Starting phenix.real_space_refine
on Sat May 10 04:36:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gt6_34245/05_2025/8gt6_34245.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gt6_34245/05_2025/8gt6_34245.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gt6_34245/05_2025/8gt6_34245.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gt6_34245/05_2025/8gt6_34245.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gt6_34245/05_2025/8gt6_34245.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gt6_34245/05_2025/8gt6_34245.cif"
  }
  resolution = 3.47
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 140 atoms to isotropic.
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: 4
    Type Number    sf(0)   Gaussians
     S      26      5.16       5
     C    3160      2.51       5
     N     859      2.21       5
     O     877      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4922
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 309, 2429
          Classifications: {'peptide': 309}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 15, 'TRANS': 293}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 23
    Chain: "B"
      Number of atoms: 2429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 309, 2429
          Classifications: {'peptide': 309}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 15, 'TRANS': 293}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 23
    Chain: "A"
      Number of atoms: 64
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 64
          Unusual residues: {'WJ6': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.93, per 1000 atoms: 0.80
  Number of scatterers: 4922
  At special positions: 0
  Unit cell: (65.331, 86.751, 102.816, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      26     16.00
     O     877      8.00
     N     859      7.00
     C    3160      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.23
  Conformation dependent library (CDL) restraints added in 592.4 milliseconds
  

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1160

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 2 sheets defined
      60.8% alpha, 7.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 36
      removed outlier: 3.621A  pdb=" N   LEU A  23 " --> pdb=" O   GLN A  19 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   VAL A  24 " --> pdb=" O   LYS A  20 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   VAL A  31 " --> pdb=" O   SER A  27 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   THR A  32 " --> pdb=" O   ALA A  28 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LEU A  33 " --> pdb=" O   CYS A  29 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU A  36 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 42 through 70
      removed outlier: 4.142A  pdb=" N   TYR A  46 " --> pdb=" O   HIS A  42 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   VAL A  48 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LEU A  49 " --> pdb=" O   ARG A  45 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLN A  55 " --> pdb=" O   LEU A  51 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER A  65 " --> pdb=" O   ASN A  61 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLU A  68 " --> pdb=" O   CYS A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 78
    Processing helix  chain 'A' and resid 80 through 88
      removed outlier: 3.852A  pdb=" N   THR A  84 " --> pdb=" O   SER A  80 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   VAL A  85 " --> pdb=" O   TYR A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 108
      removed outlier: 4.431A  pdb=" N   LEU A  98 " --> pdb=" O   ARG A  94 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ILE A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   SER A 108 " --> pdb=" O   TYR A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 134
      removed outlier: 4.114A  pdb=" N   LEU A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LEU A 126 " --> pdb=" O   ALA A 122 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   SER A 127 " --> pdb=" O   LEU A 123 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLN A 128 " --> pdb=" O   LEU A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 149
      removed outlier: 3.606A  pdb=" N   CYS A 148 " --> pdb=" O   ILE A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 167
    Processing helix  chain 'A' and resid 167 through 186
      Proline residue:  A 173  - end of helix
      removed outlier: 4.224A  pdb=" N   GLN A 176 " --> pdb=" O   LEU A 172 " (cutoff:3.500A)
      removed outlier: 5.166A  pdb=" N   ALA A 177 " --> pdb=" O   PRO A 173 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   TYR A 182 " --> pdb=" O   ARG A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 262 through 274
      removed outlier: 3.573A  pdb=" N   GLN A 266 " --> pdb=" O   ALA A 262 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   SER A 272 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 299
      removed outlier: 3.646A  pdb=" N   GLN A 287 " --> pdb=" O   ASP A 283 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LYS A 289 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU A 290 " --> pdb=" O   GLU A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 335
