Starting phenix.real_space_refine
on Tue Feb 11 12:28:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6izv_9758/02_2025/6izv_9758.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6izv_9758/02_2025/6izv_9758.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6izv_9758/02_2025/6izv_9758.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6izv_9758/02_2025/6izv_9758.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6izv_9758/02_2025/6izv_9758.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6izv_9758/02_2025/6izv_9758.cif"
  }
  resolution = 4.2
  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=   0.011 sd=   0.077
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     Mg      2      5.21       5
     S      20      5.16       5
     C    3578      2.51       5
     N     940      2.21       5
     O    1080      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-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5624
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "0"
      Number of atoms: 2784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 349, 2784
          Classifications: {'peptide': 349}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 339}
    Chain: "1"
      Number of atoms: 2784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 349, 2784
          Classifications: {'peptide': 349}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 9, 'TRANS': 339}
    Chain: "0"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "1"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 3.92, per 1000 atoms: 0.70
  Number of scatterers: 5624
  At special positions: 0
  Unit cell: (73.205, 83.853, 133.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      20     16.00
     P       4     15.00
     Mg      2     11.99
     O    1080      8.00
     N     940      7.00
     C    3578      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: 1.41
  Conformation dependent library (CDL) restraints added in 714.7 milliseconds
  

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1300

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 10 sheets defined
      40.1% alpha, 22.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.70
  Creating SS restraints...
    Processing helix  chain '0' and resid 38 through 44
      removed outlier: 3.703A  pdb=" N   PHE 0  42 " --> pdb=" O   SER 0  38 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   PHE 0  43 " --> pdb=" O   LEU 0  39 " (cutoff:3.500A)
    Processing helix  chain '0' and resid 70 through 76
      removed outlier: 3.525A  pdb=" N   ARG 0  75 " --> pdb=" O   GLU 0  71 " (cutoff:3.500A)
    Processing helix  chain '0' and resid 91 through 104
    Processing helix  chain '0' and resid 125 through 130
      removed outlier: 4.437A  pdb=" N   LYS 0 129 " --> pdb=" O   GLU 0 125 " (cutoff:3.500A)
    Processing helix  chain '0' and resid 130 through 141
      removed outlier: 4.271A  pdb=" N   LEU 0 134 " --> pdb=" O   GLN 0 130 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LYS 0 139 " --> pdb=" O   ASN 0 135 " (cutoff:3.500A)
    Processing helix  chain '0' and resid 169 through 175
      removed outlier: 4.352A  pdb=" N   ILE 0 173 " --> pdb=" O   GLY 0 169 " (cutoff:3.500A)
    Processing helix  chain '0' and resid 180 through 184
      removed outlier: 3.970A  pdb=" N   SER 0 183 " --> pdb=" O   ASP 0 180 " (cutoff:3.500A)
    Processing helix  chain '0' and resid 229 through 245
      removed outlier: 3.580A  pdb=" N   LYS 0 238 " --> pdb=" O   ASN 0 234 " (cutoff:3.500A)
    Processing helix  chain '0' and resid 251 through 262
      removed outlier: 3.697A  pdb=" N   CYS 0 259 " --> pdb=" O   LEU 0 255 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   GLU 0 260 " --> pdb=" O   MET 0 256 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   GLU 0 261 " --> pdb=" O   LEU 0 257 " (cutoff:3.500A)
    Processing helix  chain '0' and resid 273 through 296
      removed outlier: 4.358A  pdb=" N   LYS 0 291 " --> pdb=" O   ASN 0 287 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU 0 295 " --> pdb=" O   LYS 0 291 " (cutoff:3.500A)
    Processing helix  chain '0' and resid 297 through 301
      removed outlier: 3.667A  pdb=" N   LYS 0 300 " --> pdb=" O   GLY 0 297 " (cutoff:3.500A)
    Processing helix  chain '0' and resid 310 through 317
      removed outlier: 3.844A  pdb=" N   LYS 0 314 " --> pdb=" O   GLY 0 310 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   VAL 0 315 " --> pdb=" O   GLY 0 311 " (cutoff:3.500A)
    Processing helix  chain '0' and resid 319 through 324
      removed outlier: 3.733A  pdb=" N   LEU 0 322 " --> pdb=" O   HIS 0 319 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ILE 0 323 " --> pdb=" O   LEU 0 320 " (cutoff:3.500A)
    Processing helix  chain '0' and resid 336 through 345
    Processing helix  chain '1' and resid 38 through 44
      removed outlier: 3.702A  pdb=" N   PHE 1  42 " --> pdb=" O   SER 1  38 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   PHE 1  43 " --> pdb=" O   LEU 1  39 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 70 through 76
      removed outlier: 3.524A  pdb=" N   ARG 1  75 " --> pdb=" O   GLU 1  71 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 91 through 104
    Processing helix  chain '1' and resid 125 through 130
      removed outlier: 4.437A  pdb=" N   LYS 1 129 " --> pdb=" O   GLU 1 125 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 130 through 141
