Starting phenix.real_space_refine
on Fri Aug 22 15:32:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gt6_34245/08_2025/8gt6_34245.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gt6_34245/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gt6_34245/08_2025/8gt6_34245.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gt6_34245/08_2025/8gt6_34245.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gt6_34245/08_2025/8gt6_34245.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gt6_34245/08_2025/8gt6_34245.map"
  }
  resolution = 3.47
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: {'ARG:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 1}
          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: {'ARG:plan': 3, 'GLN:plan1': 1, 'GLU:plan': 1}
          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: 1.48, per 1000 atoms: 0.30
  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: 0.31
  Conformation dependent library (CDL) restraints added in 187.1 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  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: 0.15
  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: 0.46

  Time building geometry restraints manager: 0.43 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:             0.980
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.840
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.000
  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:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.210
-------------------------------------------------------------------------------
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 : 10.99
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.002   0.000   ARG A 281 
 TYR   0.018   0.002   TYR A  77 
 PHE   0.009   0.002   PHE A 291 
 TRP   0.008   0.001   TRP A  82 
 HIS   0.004   0.001   HIS A   7 

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

*********************** 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  : 0.189 
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: 0.0620
  time to fit residues: 11.3590
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  : 0.199 
-------------------------------------------------------------------------------
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 54 optimal weight:    0.9990
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    0.3980
   chunk 56 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 250 ASN
A 266 GLN
A 335 GLN
B   7 HIS
B  61 ASN
B 250 ASN
B 266 GLN
B 335 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.125415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.093306 restraints weight = 10937.319|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 3.80
r_work: 0.3196 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5031  Z= 0.136
  Angle     :  0.716  12.422   6831  Z= 0.331
  Chirality :  0.040   0.137    766
  Planarity :  0.005   0.044    859
  Dihedral  :  7.164  62.082    729
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 16.22 %
    Favored  : 82.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.53 (0.31), residues: 594
  helix: -1.57 (0.23), residues: 350
  sheet: -0.99 (0.80), residues: 46
  loop : -1.68 (0.46), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  71 
 TYR   0.009   0.001   TYR A 107 
 PHE   0.004   0.001   PHE B 323 
 TRP   0.009   0.001   TRP A 119 
 HIS   0.001   0.000   HIS A 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 5031)
  covalent geometry    : angle       0.71603 ( 6831)
  hydrogen bonds       : bond        0.05397 (  222)
  hydrogen bonds       : angle       5.92950 (  666)

*********************** 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
  151 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 143
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A  120 MET cc_start: 0.7917 (mpp) cc_final: 0.7516 (mpp)
REVERT: A  149 GLU cc_start: 0.8459 (mp0) cc_final: 0.8111 (mp0)
REVERT: A  218 ASN cc_start: 0.7751 (t0) cc_final: 0.7544 (t0)
REVERT: A  224 LYS cc_start: 0.9122 (mmtt) cc_final: 0.8896 (mmmt)
REVERT: A  237 ASP cc_start: 0.5598 (m-30) cc_final: 0.5285 (p0)
REVERT: A  238 ARG cc_start: 0.7615 (mpp-170) cc_final: 0.7180 (mmt-90)
REVERT: A  257 CYS cc_start: 0.8344 (p) cc_final: 0.8090 (p)
REVERT: B  120 MET cc_start: 0.7894 (mpp) cc_final: 0.7502 (mpp)
REVERT: B  149 GLU cc_start: 0.8462 (mp0) cc_final: 0.8105 (mp0)
REVERT: B  218 ASN cc_start: 0.7771 (t0) cc_final: 0.7567 (t0)
REVERT: B  224 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8841 (mmmt)
REVERT: B  237 ASP cc_start: 0.6419 (m-30) cc_final: 0.5315 (p0)
REVERT: B  238 ARG cc_start: 0.7572 (mpp-170) cc_final: 0.7186 (mtm-85)
  outliers start: 8
  outliers final: 4
  residues processed: 146
  average time/residue: 0.0621
  time to fit residues: 11.7128
Evaluate side-chains
  135 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 131
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
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 34 optimal weight:    5.9990
   chunk 6 optimal weight:    7.9990
   chunk 48 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   chunk 3 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 21 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9980
   overall best weight:    1.4984

