Starting phenix.real_space_refine
on Tue Aug  4 15:55:22 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9v32_64747/08_2026/9v32_64747.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9v32_64747/08_2026/9v32_64747.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9v32_64747/08_2026/9v32_64747.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9v32_64747/08_2026/9v32_64747.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9v32_64747/08_2026/9v32_64747.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9v32_64747/08_2026/9v32_64747.map"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.033
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: 4
    Type Number    sf(0)   Gaussians
     S      27      5.16       5
     C    2873      2.51       5
     N     740      2.21       5
     O     867      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4507
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 1258
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 171, 1258
          Classifications: {'peptide': 171}
          Link IDs: {'PTRANS': 2, 'TRANS': 168}
          Chain breaks: 2
    Chain: "H"
      Number of atoms: 1588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 1588
          Classifications: {'peptide': 207}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 193}
          Chain breaks: 2
    Chain: "L"
      Number of atoms: 1661
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1661
          Classifications: {'peptide': 215}
          Link IDs: {'PCIS': 3, 'PTRANS': 8, 'TRANS': 203}
  Time building chain proxies: 1.16, per 1000 atoms: 0.26
  Number of scatterers: 4507
  At special positions: 0
  Unit cell: (65.45, 68, 147.05, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      27     16.00
     O     867      8.00
     N     740      7.00
     C    2873      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  53 " - pdb=" SG  CYS A  63 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS H 145 " - pdb=" SG  CYS H 201 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  94 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L 140 " - pdb=" SG  CYS L 200 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.36
  Conformation dependent library (CDL) restraints added in 167.8 milliseconds
  

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1090

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 10 sheets defined
      22.9% alpha, 30.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 27
      removed outlier: 3.698A  pdb=" N   CYS A   6 " --> pdb=" O   ALA A   2 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 73 through 100
      removed outlier: 3.508A  pdb=" N   VAL A  79 " --> pdb=" O   MET A  75 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   ARG A  80 " --> pdb=" O   LEU A  76 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ALA A  81 " --> pdb=" O   GLN A  77 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLY A  86 " --> pdb=" O   LEU A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 143
      removed outlier: 3.604A  pdb=" N   ILE A 123 " --> pdb=" O   LEU A 119 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   MET A 124 " --> pdb=" O   THR A 120 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   PHE A 125 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   ILE A 126 " --> pdb=" O   GLY A 122 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   VAL A 127 " --> pdb=" O   ILE A 123 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY A 135 " --> pdb=" O   CYS A 131 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   VAL A 136 " --> pdb=" O   ALA A 132 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   SER A 137 " --> pdb=" O   ILE A 133 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   PHE A 139 " --> pdb=" O   GLY A 135 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   MET A 142 " --> pdb=" O   VAL A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 195
      removed outlier: 3.885A  pdb=" N   VAL A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ILE A 194 " --> pdb=" O   VAL A 190 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 61 through 65