      removed outlier: 3.968A  pdb=" N   GLU A 328 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 36
      removed outlier: 3.621A  pdb=" N   LEU B  23 " --> pdb=" O   GLN B  19 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   VAL B  24 " --> pdb=" O   LYS B  20 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   VAL B  31 " --> pdb=" O   SER B  27 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   THR B  32 " --> pdb=" O   ALA B  28 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LEU B  33 " --> pdb=" O   CYS B  29 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   LEU B  36 " --> pdb=" O   THR B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 70
      removed outlier: 4.142A  pdb=" N   TYR B  46 " --> pdb=" O   HIS B  42 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   VAL B  48 " --> pdb=" O   LEU B  44 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LEU B  49 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLN B  55 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER B  65 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLU B  68 " --> pdb=" O   CYS B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 73 through 78
    Processing helix  chain 'B' and resid 80 through 88
      removed outlier: 3.852A  pdb=" N   THR B  84 " --> pdb=" O   SER B  80 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   VAL B  85 " --> pdb=" O   TYR B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 91 through 108
      removed outlier: 4.431A  pdb=" N   LEU B  98 " --> pdb=" O   ARG B  94 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ILE B 103 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   SER B 108 " --> pdb=" O   TYR B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 134
      removed outlier: 4.114A  pdb=" N   LEU B 124 " --> pdb=" O   MET B 120 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   LEU B 126 " --> pdb=" O   ALA B 122 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   SER B 127 " --> pdb=" O   LEU B 123 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLN B 128 " --> pdb=" O   LEU B 124 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 149
      removed outlier: 3.606A  pdb=" N   CYS B 148 " --> pdb=" O   ILE B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 156 through 167
    Processing helix  chain 'B' and resid 167 through 186
      Proline residue:  B 173  - end of helix
      removed outlier: 4.224A  pdb=" N   GLN B 176 " --> pdb=" O   LEU B 172 " (cutoff:3.500A)
      removed outlier: 5.166A  pdb=" N   ALA B 177 " --> pdb=" O   PRO B 173 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   TYR B 182 " --> pdb=" O   ARG B 178 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 262 through 274
      removed outlier: 3.573A  pdb=" N   GLN B 266 " --> pdb=" O   ALA B 262 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   SER B 272 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 280 through 299
      removed outlier: 3.646A  pdb=" N   GLN B 287 " --> pdb=" O   ASP B 283 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LYS B 289 " --> pdb=" O   LEU B 285 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU B 290 " --> pdb=" O   GLU B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 335
      removed outlier: 3.968A  pdb=" N   GLU B 328 " --> pdb=" O   SER B 324 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 244 through 249
      removed outlier: 3.538A  pdb=" N   CYS A 257 " --> pdb=" O   TYR A 245 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   GLY A 255 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   GLU A 249 " --> pdb=" O   ARG A 253 " (cutoff:3.500A)
      removed outlier: 4.962A  pdb=" N   ARG A 253 " --> pdb=" O   GLU A 249 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   LEU A 198 " --> pdb=" O   ARG A 310 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   ILE A 312 " --> pdb=" O   LEU A 198 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   ILE A 200 " --> pdb=" O   ILE A 312 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   TYR A 314 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   LEU A 202 " --> pdb=" O   TYR A 314 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 244 through 249
      removed outlier: 3.570A  pdb=" N   CYS B 257 " --> pdb=" O   TYR B 245 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   GLY B 255 " --> pdb=" O   LEU B 247 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   GLU B 249 " --> pdb=" O   ARG B 253 " (cutoff:3.500A)
      removed outlier: 4.962A  pdb=" N   ARG B 253 " --> pdb=" O   GLU B 249 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   LEU B 198 " --> pdb=" O   ARG B 310 " (cutoff:3.500A)
      removed outlier: 7.134A  pdb=" N   ILE B 312 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   ILE B 200 " --> pdb=" O   ILE B 312 " (cutoff:3.500A)
      removed outlier: 7.556A  pdb=" N   TYR B 314 " --> pdb=" O   ILE B 200 " (cutoff:3.500A)
      removed outlier: 6.189A  pdb=" N   LEU B 202 " --> pdb=" O   TYR B 314 " (cutoff:3.500A)

