Starting phenix.real_space_refine
on Thu Feb 13 04:49:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zyz_60584/02_2025/8zyz_60584.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zyz_60584/02_2025/8zyz_60584.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zyz_60584/02_2025/8zyz_60584.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zyz_60584/02_2025/8zyz_60584.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zyz_60584/02_2025/8zyz_60584.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zyz_60584/02_2025/8zyz_60584.cif"
  }
  resolution = 3.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.016
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      78      5.16       5
     Na      2      4.78       5
     C    5745      2.51       5
     N    1471      2.21       5
     O    1622      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8918
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "A"
      Number of atoms: 361
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 46, 361
          Classifications: {'peptide': 46}
          Link IDs: {'PTRANS': 1, 'TRANS': 44}
    Chain: "B"
      Number of atoms: 368
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 47, 368
          Classifications: {'peptide': 47}
          Link IDs: {'PTRANS': 1, 'TRANS': 45}
    Chain: "C"
      Number of atoms: 1606
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 211, 1601
          Classifications: {'peptide': 211}
          Link IDs: {'PTRANS': 6, 'TRANS': 204}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 211, 1601
          Classifications: {'peptide': 211}
          Link IDs: {'PTRANS': 6, 'TRANS': 204}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1616
    Chain: "D"
      Number of atoms: 1621
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 214, 1621
          Classifications: {'peptide': 214}
          Link IDs: {'PTRANS': 6, 'TRANS': 207}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1613
          Classifications: {'peptide': 213}
          Link IDs: {'PTRANS': 6, 'TRANS': 206}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1729
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1729
          Classifications: {'peptide': 230}
          Link IDs: {'PTRANS': 6, 'TRANS': 223}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 1613
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1613
          Classifications: {'peptide': 213}
          Link IDs: {'PTRANS': 6, 'TRANS': 206}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NA': 1}
          Classifications: {'undetermined': 1}
    Chain: "G"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' NA': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
    Chain: "E"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 6.24, per 1000 atoms: 0.70
  Number of scatterers: 8918
  At special positions: 0
  Unit cell: (102.6, 98.55, 106.65, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      78     16.00
     Na      2     11.00
     O    1622      8.00
     N    1471      7.00
     C    5745      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.58
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2140