    Processing helix  chain 'H' and resid 161 through 163
      No H-bonds generated for 'chain 'H' and resid 161 through 163'
    Processing helix  chain 'L' and resid 85 through 89
    Processing helix  chain 'L' and resid 127 through 134
      removed outlier: 3.798A  pdb=" N   LEU L 131 " --> pdb=" O   SER L 127 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 189 through 195
      removed outlier: 4.064A  pdb=" N   HIS L 195 " --> pdb=" O   ASP L 191 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 62 through 65
      removed outlier: 6.904A  pdb=" N   ASN A  45 " --> pdb=" O   GLN A  33 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   SER A  31 " --> pdb=" O   GLN A  47 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   THR A  32 " --> pdb=" O   THR A 170 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 5
      removed outlier: 3.641A  pdb=" N   GLN H   3 " --> pdb=" O   SER H  25 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   SER H  25 " --> pdb=" O   GLN H   3 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU H  20 " --> pdb=" O   MET H  81 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   THR H  78 " --> pdb=" O   ASP H  73 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 9 through 12
      removed outlier: 6.461A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 115 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   SER H  99 " --> pdb=" O   TRP H  33 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   TRP H  33 " --> pdb=" O   SER H  99 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   ILE H  34 " --> pdb=" O   ASN H  50 " (cutoff:3.500A)
      removed outlier: 4.539A  pdb=" N   ASN H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   TYR H  57 " --> pdb=" O   TYR H  52 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 9 through 12
      removed outlier: 6.461A  pdb=" N   GLU H  10 " --> pdb=" O   THR H 115 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ARG H  98 " --> pdb=" O   ASP H 106 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ASP H 106 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 125 through 129
      removed outlier: 3.547A  pdb=" N   CYS H 145 " --> pdb=" O   SER H 185 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 156 through 159
      removed outlier: 3.920A  pdb=" N   HIS H 205 " --> pdb=" O   THR H 210 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   THR H 210 " --> pdb=" O   HIS H 205 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'L' and resid 4 through 7
      removed outlier: 3.504A  pdb=" N   SER L  22 " --> pdb=" O   SER L   7 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   VAL L  19 " --> pdb=" O   ILE L  81 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE L  77 " --> pdb=" O   CYS L  23 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   THR L  78 " --> pdb=" O   SER L  71 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   SER L  71 " --> pdb=" O   THR L  78 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 10 through 13
      removed outlier: 6.761A  pdb=" N   TRP L  41 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   LYS L  51 " --> pdb=" O   GLN L  43 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 120 through 124
      removed outlier: 3.825A  pdb=" N   ASN L 144 " --> pdb=" O   TYR L 179 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   TYR L 179 " --> pdb=" O   ASN L 144 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'L' and resid 159 through 160
      removed outlier: 3.945A  pdb=" N   LYS L 151 " --> pdb=" O   THR L 203 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   THR L 203 " --> pdb=" O   LYS L 151 " (cutoff:3.500A)

    196 hydrogen bonds defined for protein.
    525 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.64

  Time building geometry restraints manager: 0.49 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: 1400
        1.34 -     1.46: 1046
        1.46 -     1.58: 2122
        1.58 -     1.70: 0
        1.70 -     1.82: 39
  Bond restraints: 4607
  Sorted by residual:
  bond pdb=" CB  ASP L  66 "