    222 hydrogen bonds defined for protein.
    666 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.31

  Time building geometry restraints manager: 1.41 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 778
        1.30 -     1.43: 1362
        1.43 -     1.56: 2859
        1.56 -     1.68: 0
        1.68 -     1.81: 32
  Bond restraints: 5031
  Sorted by residual:
  bond pdb=" C20 WJ6 A 401 "
       pdb=" C21 WJ6 A 401 "
    ideal  model  delta    sigma   weight residual
    1.325  1.535 -0.210 2.00e-02 2.50e+03 1.10e+02
  bond pdb=" C39 WJ6 A 401 "
       pdb=" N13 WJ6 A 401 "
    ideal  model  delta    sigma   weight residual
    1.465  1.307  0.158 2.00e-02 2.50e+03 6.27e+01
  bond pdb=" C41 WJ6 A 401 "
       pdb=" N13 WJ6 A 401 "
    ideal  model  delta    sigma   weight residual
    1.468  1.314  0.154 2.00e-02 2.50e+03 5.96e+01
  bond pdb=" C27 WJ6 A 401 "
       pdb=" C28 WJ6 A 401 "
    ideal  model  delta    sigma   weight residual
    1.410  1.259  0.151 2.00e-02 2.50e+03 5.72e+01
  bond pdb=" C44 WJ6 A 401 "
       pdb=" N13 WJ6 A 401 "
    ideal  model  delta    sigma   weight residual
    1.464  1.318  0.146 2.00e-02 2.50e+03 5.32e+01
  ... (remaining 5026 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.31: 6686
        3.31 -     6.62: 117
        6.62 -     9.93: 21
        9.93 -    13.25: 3
       13.25 -    16.56: 4
  Bond angle restraints: 6831
  Sorted by residual:
  angle pdb=" C20 WJ6 A 401 "
        pdb=" C21 WJ6 A 401 "
        pdb=" C22 WJ6 A 401 "
      ideal   model   delta    sigma   weight residual
     126.79  110.23   16.56 3.00e+00 1.11e-01 3.05e+01
  angle pdb=" C4  WJ6 A 401 "
        pdb=" N1  WJ6 A 401 "
        pdb=" C9  WJ6 A 401 "
      ideal   model   delta    sigma   weight residual
     106.05  119.41  -13.36 3.00e+00 1.11e-01 1.98e+01
  angle pdb=" C3  WJ6 A 401 "
        pdb=" C8  WJ6 A 401 "
        pdb=" C7  WJ6 A 401 "
      ideal   model   delta    sigma   weight residual
     106.52  119.75  -13.23 3.00e+00 1.11e-01 1.94e+01
  angle pdb=" C19 WJ6 A 401 "
        pdb=" C20 WJ6 A 401 "
        pdb=" C21 WJ6 A 401 "
      ideal   model   delta    sigma   weight residual
     124.95  112.69   12.26 3.00e+00 1.11e-01 1.67e+01
  angle pdb=" CA  LEU B  89 "
        pdb=" CB  LEU B  89 "
        pdb=" CG  LEU B  89 "
      ideal   model   delta    sigma   weight residual
     116.30  130.03  -13.73 3.50e+00 8.16e-02 1.54e+01
  ... (remaining 6826 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.49: 2646
       17.49 -    34.97: 280
       34.97 -    52.46: 51
       52.46 -    69.95: 22
       69.95 -    87.44: 6
  Dihedral angle restraints: 3005
    sinusoidal: 1205
      harmonic: 1800
  Sorted by residual:
  dihedral pdb=" CA  ASP B 205 "
           pdb=" C   ASP B 205 "
           pdb=" N   CYS B 206 "
           pdb=" CA  CYS B 206 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -136.05  -43.95     0      5.00e+00 4.00e-02 7.73e+01
  dihedral pdb=" CA  ASP A 205 "
           pdb=" C   ASP A 205 "
           pdb=" N   CYS A 206 "
           pdb=" CA  CYS A 206 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -136.05  -43.95     0      5.00e+00 4.00e-02 7.73e+01
  dihedral pdb=" CA  CYS A 206 "
           pdb=" C   CYS A 206 "
           pdb=" N   GLY A 207 "
           pdb=" CA  GLY A 207 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.58   19.42     0      5.00e+00 4.00e-02 1.51e+01
  ... (remaining 3002 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 496
       0.043 -    0.087: 188
       0.087 -    0.130: 50
       0.130 -    0.173: 19
       0.173 -    0.216: 13
  Chirality restraints: 766
  Sorted by residual:
  chirality pdb=" CA  ILE B 244 "
            pdb=" N   ILE B 244 "
            pdb=" C   ILE B 244 "
            pdb=" CB  ILE B 244 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CB  THR B 256 "
            pdb=" CA  THR B 256 "
            pdb=" OG1 THR B 256 "
            pdb=" CG2 THR B 256 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.21 2.00e-01 2.50e+01 1.10e+00
  chirality pdb=" CB  THR A 256 "
            pdb=" CA  THR A 256 "
            pdb=" OG1 THR A 256 "
            pdb=" CG2 THR A 256 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.21 2.00e-01 2.50e+01 1.10e+00
  ... (remaining 763 not shown)

  Planarity restraints: 859
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C19 WJ6 A 401 "    0.048 2.00e-02 2.50e+03   4.79e-02 2.29e+01
        pdb=" C20 WJ6 A 401 "   -0.050 2.00e-02 2.50e+03
        pdb=" C21 WJ6 A 401 "   -0.045 2.00e-02 2.50e+03
        pdb=" C22 WJ6 A 401 "    0.047 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 205 "   -0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" C   ASP A 205 "    0.055 2.00e-02 2.50e+03
        pdb=" O   ASP A 205 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   CYS A 206 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 205 "    0.016 2.00e-02 2.50e+03   3.18e-02 1.01e+01
        pdb=" C   ASP B 205 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   ASP B 205 "    0.021 2.00e-02 2.50e+03
        pdb=" N   CYS B 206 "    0.018 2.00e-02 2.50e+03
  ... (remaining 856 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 1630
        2.84 -     3.35: 4628
        3.35 -     3.87: 7795
        3.87 -     4.38: 9040
        4.38 -     4.90: 14963
  Nonbonded interactions: 38056
  Sorted by model distance:
  nonbonded pdb=" O   PRO B 264 "
            pdb=" OG1 THR B 267 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" O   PRO A 264 "
            pdb=" OG1 THR A 267 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" O   PHE B 269 "
            pdb=" OG  SER B 272 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" O   PHE A 269 "
            pdb=" OG  SER A 272 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" OE1 GLU A 246 "
            pdb=" CD  ARG A 253 "
     model   vdw
     2.356 3.440
  ... (remaining 38051 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 5 through 337)
  selection = chain 'B'
}

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:             0.940
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     16.260
  Find NCS groups from input model:        0.200
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
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      :  0.011   0.210   5031  Z= 0.544
  Angle     :  1.125  16.558   6831  Z= 0.535
  Chirality :  0.056   0.216    766
  Planarity :  0.007   0.061    859
  Dihedral  : 16.017  87.436   1845
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 9.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  7.53 %
    Favored  : 91.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.34 %