-------------------------------------------------------------------------------
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 = 0.3892 r_free = 0.3892 target = 0.123658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.092281 restraints weight = 11007.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 3.66
r_work: 0.3172 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.3024

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= 0.153
  Angle     :  0.683  11.087   6831  Z= 0.315
  Chirality :  0.042   0.191    766
  Planarity :  0.004   0.037    859
  Dihedral  :  6.533  61.066    721
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 19.11 %
    Favored  : 78.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.45 (0.33), residues: 594
  helix: -0.54 (0.24), residues: 350
  sheet: -1.26 (0.82), residues: 46
  loop : -1.40 (0.47), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 238 
 TYR   0.017   0.001   TYR A 104 
 PHE   0.005   0.001   PHE A 279 
 TRP   0.007   0.001   TRP A  34 
 HIS   0.001   0.000   HIS B 157 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 5031)
  covalent geometry    : angle       0.68349 ( 6831)
  hydrogen bonds       : bond        0.04663 (  222)
  hydrogen bonds       : angle       5.38152 (  666)

*********************** 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
  136 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 TRP cc_start: 0.8081 (t60) cc_final: 0.7513 (t60)
REVERT: A  218 ASN cc_start: 0.7823 (t0) cc_final: 0.7619 (t0)
REVERT: A  224 LYS cc_start: 0.9115 (mmtt) cc_final: 0.8897 (mmmt)
REVERT: A  237 ASP cc_start: 0.5611 (m-30) cc_final: 0.5347 (p0)
REVERT: A  238 ARG cc_start: 0.7620 (mpp-170) cc_final: 0.7163 (mtt-85)
REVERT: A  246 GLU cc_start: 0.6067 (pp20) cc_final: 0.5691 (pp20)
REVERT: B  119 TRP cc_start: 0.8063 (t60) cc_final: 0.7484 (t60)
REVERT: B  218 ASN cc_start: 0.7805 (t0) cc_final: 0.7587 (t0)
REVERT: B  224 LYS cc_start: 0.9082 (mmtt) cc_final: 0.8833 (mmmt)
REVERT: B  237 ASP cc_start: 0.6639 (m-30) cc_final: 0.5652 (p0)
REVERT: B  238 ARG cc_start: 0.7586 (mpp-170) cc_final: 0.7217 (mtm-85)
REVERT: B  246 GLU cc_start: 0.6207 (pp20) cc_final: 0.5717 (pp20)
  outliers start: 10
  outliers final: 6
  residues processed: 132
  average time/residue: 0.0613
  time to fit residues: 10.8514
Evaluate side-chains
  131 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 125
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
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 35 optimal weight:    4.9990
   chunk 46 optimal weight:    0.9990
   chunk 59 optimal weight:    8.9990
   chunk 23 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0570
   chunk 39 optimal weight:    0.0870
   chunk 32 optimal weight:    0.9980
   chunk 48 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 13 optimal weight:    8.9990
   overall best weight:    0.5678

-------------------------------------------------------------------------------
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 = 0.3926 r_free = 0.3926 target = 0.125994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.095398 restraints weight = 10883.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 3.68
r_work: 0.3231 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.3410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5031  Z= 0.105
  Angle     :  0.666  11.636   6831  Z= 0.292
  Chirality :  0.040   0.169    766
  Planarity :  0.004   0.034    859
  Dihedral  :  6.244  61.342    721
  Min Nonbonded Distance : 2.636

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 20.27 %
    Favored  : 77.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.86 (0.34), residues: 594
  helix:  0.08 (0.26), residues: 350
  sheet: -1.87 (0.74), residues: 46
  loop : -1.23 (0.47), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  14 
 TYR   0.019   0.001   TYR A 104 
 PHE   0.003   0.001   PHE A 105 
 TRP   0.007   0.001   TRP B 161 
 HIS   0.001   0.000   HIS B  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 5031)
  covalent geometry    : angle       0.66579 ( 6831)
  hydrogen bonds       : bond        0.03806 (  222)
  hydrogen bonds       : angle       4.82176 (  666)