       pdb=" CG  ASP L  66 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 2.50e-02 1.60e+03 8.87e-01
  bond pdb=" C   ILE A 194 "
       pdb=" O   ILE A 194 "
    ideal  model  delta    sigma   weight residual
    1.233  1.242 -0.009 1.02e-02 9.61e+03 8.61e-01
  bond pdb=" CB  GLN L  44 "
       pdb=" CG  GLN L  44 "
    ideal  model  delta    sigma   weight residual
    1.520  1.493  0.027 3.00e-02 1.11e+03 8.05e-01
  bond pdb=" CB  GLN L  48 "
       pdb=" CG  GLN L  48 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 7.01e-01
  bond pdb=" CB  PRO L 147 "
       pdb=" CG  PRO L 147 "
    ideal  model  delta    sigma   weight residual
    1.506  1.475  0.031 3.90e-02 6.57e+02 6.20e-01
  ... (remaining 4602 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.33: 6021
        1.33 -     2.66: 172
        2.66 -     3.99: 53
        3.99 -     5.32: 16
        5.32 -     6.65: 3
  Bond angle restraints: 6265
  Sorted by residual:
  angle pdb=" C   ALA L  57 "
        pdb=" CA  ALA L  57 "
        pdb=" CB  ALA L  57 "
      ideal   model   delta    sigma   weight residual
     110.42  115.95   -5.53 1.99e+00 2.53e-01 7.73e+00
  angle pdb=" C   TYR H 107 "
        pdb=" N   TRP H 108 "
        pdb=" CA  TRP H 108 "
      ideal   model   delta    sigma   weight residual
     121.39  116.82    4.57 1.66e+00 3.63e-01 7.57e+00
  angle pdb=" CA  LYS H 206 "
        pdb=" C   LYS H 206 "
        pdb=" N   PRO H 207 "
      ideal   model   delta    sigma   weight residual
     118.44  122.39   -3.95 1.59e+00 3.96e-01 6.19e+00
  angle pdb=" CA  LYS L 151 "
        pdb=" CB  LYS L 151 "
        pdb=" CG  LYS L 151 "
      ideal   model   delta    sigma   weight residual
     114.10  118.69   -4.59 2.00e+00 2.50e-01 5.27e+00
  angle pdb=" N   LYS H 206 "
        pdb=" CA  LYS H 206 "
        pdb=" C   LYS H 206 "
      ideal   model   delta    sigma   weight residual
     109.81  114.78   -4.97 2.21e+00 2.05e-01 5.05e+00
  ... (remaining 6260 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 2501
       17.66 -    35.33: 188
       35.33 -    52.99: 27
       52.99 -    70.65: 2
       70.65 -    88.32: 2
  Dihedral angle restraints: 2720
    sinusoidal: 1017
      harmonic: 1703
  Sorted by residual:
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  94 "
           pdb=" CB  CYS L  94 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   56.97   36.03     1      1.00e+01 1.00e-02 1.84e+01
  dihedral pdb=" CA  LYS H  63 "
           pdb=" C   LYS H  63 "
           pdb=" N   PHE H  64 "
           pdb=" CA  PHE H  64 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.85   21.15     0      5.00e+00 4.00e-02 1.79e+01
  dihedral pdb=" CA  GLN H 176 "
           pdb=" C   GLN H 176 "
           pdb=" N   SER H 177 "
           pdb=" CA  SER H 177 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.18  -18.82     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 2717 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.026: 425
       0.026 -    0.053: 183
       0.053 -    0.079: 63
       0.079 -    0.106: 31
       0.106 -    0.132: 20
  Chirality restraints: 722
  Sorted by residual:
  chirality pdb=" CA  LYS H  63 "
            pdb=" N   LYS H  63 "
            pdb=" C   LYS H  63 "
            pdb=" CB  LYS H  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.39e-01
  chirality pdb=" CA  MET L   4 "
            pdb=" N   MET L   4 "
            pdb=" C   MET L   4 "
            pdb=" CB  MET L   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.64   -0.13 2.00e-01 2.50e+01 4.11e-01
  chirality pdb=" CA  ILE H  34 "
            pdb=" N   ILE H  34 "
            pdb=" C   ILE H  34 "
            pdb=" CB  ILE H  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.10e-01
  ... (remaining 719 not shown)

  Planarity restraints: 783
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER L   7 "    0.048 5.00e-02 4.00e+02   7.25e-02 8.41e+00
        pdb=" N   PRO L   8 "   -0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO L   8 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO L   8 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP H 108 "    0.017 2.00e-02 2.50e+03   1.72e-02 7.39e+00