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: -4.60 (0.26), residues: 594
  helix: -3.69 (0.15), residues: 306
  sheet: -2.07 (0.54), residues: 74
  loop : -1.98 (0.39), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  82 
 HIS   0.004   0.001   HIS A   7 
 PHE   0.009   0.002   PHE A 291 
 TYR   0.018   0.002   TYR A  77 
 ARG   0.002   0.000   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.32829 (  222)
  hydrogen bonds       : angle      10.55409 (  666)
  covalent geometry    : bond        0.01084 ( 5031)
  covalent geometry    : angle       1.12519 ( 6831)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 140
  time to evaluate  : 0.605 
Fit side-chains
REVERT: A   56 LEU cc_start: 0.9596 (mt) cc_final: 0.9380 (mt)
REVERT: A  120 MET cc_start: 0.7522 (mpp) cc_final: 0.7286 (mpp)
REVERT: A  174 GLU cc_start: 0.7738 (tp30) cc_final: 0.7512 (tp30)
REVERT: A  223 ASP cc_start: 0.8192 (t0) cc_final: 0.7617 (t0)
REVERT: A  238 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6302 (mmt-90)
REVERT: B   56 LEU cc_start: 0.9596 (mt) cc_final: 0.9379 (mt)
REVERT: B  120 MET cc_start: 0.7526 (mpp) cc_final: 0.7289 (mpp)
REVERT: B  174 GLU cc_start: 0.7745 (tp30) cc_final: 0.7514 (tp30)
REVERT: B  218 ASN cc_start: 0.7978 (t0) cc_final: 0.7665 (t0)
REVERT: B  223 ASP cc_start: 0.8426 (t0) cc_final: 0.7851 (t0)
REVERT: B  237 ASP cc_start: 0.6115 (m-30) cc_final: 0.5220 (p0)
  outliers start: 4
  outliers final: 2
  residues processed: 142
  average time/residue: 0.1563
  time to fit residues: 28.6960
Evaluate side-chains
  128 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 125
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 ASP
Chi-restraints excluded: chain A residue  238 ARG
Chi-restraints excluded: chain A residue  244 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0770
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0670
   chunk 24 optimal weight:    0.0670
   chunk 47 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 28 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.6216

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

Flipped N/Q/H residues before XYZ refinement:
A   7 HIS
A  61 ASN
A 266 GLN
A 335 GLN
B   7 HIS
B  61 ASN
B 266 GLN
B 335 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3935 r_free = 0.3935 target = 0.126203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.094717 restraints weight = 10842.861|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 3.75
r_work: 0.3219 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.3219
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8278
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5031  Z= 0.129
  Angle     :  0.708  11.961   6831  Z= 0.328
  Chirality :  0.040   0.137    766
  Planarity :  0.005   0.044    859
  Dihedral  :  7.136  62.694    729
  Min Nonbonded Distance : 2.628

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 15.83 %
    Favored  : 82.63 %
  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: -2.56 (0.31), residues: 594
  helix: -1.59 (0.23), residues: 350
  sheet: -1.07 (0.80), residues: 46
  loop : -1.70 (0.46), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 119 
 HIS   0.001   0.000   HIS B  42 
 PHE   0.003   0.001   PHE B 269 
 TYR   0.009   0.001   TYR A 107 
 ARG   0.002   0.000   ARG A  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05249 (  222)
  hydrogen bonds       : angle       5.88428 (  666)
  covalent geometry    : bond        0.00264 ( 5031)
  covalent geometry    : angle       0.70840 ( 6831)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 151
  time to evaluate  : 0.528 
Fit side-chains
REVERT: A  119 TRP cc_start: 0.7879 (t60) cc_final: 0.7571 (t60)
REVERT: A  120 MET cc_start: 0.7894 (mpp) cc_final: 0.7491 (mpp)
REVERT: A  218 ASN cc_start: 0.7739 (t0) cc_final: 0.7532 (t0)
REVERT: A  224 LYS cc_start: 0.9119 (mmtt) cc_final: 0.8893 (mmmt)
REVERT: A  238 ARG cc_start: 0.7585 (mpp-170) cc_final: 0.7227 (mmt-90)
REVERT: A  257 CYS cc_start: 0.8317 (p) cc_final: 0.8069 (p)
REVERT: B  119 TRP cc_start: 0.7881 (t60) cc_final: 0.7576 (t60)
REVERT: B  120 MET cc_start: 0.7873 (mpp) cc_final: 0.7480 (mpp)
REVERT: B  218 ASN cc_start: 0.7776 (t0) cc_final: 0.7571 (t0)
REVERT: B  224 LYS cc_start: 0.9079 (mmtt) cc_final: 0.8823 (mmmt)
REVERT: B  237 ASP cc_start: 0.6466 (m-30) cc_final: 0.5391 (p0)
REVERT: B  238 ARG cc_start: 0.7533 (mpp-170) cc_final: 0.7142 (mtm-85)
REVERT: B  257 CYS cc_start: 0.8310 (p) cc_final: 0.8061 (p)
  outliers start: 8
  outliers final: 4
  residues processed: 154
  average time/residue: 0.1605
  time to fit residues: 31.5211
Evaluate side-chains
  138 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 134
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 CYS
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   25 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 57 optimal weight:    0.0170
   chunk 26 optimal weight:    0.9980
   chunk 3 optimal weight:   10.0000
   chunk 53 optimal weight:    2.9990
   chunk 51 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   chunk 2 optimal weight:    4.9990
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.6022