      removed outlier: 4.271A  pdb=" N   LEU 1 134 " --> pdb=" O   GLN 1 130 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LYS 1 139 " --> pdb=" O   ASN 1 135 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 169 through 175
      removed outlier: 4.352A  pdb=" N   ILE 1 173 " --> pdb=" O   GLY 1 169 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 180 through 184
      removed outlier: 3.969A  pdb=" N   SER 1 183 " --> pdb=" O   ASP 1 180 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 229 through 245
      removed outlier: 3.580A  pdb=" N   LYS 1 238 " --> pdb=" O   ASN 1 234 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 251 through 262
      removed outlier: 3.697A  pdb=" N   CYS 1 259 " --> pdb=" O   LEU 1 255 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   GLU 1 260 " --> pdb=" O   MET 1 256 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   GLU 1 261 " --> pdb=" O   LEU 1 257 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 273 through 296
      removed outlier: 4.359A  pdb=" N   LYS 1 291 " --> pdb=" O   ASN 1 287 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU 1 295 " --> pdb=" O   LYS 1 291 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 297 through 301
      removed outlier: 3.667A  pdb=" N   LYS 1 300 " --> pdb=" O   GLY 1 297 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 310 through 317
      removed outlier: 3.844A  pdb=" N   LYS 1 314 " --> pdb=" O   GLY 1 310 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   VAL 1 315 " --> pdb=" O   GLY 1 311 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 319 through 324
      removed outlier: 3.733A  pdb=" N   LEU 1 322 " --> pdb=" O   HIS 1 319 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ILE 1 323 " --> pdb=" O   LEU 1 320 " (cutoff:3.500A)
    Processing helix  chain '1' and resid 336 through 345
    Processing sheet with id=AA1, first strand: chain '0' and resid 24 through 28
      removed outlier: 6.182A  pdb=" N   TYR 0   4 " --> pdb=" O   HIS 0 117 " (cutoff:3.500A)
      removed outlier: 7.535A  pdb=" N   VAL 0 119 " --> pdb=" O   TYR 0   4 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   ILE 0   6 " --> pdb=" O   VAL 0 119 " (cutoff:3.500A)
      removed outlier: 8.852A  pdb=" N   GLY 0 121 " --> pdb=" O   ILE 0   6 " (cutoff:3.500A)
      removed outlier: 8.914A  pdb=" N   ILE 0   8 " --> pdb=" O   GLY 0 121 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   PHE 0 166 " --> pdb=" O   THR 0 120 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LEU 0 122 " --> pdb=" O   PHE 0 166 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain '0' and resid 31 through 33
    Processing sheet with id=AA3, first strand: chain '0' and resid 214 through 216
    Processing sheet with id=AA4, first strand: chain '0' and resid 214 through 216
      removed outlier: 7.422A  pdb=" N   PHE 0 190 " --> pdb=" O   SER 0 305 " (cutoff:3.500A)
      removed outlier: 7.908A  pdb=" N   MET 0 307 " --> pdb=" O   PHE 0 190 " (cutoff:3.500A)
      removed outlier: 5.820A  pdb=" N   GLY 0 192 " --> pdb=" O   MET 0 307 " (cutoff:3.500A)
      removed outlier: 7.302A  pdb=" N   ALA 0 309 " --> pdb=" O   GLY 0 192 " (cutoff:3.500A)
      removed outlier: 6.045A  pdb=" N   ILE 0 194 " --> pdb=" O   ALA 0 309 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   GLN 0 329 " --> pdb=" O   ASN 0 304 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   ILE 0 306 " --> pdb=" O   GLN 0 329 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain '0' and resid 263 through 265
      removed outlier: 3.784A  pdb=" N   ILE 0 264 " --> pdb=" O   ILE 0 271 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain '1' and resid 24 through 28
      removed outlier: 6.184A  pdb=" N   TYR 1   4 " --> pdb=" O   HIS 1 117 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   VAL 1 119 " --> pdb=" O   TYR 1   4 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   ILE 1   6 " --> pdb=" O   VAL 1 119 " (cutoff:3.500A)
      removed outlier: 8.852A  pdb=" N   GLY 1 121 " --> pdb=" O   ILE 1   6 " (cutoff:3.500A)
      removed outlier: 8.913A  pdb=" N   ILE 1   8 " --> pdb=" O   GLY 1 121 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   PHE 1 166 " --> pdb=" O   THR 1 120 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   LEU 1 122 " --> pdb=" O   PHE 1 166 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain '1' and resid 31 through 33
    Processing sheet with id=AA8, first strand: chain '1' and resid 214 through 216
    Processing sheet with id=AA9, first strand: chain '1' and resid 214 through 216
      removed outlier: 7.422A  pdb=" N   PHE 1 190 " --> pdb=" O   SER 1 305 " (cutoff:3.500A)
      removed outlier: 7.909A  pdb=" N   MET 1 307 " --> pdb=" O   PHE 1 190 " (cutoff:3.500A)
      removed outlier: 5.821A  pdb=" N   GLY 1 192 " --> pdb=" O   MET 1 307 " (cutoff:3.500A)
      removed outlier: 7.303A  pdb=" N   ALA 1 309 " --> pdb=" O   GLY 1 192 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   ILE 1 194 " --> pdb=" O   ALA 1 309 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   GLN 1 329 " --> pdb=" O   ASN 1 304 " (cutoff:3.500A)
      removed outlier: 6.380A  pdb=" N   ILE 1 306 " --> pdb=" O   GLN 1 329 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain '1' and resid 263 through 265
      removed outlier: 3.784A  pdb=" N   ILE 1 264 " --> pdb=" O   ILE 1 271 " (cutoff:3.500A)