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 1 sheets defined
      91.1% alpha, 0.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 39
      removed outlier: 3.820A  pdb=" N   GLY A  20 " --> pdb=" O   PRO A  16 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   PHE A  39 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 59
    Processing helix  chain 'B' and resid 18 through 39
      removed outlier: 3.943A  pdb=" N   PHE B  39 " --> pdb=" O   LEU B  35 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 58
    Processing helix  chain 'C' and resid 31 through 50
    Processing helix  chain 'C' and resid 51 through 68
      removed outlier: 3.548A  pdb=" N   PHE C  68 " --> pdb=" O   LYS C  64 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 72 through 87
    Processing helix  chain 'C' and resid 102 through 114
      removed outlier: 3.512A  pdb=" N   ASP C 114 " --> pdb=" O   ASP C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 168
      removed outlier: 3.500A  pdb=" N   VAL C 121 " --> pdb=" O   ASP C 117 " (cutoff:3.500A)
      Proline residue:  C 151  - end of helix
    Processing helix  chain 'C' and resid 171 through 173
      No H-bonds generated for 'chain 'C' and resid 171 through 173'
    Processing helix  chain 'C' and resid 174 through 195
      removed outlier: 3.623A  pdb=" N   ALA C 178 " --> pdb=" O   ALA C 174 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   MET C 179 " --> pdb=" O   ILE C 175 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ALA C 180 " --> pdb=" O   GLY C 176 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   THR C 185 " --> pdb=" O   VAL C 181 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   THR C 186 " --> pdb=" O   ALA C 182 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 196 through 228
    Processing helix  chain 'C' and resid 230 through 240
    Processing helix  chain 'C' and resid 241 through 244
      removed outlier: 3.609A  pdb=" N   GLU C 244 " --> pdb=" O   TYR C 241 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 241 through 244'
    Processing helix  chain 'D' and resid 31 through 48
    Processing helix  chain 'D' and resid 51 through 68
    Processing helix  chain 'D' and resid 72 through 85
      removed outlier: 3.989A  pdb=" N   ASP D  85 " --> pdb=" O   VAL D  81 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 102 through 115
    Processing helix  chain 'D' and resid 117 through 167
      Proline residue:  D 151  - end of helix
    Processing helix  chain 'D' and resid 175 through 196
      removed outlier: 3.771A  pdb=" N   VAL D 181 " --> pdb=" O   PRO D 177 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   ALA D 182 " --> pdb=" O   ALA D 178 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 196 through 228
    Processing helix  chain 'D' and resid 230 through 239
      removed outlier: 4.067A  pdb=" N   ILE D 234 " --> pdb=" O   ASN D 230 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   ASP D 235 " --> pdb=" O   PRO D 231 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   SER D 236 " --> pdb=" O   ARG D 232 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   TYR D 237 " --> pdb=" O   VAL D 233 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   LYS D 239 " --> pdb=" O   ASP D 235 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 244 through 250
      removed outlier: 3.523A  pdb=" N   ARG D 247 " --> pdb=" O   GLU D 244 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LEU D 249 " --> pdb=" O   LYS D 246 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 27 through 50
      removed outlier: 3.795A  pdb=" N   ASP E  31 " --> pdb=" O   GLY E  27 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   MET E  48 " --> pdb=" O   PHE E  44 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LYS E  49 " --> pdb=" O   VAL E  45 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 68
    Processing helix  chain 'E' and resid 72 through 87
    Processing helix  chain 'E' and resid 102 through 114
    Processing helix  chain 'E' and resid 117 through 168
      Proline residue:  E 151  - end of helix
    Processing helix  chain 'E' and resid 171 through 196
      removed outlier: 3.552A  pdb=" N   ILE E 175 " --> pdb=" O   ASP E 171 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   GLY E 176 " --> pdb=" O   PRO E 172 " (cutoff:3.500A)
      Proline residue:  E 177  - end of helix
    Processing helix  chain 'E' and resid 196 through 228
    Processing helix  chain 'E' and resid 230 through 240
    Processing helix  chain 'E' and resid 241 through 244
    Processing helix  chain 'F' and resid 4 through 23
    Processing helix  chain 'F' and resid 32 through 47
      removed outlier: 3.536A  pdb=" N   VAL F  38 " --> pdb=" O   SER F  34 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 51 through 68
    Processing helix  chain 'F' and resid 72 through 87
    Processing helix  chain 'F' and resid 102 through 115
    Processing helix  chain 'F' and resid 117 through 167
      Proline residue:  F 151  - end of helix
    Processing helix  chain 'F' and resid 171 through 173
      No H-bonds generated for 'chain 'F' and resid 171 through 173'
    Processing helix  chain 'F' and resid 174 through 195
      removed outlier: 3.734A  pdb=" N   THR F 185 " --> pdb=" O   VAL F 181 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   THR F 186 " --> pdb=" O   ALA F 182 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 196 through 227
    Processing helix  chain 'F' and resid 230 through 243
    Processing helix  chain 'F' and resid 244 through 251
      removed outlier: 3.700A  pdb=" N   ARG F 247 " --> pdb=" O   GLU F 244 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ILE F 251 " --> pdb=" O   ALA F 248 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 28 through 50
    Processing helix  chain 'G' and resid 51 through 67
    Processing helix  chain 'G' and resid 72 through 87
    Processing helix  chain 'G' and resid 102 through 115
      removed outlier: 3.610A  pdb=" N   ASP G 114 " --> pdb=" O   ASP G 110 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 118 through 169
      Proline residue:  G 151  - end of helix
    Processing helix  chain 'G' and resid 171 through 196
      removed outlier: 3.565A  pdb=" N   GLY G 176 " --> pdb=" O   PRO G 172 " (cutoff:3.500A)
      Proline residue:  G 177  - end of helix
    Processing helix  chain 'G' and resid 196 through 228
    Processing helix  chain 'G' and resid 230 through 243
      removed outlier: 3.937A  pdb=" N   ASN G 240 " --> pdb=" O   SER G 236 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   TYR G 241 " --> pdb=" O   TYR G 237 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ASN G 243 " --> pdb=" O   LYS G 239 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 244 through 249
      removed outlier: 3.791A  pdb=" N   ARG G 247 " --> pdb=" O   GLU G 244 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 40 through 42

    812 hydrogen bonds defined for protein.
    2411 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.73