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

Flipped N/Q/H residues before XYZ refinement:
A 250 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.123788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.092771 restraints weight = 10984.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3370 rms_B_bonded: 3.65
r_work: 0.3173 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   5031  Z= 0.158
  Angle     :  0.686  11.129   6831  Z= 0.316
  Chirality :  0.042   0.171    766
  Planarity :  0.004   0.037    859
  Dihedral  :  6.561  61.356    721
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 6.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 18.92 %
    Favored  : 79.15 %
  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: -1.52 (0.33), residues: 594
  helix: -0.60 (0.24), residues: 350
  sheet: -1.26 (0.81), residues: 46
  loop : -1.44 (0.47), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  34 
 HIS   0.001   0.000   HIS B 157 
 PHE   0.005   0.001   PHE B 279 
 TYR   0.017   0.001   TYR A 104 
 ARG   0.002   0.000   ARG A 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04690 (  222)
  hydrogen bonds       : angle       5.43547 (  666)
  covalent geometry    : bond        0.00346 ( 5031)
  covalent geometry    : angle       0.68621 ( 6831)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.514 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 TRP cc_start: 0.8063 (t60) cc_final: 0.7489 (t60)
REVERT: A  218 ASN cc_start: 0.7825 (t0) cc_final: 0.7624 (t0)
REVERT: A  224 LYS cc_start: 0.9115 (mmtt) cc_final: 0.8894 (mmmt)
REVERT: A  238 ARG cc_start: 0.7646 (mpp-170) cc_final: 0.7232 (mmt-90)
REVERT: A  246 GLU cc_start: 0.5987 (pp20) cc_final: 0.5577 (pp20)
REVERT: B  119 TRP cc_start: 0.8054 (t60) cc_final: 0.7477 (t60)
REVERT: B  224 LYS cc_start: 0.9076 (mmtt) cc_final: 0.8830 (mmmt)
REVERT: B  237 ASP cc_start: 0.6617 (m-30) cc_final: 0.5642 (p0)
REVERT: B  238 ARG cc_start: 0.7557 (mpp-170) cc_final: 0.7133 (mtm-85)
REVERT: B  246 GLU cc_start: 0.6049 (pp20) cc_final: 0.5574 (pp20)
  outliers start: 10
  outliers final: 6
  residues processed: 130
  average time/residue: 0.1429
  time to fit residues: 24.7125
Evaluate side-chains
  127 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 121
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 CYS
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   33 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 33 optimal weight:    9.9990
   chunk 20 optimal weight:    6.9990
   chunk 13 optimal weight:    9.9990
   chunk 2 optimal weight:    2.9990
   chunk 52 optimal weight:    0.4980
   chunk 49 optimal weight:    7.9990
   chunk 44 optimal weight:    0.7980
   chunk 17 optimal weight:   10.0000
   chunk 28 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    1.8586

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

Flipped N/Q/H residues before XYZ refinement:
A  74 HIS
B  74 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.123141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.091738 restraints weight = 11180.790|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 3.76
r_work: 0.3148 rms_B_bonded: 4.74 restraints_weight: 0.5000
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8330
moved from start:          0.3256