    206 hydrogen bonds defined for protein.
    576 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: 1.66

  Time building geometry restraints manager: 1.63 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1825
        1.34 -     1.46: 1065
        1.46 -     1.57: 2790
        1.57 -     1.69: 6
        1.69 -     1.80: 36
  Bond restraints: 5722
  Sorted by residual:
  bond pdb=" C   ASN 0 162 "
       pdb=" N   ILE 0 163 "
    ideal  model  delta    sigma   weight residual
    1.334  1.316  0.018 1.29e-02 6.01e+03 1.92e+00
  bond pdb=" C   ASN 1 162 "
       pdb=" N   ILE 1 163 "
    ideal  model  delta    sigma   weight residual
    1.334  1.317  0.017 1.29e-02 6.01e+03 1.81e+00
  bond pdb=" C4  ADP 1 401 "
       pdb=" C5  ADP 1 401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.464  0.026 2.00e-02 2.50e+03 1.73e+00
  bond pdb=" C4  ADP 0 401 "
       pdb=" C5  ADP 0 401 "
    ideal  model  delta    sigma   weight residual
    1.490  1.464  0.026 2.00e-02 2.50e+03 1.69e+00
  bond pdb=" CA  VAL 1 196 "
       pdb=" CB  VAL 1 196 "
    ideal  model  delta    sigma   weight residual
    1.540  1.524  0.016 1.36e-02 5.41e+03 1.36e+00
  ... (remaining 5717 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 7295
        1.73 -     3.46: 357
        3.46 -     5.19: 38
        5.19 -     6.91: 12
        6.91 -     8.64: 10
  Bond angle restraints: 7712
  Sorted by residual:
  angle pdb=" C   SER 0 175 "
        pdb=" N   LYS 0 176 "
        pdb=" CA  LYS 0 176 "
      ideal   model   delta    sigma   weight residual
     121.54  128.77   -7.23 1.91e+00 2.74e-01 1.43e+01
  angle pdb=" C   SER 1 175 "
        pdb=" N   LYS 1 176 "
        pdb=" CA  LYS 1 176 "
      ideal   model   delta    sigma   weight residual
     121.54  128.77   -7.23 1.91e+00 2.74e-01 1.43e+01
  angle pdb=" N   ILE 0  83 "
        pdb=" CA  ILE 0  83 "
        pdb=" C   ILE 0  83 "
      ideal   model   delta    sigma   weight residual
     113.42  109.34    4.08 1.17e+00 7.31e-01 1.22e+01
  angle pdb=" N   ILE 1  83 "
        pdb=" CA  ILE 1  83 "
        pdb=" C   ILE 1  83 "
      ideal   model   delta    sigma   weight residual
     113.42  109.35    4.07 1.17e+00 7.31e-01 1.21e+01
  angle pdb=" C   PRO 0 325 "
        pdb=" N   ASN 0 326 "
        pdb=" CA  ASN 0 326 "
      ideal   model   delta    sigma   weight residual
     121.54  128.07   -6.53 1.91e+00 2.74e-01 1.17e+01
  ... (remaining 7707 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.87: 3412
       29.87 -    59.74: 37
       59.74 -    89.61: 8
       89.61 -   119.48: 0
      119.48 -   149.35: 1
  Dihedral angle restraints: 3458
    sinusoidal: 1446
      harmonic: 2012
  Sorted by residual:
  dihedral pdb=" O1B ADP 0 401 "
           pdb=" O3A ADP 0 401 "
           pdb=" PB  ADP 0 401 "
           pdb=" PA  ADP 0 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  150.64  149.35     1      2.00e+01 2.50e-03 4.46e+01
  dihedral pdb=" CA  CYS 0 259 "
           pdb=" C   CYS 0 259 "
           pdb=" N   GLU 0 260 "
           pdb=" CA  GLU 0 260 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.95   26.05     0      5.00e+00 4.00e-02 2.72e+01
  dihedral pdb=" CA  CYS 1 259 "
           pdb=" C   CYS 1 259 "
           pdb=" N   GLU 1 260 "
           pdb=" CA  GLU 1 260 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.95   26.05     0      5.00e+00 4.00e-02 2.71e+01
  ... (remaining 3455 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 594
       0.049 -    0.097: 205
       0.097 -    0.146: 54
       0.146 -    0.194: 3
       0.194 -    0.242: 4
  Chirality restraints: 860
  Sorted by residual:
  chirality pdb=" CB  VAL 0  55 "
            pdb=" CA  VAL 0  55 "
            pdb=" CG1 VAL 0  55 "
            pdb=" CG2 VAL 0  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CB  VAL 1  55 "
            pdb=" CA  VAL 1  55 "
            pdb=" CG1 VAL 1  55 "
            pdb=" CG2 VAL 1  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" CB  ILE 0  26 "
            pdb=" CA  ILE 0  26 "
            pdb=" CG1 ILE 0  26 "
            pdb=" CG2 ILE 0  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.19 2.00e-01 2.50e+01 9.42e-01
  ... (remaining 857 not shown)

  Planarity restraints: 992
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE 0 345 "   -0.016 2.00e-02 2.50e+03   1.85e-02 5.99e+00
        pdb=" CG  PHE 0 345 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 PHE 0 345 "   -0.020 2.00e-02 2.50e+03
        pdb=" CD2 PHE 0 345 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE 0 345 "    0.009 2.00e-02 2.50e+03
        pdb=" CE2 PHE 0 345 "   -0.014 2.00e-02 2.50e+03
        pdb=" CZ  PHE 0 345 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE 1 345 "    0.016 2.00e-02 2.50e+03   1.84e-02 5.91e+00
        pdb=" CG  PHE 1 345 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 PHE 1 345 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 PHE 1 345 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE1 PHE 1 345 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 PHE 1 345 "    0.014 2.00e-02 2.50e+03
        pdb=" CZ  PHE 1 345 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL 1 148 "   -0.009 2.00e-02 2.50e+03   1.90e-02 3.63e+00
        pdb=" C   VAL 1 148 "    0.033 2.00e-02 2.50e+03
        pdb=" O   VAL 1 148 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ASP 1 149 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 989 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 214
        2.72 -     3.26: 5427
        3.26 -     3.81: 8816
        3.81 -     4.35: 11096
        4.35 -     4.90: 18565
  Nonbonded interactions: 44118
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN 1 168 "
            pdb="MG    MG 1 402 "
     model   vdw
     2.170 2.250
  nonbonded pdb=" NE2 GLN 0 168 "
            pdb="MG    MG 0 402 "
     model   vdw
     2.171 2.250
  nonbonded pdb=" O1B ADP 1 401 "
            pdb="MG    MG 1 402 "
     model   vdw
     2.265 2.170
  nonbonded pdb=" O2B ADP 0 401 "
            pdb="MG    MG 0 402 "
     model   vdw
     2.265 2.170
  nonbonded pdb=" OH  TYR 1 233 "
            pdb=" O2' ADP 1 401 "
     model   vdw
     2.281 3.040
  ... (remaining 44113 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain '1'
  selection = chain '0'
}