  Time building geometry restraints manager: 2.89 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2896
        1.34 -     1.46: 1892
        1.46 -     1.59: 4093
        1.59 -     1.71: 0
        1.71 -     1.83: 154
  Bond restraints: 9035
  Sorted by residual:
  bond pdb=" CB  MET C 179 "
       pdb=" CG  MET C 179 "
    ideal  model  delta    sigma   weight residual
    1.520  1.483  0.037 3.00e-02 1.11e+03 1.51e+00
  bond pdb=" CB  ASN G 243 "
       pdb=" CG  ASN G 243 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 2.50e-02 1.60e+03 1.24e+00
  bond pdb=" CB  MET D 179 "
       pdb=" CG  MET D 179 "
    ideal  model  delta    sigma   weight residual
    1.520  1.490  0.030 3.00e-02 1.11e+03 1.02e+00
  bond pdb=" CB  THR C 158 "
       pdb=" CG2 THR C 158 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.30e-01
  bond pdb=" CB  ILE C  61 "
       pdb=" CG2 ILE C  61 "
    ideal  model  delta    sigma   weight residual
    1.521  1.490  0.031 3.30e-02 9.18e+02 8.86e-01
  ... (remaining 9030 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.58: 12099
        2.58 -     5.17: 62
        5.17 -     7.75: 6
        7.75 -    10.34: 1
       10.34 -    12.92: 1
  Bond angle restraints: 12169
  Sorted by residual:
  angle pdb=" CB  MET G  83 "
        pdb=" CG  MET G  83 "
        pdb=" SD  MET G  83 "
      ideal   model   delta    sigma   weight residual
     112.70  125.62  -12.92 3.00e+00 1.11e-01 1.86e+01
  angle pdb=" CG  MET G  83 "
        pdb=" SD  MET G  83 "
        pdb=" CE  MET G  83 "
      ideal   model   delta    sigma   weight residual
     100.90  106.34   -5.44 2.20e+00 2.07e-01 6.12e+00
  angle pdb=" CB  MET F  52 "
        pdb=" CG  MET F  52 "
        pdb=" SD  MET F  52 "
      ideal   model   delta    sigma   weight residual
     112.70  120.06   -7.36 3.00e+00 1.11e-01 6.02e+00
  angle pdb=" C   ASP E 148 "
        pdb=" N   VAL E 149 "
        pdb=" CA  VAL E 149 "
      ideal   model   delta    sigma   weight residual
     121.55  118.18    3.37 1.42e+00 4.96e-01 5.63e+00
  angle pdb=" CB  MET B  30 "
        pdb=" CG  MET B  30 "
        pdb=" SD  MET B  30 "
      ideal   model   delta    sigma   weight residual
     112.70  105.71    6.99 3.00e+00 1.11e-01 5.43e+00
  ... (remaining 12164 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.90: 4577
       17.90 -    35.79: 655
       35.79 -    53.69: 175
       53.69 -    71.59: 32
       71.59 -    89.48: 11
  Dihedral angle restraints: 5450
    sinusoidal: 2132
      harmonic: 3318
  Sorted by residual:
  dihedral pdb=" CA  ASP D 133 "
           pdb=" CB  ASP D 133 "
           pdb=" CG  ASP D 133 "
           pdb=" OD1 ASP D 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.40   59.40     1      2.00e+01 2.50e-03 1.18e+01
  dihedral pdb=" CB  GLU C 211 "
           pdb=" CG  GLU C 211 "
           pdb=" CD  GLU C 211 "
           pdb=" OE1 GLU C 211 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.48   89.48     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CA  ASP F  31 "
           pdb=" CB  ASP F  31 "
           pdb=" CG  ASP F  31 "
           pdb=" OD1 ASP F  31 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -85.55   55.55     1      2.00e+01 2.50e-03 1.04e+01
  ... (remaining 5447 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 909
       0.029 -    0.059: 370
       0.059 -    0.088: 119
       0.088 -    0.118: 44
       0.118 -    0.147: 5
  Chirality restraints: 1447
  Sorted by residual:
  chirality pdb=" CA  ASP E 148 "
            pdb=" N   ASP E 148 "
            pdb=" C   ASP E 148 "
            pdb=" CB  ASP E 148 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.40e-01
  chirality pdb=" CA  ASN G 243 "
            pdb=" N   ASN G 243 "
            pdb=" C   ASN G 243 "
            pdb=" CB  ASN G 243 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.25e-01
  chirality pdb=" CA  PRO D 151 "
            pdb=" N   PRO D 151 "
            pdb=" C   PRO D 151 "
            pdb=" CB  PRO D 151 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.21e-01
  ... (remaining 1444 not shown)

  Planarity restraints: 1544
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN G 243 "    0.014 2.00e-02 2.50e+03   2.77e-02 7.67e+00
        pdb=" C   ASN G 243 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   ASN G 243 "    0.018 2.00e-02 2.50e+03
        pdb=" N   GLU G 244 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP C 148 "   -0.009 2.00e-02 2.50e+03   1.79e-02 3.20e+00
        pdb=" CG  ASP C 148 "    0.031 2.00e-02 2.50e+03
        pdb=" OD1 ASP C 148 "   -0.011 2.00e-02 2.50e+03
        pdb=" OD2 ASP C 148 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B  15 "   -0.028 5.00e-02 4.00e+02   4.21e-02 2.84e+00
        pdb=" N   PRO B  16 "    0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO B  16 "   -0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B  16 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 1541 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 50
        2.65 -     3.21: 8360
        3.21 -     3.77: 14464
        3.77 -     4.34: 18178
        4.34 -     4.90: 31349
  Nonbonded interactions: 72401
  Sorted by model distance:
  nonbonded pdb=" OG1 THR E 158 "
            pdb=" OG1 THR E 186 "
     model   vdw
     2.087 3.040
  nonbonded pdb=" O   PHE D  29 "
            pdb=" OH  TYR D 188 "
     model   vdw
     2.146 3.040
  nonbonded pdb=" O   ASN G 243 "
            pdb=" ND2 ASN G 243 "
     model   vdw
     2.157 3.120
  nonbonded pdb=" OD1 ASP E  31 "
            pdb=" OH  TYR E 188 "
     model   vdw
     2.166 3.040
  nonbonded pdb=" O   LEU A  35 "
            pdb=" OG  SER A  38 "
     model   vdw
     2.201 3.040
  ... (remaining 72396 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'
  selection = (chain 'B' and resid 14 through 59)
}
ncs_group {
  reference = (chain 'C' and (resid 29 through 154 or resid 156 through 250))
  selection = (chain 'D' and (resid 29 through 154 or resid 156 through 250))
  selection = (chain 'E' and (resid 29 through 154 or resid 156 through 250))
  selection = (chain 'F' and (resid 15 through 16 or resid 31 through 154 or resid 156 through \ 
 250))
  selection = (chain 'G' and (resid 29 through 154 or resid 156 through 250))
}