        pdb=" CG  TRP H 108 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP H 108 "    0.023 2.00e-02 2.50e+03
        pdb=" CD2 TRP H 108 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP H 108 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP H 108 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP H 108 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP H 108 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP H 108 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP H 108 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 153 "   -0.040 5.00e-02 4.00e+02   6.09e-02 5.93e+00
        pdb=" N   PRO H 154 "    0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO H 154 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO H 154 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 780 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 627
        2.76 -     3.29: 4405
        3.29 -     3.83: 6892
        3.83 -     4.36: 7681
        4.36 -     4.90: 13380
  Nonbonded interactions: 32985
  Sorted by model distance:
  nonbonded pdb=" O   LEU A  76 "
            pdb=" NH1 ARG A  80 "
     model   vdw
     2.223 3.120
  nonbonded pdb=" OH  TYR H  60 "
            pdb=" N   LEU H  70 "
     model   vdw
     2.282 3.120
  nonbonded pdb=" OG  SER L  83 "
            pdb=" NE2 GLN L  85 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" O   VAL A   3 "
            pdb=" NE2 GLN A   7 "
     model   vdw
     2.302 3.120
  nonbonded pdb=" NH1 ARG L 114 "
            pdb=" O   THR L 115 "
     model   vdw
     2.331 3.120
  ... (remaining 32980 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.440
  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:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.010
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7523
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      :  0.003   0.033   4612  Z= 0.117
  Angle     :  0.616   6.647   6275  Z= 0.320
  Chirality :  0.040   0.132    722
  Planarity :  0.005   0.073    783
  Dihedral  : 12.141  88.318   1615
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.40 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.86 (0.37), residues: 579
  helix:  2.86 (0.50), residues: 114
  sheet:  1.55 (0.39), residues: 201
  loop : -1.37 (0.36), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  80 
 TYR   0.023   0.001   TYR A  46 
 PHE   0.013   0.001   PHE H  64 
 TRP   0.046   0.002   TRP H 108 
 HIS   0.001   0.000   HIS L 204 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.12 ( 4607)
  covalent geometry    : angle       0.61273 /  0.32 ( 6265)
  SS BOND              : bond        0.00442 /  0.23 (    5)
  SS BOND              : angle       1.72539 /  1.02 (   10)
  hydrogen bonds       : bond        0.28181 / 18.69 (  192)
  hydrogen bonds       : angle       8.12724 /  5.82 (  525)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 181
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 GLN cc_start: 0.8467 (mp-120) cc_final: 0.8226 (mm-40)
REVERT: A   53 CYS cc_start: 0.4757 (m) cc_final: 0.4073 (m)
REVERT: A   87 ILE cc_start: 0.8924 (mt) cc_final: 0.8454 (mt)
REVERT: A  142 MET cc_start: 0.7181 (mmp) cc_final: 0.6754 (mmp)
REVERT: A  191 MET cc_start: 0.7182 (tpt) cc_final: 0.6175 (tpt)
REVERT: A  192 MET cc_start: 0.7781 (tpt) cc_final: 0.7214 (tpt)
REVERT: H    5 GLN cc_start: 0.7744 (tt0) cc_final: 0.7383 (tt0)
REVERT: H   82 GLN cc_start: 0.7289 (tp40) cc_final: 0.6892 (tp40)
REVERT: H  112 THR cc_start: 0.8134 (t) cc_final: 0.7721 (t)
REVERT: L    4 MET cc_start: 0.7130 (tpt) cc_final: 0.6900 (tpt)
REVERT: L   43 GLN cc_start: 0.8144 (tt0) cc_final: 0.7930 (tt0)
REVERT: L  145 PHE cc_start: 0.7468 (p90) cc_final: 0.6792 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 182
  average time/residue: 0.0745
  time to fit residues: 17.1104
Evaluate side-chains
  175 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    5.9990
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 32 optimal weight:    0.0980
   chunk 31 optimal weight:    0.0370