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 group one per residue
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:             0.050
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     17.000
  Find NCS groups from input model:        0.100
  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:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   5722  Z= 0.308
  Angle     :  0.899   8.642   7712  Z= 0.495
  Chirality :  0.052   0.242    860
  Planarity :  0.005   0.038    992
  Dihedral  : 10.554 149.352   2158
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 5.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  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: -3.60 (0.28), residues: 694
  helix: -3.74 (0.19), residues: 218
  sheet: -2.24 (0.39), residues: 176
  loop : -1.09 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.004   TRP 0 296 
 HIS   0.007   0.002   HIS 1  54 
 PHE   0.038   0.003   PHE 0 345 
 TYR   0.010   0.002   TYR 1 270 
 ARG   0.003   0.001   ARG 0  37 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 0   30 ILE cc_start: 0.9504 (mt) cc_final: 0.9270 (tp)
REVERT: 0   71 GLU cc_start: 0.8287 (tp30) cc_final: 0.8014 (tp30)
REVERT: 0  130 GLN cc_start: 0.8460 (mt0) cc_final: 0.8195 (mt0)
REVERT: 0  135 ASN cc_start: 0.8874 (t0) cc_final: 0.8500 (m-40)
REVERT: 0  193 LEU cc_start: 0.9151 (tp) cc_final: 0.8758 (tp)
REVERT: 0  219 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7737 (tm-30)
REVERT: 0  220 MET cc_start: 0.8693 (mtp) cc_final: 0.7974 (mtt)
REVERT: 0  246 ASP cc_start: 0.8716 (t70) cc_final: 0.8161 (t70)
REVERT: 0  256 MET cc_start: 0.8183 (mtp) cc_final: 0.7938 (tpt)
REVERT: 0  261 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8634 (mm-30)
REVERT: 1  130 GLN cc_start: 0.8053 (mt0) cc_final: 0.7834 (mt0)
REVERT: 1  211 ASP cc_start: 0.8052 (m-30) cc_final: 0.7725 (t70)
REVERT: 1  220 MET cc_start: 0.8062 (mtp) cc_final: 0.6374 (mtp)
REVERT: 1  256 MET cc_start: 0.8304 (mtp) cc_final: 0.7920 (tpt)
REVERT: 1  319 HIS cc_start: 0.8278 (m-70) cc_final: 0.8036 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 211
  average time/residue: 0.2180
  time to fit residues: 56.3700
Evaluate side-chains
  100 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.638 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 57 optimal weight:    4.9990
   chunk 51 optimal weight:    9.9990
   chunk 28 optimal weight:   10.0000
   chunk 17 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 20 optimal weight:    7.9990
   chunk 32 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 61 optimal weight:    8.9990
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** 0  14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
0  52 ASN
0 150 HIS
** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
1  14 GLN
1 150 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.075943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.062651 restraints weight = 17323.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.064864 restraints weight = 9896.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.066439 restraints weight = 6684.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3046
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.3807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   5722  Z= 0.328
  Angle     :  0.760   6.777   7712  Z= 0.393
  Chirality :  0.050   0.305    860
  Planarity :  0.005   0.038    992
  Dihedral  :  9.004 101.451    754
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.77 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.38 %
    Favored  : 96.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.36 (0.31), residues: 694
  helix: -1.65 (0.30), residues: 212
  sheet: -2.09 (0.38), residues: 182
  loop : -0.88 (0.37), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP 1 296 
 HIS   0.009   0.002   HIS 0  54 
 PHE   0.032   0.002   PHE 1 345 
 TYR   0.017   0.002   TYR 0 270 
 ARG   0.005   0.001   ARG 1 207 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.725 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 0    4 TYR cc_start: 0.7715 (t80) cc_final: 0.7187 (t80)
REVERT: 0   60 GLU cc_start: 0.8561 (pt0) cc_final: 0.8319 (pm20)
REVERT: 0   67 TYR cc_start: 0.8888 (m-80) cc_final: 0.8437 (m-80)
REVERT: 0   71 GLU cc_start: 0.8530 (tp30) cc_final: 0.8314 (tp30)
REVERT: 0  130 GLN cc_start: 0.8524 (mt0) cc_final: 0.8133 (mt0)
REVERT: 0  135 ASN cc_start: 0.8602 (t0) cc_final: 0.7927 (m-40)
REVERT: 0  137 MET cc_start: 0.8664 (tmm) cc_final: 0.8098 (tmm)
REVERT: 0  139 LYS cc_start: 0.8445 (mtmt) cc_final: 0.7581 (ptpt)
REVERT: 0  213 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8919 (mt-10)
REVERT: 0  220 MET cc_start: 0.8368 (mtp) cc_final: 0.8040 (mtt)
REVERT: 0  246 ASP cc_start: 0.8715 (t70) cc_final: 0.8130 (t0)
REVERT: 0  327 MET cc_start: 0.8330 (ttp) cc_final: 0.8091 (ttp)
REVERT: 1   67 TYR cc_start: 0.8948 (m-80) cc_final: 0.8592 (m-80)
REVERT: 1  130 GLN cc_start: 0.8063 (mt0) cc_final: 0.7844 (mt0)
REVERT: 1  136 ASP cc_start: 0.8725 (m-30) cc_final: 0.8211 (p0)
REVERT: 1  137 MET cc_start: 0.7744 (ttm) cc_final: 0.7454 (ttm)
REVERT: 1  145 ILE cc_start: 0.8731 (tt) cc_final: 0.8528 (tt)
REVERT: 1  211 ASP cc_start: 0.8219 (m-30) cc_final: 0.7853 (t70)
REVERT: 1  220 MET cc_start: 0.7642 (mtp) cc_final: 0.7409 (mtp)
REVERT: 1  256 MET cc_start: 0.8078 (mtp) cc_final: 0.7867 (tpt)
  outliers start: 1
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1597
  time to fit residues: 26.1268
Evaluate side-chains
  78 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.640 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 56 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 16 optimal weight:   20.0000
   chunk 47 optimal weight:    5.9990
   chunk 66 optimal weight:    7.9990
   chunk 28 optimal weight:   10.0000
   chunk 58 optimal weight:    0.1980
   chunk 3 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 2 optimal weight:   20.0000
   overall best weight:    2.8388