*********************** 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
  158 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 147
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  119 TRP cc_start: 0.7955 (t60) cc_final: 0.7385 (t60)
REVERT: A  218 ASN cc_start: 0.7696 (t0) cc_final: 0.7473 (t0)
REVERT: A  224 LYS cc_start: 0.9114 (mmtt) cc_final: 0.8808 (mmmt)
REVERT: A  238 ARG cc_start: 0.7726 (mpp-170) cc_final: 0.7398 (mtt-85)
REVERT: A  246 GLU cc_start: 0.6075 (pp20) cc_final: 0.5849 (pp20)
REVERT: B  119 TRP cc_start: 0.7944 (t60) cc_final: 0.7369 (t60)
REVERT: B  224 LYS cc_start: 0.9072 (mmtt) cc_final: 0.8782 (mmmt)
REVERT: B  237 ASP cc_start: 0.6620 (m-30) cc_final: 0.5823 (p0)
REVERT: B  238 ARG cc_start: 0.7573 (mpp-170) cc_final: 0.7237 (mtm-85)
REVERT: B  246 GLU cc_start: 0.6148 (pp20) cc_final: 0.5850 (pp20)
  outliers start: 11
  outliers final: 5
  residues processed: 156
  average time/residue: 0.0599
  time to fit residues: 12.3544
Evaluate side-chains
  135 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 130
  time to evaluate  : 0.131 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 18 optimal weight:    0.4980
   chunk 57 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 58 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 29 optimal weight:   10.0000
   overall best weight:    1.4988

-------------------------------------------------------------------------------
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
B 218 ASN
B 242 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.124284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.092691 restraints weight = 11019.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3373 rms_B_bonded: 3.74
r_work: 0.3176 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8316
moved from start:          0.3466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5031  Z= 0.145
  Angle     :  0.698  11.447   6831  Z= 0.307
  Chirality :  0.043   0.211    766
  Planarity :  0.004   0.035    859
  Dihedral  :  6.288  60.738    721
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 21.43 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.61 (0.34), residues: 594
  helix:  0.41 (0.27), residues: 350
  sheet: -3.05 (0.78), residues: 32
  loop : -1.23 (0.46), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 281 
 TYR   0.015   0.001   TYR A 104 
 PHE   0.022   0.002   PHE A 117 
 TRP   0.005   0.001   TRP A  34 
 HIS   0.001   0.001   HIS B  72 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 5031)
  covalent geometry    : angle       0.69833 ( 6831)
  hydrogen bonds       : bond        0.03768 (  222)
  hydrogen bonds       : angle       4.88402 (  666)

*********************** 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
  136 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.198 
Fit side-chains
REVERT: A   72 HIS cc_start: 0.7991 (m90) cc_final: 0.7672 (m-70)
REVERT: A  119 TRP cc_start: 0.8030 (t60) cc_final: 0.7542 (t60)
REVERT: A  218 ASN cc_start: 0.7772 (t0) cc_final: 0.7564 (t0)
REVERT: A  224 LYS cc_start: 0.9126 (mmtt) cc_final: 0.8913 (mmmt)
REVERT: A  238 ARG cc_start: 0.7733 (mpp-170) cc_final: 0.7286 (mtt-85)
REVERT: B   72 HIS cc_start: 0.7948 (m90) cc_final: 0.7635 (m-70)
REVERT: B  119 TRP cc_start: 0.8022 (t60) cc_final: 0.7533 (t60)
REVERT: B  224 LYS cc_start: 0.9079 (mmtt) cc_final: 0.8827 (mmmt)
REVERT: B  237 ASP cc_start: 0.6705 (m-30) cc_final: 0.5833 (p0)
REVERT: B  238 ARG cc_start: 0.7588 (mpp-170) cc_final: 0.7362 (mtm-85)
  outliers start: 14
  outliers final: 10
  residues processed: 131
  average time/residue: 0.0473
  time to fit residues: 8.3936
Evaluate side-chains
  127 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 12 optimal weight:    0.2980
   chunk 42 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 19 optimal weight:    8.9990
   chunk 54 optimal weight:    0.4980
   chunk 7 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 25 optimal weight:    6.9990
   chunk 33 optimal weight:    8.9990
   chunk 3 optimal weight:   10.0000
   overall best weight:    0.7384