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=0.39 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:             0.320
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     24.260
  Find NCS groups from input model:        0.460
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.860
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
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      :  0.004   0.039   9035  Z= 0.223
  Angle     :  0.530  12.923  12169  Z= 0.271
  Chirality :  0.037   0.147   1447
  Planarity :  0.004   0.042   1544
  Dihedral  : 18.051  89.484   3310
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  : 29.12 %
    Favored  : 70.78 %
  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:  3.30 (0.25), residues: 1149
  helix:  2.52 (0.16), residues: 996
  sheet:  None (None), residues: 0
  loop : -0.18 (0.54), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.002   TRP A  18 
 HIS   0.004   0.001   HIS E 136 
 PHE   0.014   0.002   PHE E 143 
 TYR   0.008   0.001   TYR D 241 
 ARG   0.009   0.001   ARG G 216 

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.898 
Fit side-chains
REVERT: B   30 MET cc_start: 0.8053 (ttt) cc_final: 0.7768 (ttm)
REVERT: E   75 ASP cc_start: 0.8422 (m-30) cc_final: 0.7674 (t70)
  outliers start: 1
  outliers final: 1
  residues processed: 125
  average time/residue: 0.2028
  time to fit residues: 36.5161
Evaluate side-chains
  127 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain G residue  243 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    1.9990
   chunk 87 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 58 optimal weight:    8.9990
   chunk 46 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9980
   chunk 34 optimal weight:    7.9990
   chunk 54 optimal weight:    7.9990
   chunk 67 optimal weight:    4.9990
   chunk 104 optimal weight:    0.6980
   overall best weight:    1.3386

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.183249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 98)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.120622 restraints weight = 10321.647|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 1.82
r_work: 0.3051 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3051
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3020
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3020 r_free = 0.3020    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3020 r_free = 0.3020    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3020
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.0590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9035  Z= 0.197
  Angle     :  0.478   7.584  12169  Z= 0.248
  Chirality :  0.036   0.122   1447
  Planarity :  0.004   0.042   1544
  Dihedral  :  3.441  13.392   1225
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 26.67 %
    Favored  : 71.94 %
  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:  3.64 (0.25), residues: 1149
  helix:  2.73 (0.16), residues: 1005
  sheet:  None (None), residues: 0
  loop : -0.18 (0.55), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A  18 
 HIS   0.003   0.001   HIS E 136 
 PHE   0.018   0.001   PHE A  39 
 TYR   0.006   0.001   TYR D 241 
 ARG   0.003   0.000   ARG G 216 

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.971 
Fit side-chains
REVERT: C   56 PHE cc_start: 0.7102 (m-10) cc_final: 0.6736 (m-80)
REVERT: C   67 MET cc_start: 0.7695 (ptt) cc_final: 0.7173 (ptp)
REVERT: C  239 LYS cc_start: 0.7473 (mtpp) cc_final: 0.7210 (mtpp)
REVERT: E   75 ASP cc_start: 0.8553 (m-30) cc_final: 0.7510 (t70)
  outliers start: 13
  outliers final: 6
  residues processed: 136
  average time/residue: 0.1948
  time to fit residues: 38.6572
Evaluate side-chains
  131 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 125
  time to evaluate  : 0.915 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  205 SER
Chi-restraints excluded: chain F residue  242 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 2 optimal weight:    0.4980
   chunk 55 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0870
   chunk 80 optimal weight:   10.0000
   chunk 97 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.7164

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.185258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.132366 restraints weight = 15425.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3406 rms_B_bonded: 1.82
r_work: 0.3118 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2962 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2909
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2909 r_free = 0.2909    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2909
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.0859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9035  Z= 0.145
  Angle     :  0.439   8.066  12169  Z= 0.228
  Chirality :  0.035   0.113   1447
  Planarity :  0.003   0.041   1544
  Dihedral  :  3.310  13.099   1223
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 26.99 %
    Favored  : 71.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.99 (0.25), residues: 1149
  helix:  2.97 (0.16), residues: 1008
  sheet:  None (None), residues: 0
  loop : -0.16 (0.56), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  18 
 HIS   0.002   0.001   HIS E 136 
 PHE   0.015   0.001   PHE A  39 
 TYR   0.004   0.001   TYR F 188 
 ARG   0.004   0.000   ARG G 216 

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 133
  time to evaluate  : 0.993 
Fit side-chains
REVERT: C   67 MET cc_start: 0.7721 (ptt) cc_final: 0.7181 (ptp)
REVERT: C  239 LYS cc_start: 0.7313 (mtpp) cc_final: 0.7047 (mtpp)
REVERT: E   75 ASP cc_start: 0.8556 (m-30) cc_final: 0.7554 (t70)
REVERT: F  148 ASP cc_start: 0.8609 (m-30) cc_final: 0.8260 (m-30)
REVERT: F  207 ARG cc_start: 0.8962 (tpt-90) cc_final: 0.8635 (tpp80)
REVERT: G  135 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.7354 (mtp180)
  outliers start: 13
  outliers final: 8
  residues processed: 141
  average time/residue: 0.1837
  time to fit residues: 37.8072
Evaluate side-chains
  134 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 125
  time to evaluate  : 1.006 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain C residue  165 MET
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain E residue  105 MET
Chi-restraints excluded: chain E residue  205 SER
Chi-restraints excluded: chain G residue  135 ARG
Chi-restraints excluded: chain G residue  175 ILE
Chi-restraints excluded: chain G residue  183 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 15 optimal weight:    7.9990
   chunk 82 optimal weight:    3.9990
   chunk 92 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 102 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   chunk 112 optimal weight:    2.9990
   chunk 111 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 79 optimal weight:    5.9990
   overall best weight:    2.5988

