 (m-30) cc_final: 0.7843 (p0)
REVERT: B  214 ARG cc_start: 0.8632 (mmm160) cc_final: 0.8367 (mmm-85)
REVERT: B  261 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8605 (mp)
REVERT: N   80 TYR cc_start: 0.8374 (m-80) cc_final: 0.8138 (m-80)
REVERT: N  120 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8410 (mp10)
REVERT: R   95 ASP cc_start: 0.8930 (m-30) cc_final: 0.8712 (m-30)
REVERT: R   99 ILE cc_start: 0.8404 (pt) cc_final: 0.8183 (pp)
REVERT: R  310 ASN cc_start: 0.7500 (m-40) cc_final: 0.7182 (m-40)
  outliers start: 31
  outliers final: 15
  residues processed: 147
  average time/residue: 1.2111
  time to fit residues: 189.4509
Evaluate side-chains
  142 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 1.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ASP
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain N residue   69 THR
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue  170 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 83 optimal weight:    0.1980
   chunk 47 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 60 optimal weight:    8.9990
   chunk 59 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9980
   chunk 19 optimal weight:    7.9990
   chunk 96 optimal weight:    0.9980
   chunk 91 optimal weight:    7.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    1.1782

-------------------------------------------------------------------------------
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 = 0.3956 r_free = 0.3956 target = 0.157135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.115695 restraints weight = 10065.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 2.46
r_work: 0.3366 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8171
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8187  Z= 0.132
  Angle     :  0.536  10.115  11087  Z= 0.276
  Chirality :  0.042   0.277   1256
  Planarity :  0.003   0.046   1411
  Dihedral  :  5.636  75.519   1114
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  4.05 %
    Allowed  : 18.27 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.49 (0.27), residues: 997
  helix:  2.69 (0.26), residues: 391
  sheet: -0.22 (0.32), residues: 230
  loop :  0.03 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  82 
 HIS   0.008   0.001   HIS R 245 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.016   0.001   TYR R 156 
 ARG   0.008   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03877 (  440)
  hydrogen bonds       : angle       4.33263 ( 1257)
  SS BOND              : bond        0.00035 (    1)
  SS BOND              : angle       1.58201 (    2)
  covalent geometry    : bond        0.00300 ( 8186)
  covalent geometry    : angle       0.53549 (11085)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 132
  time to evaluate  : 0.939 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.6912 (mptp) cc_final: 0.6680 (mptt)
REVERT: A  370 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7921 (pm20)
REVERT: A  391 TYR cc_start: 0.8643 (OUTLIER) cc_final: 0.7859 (t80)
REVERT: B   16 ASN cc_start: 0.8126 (m-40) cc_final: 0.7727 (m-40)
REVERT: B   42 ARG cc_start: 0.7340 (ttt-90) cc_final: 0.6766 (ttp80)
REVERT: B   44 GLN cc_start: 0.7995 (tt0) cc_final: 0.7628 (tt0)
REVERT: B   46 ARG cc_start: 0.7973 (mtt180) cc_final: 0.7425 (mtm-85)
REVERT: B  153 ASP cc_start: 0.8173 (m-30) cc_final: 0.7851 (p0)
REVERT: B  214 ARG cc_start: 0.8627 (mmm160) cc_final: 0.8363 (mmm-85)
REVERT: B  261 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8611 (mp)
REVERT: N   80 TYR cc_start: 0.8388 (m-80) cc_final: 0.8162 (m-80)
REVERT: N  120 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8426 (mp10)
REVERT: R   88 ARG cc_start: 0.6540 (OUTLIER) cc_final: 0.6119 (ttt180)
REVERT: R   95 ASP cc_start: 0.8917 (m-30) cc_final: 0.8699 (m-30)
REVERT: R   99 ILE cc_start: 0.8420 (pt) cc_final: 0.8202 (pp)
REVERT: R  326 PHE cc_start: 0.8438 (m-10) cc_final: 0.8190 (m-10)
  outliers start: 35
  outliers final: 18
  residues processed: 153
  average time/residue: 1.1529
  time to fit residues: 187.5087
Evaluate side-chains
  150 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  235 ILE
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   88 ARG
Chi-restraints excluded: chain R residue  108 LEU
Chi-restraints excluded: chain R residue  170 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   chunk 75 optimal weight:    0.8980
   chunk 64 optimal weight:    9.9990
   chunk 93 optimal weight:    0.9990
   chunk 3 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0010
   chunk 56 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 2 optimal weight:    2.9990
   overall best weight:    0.9590