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

Flipped N/Q/H residues before XYZ refinement:
0  14 GLN
0  52 ASN
** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.077922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.064622 restraints weight = 16854.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.066915 restraints weight = 9488.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.068532 restraints weight = 6312.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.4268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5722  Z= 0.202
  Angle     :  0.627   6.106   7712  Z= 0.322
  Chirality :  0.045   0.151    860
  Planarity :  0.003   0.031    992
  Dihedral  :  8.293  90.151    754
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  1.93 %
    Favored  : 97.91 %
  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: -1.85 (0.32), residues: 694
  helix: -0.88 (0.34), residues: 228
  sheet: -1.99 (0.39), residues: 172
  loop : -0.76 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP 1 296 
 HIS   0.005   0.001   HIS 1  54 
 PHE   0.015   0.002   PHE 1 174 
 TYR   0.008   0.001   TYR 0 317 
 ARG   0.004   0.001   ARG 0  37 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.675 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 0  130 GLN cc_start: 0.8597 (mt0) cc_final: 0.8394 (mt0)
REVERT: 0  135 ASN cc_start: 0.8635 (t0) cc_final: 0.7962 (m-40)
REVERT: 0  137 MET cc_start: 0.8760 (tmm) cc_final: 0.8069 (tmm)
REVERT: 0  139 LYS cc_start: 0.8382 (mtmt) cc_final: 0.7513 (ptpt)
REVERT: 0  193 LEU cc_start: 0.9075 (tp) cc_final: 0.8769 (tt)
REVERT: 0  213 GLU cc_start: 0.9302 (mt-10) cc_final: 0.8964 (mt-10)
REVERT: 0  218 GLN cc_start: 0.8145 (tt0) cc_final: 0.7830 (mt0)
REVERT: 0  220 MET cc_start: 0.7857 (mtp) cc_final: 0.7591 (mtt)
REVERT: 0  246 ASP cc_start: 0.8613 (t70) cc_final: 0.8022 (t0)
REVERT: 0  317 TYR cc_start: 0.9109 (t80) cc_final: 0.8816 (t80)
REVERT: 0  327 MET cc_start: 0.8372 (ttp) cc_final: 0.8147 (ttp)
REVERT: 1   67 TYR cc_start: 0.8877 (m-80) cc_final: 0.8497 (m-80)
REVERT: 1  130 GLN cc_start: 0.8100 (mt0) cc_final: 0.7503 (mt0)
REVERT: 1  136 ASP cc_start: 0.8562 (m-30) cc_final: 0.8016 (p0)
REVERT: 1  137 MET cc_start: 0.7923 (ttm) cc_final: 0.7377 (ttm)
REVERT: 1  211 ASP cc_start: 0.7949 (m-30) cc_final: 0.7618 (t70)
REVERT: 1  218 GLN cc_start: 0.8457 (tm-30) cc_final: 0.7857 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1525
  time to fit residues: 24.0341
Evaluate side-chains
  83 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 34 optimal weight:   20.0000
   chunk 38 optimal weight:    8.9990
   chunk 11 optimal weight:    0.0170
   chunk 27 optimal weight:   10.0000
   chunk 18 optimal weight:    9.9990
   chunk 9 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9980
   chunk 31 optimal weight:    9.9990
   chunk 33 optimal weight:    7.9990
   chunk 15 optimal weight:   20.0000
   chunk 49 optimal weight:    4.9990
   overall best weight:    4.0024

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

Flipped N/Q/H residues before XYZ refinement:
0  52 ASN
** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 1 126 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.074334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.061694 restraints weight = 17683.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2996 r_free = 0.2996 target = 0.063847 restraints weight = 9932.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.065387 restraints weight = 6582.355|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.4680

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5722  Z= 0.237
  Angle     :  0.643   7.645   7712  Z= 0.326
  Chirality :  0.045   0.149    860
  Planarity :  0.004   0.031    992
  Dihedral  :  7.949  88.215    754
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.89 %
    Favored  : 97.11 %
  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: -1.64 (0.32), residues: 694
  helix: -0.62 (0.36), residues: 228
  sheet: -1.94 (0.37), residues: 182
  loop : -0.61 (0.38), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP 1 296 
 HIS   0.005   0.002   HIS 1  54 
 PHE   0.017   0.002   PHE 1 345 
 TYR   0.019   0.001   TYR 1 317 
 ARG   0.004   0.001   ARG 1 299 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.696 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 0   60 GLU cc_start: 0.8423 (pp20) cc_final: 0.7318 (pm20)
REVERT: 0   71 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8188 (mm-30)
REVERT: 0  130 GLN cc_start: 0.8566 (mt0) cc_final: 0.8352 (mt0)
REVERT: 0  135 ASN cc_start: 0.8611 (t0) cc_final: 0.7924 (m-40)
REVERT: 0  137 MET cc_start: 0.8732 (tmm) cc_final: 0.8054 (tmm)
REVERT: 0  139 LYS cc_start: 0.8419 (mtmt) cc_final: 0.7571 (ptpt)
REVERT: 0  193 LEU cc_start: 0.9068 (tp) cc_final: 0.8823 (tt)
REVERT: 0  246 ASP cc_start: 0.8614 (t70) cc_final: 0.8183 (t70)
REVERT: 0  317 TYR cc_start: 0.9104 (t80) cc_final: 0.8776 (t80)
REVERT: 0  327 MET cc_start: 0.8308 (ttp) cc_final: 0.8103 (ttp)
REVERT: 1   67 TYR cc_start: 0.8852 (m-80) cc_final: 0.8501 (m-80)
REVERT: 1  130 GLN cc_start: 0.8130 (mt0) cc_final: 0.7868 (mt0)
REVERT: 1  136 ASP cc_start: 0.8619 (m-30) cc_final: 0.7952 (p0)
REVERT: 1  137 MET cc_start: 0.8086 (ttm) cc_final: 0.7484 (ttm)
REVERT: 1  211 ASP cc_start: 0.7992 (m-30) cc_final: 0.7677 (t70)
REVERT: 1  218 GLN cc_start: 0.8514 (tm-30) cc_final: 0.8239 (tm-30)
REVERT: 1  256 MET cc_start: 0.8083 (tmm) cc_final: 0.7807 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 105
  average time/residue: 0.1432
  time to fit residues: 20.7275
Evaluate side-chains
  77 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.601 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 27 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9990
   chunk 58 optimal weight:    5.9990
   chunk 34 optimal weight:   20.0000
   chunk 33 optimal weight:   10.0000
   chunk 41 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 51 optimal weight:   20.0000
   chunk 30 optimal weight:    6.9990
   chunk 6 optimal weight:    0.4980
   overall best weight:    4.2988