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.179765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 93)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.119942 restraints weight = 10386.476|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 1.86
r_work: 0.2989 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.2989
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2951
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2951 r_free = 0.2951    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2951 r_free = 0.2951    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2951
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7699
moved from start:          0.1048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   9035  Z= 0.310
  Angle     :  0.539   7.438  12169  Z= 0.278
  Chirality :  0.040   0.135   1447
  Planarity :  0.004   0.046   1544
  Dihedral  :  3.596  13.500   1223
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 25.82 %
    Favored  : 71.73 %
  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:  3.44 (0.25), residues: 1149
  helix:  2.59 (0.16), residues: 1008
  sheet:  None (None), residues: 0
  loop : -0.24 (0.56), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.002   TRP A  18 
 HIS   0.005   0.002   HIS D 136 
 PHE   0.018   0.002   PHE A  39 
 TYR   0.009   0.001   TYR D 241 
 ARG   0.004   0.001   ARG G 216 

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 129
  time to evaluate  : 0.982 
Fit side-chains
   revert: symmetry clash
REVERT: B   56 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.6558 (m-10)
REVERT: C   67 MET cc_start: 0.7758 (ptt) cc_final: 0.7175 (ptp)
REVERT: C  239 LYS cc_start: 0.7336 (mtpp) cc_final: 0.7086 (mtpp)
REVERT: E   67 MET cc_start: 0.7403 (mmt) cc_final: 0.7166 (ttm)
REVERT: G   83 MET cc_start: 0.5159 (mmp) cc_final: 0.4758 (mmm)
REVERT: G  135 ARG cc_start: 0.7391 (OUTLIER) cc_final: 0.7048 (mtp180)
  outliers start: 23
  outliers final: 19
  residues processed: 145
  average time/residue: 0.2005
  time to fit residues: 41.6276
Evaluate side-chains
  146 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain B residue   56 PHE
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  113 VAL
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain C residue  175 ILE
Chi-restraints excluded: chain C residue  205 SER
Chi-restraints excluded: chain D residue   36 LEU
Chi-restraints excluded: chain D residue   51 THR
Chi-restraints excluded: chain D residue   83 MET
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  205 SER
Chi-restraints excluded: chain E residue  250 GLU
Chi-restraints excluded: chain F residue  212 THR
Chi-restraints excluded: chain G residue  135 ARG
Chi-restraints excluded: chain G residue  175 ILE
Chi-restraints excluded: chain G residue  183 LEU
Chi-restraints excluded: chain G residue  212 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 26 optimal weight:    0.3980
   chunk 37 optimal weight:    8.9990
   chunk 108 optimal weight:    0.9990
   chunk 107 optimal weight:    0.6980
   chunk 102 optimal weight:   10.0000
   chunk 6 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 48 optimal weight:    7.9990
   chunk 9 optimal weight:    0.6980
   chunk 61 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 106 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.184073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.128879 restraints weight = 11641.230|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 1.52
r_work: 0.3126 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2972 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2972
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2923
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2923 r_free = 0.2923    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2923
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7764
moved from start:          0.1138

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9035  Z= 0.147
  Angle     :  0.436   6.030  12169  Z= 0.229
  Chirality :  0.035   0.115   1447
  Planarity :  0.003   0.042   1544
  Dihedral  :  3.365  12.724   1223
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 26.89 %
    Favored  : 71.09 %
  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:  3.92 (0.25), residues: 1149
  helix:  2.91 (0.16), residues: 1012
  sheet:  None (None), residues: 0
  loop : -0.17 (0.55), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  18 
 HIS   0.002   0.001   HIS D 136 
 PHE   0.015   0.001   PHE A  39 
 TYR   0.005   0.001   TYR F 188 
 ARG   0.003   0.000   ARG G 216 