-------------------------------------------------------------------------------
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 = 0.3963 r_free = 0.3963 target = 0.157737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.116279 restraints weight = 10173.802|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 2.48
r_work: 0.3374 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3257 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8161
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8187  Z= 0.122
  Angle     :  0.551  14.859  11087  Z= 0.278
  Chirality :  0.042   0.315   1256
  Planarity :  0.004   0.046   1411
  Dihedral  :  5.572  76.002   1114
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 4.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 19.77 %
    Favored  : 77.23 %
  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:  1.53 (0.27), residues: 997
  helix:  2.74 (0.26), residues: 391
  sheet: -0.19 (0.32), residues: 230
  loop :  0.02 (0.34), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 234 
 HIS   0.008   0.001   HIS R 245 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.016   0.001   TYR R 156 
 ARG   0.008   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03807 (  440)
  hydrogen bonds       : angle       4.29487 ( 1257)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       1.53409 (    2)
  covalent geometry    : bond        0.00272 ( 8186)
  covalent geometry    : angle       0.55056 (11085)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 0.843 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.6860 (mptp) cc_final: 0.6632 (mptt)
REVERT: A  331 ASP cc_start: 0.7916 (t0) cc_final: 0.7202 (t70)
REVERT: A  370 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7916 (pm20)
REVERT: A  391 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.7853 (t80)
REVERT: B   16 ASN cc_start: 0.8178 (m-40) cc_final: 0.7744 (m-40)
REVERT: B   46 ARG cc_start: 0.7994 (mtt180) cc_final: 0.7435 (mtm-85)
REVERT: B  153 ASP cc_start: 0.8160 (m-30) cc_final: 0.7853 (p0)
REVERT: B  214 ARG cc_start: 0.8625 (mmm160) cc_final: 0.8358 (mmm-85)
REVERT: B  261 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8604 (mp)
REVERT: N   80 TYR cc_start: 0.8363 (m-80) cc_final: 0.8028 (m-80)
REVERT: N  120 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8423 (mp10)
REVERT: R   88 ARG cc_start: 0.6516 (OUTLIER) cc_final: 0.6131 (ttt180)
REVERT: R   95 ASP cc_start: 0.8919 (m-30) cc_final: 0.8700 (m-30)
REVERT: R   99 ILE cc_start: 0.8435 (pt) cc_final: 0.8206 (pp)
REVERT: R  326 PHE cc_start: 0.8443 (m-10) cc_final: 0.8197 (m-10)
  outliers start: 26
  outliers final: 16
  residues processed: 147
  average time/residue: 1.1667
  time to fit residues: 182.0134
Evaluate side-chains
  146 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   88 ARG
Chi-restraints excluded: chain R residue  170 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 85 optimal weight:    4.9990
   chunk 32 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.1384

-------------------------------------------------------------------------------
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 = 0.3960 r_free = 0.3960 target = 0.157564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.115881 restraints weight = 10185.630|
|-----------------------------------------------------------------------------|
r_work (start): 0.3469 rms_B_bonded: 2.49
r_work: 0.3369 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3252 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8187  Z= 0.131
  Angle     :  0.544  10.990  11087  Z= 0.283
  Chirality :  0.042   0.239   1256
  Planarity :  0.003   0.046   1411
  Dihedral  :  5.552  74.950   1114
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 20.12 %
    Favored  : 76.88 %
  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:  1.48 (0.27), residues: 997
  helix:  2.66 (0.25), residues: 391
  sheet: -0.24 (0.32), residues: 232
  loop :  0.05 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.008   0.001   HIS R 245 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.024   0.002   TYR N  60 
 ARG   0.009   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03821 (  440)
  hydrogen bonds       : angle       4.30891 ( 1257)
  SS BOND              : bond        0.00041 (    1)
  SS BOND              : angle       1.52271 (    2)
  covalent geometry    : bond        0.00296 ( 8186)
  covalent geometry    : angle       0.54357 (11085)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 127
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.6858 (mptp) cc_final: 0.6630 (mptt)
REVERT: A  370 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7948 (pm20)
REVERT: B   46 ARG cc_start: 0.8012 (mtt180) cc_final: 0.7452 (mtm-85)
REVERT: B  153 ASP cc_start: 0.8172 (m-30) cc_final: 0.7856 (p0)
REVERT: B  214 ARG cc_start: 0.8611 (mmm160) cc_final: 0.8338 (mmm-85)
REVERT: B  261 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8585 (mp)
REVERT: N   80 TYR cc_start: 0.8383 (m-80) cc_final: 0.8056 (m-80)
REVERT: N  120 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8416 (mp10)
REVERT: R   88 ARG cc_start: 0.6583 (OUTLIER) cc_final: 0.6155 (ttt180)
REVERT: R   95 ASP cc_start: 0.8907 (m-30) cc_final: 0.8658 (m-30)
REVERT: R   99 ILE cc_start: 0.8431 (pt) cc_final: 0.8203 (pp)
REVERT: R  326 PHE cc_start: 0.8452 (m-10) cc_final: 0.8190 (m-10)
  outliers start: 26
  outliers final: 19
  residues processed: 143
  average time/residue: 1.2144
  time to fit residues: 184.8319
Evaluate side-chains
  149 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 0.854 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   49 ASP
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   59 LEU
Chi-restraints excluded: chain R residue   88 ARG
Chi-restraints excluded: chain R residue  170 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 96 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 85 optimal weight:    4.9990
   chunk 94 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9990
   chunk 28 optimal weight:    3.9990
   chunk 57 optimal weight:    5.9990
   chunk 79 optimal weight:    9.9990
   chunk 92 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 56 optimal weight:    7.9990
   overall best weight:    1.1386