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

Flipped N/Q/H residues before XYZ refinement:
0  14 GLN
0  52 ASN
** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 126 HIS
1 329 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.076769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2975 r_free = 0.2975 target = 0.063426 restraints weight = 17319.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.065702 restraints weight = 9780.404|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.067313 restraints weight = 6527.364|
|-----------------------------------------------------------------------------|
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.4976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5722  Z= 0.249
  Angle     :  0.657   7.981   7712  Z= 0.333
  Chirality :  0.046   0.151    860
  Planarity :  0.003   0.025    992
  Dihedral  :  7.639  82.828    754
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 11.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.33), residues: 694
  helix: -0.43 (0.36), residues: 224
  sheet: -1.71 (0.40), residues: 170
  loop : -0.44 (0.38), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP 1 296 
 HIS   0.006   0.002   HIS 1  54 
 PHE   0.035   0.002   PHE 1 345 
 TYR   0.020   0.002   TYR 1 317 
 ARG   0.003   0.000   ARG 1  85 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.697 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 0  130 GLN cc_start: 0.8646 (mt0) cc_final: 0.8263 (mt0)
REVERT: 0  135 ASN cc_start: 0.8612 (t0) cc_final: 0.8183 (m110)
REVERT: 0  137 MET cc_start: 0.8752 (tmm) cc_final: 0.8076 (tmm)
REVERT: 0  139 LYS cc_start: 0.8570 (mtmt) cc_final: 0.8365 (mtpt)
REVERT: 0  246 ASP cc_start: 0.8657 (t70) cc_final: 0.8278 (t70)
REVERT: 0  261 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8389 (mm-30)
REVERT: 0  317 TYR cc_start: 0.9150 (t80) cc_final: 0.8779 (t80)
REVERT: 1   49 ILE cc_start: 0.8976 (tt) cc_final: 0.8681 (tt)
REVERT: 1   67 TYR cc_start: 0.8809 (m-80) cc_final: 0.8535 (m-80)
REVERT: 1  130 GLN cc_start: 0.8361 (mt0) cc_final: 0.8159 (mt0)
REVERT: 1  136 ASP cc_start: 0.8639 (m-30) cc_final: 0.7869 (p0)
REVERT: 1  142 GLU cc_start: 0.8276 (tp30) cc_final: 0.7576 (pm20)
REVERT: 1  211 ASP cc_start: 0.8079 (m-30) cc_final: 0.7816 (t70)
REVERT: 1  218 GLN cc_start: 0.8564 (tm-30) cc_final: 0.8186 (tm-30)
REVERT: 1  220 MET cc_start: 0.7790 (mtt) cc_final: 0.6794 (mtt)
REVERT: 1  236 MET cc_start: 0.9028 (mmm) cc_final: 0.8819 (mmm)
REVERT: 1  256 MET cc_start: 0.8057 (tmm) cc_final: 0.7675 (tpt)
REVERT: 1  261 GLU cc_start: 0.8465 (mm-30) cc_final: 0.8192 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.1631
  time to fit residues: 22.5244
Evaluate side-chains
  77 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 60 optimal weight:    7.9990
   chunk 24 optimal weight:   20.0000
   chunk 7 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   chunk 66 optimal weight:    9.9990
   chunk 37 optimal weight:   10.0000
   chunk 39 optimal weight:    7.9990
   chunk 51 optimal weight:    9.9990
   chunk 63 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   overall best weight:    4.5988

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

Flipped N/Q/H residues before XYZ refinement:
0  52 ASN
** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
0 319 HIS
1 329 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.076455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.063380 restraints weight = 17242.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.065684 restraints weight = 9732.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.067322 restraints weight = 6459.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.5175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5722  Z= 0.258
  Angle     :  0.646   7.272   7712  Z= 0.327
  Chirality :  0.045   0.148    860
  Planarity :  0.003   0.028    992
  Dihedral  :  7.452  79.907    754
  Min Nonbonded Distance : 1.904