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5031  Z= 0.168
  Angle     :  0.705  11.262   6831  Z= 0.316
  Chirality :  0.042   0.173    766
  Planarity :  0.004   0.036    859
  Dihedral  :  6.499  61.678    721
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 20.46 %
    Favored  : 77.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.89 (0.34), residues: 594
  helix:  0.02 (0.26), residues: 350
  sheet: -1.66 (0.76), residues: 46
  loop : -1.23 (0.50), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  34 
 HIS   0.001   0.000   HIS A 157 
 PHE   0.006   0.001   PHE A 279 
 TYR   0.018   0.001   TYR A 104 
 ARG   0.001   0.000   ARG A 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04266 (  222)
  hydrogen bonds       : angle       5.15505 (  666)
  covalent geometry    : bond        0.00377 ( 5031)
  covalent geometry    : angle       0.70508 ( 6831)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 TRP cc_start: 0.8024 (t60) cc_final: 0.7446 (t60)
REVERT: A  218 ASN cc_start: 0.7826 (t0) cc_final: 0.7597 (t0)
REVERT: A  224 LYS cc_start: 0.9133 (mmtt) cc_final: 0.8900 (mmmt)
REVERT: A  238 ARG cc_start: 0.7707 (mpp-170) cc_final: 0.7287 (mtt-85)
REVERT: B  119 TRP cc_start: 0.8025 (t60) cc_final: 0.7448 (t60)
REVERT: B  224 LYS cc_start: 0.9118 (mmtt) cc_final: 0.8862 (mmmt)
REVERT: B  237 ASP cc_start: 0.6585 (m-30) cc_final: 0.5722 (p0)
REVERT: B  238 ARG cc_start: 0.7563 (mpp-170) cc_final: 0.7211 (mtm-85)
  outliers start: 13
  outliers final: 8
  residues processed: 131
  average time/residue: 0.1422
  time to fit residues: 24.4020
Evaluate side-chains
  121 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 0.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 CYS
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  132 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 51 optimal weight:    6.9990
   chunk 45 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 9 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 26 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
A  74 HIS
B  74 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.123325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.091583 restraints weight = 11040.716|
|-----------------------------------------------------------------------------|
r_work (start): 0.3353 rms_B_bonded: 3.73
r_work: 0.3155 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8326
moved from start:          0.3431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5031  Z= 0.162
  Angle     :  0.694  11.379   6831  Z= 0.314
  Chirality :  0.042   0.160    766
  Planarity :  0.004   0.037    859
  Dihedral  :  6.441  61.424    721
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 8.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 21.43 %
    Favored  : 75.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.35), residues: 594
  helix:  0.36 (0.26), residues: 350
  sheet: -1.66 (0.77), residues: 46
  loop : -1.15 (0.49), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP B  34 
 HIS   0.001   0.001   HIS B  74 
 PHE   0.006   0.001   PHE A 279 
 TYR   0.015   0.001   TYR A 104 
 ARG   0.006   0.000   ARG B 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04024 (  222)
  hydrogen bonds       : angle       5.05140 (  666)
  covalent geometry    : bond        0.00365 ( 5031)
  covalent geometry    : angle       0.69445 ( 6831)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 0.570 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 TRP cc_start: 0.8063 (t60) cc_final: 0.7501 (t60)
REVERT: A  183 ASN cc_start: 0.8753 (m-40) cc_final: 0.8398 (m110)
REVERT: A  218 ASN cc_start: 0.7862 (t0) cc_final: 0.7659 (t0)
REVERT: A  224 LYS cc_start: 0.9148 (mmtt) cc_final: 0.8922 (mmmt)
REVERT: A  238 ARG cc_start: 0.7615 (mpp-170) cc_final: 0.7397 (mtt-85)
REVERT: B  119 TRP cc_start: 0.8050 (t60) cc_final: 0.7485 (t60)
REVERT: B  183 ASN cc_start: 0.8728 (m-40) cc_final: 0.8349 (m110)
REVERT: B  224 LYS cc_start: 0.9123 (mmtt) cc_final: 0.8863 (mmmt)
REVERT: B  237 ASP cc_start: 0.6654 (m-30) cc_final: 0.5907 (p0)
REVERT: B  238 ARG cc_start: 0.7526 (mpp-170) cc_final: 0.7304 (mtm-85)
  outliers start: 17
  outliers final: 13
  residues processed: 139
  average time/residue: 0.1402
  time to fit residues: 25.6754
Evaluate side-chains
  133 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 CYS
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  147 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 19 optimal weight:    5.9990
   chunk 20 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 26 optimal weight:    0.8980
   chunk 5 optimal weight:    7.9990
   chunk 30 optimal weight:    0.4980
   chunk 10 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
B 250 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.124463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.093520 restraints weight = 10850.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3385 rms_B_bonded: 3.66
r_work: 0.3189 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.3601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5031  Z= 0.122
  Angle     :  0.677  11.234   6831  Z= 0.301
  Chirality :  0.042   0.174    766
  Planarity :  0.004   0.038    859
  Dihedral  :  6.306  61.161    721
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 21.62 %
    Favored  : 75.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.35), residues: 594
  helix:  0.60 (0.27), residues: 350
  sheet: -3.04 (0.76), residues: 32
  loop : -1.11 (0.48), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B  34 
 HIS   0.001   0.000   HIS A  42 
 PHE   0.004   0.001   PHE A 279 
 TYR   0.014   0.001   TYR A 104 
 ARG   0.007   0.000   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03659 (  222)
  hydrogen bonds       : angle       4.86483 (  666)
  covalent geometry    : bond        0.00267 ( 5031)
  covalent geometry    : angle       0.67707 ( 6831)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 126
  time to evaluate  : 0.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 TRP cc_start: 0.8006 (t60) cc_final: 0.7465 (t60)
REVERT: A  224 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8856 (mmmt)
REVERT: A  238 ARG cc_start: 0.7793 (mpp-170) cc_final: 0.7523 (mtt-85)
REVERT: B  119 TRP cc_start: 0.7991 (t60) cc_final: 0.7447 (t60)
REVERT: B  224 LYS cc_start: 0.9104 (mmtt) cc_final: 0.8852 (mmmt)
REVERT: B  237 ASP cc_start: 0.6599 (m-30) cc_final: 0.5999 (p0)
REVERT: B  246 GLU cc_start: 0.6087 (pp20) cc_final: 0.5847 (pp20)
  outliers start: 13
  outliers final: 11
  residues processed: 133
  average time/residue: 0.1412
  time to fit residues: 25.0952
Evaluate side-chains
  127 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 CYS
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  147 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 55 optimal weight:    0.3980
   chunk 45 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 19 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 35 optimal weight:    6.9990
   chunk 47 optimal weight:   10.0000
   chunk 56 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   overall best weight:    1.4584