-------------------------------------------------------------------------------
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 = 0.3959 r_free = 0.3959 target = 0.157518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.115733 restraints weight = 10293.575|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 2.50
r_work: 0.3367 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.1996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8187  Z= 0.133
  Angle     :  0.556  11.947  11087  Z= 0.287
  Chirality :  0.042   0.254   1256
  Planarity :  0.004   0.046   1411
  Dihedral  :  5.541  74.988   1114
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 20.69 %
    Favored  : 76.30 %
  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:  1.48 (0.27), residues: 997
  helix:  2.69 (0.25), residues: 391
  sheet: -0.24 (0.32), residues: 232
  loop :  0.01 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  82 
 HIS   0.008   0.001   HIS R 245 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.017   0.001   TYR R 156 
 ARG   0.009   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03857 (  440)
  hydrogen bonds       : angle       4.29506 ( 1257)
  SS BOND              : bond        0.00042 (    1)
  SS BOND              : angle       1.49480 (    2)
  covalent geometry    : bond        0.00299 ( 8186)
  covalent geometry    : angle       0.55558 (11085)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 129
  time to evaluate  : 0.855 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.6859 (mptp) cc_final: 0.6634 (mptt)
REVERT: A   58 LYS cc_start: 0.7868 (mttp) cc_final: 0.7559 (ttmm)
REVERT: A  370 GLU cc_start: 0.8250 (OUTLIER) cc_final: 0.7949 (pm20)
REVERT: A  386 MET cc_start: 0.8109 (mtm) cc_final: 0.7752 (ttm)
REVERT: B   44 GLN cc_start: 0.7771 (tt0) cc_final: 0.7474 (pm20)
REVERT: B   46 ARG cc_start: 0.8015 (mtt180) cc_final: 0.7465 (mtm-85)
REVERT: B  153 ASP cc_start: 0.8166 (m-30) cc_final: 0.7852 (p0)
REVERT: B  214 ARG cc_start: 0.8618 (mmm160) cc_final: 0.8349 (mmm-85)
REVERT: B  261 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8577 (mp)
REVERT: N   80 TYR cc_start: 0.8378 (m-80) cc_final: 0.8055 (m-80)
REVERT: N  120 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8421 (mp10)
REVERT: R   88 ARG cc_start: 0.6538 (OUTLIER) cc_final: 0.6171 (ttt180)
REVERT: R   95 ASP cc_start: 0.8896 (m-30) cc_final: 0.8668 (m-30)
REVERT: R   99 ILE cc_start: 0.8413 (pt) cc_final: 0.8180 (pp)
REVERT: R  326 PHE cc_start: 0.8455 (m-10) cc_final: 0.8193 (m-10)
  outliers start: 26
  outliers final: 19
  residues processed: 144
  average time/residue: 1.1661
  time to fit residues: 178.2586
Evaluate side-chains
  150 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 127
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain N residue  125 THR
Chi-restraints excluded: chain R residue   59 LEU
Chi-restraints excluded: chain R residue   88 ARG
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  170 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   chunk 24 optimal weight:    9.9990
   chunk 79 optimal weight:    0.2980
   chunk 76 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0970
   chunk 70 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.6182

-------------------------------------------------------------------------------
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 = 0.3979 r_free = 0.3979 target = 0.159545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.118285 restraints weight = 10055.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 2.48
r_work: 0.3400 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.3284 rms_B_bonded: 4.70 restraints_weight: 0.2500
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.2156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   8187  Z= 0.109
  Angle     :  0.557  16.170  11087  Z= 0.282
  Chirality :  0.042   0.225   1256
  Planarity :  0.003   0.046   1411
  Dihedral  :  5.423  75.378   1114
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 20.92 %
    Favored  : 76.30 %
  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:  1.50 (0.27), residues: 997
  helix:  2.76 (0.25), residues: 388
  sheet: -0.26 (0.32), residues: 235
  loop :  0.02 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.008   0.001   HIS R 245 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.016   0.001   TYR R 156 
 ARG   0.010   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03661 (  440)
  hydrogen bonds       : angle       4.17675 ( 1257)
  SS BOND              : bond        0.00030 (    1)
  SS BOND              : angle       1.45558 (    2)
  covalent geometry    : bond        0.00238 ( 8186)
  covalent geometry    : angle       0.55639 (11085)