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.936 
Fit side-chains
REVERT: B   56 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.6703 (m-10)
REVERT: C   56 PHE cc_start: 0.7366 (m-10) cc_final: 0.7031 (m-80)
REVERT: C   67 MET cc_start: 0.7145 (ptt) cc_final: 0.6553 (ptp)
REVERT: C  239 LYS cc_start: 0.7252 (mtpp) cc_final: 0.7048 (mtpp)
REVERT: D  179 MET cc_start: 0.7991 (ttm) cc_final: 0.7725 (ttt)
REVERT: E   67 MET cc_start: 0.7564 (mmt) cc_final: 0.7244 (ttm)
REVERT: E   75 ASP cc_start: 0.8555 (m-30) cc_final: 0.7543 (t70)
REVERT: F  148 ASP cc_start: 0.8491 (m-30) cc_final: 0.8082 (m-30)
REVERT: G   83 MET cc_start: 0.5024 (mmp) cc_final: 0.4694 (mmm)
REVERT: G  135 ARG cc_start: 0.7517 (OUTLIER) cc_final: 0.7198 (mtp180)
  outliers start: 19
  outliers final: 10
  residues processed: 149
  average time/residue: 0.1870
  time to fit residues: 40.3592
Evaluate side-chains
  138 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain B residue   56 PHE
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain D residue   51 THR
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain E residue  175 ILE
Chi-restraints excluded: chain E residue  205 SER
Chi-restraints excluded: chain G residue  135 ARG
Chi-restraints excluded: chain G residue  175 ILE
Chi-restraints excluded: chain G residue  183 LEU
Chi-restraints excluded: chain G residue  212 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 112 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9990
   chunk 75 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 76 optimal weight:    2.9990
   chunk 16 optimal weight:    0.4980
   chunk 79 optimal weight:    8.9990
   chunk 24 optimal weight:    0.8980
   chunk 6 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.184833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.132987 restraints weight = 15400.763|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 1.92
r_work: 0.3110 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3083
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3083 r_free = 0.3083    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3083
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.1236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   9035  Z= 0.151
  Angle     :  0.445   7.567  12169  Z= 0.232
  Chirality :  0.035   0.135   1447
  Planarity :  0.003   0.042   1544
  Dihedral  :  3.328  13.133   1223
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 27.31 %
    Favored  : 70.78 %
  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:  4.13 (0.25), residues: 1149
  helix:  3.06 (0.16), residues: 1011
  sheet:  None (None), residues: 0
  loop : -0.15 (0.55), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  18 
 HIS   0.002   0.001   HIS D 136 
 PHE   0.020   0.001   PHE A  32 
 TYR   0.004   0.001   TYR F 188 
 ARG   0.004   0.000   ARG G 216 

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 1.054 
Fit side-chains
REVERT: B   56 PHE cc_start: 0.7707 (OUTLIER) cc_final: 0.6659 (m-10)
REVERT: C   56 PHE cc_start: 0.7201 (m-10) cc_final: 0.6967 (m-80)
REVERT: C  239 LYS cc_start: 0.7370 (mtpp) cc_final: 0.7158 (mtpp)
REVERT: D  179 MET cc_start: 0.7781 (ttm) cc_final: 0.7518 (ttt)
REVERT: E   75 ASP cc_start: 0.8563 (m-30) cc_final: 0.7549 (t70)
REVERT: F  148 ASP cc_start: 0.8308 (m-30) cc_final: 0.7912 (m-30)
REVERT: G   83 MET cc_start: 0.4952 (mmp) cc_final: 0.4716 (mmm)
REVERT: G  135 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7285 (mtp180)
  outliers start: 18
  outliers final: 12
  residues processed: 144
  average time/residue: 0.1803
  time to fit residues: 37.6882
Evaluate side-chains
  142 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain B residue   56 PHE
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain D residue   51 THR
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  175 ILE
Chi-restraints excluded: chain E residue  205 SER
Chi-restraints excluded: chain E residue  238 LEU
Chi-restraints excluded: chain G residue  135 ARG
Chi-restraints excluded: chain G residue  175 ILE
Chi-restraints excluded: chain G residue  183 LEU
Chi-restraints excluded: chain G residue  212 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 113 optimal weight:    0.0370
   chunk 61 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 110 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 99 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.9664

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.184430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 132)---------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.125343 restraints weight = 10685.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3316 rms_B_bonded: 2.08
r_work: 0.3129 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2939
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2939 r_free = 0.2939    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2939 r_free = 0.2939    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2939
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7679
moved from start:          0.1283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9035  Z= 0.166
  Angle     :  0.458   6.566  12169  Z= 0.237
  Chirality :  0.036   0.131   1447
  Planarity :  0.003   0.042   1544
  Dihedral  :  3.347  12.420   1223
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 27.63 %
    Favored  : 70.78 %
  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:  4.12 (0.24), residues: 1149
  helix:  3.07 (0.16), residues: 1006
  sheet:  None (None), residues: 0
  loop : -0.18 (0.53), residues: 143

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP B  18 
 HIS   0.002   0.001   HIS D 136 
 PHE   0.015   0.001   PHE A  39 
 TYR   0.005   0.001   TYR F 188 
 ARG   0.004   0.000   ARG G 216 