-------------------------------------------------------------------------------
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 = 0.3887 r_free = 0.3887 target = 0.123483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.092707 restraints weight = 10846.644|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 3.62
r_work: 0.3171 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.3711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5031  Z= 0.142
  Angle     :  0.706  11.778   6831  Z= 0.310
  Chirality :  0.043   0.186    766
  Planarity :  0.004   0.039    859
  Dihedral  :  6.287  60.902    721
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 23.17 %
    Favored  : 74.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.35), residues: 594
  helix:  0.72 (0.27), residues: 350
  sheet: -3.00 (0.77), residues: 32
  loop : -1.09 (0.48), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A 161 
 HIS   0.001   0.000   HIS A  42 
 PHE   0.006   0.001   PHE B 279 
 TYR   0.012   0.001   TYR B 104 
 ARG   0.006   0.000   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03623 (  222)
  hydrogen bonds       : angle       4.87246 (  666)
  covalent geometry    : bond        0.00320 ( 5031)
  covalent geometry    : angle       0.70575 ( 6831)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 117
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 TRP cc_start: 0.8016 (t60) cc_final: 0.7484 (t60)
REVERT: A  224 LYS cc_start: 0.9125 (mmtt) cc_final: 0.8902 (mmmt)
REVERT: A  238 ARG cc_start: 0.7804 (mpp-170) cc_final: 0.7534 (mtt-85)
REVERT: A  246 GLU cc_start: 0.6134 (pp20) cc_final: 0.5903 (pp20)
REVERT: B  119 TRP cc_start: 0.8002 (t60) cc_final: 0.7467 (t60)
REVERT: B  218 ASN cc_start: 0.7425 (t0) cc_final: 0.7068 (t0)
REVERT: B  224 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8853 (mmmt)
REVERT: B  237 ASP cc_start: 0.6669 (m-30) cc_final: 0.6033 (p0)
REVERT: B  246 GLU cc_start: 0.6145 (pp20) cc_final: 0.5900 (pp20)
  outliers start: 13
  outliers final: 13
  residues processed: 122
  average time/residue: 0.1375
  time to fit residues: 22.2895
Evaluate side-chains
  127 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 114
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 CYS
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  147 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 19 optimal weight:    5.9990
   chunk 33 optimal weight:    5.9990
   chunk 0 optimal weight:    5.9990
   chunk 42 optimal weight:    6.9990
   chunk 47 optimal weight:    0.5980
   chunk 46 optimal weight:    0.5980
   chunk 30 optimal weight:    0.3980
   chunk 9 optimal weight:    8.9990
   overall best weight:    0.7182

-------------------------------------------------------------------------------
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 = 0.3919 r_free = 0.3919 target = 0.125823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.095160 restraints weight = 10962.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3408 rms_B_bonded: 3.69
r_work: 0.3216 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.3903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5031  Z= 0.110
  Angle     :  0.689  11.904   6831  Z= 0.300
  Chirality :  0.042   0.225    766
  Planarity :  0.004   0.039    859
  Dihedral  :  6.133  60.885    721
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 24.32 %
    Favored  : 73.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.36), residues: 594
  helix:  0.86 (0.27), residues: 350
  sheet: -3.05 (0.77), residues: 32
  loop : -1.09 (0.47), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP B 161 
 HIS   0.002   0.000   HIS B  42 
 PHE   0.003   0.001   PHE A 291 
 TYR   0.012   0.001   TYR A 104 
 ARG   0.005   0.000   ARG B 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03369 (  222)
  hydrogen bonds       : angle       4.72271 (  666)
  covalent geometry    : bond        0.00234 ( 5031)
  covalent geometry    : angle       0.68861 ( 6831)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.561 
Fit side-chains
REVERT: A   30 LEU cc_start: 0.9074 (tp) cc_final: 0.8871 (mp)
REVERT: A  119 TRP cc_start: 0.7997 (t60) cc_final: 0.7544 (t60)
REVERT: A  224 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8812 (mmmt)
REVERT: A  238 ARG cc_start: 0.7766 (mpp-170) cc_final: 0.7536 (mtt-85)
REVERT: A  246 GLU cc_start: 0.6119 (pp20) cc_final: 0.5895 (pp20)
REVERT: B  119 TRP cc_start: 0.7980 (t60) cc_final: 0.7522 (t60)
REVERT: B  218 ASN cc_start: 0.7495 (t0) cc_final: 0.7126 (t0)
REVERT: B  224 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8797 (mmmt)
REVERT: B  237 ASP cc_start: 0.6564 (m-30) cc_final: 0.6066 (p0)
  outliers start: 12
  outliers final: 10
  residues processed: 128
  average time/residue: 0.1354
  time to fit residues: 23.0628
Evaluate side-chains
  124 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 114
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 CYS
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  136 LEU
Chi-restraints excluded: chain B residue  147 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 19 optimal weight:    9.9990
   chunk 20 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 49 optimal weight:    6.9990
   chunk 14 optimal weight:    2.9990
   chunk 31 optimal weight:    0.0170
   chunk 4 optimal weight:    1.9990
   chunk 8 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    1.2026