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  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: -1.16 (0.33), residues: 694
  helix: -0.07 (0.37), residues: 216
  sheet: -1.72 (0.40), residues: 170
  loop : -0.50 (0.38), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP 1 296 
 HIS   0.005   0.002   HIS 1  54 
 PHE   0.014   0.002   PHE 1 174 
 TYR   0.021   0.002   TYR 1 317 
 ARG   0.006   0.001   ARG 1  85 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.681 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 0  130 GLN cc_start: 0.8636 (mt0) cc_final: 0.8276 (mt0)
REVERT: 0  135 ASN cc_start: 0.8705 (t0) cc_final: 0.8495 (m110)
REVERT: 0  137 MET cc_start: 0.8740 (tmm) cc_final: 0.8102 (tmm)
REVERT: 0  139 LYS cc_start: 0.8586 (mtmt) cc_final: 0.8367 (mtpt)
REVERT: 0  246 ASP cc_start: 0.8604 (t70) cc_final: 0.8220 (t70)
REVERT: 0  261 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8374 (mm-30)
REVERT: 0  317 TYR cc_start: 0.9225 (t80) cc_final: 0.8709 (t80)
REVERT: 1  130 GLN cc_start: 0.8389 (mt0) cc_final: 0.8186 (mt0)
REVERT: 1  136 ASP cc_start: 0.8663 (m-30) cc_final: 0.7834 (p0)
REVERT: 1  211 ASP cc_start: 0.8207 (m-30) cc_final: 0.7821 (t70)
REVERT: 1  218 GLN cc_start: 0.8606 (tm-30) cc_final: 0.8291 (tm-30)
REVERT: 1  261 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8188 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1662
  time to fit residues: 23.4385
Evaluate side-chains
  73 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 46 optimal weight:    0.7980
   chunk 6 optimal weight:    6.9990
   chunk 37 optimal weight:   20.0000
   chunk 25 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 13 optimal weight:    9.9990
   chunk 12 optimal weight:    7.9990
   chunk 61 optimal weight:    9.9990
   chunk 27 optimal weight:   20.0000
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
0  52 ASN
** 0 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
0 218 GLN
1 329 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.077300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.064184 restraints weight = 17217.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.066507 restraints weight = 9660.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.068136 restraints weight = 6387.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3087
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.5314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5722  Z= 0.219
  Angle     :  0.624   6.793   7712  Z= 0.316
  Chirality :  0.045   0.149    860
  Planarity :  0.003   0.029    992
  Dihedral  :  7.249  77.895    754
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  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: -0.97 (0.34), residues: 694
  helix:  0.14 (0.38), residues: 216
  sheet: -1.54 (0.42), residues: 166
  loop : -0.51 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP 1 296 
 HIS   0.005   0.002   HIS 1  54 
 PHE   0.014   0.002   PHE 1 345 
 TYR   0.018   0.002   TYR 1 317 
 ARG   0.006   0.000   ARG 1  85 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 0  130 GLN cc_start: 0.8639 (mt0) cc_final: 0.8264 (mt0)
REVERT: 0  137 MET cc_start: 0.8757 (tmm) cc_final: 0.8112 (tmm)
REVERT: 0  193 LEU cc_start: 0.9008 (tp) cc_final: 0.8681 (tt)
REVERT: 0  246 ASP cc_start: 0.8562 (t70) cc_final: 0.8175 (t70)
REVERT: 0  261 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8343 (mm-30)
REVERT: 0  317 TYR cc_start: 0.9235 (t80) cc_final: 0.8787 (t80)
REVERT: 1  136 ASP cc_start: 0.8620 (m-30) cc_final: 0.7823 (p0)
REVERT: 1  211 ASP cc_start: 0.8218 (m-30) cc_final: 0.7820 (t70)
REVERT: 1  218 GLN cc_start: 0.8647 (tm-30) cc_final: 0.8222 (tm-30)
REVERT: 1  256 MET cc_start: 0.7986 (tmm) cc_final: 0.7609 (tmm)
REVERT: 1  261 GLU cc_start: 0.8402 (mm-30) cc_final: 0.8104 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.1528
  time to fit residues: 21.3234
Evaluate side-chains
  72 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 30 optimal weight:   10.0000
   chunk 57 optimal weight:    0.9980
   chunk 12 optimal weight:    0.3980
   chunk 3 optimal weight:    7.9990
   chunk 26 optimal weight:    6.9990
   chunk 13 optimal weight:    2.9990
   chunk 39 optimal weight:    8.9990
   chunk 20 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
0  52 ASN
0 162 ASN
1 155 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.079480 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.066081 restraints weight = 16878.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.068515 restraints weight = 9406.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.070217 restraints weight = 6198.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.5563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5722  Z= 0.154
  Angle     :  0.610   8.970   7712  Z= 0.308
  Chirality :  0.045   0.152    860
  Planarity :  0.003   0.030    992
  Dihedral  :  6.916  74.461    754
  Min Nonbonded Distance : 2.000

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  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: -0.92 (0.33), residues: 694
  helix:  0.42 (0.38), residues: 214
  sheet: -1.47 (0.43), residues: 156
  loop : -0.74 (0.36), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP 1 296 
 HIS   0.005   0.001   HIS 1  54 
 PHE   0.012   0.001   PHE 1 141 
 TYR   0.016   0.001   TYR 1 317 
 ARG   0.006   0.001   ARG 1 299 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 0.637 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 0  130 GLN cc_start: 0.8764 (mt0) cc_final: 0.8445 (mt0)
REVERT: 0  137 MET cc_start: 0.8586 (tmm) cc_final: 0.7918 (tmm)
REVERT: 0  246 ASP cc_start: 0.8565 (t70) cc_final: 0.8104 (t70)
REVERT: 0  261 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8296 (mm-30)
REVERT: 0  317 TYR cc_start: 0.9166 (t80) cc_final: 0.8758 (t80)
REVERT: 1  136 ASP cc_start: 0.8505 (m-30) cc_final: 0.7829 (p0)
REVERT: 1  211 ASP cc_start: 0.8145 (m-30) cc_final: 0.7805 (t70)
REVERT: 1  218 GLN cc_start: 0.8490 (tm-30) cc_final: 0.7869 (tm-30)
REVERT: 1  256 MET cc_start: 0.7947 (tmm) cc_final: 0.7630 (tmm)
REVERT: 1  261 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8087 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1531
  time to fit residues: 21.4964
Evaluate side-chains
  70 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 67 optimal weight:    8.9990
   chunk 9 optimal weight:    5.9990
   chunk 36 optimal weight:   10.0000
   chunk 59 optimal weight:    9.9990
   chunk 1 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0030
   chunk 33 optimal weight:    8.9990
   chunk 56 optimal weight:   20.0000
   chunk 7 optimal weight:    0.9980
   chunk 52 optimal weight:    6.9990
   overall best weight:    1.7592