-------------------------------------------------------------------------------
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 = 0.3928 r_free = 0.3928 target = 0.126233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.095243 restraints weight = 11065.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 3.70
r_work: 0.3222 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.3222
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.3718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5031  Z= 0.113
  Angle     :  0.683  11.444   6831  Z= 0.301
  Chirality :  0.042   0.174    766
  Planarity :  0.004   0.035    859
  Dihedral  :  6.173  61.104    721
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.16 %
    Allowed  : 24.71 %
    Favored  : 74.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.46 (0.35), residues: 594
  helix:  0.55 (0.27), residues: 350
  sheet: -3.15 (0.78), residues: 32
  loop : -1.15 (0.46), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 281 
 TYR   0.014   0.001   TYR B 104 
 PHE   0.004   0.001   PHE A 117 
 TRP   0.006   0.001   TRP A 119 
 HIS   0.001   0.000   HIS B  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 5031)
  covalent geometry    : angle       0.68282 ( 6831)
  hydrogen bonds       : bond        0.03526 (  222)
  hydrogen bonds       : angle       4.71805 (  666)

*********************** 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
  138 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 132
  time to evaluate  : 0.199 
Fit side-chains
REVERT: A  119 TRP cc_start: 0.8107 (t60) cc_final: 0.7509 (t60)
REVERT: A  224 LYS cc_start: 0.9111 (mmtt) cc_final: 0.8815 (mmmt)
REVERT: A  238 ARG cc_start: 0.7747 (mpp-170) cc_final: 0.7431 (mtt-85)
REVERT: B  119 TRP cc_start: 0.8100 (t60) cc_final: 0.7499 (t60)
REVERT: B  224 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8780 (mmmt)
REVERT: B  237 ASP cc_start: 0.6805 (m-30) cc_final: 0.5943 (p0)
  outliers start: 6
  outliers final: 5
  residues processed: 135
  average time/residue: 0.0531
  time to fit residues: 9.6791
Evaluate side-chains
  126 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 121
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
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  258 VAL
Chi-restraints excluded: chain B residue   12 CYS
Chi-restraints excluded: chain B residue   25 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   chunk 43 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 52 optimal weight:    4.9990
   chunk 54 optimal weight:    0.7980
   chunk 2 optimal weight:    9.9990
   chunk 30 optimal weight:    0.0060
   overall best weight:    1.1602

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.125459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.093939 restraints weight = 10899.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.3382 rms_B_bonded: 3.77
r_work: 0.3185 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.3774

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= 0.127
  Angle     :  0.698  11.286   6831  Z= 0.305
  Chirality :  0.043   0.223    766
  Planarity :  0.004   0.036    859
  Dihedral  :  6.162  60.506    721
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 23.17 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.33 (0.35), residues: 594
  helix:  0.65 (0.27), residues: 350
  sheet: -3.15 (0.78), residues: 32
  loop : -1.09 (0.47), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 238 
 TYR   0.012   0.001   TYR A 104 
 PHE   0.028   0.002   PHE B 117 
 TRP   0.007   0.001   TRP B 119 
 HIS   0.001   0.000   HIS B 332 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 5031)
  covalent geometry    : angle       0.69822 ( 6831)
  hydrogen bonds       : bond        0.03531 (  222)
  hydrogen bonds       : angle       4.76130 (  666)

*********************** 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
  133 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 0.164 
Fit side-chains
REVERT: A  119 TRP cc_start: 0.8162 (t60) cc_final: 0.7495 (t60)
REVERT: A  224 LYS cc_start: 0.9119 (mmtt) cc_final: 0.8821 (mmmt)
REVERT: A  238 ARG cc_start: 0.7775 (mpp-170) cc_final: 0.7477 (mtt-85)
REVERT: A  246 GLU cc_start: 0.6068 (pp20) cc_final: 0.5788 (pp20)
REVERT: B   72 HIS cc_start: 0.7987 (m90) cc_final: 0.7659 (m-70)
REVERT: B  119 TRP cc_start: 0.8164 (t60) cc_final: 0.7889 (t60)
REVERT: B  224 LYS cc_start: 0.9088 (mmtt) cc_final: 0.8829 (mmmt)
REVERT: B  237 ASP cc_start: 0.6806 (m-30) cc_final: 0.5965 (p0)
REVERT: B  246 GLU cc_start: 0.6148 (pp20) cc_final: 0.5855 (pp20)
  outliers start: 11
  outliers final: 10
  residues processed: 128
  average time/residue: 0.0534
  time to fit residues: 9.1946
Evaluate side-chains
  128 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 118
  time to evaluate  : 0.139 
-------------------------------------------------------------------------------
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 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 43 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 6 optimal weight:    7.9990
   chunk 26 optimal weight:    0.9990
   chunk 32 optimal weight:    0.5980
   chunk 29 optimal weight:    0.0070
   chunk 11 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.7202