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

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

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1994 Ramachandran restraints generated.
    997 Oldfield, 0 Emsley, 997 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
REVERT: A   17 LYS cc_start: 0.6882 (mptp) cc_final: 0.6665 (mptt)
REVERT: A   27 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7926 (mm-30)
REVERT: A   58 LYS cc_start: 0.7853 (mttp) cc_final: 0.7538 (ttmm)
REVERT: A  370 GLU cc_start: 0.8222 (OUTLIER) cc_final: 0.7923 (pm20)
REVERT: A  386 MET cc_start: 0.8078 (mtm) cc_final: 0.7718 (ttm)
REVERT: B   42 ARG cc_start: 0.7338 (ttt-90) cc_final: 0.7121 (ttt-90)
REVERT: B   46 ARG cc_start: 0.8025 (mtt180) cc_final: 0.7444 (mtm-85)
REVERT: B  153 ASP cc_start: 0.8162 (m-30) cc_final: 0.7916 (p0)
REVERT: B  214 ARG cc_start: 0.8611 (mmm160) cc_final: 0.8342 (mmm-85)
REVERT: B  261 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8524 (mp)
REVERT: G   21 MET cc_start: 0.7191 (ttt) cc_final: 0.6978 (tmm)
REVERT: N   80 TYR cc_start: 0.8371 (m-80) cc_final: 0.8058 (m-80)
REVERT: N  120 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8368 (mp10)
REVERT: R   88 ARG cc_start: 0.6434 (OUTLIER) cc_final: 0.6169 (ttt180)
REVERT: R   95 ASP cc_start: 0.8881 (m-30) cc_final: 0.8660 (m-30)
REVERT: R   99 ILE cc_start: 0.8411 (pt) cc_final: 0.8183 (pp)
REVERT: R  326 PHE cc_start: 0.8429 (m-10) cc_final: 0.8215 (m-10)
  outliers start: 24
  outliers final: 17
  residues processed: 142
  average time/residue: 1.2140
  time to fit residues: 183.2484
Evaluate side-chains
  147 residues out of total 876 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 126
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  370 GLU
Chi-restraints excluded: chain A residue  391 TYR
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  178 THR
Chi-restraints excluded: chain B residue  205 ASP
Chi-restraints excluded: chain B residue  261 LEU
Chi-restraints excluded: chain B residue  263 THR
Chi-restraints excluded: chain B residue  281 SER
Chi-restraints excluded: chain B residue  292 PHE
Chi-restraints excluded: chain B residue  325 MET
Chi-restraints excluded: chain G residue   31 SER
Chi-restraints excluded: chain N residue   78 THR
Chi-restraints excluded: chain N residue   99 CYS
Chi-restraints excluded: chain N residue  108 PHE
Chi-restraints excluded: chain N residue  120 GLN
Chi-restraints excluded: chain R residue   59 LEU
Chi-restraints excluded: chain R residue   88 ARG
Chi-restraints excluded: chain R residue  167 LEU
Chi-restraints excluded: chain R residue  170 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0370
   chunk 36 optimal weight:    5.9990
   chunk 95 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 81 optimal weight:    4.9990
   overall best weight:    1.7864

-------------------------------------------------------------------------------
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 = 0.3945 r_free = 0.3945 target = 0.156082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.114240 restraints weight = 10199.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 2.49
r_work: 0.3353 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   8187  Z= 0.170
  Angle     :  0.571  12.029  11087  Z= 0.298
  Chirality :  0.044   0.240   1256
  Planarity :  0.004   0.045   1411
  Dihedral  :  5.594  72.725   1114
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 21.16 %
    Favored  : 76.07 %
  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:  1.42 (0.27), residues: 997
  helix:  2.70 (0.25), residues: 388
  sheet: -0.35 (0.32), residues: 235
  loop :  0.01 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 234 
 HIS   0.008   0.001   HIS R 245 
 PHE   0.013   0.001   PHE A 212 
 TYR   0.025   0.002   TYR N  60 
 ARG   0.009   0.000   ARG B 197 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04047 (  440)
  hydrogen bonds       : angle       4.34327 ( 1257)
  SS BOND              : bond        0.00073 (    1)
  SS BOND              : angle       1.52709 (    2)
  covalent geometry    : bond        0.00394 ( 8186)
  covalent geometry    : angle       0.57061 (11085)
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 7424.19 seconds
wall clock time: 126 minutes 56.03 seconds (7616.03 seconds total)