-------------------------------------------------------------------------------
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 = 0.3906 r_free = 0.3906 target = 0.125107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.094428 restraints weight = 10628.263|
|-----------------------------------------------------------------------------|
r_work (start): 0.3390 rms_B_bonded: 3.59
r_work: 0.3194 rms_B_bonded: 4.65 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.3914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5031  Z= 0.133
  Angle     :  0.738  11.688   6831  Z= 0.321
  Chirality :  0.043   0.259    766
  Planarity :  0.004   0.039    859
  Dihedral  :  6.152  60.340    721
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 24.32 %
    Favored  : 73.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.36), residues: 594
  helix:  0.81 (0.27), residues: 354
  sheet: -3.16 (0.77), residues: 32
  loop : -0.98 (0.49), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 119 
 HIS   0.001   0.000   HIS A  42 
 PHE   0.005   0.001   PHE B 117 
 TYR   0.011   0.001   TYR B 104 
 ARG   0.005   0.000   ARG B 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03539 (  222)
  hydrogen bonds       : angle       4.77081 (  666)
  covalent geometry    : bond        0.00297 ( 5031)
  covalent geometry    : angle       0.73818 ( 6831)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.570 
Fit side-chains
REVERT: A  119 TRP cc_start: 0.8151 (t60) cc_final: 0.7599 (t60)
REVERT: A  224 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8817 (mmmt)
REVERT: A  238 ARG cc_start: 0.7783 (mpp-170) cc_final: 0.7523 (mtt-85)
REVERT: A  246 GLU cc_start: 0.6060 (pp20) cc_final: 0.5784 (pp20)
REVERT: B  119 TRP cc_start: 0.8165 (t60) cc_final: 0.7618 (t60)
REVERT: B  218 ASN cc_start: 0.7548 (t0) cc_final: 0.7195 (t0)
REVERT: B  224 LYS cc_start: 0.9099 (mmtt) cc_final: 0.8833 (mmmt)
REVERT: B  237 ASP cc_start: 0.6457 (m-30) cc_final: 0.6056 (p0)
  outliers start: 10
  outliers final: 10
  residues processed: 121
  average time/residue: 0.1420
  time to fit residues: 22.9296
Evaluate side-chains
  121 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 111
  time to evaluate  : 0.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 CYS
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  147 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 17 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0020
   chunk 55 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 9 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   overall best weight:    0.6988

-------------------------------------------------------------------------------
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 = 0.3934 r_free = 0.3934 target = 0.127063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.096623 restraints weight = 10838.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 3.66
r_work: 0.3229 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.3229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.4109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5031  Z= 0.114
  Angle     :  0.732  11.831   6831  Z= 0.315
  Chirality :  0.043   0.276    766
  Planarity :  0.004   0.039    859
  Dihedral  :  6.046  60.216    721
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 23.94 %
    Favored  : 73.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.36), residues: 594
  helix:  0.90 (0.27), residues: 354
  sheet: -3.21 (0.78), residues: 32
  loop : -0.99 (0.48), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 119 
 HIS   0.002   0.000   HIS B  42 
 PHE   0.006   0.001   PHE B 117 
 TYR   0.012   0.001   TYR B 104 
 ARG   0.005   0.000   ARG B 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03359 (  222)
  hydrogen bonds       : angle       4.64828 (  666)
  covalent geometry    : bond        0.00246 ( 5031)
  covalent geometry    : angle       0.73152 ( 6831)

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

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

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1188 Ramachandran restraints generated.
    594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.538 
Fit side-chains
REVERT: A  119 TRP cc_start: 0.8148 (t60) cc_final: 0.7473 (t60)
REVERT: A  120 MET cc_start: 0.7452 (mpt) cc_final: 0.7179 (mpt)
REVERT: A  205 ASP cc_start: 0.6297 (OUTLIER) cc_final: 0.6045 (p0)
REVERT: A  224 LYS cc_start: 0.9060 (mmtt) cc_final: 0.8778 (mmmt)
REVERT: A  238 ARG cc_start: 0.7753 (mpp-170) cc_final: 0.7476 (mtt-85)
REVERT: B  119 TRP cc_start: 0.8135 (t60) cc_final: 0.7460 (t60)
REVERT: B  120 MET cc_start: 0.7423 (mpt) cc_final: 0.7154 (mpt)
REVERT: B  224 LYS cc_start: 0.9084 (mmtt) cc_final: 0.8815 (mmmt)
REVERT: B  237 ASP cc_start: 0.6458 (m-30) cc_final: 0.6117 (p0)
  outliers start: 14
  outliers final: 10
  residues processed: 128
  average time/residue: 0.1487
  time to fit residues: 24.9115
Evaluate side-chains
  123 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 112
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   12 CYS
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  132 ILE
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  205 ASP
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   25 LEU
Chi-restraints excluded: chain B residue   33 LEU
Chi-restraints excluded: chain B residue  132 ILE
Chi-restraints excluded: chain B residue  147 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 54 optimal weight:    0.7980
   chunk 6 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 28 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
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 = 0.3929 r_free = 0.3929 target = 0.126819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.096368 restraints weight = 10709.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 3.62
r_work: 0.3234 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.4189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5031  Z= 0.119
  Angle     :  0.750  11.785   6831  Z= 0.325
  Chirality :  0.044   0.273    766
  Planarity :  0.004   0.039    859
  Dihedral  :  5.992  59.480    721
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 23.94 %
    Favored  : 73.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.36), residues: 594
  helix:  0.95 (0.27), residues: 354
  sheet: -3.21 (0.78), residues: 32
  loop : -0.99 (0.48), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 119 
 HIS   0.001   0.000   HIS A  42 
 PHE   0.003   0.001   PHE B 291 
 TYR   0.011   0.001   TYR B 104 
 ARG   0.005   0.000   ARG B 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03315 (  222)
  hydrogen bonds       : angle       4.60761 (  666)
  covalent geometry    : bond        0.00265 ( 5031)
  covalent geometry    : angle       0.75020 ( 6831)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2552.20 seconds
wall clock time: 45 minutes 16.84 seconds (2716.84 seconds total)