-------------------------------------------------------------------------------
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 = 0.126954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.096082 restraints weight = 10962.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.3429 rms_B_bonded: 3.67
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: 0.8269
moved from start:          0.3974

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= 0.111
  Angle     :  0.692  11.424   6831  Z= 0.301
  Chirality :  0.042   0.253    766
  Planarity :  0.004   0.036    859
  Dihedral  :  6.062  60.480    721
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 22.97 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.35), residues: 594
  helix:  0.75 (0.27), residues: 350
  sheet: -3.20 (0.78), residues: 32
  loop : -1.04 (0.47), residues: 212

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

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 ( 5031)
  covalent geometry    : angle       0.69208 ( 6831)
  hydrogen bonds       : bond        0.03350 (  222)
  hydrogen bonds       : angle       4.67394 (  666)

*********************** 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
  135 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A   72 HIS cc_start: 0.7951 (m90) cc_final: 0.7635 (m-70)
REVERT: A  119 TRP cc_start: 0.8133 (t60) cc_final: 0.7393 (t60)
REVERT: A  224 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8798 (mmmt)
REVERT: A  238 ARG cc_start: 0.7764 (mpp-170) cc_final: 0.7519 (mtt-85)
REVERT: A  246 GLU cc_start: 0.5975 (pp20) cc_final: 0.5755 (pp20)
REVERT: B  119 TRP cc_start: 0.8132 (t60) cc_final: 0.7387 (t60)
REVERT: B  224 LYS cc_start: 0.9072 (mmtt) cc_final: 0.8778 (mmmt)
REVERT: B  237 ASP cc_start: 0.6688 (m-30) cc_final: 0.6177 (p0)
  outliers start: 12
  outliers final: 11
  residues processed: 130
  average time/residue: 0.0547
  time to fit residues: 9.5780
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  : 0.183 
-------------------------------------------------------------------------------
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 A residue  261 TYR
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 49 optimal weight:    0.0270
   chunk 44 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 37 optimal weight:    0.2980
   chunk 55 optimal weight:    0.8980
   chunk 21 optimal weight:    8.9990
   chunk 10 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 50 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.6438

-------------------------------------------------------------------------------
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 = 0.3941 r_free = 0.3941 target = 0.127401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.096550 restraints weight = 10829.189|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 3.67
r_work: 0.3236 rms_B_bonded: 4.67 restraints_weight: 0.5000
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.4085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   5031  Z= 0.113
  Angle     :  0.738  12.404   6831  Z= 0.316
  Chirality :  0.043   0.280    766
  Planarity :  0.004   0.036    859
  Dihedral  :  5.981  59.460    721
  Min Nonbonded Distance : 2.633

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 22.78 %
    Favored  : 74.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.21 (0.36), residues: 594
  helix:  0.64 (0.27), residues: 354
  sheet: -2.50 (0.63), residues: 60
  loop : -0.59 (0.54), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 238 
 TYR   0.011   0.001   TYR B 104 
 PHE   0.003   0.001   PHE A 279 
 TRP   0.005   0.001   TRP A 119 
 HIS   0.001   0.000   HIS B  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 5031)
  covalent geometry    : angle       0.73757 ( 6831)
  hydrogen bonds       : bond        0.03296 (  222)
  hydrogen bonds       : angle       4.71255 (  666)

*********************** 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
  131 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A  119 TRP cc_start: 0.8148 (t60) cc_final: 0.7426 (t60)
REVERT: A  120 MET cc_start: 0.7201 (mpt) cc_final: 0.6979 (mpt)
REVERT: A  224 LYS cc_start: 0.9089 (mmtt) cc_final: 0.8791 (mmmt)
REVERT: A  238 ARG cc_start: 0.7758 (mpp-170) cc_final: 0.7528 (mtt-85)
REVERT: B  119 TRP cc_start: 0.8141 (t60) cc_final: 0.7414 (t60)
REVERT: B  120 MET cc_start: 0.7175 (mpt) cc_final: 0.6955 (mpt)
REVERT: B  224 LYS cc_start: 0.9067 (mmtt) cc_final: 0.8787 (mmmt)
REVERT: B  237 ASP cc_start: 0.6581 (m-30) cc_final: 0.6151 (p0)
REVERT: B  271 MET cc_start: 0.8058 (mtp) cc_final: 0.7762 (mtp)
  outliers start: 12
  outliers final: 12
  residues processed: 125
  average time/residue: 0.0533
  time to fit residues: 8.9640
Evaluate side-chains
  128 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 116
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
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  136 LEU
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  261 TYR
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  147 VAL
Chi-restraints excluded: chain B residue  261 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 53 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 29 optimal weight:    5.9990
   chunk 37 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 50 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0040
   overall best weight:    1.0994