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

Flipped N/Q/H residues before XYZ refinement:
0  14 GLN
0  52 ASN
1 155 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.080204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.066798 restraints weight = 17048.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.069200 restraints weight = 9515.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.070872 restraints weight = 6288.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8194
moved from start:          0.5691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5722  Z= 0.173
  Angle     :  0.630   7.911   7712  Z= 0.315
  Chirality :  0.045   0.158    860
  Planarity :  0.003   0.030    992
  Dihedral  :  6.848  71.469    754
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.48 %
    Favored  : 99.36 %
  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: -0.89 (0.33), residues: 694
  helix:  0.45 (0.38), residues: 214
  sheet: -1.36 (0.40), residues: 172
  loop : -0.72 (0.37), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.000   TRP 1 296 
 HIS   0.005   0.001   HIS 1  54 
 PHE   0.032   0.002   PHE 1 345 
 TYR   0.023   0.001   TYR 1 317 
 ARG   0.005   0.000   ARG 1  85 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 0  130 GLN cc_start: 0.8656 (mt0) cc_final: 0.8336 (mt0)
REVERT: 0  137 MET cc_start: 0.8384 (tmm) cc_final: 0.7721 (tmm)
REVERT: 0  242 ASP cc_start: 0.8889 (m-30) cc_final: 0.8647 (m-30)
REVERT: 0  246 ASP cc_start: 0.8612 (t70) cc_final: 0.8152 (t70)
REVERT: 0  261 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8324 (mm-30)
REVERT: 0  317 TYR cc_start: 0.9148 (t80) cc_final: 0.8717 (t80)
REVERT: 1  136 ASP cc_start: 0.8475 (m-30) cc_final: 0.7830 (p0)
REVERT: 1  211 ASP cc_start: 0.8157 (m-30) cc_final: 0.7803 (t70)
REVERT: 1  218 GLN cc_start: 0.8513 (tm-30) cc_final: 0.7862 (tm-30)
REVERT: 1  256 MET cc_start: 0.7956 (tmm) cc_final: 0.7632 (tmm)
REVERT: 1  261 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8064 (mm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 97
  average time/residue: 0.1366
  time to fit residues: 18.8258
Evaluate side-chains
  76 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   chunk 23 optimal weight:    8.9990
   chunk 43 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 8 optimal weight:    8.9990
   chunk 33 optimal weight:   10.0000
   chunk 34 optimal weight:   20.0000
   chunk 45 optimal weight:    7.9990
   chunk 56 optimal weight:   20.0000
   chunk 4 optimal weight:   10.0000
   overall best weight:    5.9990

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

Flipped N/Q/H residues before XYZ refinement:
** 0  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
1 329 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.075656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.062746 restraints weight = 17845.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.064966 restraints weight = 10040.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.066528 restraints weight = 6664.915|
|-----------------------------------------------------------------------------|
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8287
moved from start:          0.5788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   5722  Z= 0.328
  Angle     :  0.724   7.736   7712  Z= 0.365
  Chirality :  0.047   0.153    860
  Planarity :  0.004   0.026    992
  Dihedral  :  7.085  71.540    754
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 13.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.93 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.04 (0.33), residues: 694
  helix:  0.18 (0.37), residues: 212
  sheet: -1.42 (0.40), residues: 170
  loop : -0.71 (0.38), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP 0 296 
 HIS   0.006   0.002   HIS 0 143 
 PHE   0.021   0.002   PHE 1 345 
 TYR   0.025   0.002   TYR 1 317 
 ARG   0.005   0.001   ARG 1  85 

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

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

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1388 Ramachandran restraints generated.
    694 Oldfield, 0 Emsley, 694 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.691 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: 0  130 GLN cc_start: 0.8621 (mt0) cc_final: 0.8254 (mt0)
REVERT: 0  137 MET cc_start: 0.8337 (tmm) cc_final: 0.7693 (tmm)
REVERT: 0  142 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6516 (mm-30)
REVERT: 0  174 PHE cc_start: 0.8052 (t80) cc_final: 0.7652 (t80)
REVERT: 0  213 GLU cc_start: 0.9304 (mt-10) cc_final: 0.8892 (mt-10)
REVERT: 0  242 ASP cc_start: 0.8968 (m-30) cc_final: 0.8749 (m-30)
REVERT: 0  261 GLU cc_start: 0.8581 (mm-30) cc_final: 0.8364 (mm-30)
REVERT: 0  317 TYR cc_start: 0.9166 (t80) cc_final: 0.8647 (t80)
REVERT: 1  130 GLN cc_start: 0.8350 (mt0) cc_final: 0.8145 (mt0)
REVERT: 1  136 ASP cc_start: 0.8616 (m-30) cc_final: 0.7790 (p0)
REVERT: 1  211 ASP cc_start: 0.8370 (m-30) cc_final: 0.8005 (t70)
REVERT: 1  218 GLN cc_start: 0.8561 (tm-30) cc_final: 0.8143 (tm-30)
REVERT: 1  225 ASP cc_start: 0.8347 (t70) cc_final: 0.8117 (t0)
REVERT: 1  256 MET cc_start: 0.8011 (tmm) cc_final: 0.7567 (tmm)
REVERT: 1  261 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8134 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1300
  time to fit residues: 15.8256
Evaluate side-chains
  69 residues out of total 622 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.618 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 50 optimal weight:    5.9990
   chunk 33 optimal weight:    9.9990
   chunk 42 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    0.0470
   chunk 18 optimal weight:    5.9990
   chunk 24 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   chunk 64 optimal weight:    1.9990
   chunk 31 optimal weight:    9.9990
   overall best weight:    2.2086

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

Flipped N/Q/H residues before XYZ refinement:
1 319 HIS
1 329 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.079358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.065856 restraints weight = 17336.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.068224 restraints weight = 9827.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.069917 restraints weight = 6544.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.5879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5722  Z= 0.181
  Angle     :  0.631   7.851   7712  Z= 0.317
  Chirality :  0.045   0.153    860
  Planarity :  0.003   0.028    992
  Dihedral  :  6.698  67.431    754
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.94 (0.33), residues: 694
  helix:  0.39 (0.38), residues: 214
  sheet: -1.27 (0.44), residues: 144
  loop : -0.90 (0.35), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP 1 296 
 HIS   0.005   0.001   HIS 1  54 
 PHE   0.019   0.001   PHE 0 141 
 TYR   0.021   0.001   TYR 1 317 
 ARG   0.005   0.001   ARG 1 299 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1583.63 seconds
wall clock time: 29 minutes 19.53 seconds (1759.53 seconds total)