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.989 
Fit side-chains
REVERT: B   56 PHE cc_start: 0.7644 (OUTLIER) cc_final: 0.6579 (m-10)
REVERT: C   56 PHE cc_start: 0.7209 (m-10) cc_final: 0.6870 (m-80)
REVERT: C   67 MET cc_start: 0.7282 (ptt) cc_final: 0.6797 (ptp)
REVERT: D  179 MET cc_start: 0.8013 (ttm) cc_final: 0.7748 (ttt)
REVERT: E   75 ASP cc_start: 0.8450 (m-30) cc_final: 0.7520 (t70)
REVERT: F  148 ASP cc_start: 0.8562 (m-30) cc_final: 0.8087 (m-30)
REVERT: G   83 MET cc_start: 0.4905 (mmp) cc_final: 0.4644 (mmm)
REVERT: G  135 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.7185 (mtp180)
  outliers start: 15
  outliers final: 11
  residues processed: 138
  average time/residue: 0.1812
  time to fit residues: 36.2958
Evaluate side-chains
  140 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain B residue   56 PHE
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain D residue   51 THR
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  175 ILE
Chi-restraints excluded: chain E residue  205 SER
Chi-restraints excluded: chain E residue  238 LEU
Chi-restraints excluded: chain G residue  135 ARG
Chi-restraints excluded: chain G residue  175 ILE
Chi-restraints excluded: chain G residue  183 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 100 optimal weight:    5.9990
   chunk 87 optimal weight:    3.9990
   chunk 29 optimal weight:    6.9990
   chunk 39 optimal weight:    4.9990
   chunk 108 optimal weight:    5.9990
   chunk 64 optimal weight:    0.6980
   chunk 103 optimal weight:    3.9990
   chunk 90 optimal weight:    9.9990
   chunk 54 optimal weight:    4.9990
   chunk 109 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.179785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 156)---------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.126580 restraints weight = 12375.160|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 1.57
r_work: 0.3059 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.2898 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2845
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2845
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.1332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   9035  Z= 0.301
  Angle     :  0.539   7.926  12169  Z= 0.279
  Chirality :  0.040   0.139   1447
  Planarity :  0.004   0.045   1544
  Dihedral  :  3.642  13.905   1223
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 26.67 %
    Favored  : 70.78 %
  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:  3.54 (0.25), residues: 1149
  helix:  2.69 (0.16), residues: 1009
  sheet:  None (None), residues: 0
  loop : -0.44 (0.54), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.002   TRP A  18 
 HIS   0.005   0.001   HIS D 136 
 PHE   0.018   0.002   PHE E 143 
 TYR   0.007   0.001   TYR D 241 
 ARG   0.007   0.001   ARG G 216 

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 1.009 
Fit side-chains
   revert: symmetry clash
REVERT: B   56 PHE cc_start: 0.7732 (OUTLIER) cc_final: 0.6659 (m-10)
REVERT: C   56 PHE cc_start: 0.7675 (m-10) cc_final: 0.7256 (m-80)
REVERT: C   67 MET cc_start: 0.7776 (ptt) cc_final: 0.7299 (ptp)
REVERT: E   75 ASP cc_start: 0.8545 (m-30) cc_final: 0.7606 (t70)
REVERT: F  148 ASP cc_start: 0.8714 (m-30) cc_final: 0.8231 (m-30)
REVERT: G   83 MET cc_start: 0.5070 (mmp) cc_final: 0.4740 (mmm)
REVERT: G  135 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7282 (mtp180)
  outliers start: 24
  outliers final: 18
  residues processed: 142
  average time/residue: 0.1890
  time to fit residues: 38.7686
Evaluate side-chains
  145 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 1.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain B residue   56 PHE
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain C residue  205 SER
Chi-restraints excluded: chain D residue   51 THR
Chi-restraints excluded: chain D residue   83 MET
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  185 THR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  237 TYR
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  175 ILE
Chi-restraints excluded: chain E residue  205 SER
Chi-restraints excluded: chain E residue  238 LEU
Chi-restraints excluded: chain F residue   81 VAL
Chi-restraints excluded: chain G residue  135 ARG
Chi-restraints excluded: chain G residue  175 ILE
Chi-restraints excluded: chain G residue  212 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 4 optimal weight:    0.4980
   chunk 73 optimal weight:   10.0000
   chunk 8 optimal weight:    4.9990
   chunk 114 optimal weight:    5.9990
   chunk 44 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 36 optimal weight:    0.5980
   chunk 79 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.184658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.134697 restraints weight = 12340.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3435 rms_B_bonded: 1.59
r_work: 0.3143 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2977 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2977
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2927
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2927 r_free = 0.2927    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2927 r_free = 0.2927    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2927
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9035  Z= 0.150
  Angle     :  0.451   8.135  12169  Z= 0.236
  Chirality :  0.035   0.132   1447
  Planarity :  0.004   0.043   1544
  Dihedral  :  3.435  12.742   1223
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 27.63 %
    Favored  : 70.56 %
  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:  4.03 (0.25), residues: 1149
  helix:  3.00 (0.16), residues: 1012
  sheet:  None (None), residues: 0
  loop : -0.30 (0.54), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A  18 
 HIS   0.002   0.001   HIS D 136 
 PHE   0.022   0.001   PHE F  44 
 TYR   0.005   0.001   TYR F 188 
 ARG   0.007   0.000   ARG G 216 