-------------------------------------------------------------------------------
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 = 0.3927 r_free = 0.3927 target = 0.126336 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.094891 restraints weight = 11109.578|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 3.76
r_work: 0.3205 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.4063

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= 0.131
  Angle     :  0.776  13.852   6831  Z= 0.330
  Chirality :  0.045   0.289    766
  Planarity :  0.004   0.036    859
  Dihedral  :  6.059  60.088    721
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 23.75 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.22 (0.36), residues: 594
  helix:  0.60 (0.26), residues: 354
  sheet: -2.44 (0.65), residues: 60
  loop : -0.55 (0.54), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 238 
 TYR   0.011   0.001   TYR A 104 
 PHE   0.003   0.001   PHE A 221 
 TRP   0.006   0.001   TRP B 161 
 HIS   0.001   0.000   HIS B  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 5031)
  covalent geometry    : angle       0.77627 ( 6831)
  hydrogen bonds       : bond        0.03355 (  222)
  hydrogen bonds       : angle       4.82307 (  666)

********************** 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
  125 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.170 
Fit side-chains
REVERT: A  119 TRP cc_start: 0.8179 (t60) cc_final: 0.7783 (t60)
REVERT: A  224 LYS cc_start: 0.9120 (mmtt) cc_final: 0.8824 (mmmt)
REVERT: A  238 ARG cc_start: 0.7791 (mpp-170) cc_final: 0.7536 (mtt-85)
REVERT: B  119 TRP cc_start: 0.8175 (t60) cc_final: 0.7779 (t60)
REVERT: B  224 LYS cc_start: 0.9081 (mmtt) cc_final: 0.8792 (mmmt)
REVERT: B  237 ASP cc_start: 0.6580 (m-30) cc_final: 0.6171 (p0)
REVERT: B  246 GLU cc_start: 0.6137 (pp20) cc_final: 0.5782 (pp20)
  outliers start: 10
  outliers final: 9
  residues processed: 122
  average time/residue: 0.0494
  time to fit residues: 8.2830
Evaluate side-chains
  121 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 112
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
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  147 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 45 optimal weight:    0.9990
   chunk 52 optimal weight:    9.9990
   chunk 57 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 5 optimal weight:    8.9990
   chunk 18 optimal weight:    4.9990
   chunk 56 optimal weight:    0.5980
   chunk 55 optimal weight:    0.7980
   chunk 19 optimal weight:    9.9990
   chunk 42 optimal weight:    0.0070
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.6600

-------------------------------------------------------------------------------
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 = 0.3947 r_free = 0.3947 target = 0.127428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.096412 restraints weight = 10831.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 3.68
r_work: 0.3244 rms_B_bonded: 4.73 restraints_weight: 0.5000
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.4244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5031  Z= 0.115
  Angle     :  0.763  11.809   6831  Z= 0.322
  Chirality :  0.044   0.287    766
  Planarity :  0.004   0.036    859
  Dihedral  :  5.946  59.617    721
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 23.36 %
    Favored  : 74.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.23 (0.35), residues: 594
  helix:  0.67 (0.27), residues: 354
  sheet: -3.18 (0.78), residues: 32
  loop : -0.93 (0.48), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 238 
 TYR   0.011   0.001   TYR A 104 
 PHE   0.004   0.001   PHE A 279 
 TRP   0.006   0.001   TRP A 161 
 HIS   0.001   0.000   HIS A  42 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 5031)
  covalent geometry    : angle       0.76272 ( 6831)
  hydrogen bonds       : bond        0.03247 (  222)
  hydrogen bonds       : angle       4.75140 (  666)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1255.82 seconds
wall clock time: 22 minutes 11.21 seconds (1331.21 seconds total)