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 132
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
REVERT: B   56 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.6665 (m-10)
REVERT: C   56 PHE cc_start: 0.7478 (m-10) cc_final: 0.7119 (m-80)
REVERT: C   67 MET cc_start: 0.7508 (ptt) cc_final: 0.7041 (ptp)
REVERT: C  179 MET cc_start: 0.8035 (mtt) cc_final: 0.7826 (mtm)
REVERT: C  195 MET cc_start: 0.8838 (mmm) cc_final: 0.8616 (mmm)
REVERT: D  179 MET cc_start: 0.8033 (tpp) cc_final: 0.7713 (ttt)
REVERT: E   75 ASP cc_start: 0.8525 (m-30) cc_final: 0.7681 (t70)
REVERT: E  148 ASP cc_start: 0.8044 (m-30) cc_final: 0.7789 (m-30)
REVERT: F  148 ASP cc_start: 0.8515 (m-30) cc_final: 0.8028 (m-30)
REVERT: G   83 MET cc_start: 0.4958 (mmp) cc_final: 0.4627 (mmm)
REVERT: G  135 ARG cc_start: 0.7645 (OUTLIER) cc_final: 0.7345 (mtp180)
  outliers start: 17
  outliers final: 12
  residues processed: 143
  average time/residue: 0.1814
  time to fit residues: 37.7063
Evaluate side-chains
  142 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain B residue   56 PHE
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain D residue   51 THR
Chi-restraints excluded: chain D residue   83 MET
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  237 TYR
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  175 ILE
Chi-restraints excluded: chain E residue  205 SER
Chi-restraints excluded: chain G residue  135 ARG
Chi-restraints excluded: chain G residue  175 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 86 optimal weight:    2.9990
   chunk 79 optimal weight:    3.9990
   chunk 114 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 108 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 168 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.184314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.135851 restraints weight = 15555.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.84
r_work: 0.3120 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.2946 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2946
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2892
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2892 r_free = 0.2892    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2892 r_free = 0.2892    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2892
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.1408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9035  Z= 0.159
  Angle     :  0.456   8.398  12169  Z= 0.239
  Chirality :  0.036   0.129   1447
  Planarity :  0.003   0.042   1544
  Dihedral  :  3.394  13.189   1223
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 28.06 %
    Favored  : 70.35 %
  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:  4.11 (0.24), residues: 1149
  helix:  3.05 (0.16), residues: 1012
  sheet:  None (None), residues: 0
  loop : -0.27 (0.54), residues: 137

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.002   0.001   TRP A  18 
 HIS   0.002   0.001   HIS D 136 
 PHE   0.015   0.001   PHE A  33 
 TYR   0.005   0.001   TYR F 188 
 ARG   0.005   0.000   ARG G 216 

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

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

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2298 Ramachandran restraints generated.
    1149 Oldfield, 0 Emsley, 1149 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
REVERT: B   56 PHE cc_start: 0.7680 (OUTLIER) cc_final: 0.6568 (m-10)
REVERT: C   56 PHE cc_start: 0.7369 (m-10) cc_final: 0.7006 (m-80)
REVERT: C   67 MET cc_start: 0.7455 (ptt) cc_final: 0.6975 (ptp)
REVERT: E   75 ASP cc_start: 0.8406 (m-30) cc_final: 0.7529 (t70)
REVERT: E  148 ASP cc_start: 0.8057 (m-30) cc_final: 0.7838 (m-30)
REVERT: F  148 ASP cc_start: 0.8659 (m-30) cc_final: 0.8159 (m-30)
REVERT: G   83 MET cc_start: 0.4918 (mmp) cc_final: 0.4602 (mmm)
REVERT: G  135 ARG cc_start: 0.7611 (OUTLIER) cc_final: 0.7267 (mtp180)
  outliers start: 15
  outliers final: 12
  residues processed: 142
  average time/residue: 0.1879
  time to fit residues: 38.7307
Evaluate side-chains
  144 residues out of total 939 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 0.989 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain B residue   56 PHE
Chi-restraints excluded: chain C residue  110 ASP
Chi-restraints excluded: chain C residue  119 ASP
Chi-restraints excluded: chain D residue   51 THR
Chi-restraints excluded: chain D residue  100 ILE
Chi-restraints excluded: chain D residue  237 TYR
Chi-restraints excluded: chain E residue  132 THR
Chi-restraints excluded: chain E residue  175 ILE
Chi-restraints excluded: chain E residue  205 SER
Chi-restraints excluded: chain G residue  135 ARG
Chi-restraints excluded: chain G residue  175 ILE
Chi-restraints excluded: chain G residue  183 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 83 optimal weight:    0.9980
   chunk 17 optimal weight:    4.9990
   chunk 24 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   chunk 84 optimal weight:    2.9990
   chunk 93 optimal weight:    5.9990
   chunk 100 optimal weight:    4.9990
   chunk 4 optimal weight:    0.6980
   chunk 109 optimal weight:    3.9990
   chunk 31 optimal weight:    4.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
** C  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 168 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.183383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 25)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.136793 restraints weight = 18535.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3449 rms_B_bonded: 6.53
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3449
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3449 r_free = 0.3449    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3449
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7442
moved from start:          0.1417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9035  Z= 0.191
  Angle     :  0.473   8.308  12169  Z= 0.247
  Chirality :  0.037   0.132   1447
  Planarity :  0.004   0.043   1544
  Dihedral  :  3.434  13.267   1223
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 28.27 %
    Favored  : 70.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  3.98 (0.25), residues: 1149
  helix:  2.96 (0.16), residues: 1014
  sheet:  None (None), residues: 0
  loop : -0.20 (0.54), residues: 135

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP A  18 
 HIS   0.003   0.001   HIS D 136 
 PHE   0.026   0.001   PHE F  44 
 TYR   0.006   0.001   TYR F 188 
 ARG   0.008   0.000   ARG G 216 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5145.76 seconds
wall clock time: 91 minutes 22.18 seconds (5482.18 seconds total)