   chunk 25 optimal weight:    3.9990
   chunk 50 optimal weight:    7.9990
   overall best weight:    1.8264

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  45 ASN
H 176 GLN
L   6 GLN
L  48 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.110971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.092983 restraints weight = 9276.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.096554 restraints weight = 4740.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.098890 restraints weight = 2884.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.100429 restraints weight = 1974.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.101561 restraints weight = 1481.018|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.2051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   4612  Z= 0.262
  Angle     :  0.640   6.952   6275  Z= 0.349
  Chirality :  0.042   0.135    722
  Planarity :  0.005   0.058    783
  Dihedral  :  4.863  18.513    627
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 10.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  3.59 %
    Favored  : 96.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.36), residues: 579
  helix:  2.57 (0.48), residues: 120
  sheet:  1.25 (0.39), residues: 202
  loop : -1.48 (0.37), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  80 
 TYR   0.022   0.002   TYR A  66 
 PHE   0.015   0.001   PHE H 171 
 TRP   0.022   0.002   TRP H  33 
 HIS   0.003   0.001   HIS L 204 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00542 /  0.26 ( 4607)
  covalent geometry    : angle       0.63409 /  0.35 ( 6265)
  SS BOND              : bond        0.01143 /  0.58 (    5)
  SS BOND              : angle       2.25465 /  1.30 (   10)
  hydrogen bonds       : bond        0.04590 /  3.24 (  192)
  hydrogen bonds       : angle       5.74494 /  4.12 (  525)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 202
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 VAL cc_start: 0.8890 (p) cc_final: 0.8634 (p)
REVERT: A    7 GLN cc_start: 0.8553 (mp-120) cc_final: 0.8321 (mm-40)
REVERT: A   15 LEU cc_start: 0.8867 (tp) cc_final: 0.8653 (tp)
REVERT: A   29 GLN cc_start: 0.8428 (mt0) cc_final: 0.8021 (mt0)
REVERT: A   46 TYR cc_start: 0.7839 (p90) cc_final: 0.7507 (p90)
REVERT: A   54 VAL cc_start: 0.8235 (t) cc_final: 0.7943 (m)
REVERT: A   87 ILE cc_start: 0.8918 (mt) cc_final: 0.8141 (mt)
REVERT: A   89 LEU cc_start: 0.7720 (tt) cc_final: 0.7473 (tt)
REVERT: A  142 MET cc_start: 0.7016 (mmp) cc_final: 0.6400 (mmp)
REVERT: A  191 MET cc_start: 0.7096 (tpt) cc_final: 0.6109 (tpt)
REVERT: A  192 MET cc_start: 0.7678 (tpt) cc_final: 0.7074 (tpt)
REVERT: H    5 GLN cc_start: 0.7832 (tt0) cc_final: 0.7566 (tt0)
REVERT: H    6 GLN cc_start: 0.8184 (tt0) cc_final: 0.7903 (tt0)
REVERT: H   19 LYS cc_start: 0.7913 (mppt) cc_final: 0.7634 (tttp)
REVERT: H  150 TYR cc_start: 0.7010 (p90) cc_final: 0.6788 (p90)
REVERT: H  158 SER cc_start: 0.7677 (t) cc_final: 0.7133 (p)
REVERT: H  159 TRP cc_start: 0.8148 (m100) cc_final: 0.7905 (m-10)
REVERT: H  175 LEU cc_start: 0.8689 (tt) cc_final: 0.8457 (tt)
REVERT: H  183 LEU cc_start: 0.7501 (pt) cc_final: 0.7243 (pt)
REVERT: H  184 SER cc_start: 0.8512 (m) cc_final: 0.8075 (t)
REVERT: H  211 LYS cc_start: 0.8795 (tttt) cc_final: 0.8375 (ttpp)
REVERT: L   43 GLN cc_start: 0.8321 (tt0) cc_final: 0.7950 (tt0)
REVERT: L   85 GLN cc_start: 0.8539 (mp10) cc_final: 0.8035 (mp10)
REVERT: L   88 ASP cc_start: 0.8635 (m-30) cc_final: 0.8275 (m-30)
REVERT: L  122 PHE cc_start: 0.7413 (m-10) cc_final: 0.7032 (m-10)
REVERT: L  145 PHE cc_start: 0.7289 (p90) cc_final: 0.6619 (p90)
REVERT: L  153 GLN cc_start: 0.8026 (mp10) cc_final: 0.7715 (mp10)
REVERT: L  176 ASP cc_start: 0.8763 (t0) cc_final: 0.8551 (t0)
REVERT: L  204 HIS cc_start: 0.8038 (t70) cc_final: 0.7765 (t70)
REVERT: L  213 LYS cc_start: 0.8684 (mmpt) cc_final: 0.8474 (mmpt)
  outliers start: 1
  outliers final: 0
  residues processed: 203
  average time/residue: 0.0755
  time to fit residues: 19.1524
Evaluate side-chains
  196 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 31 optimal weight:    0.5980
   chunk 21 optimal weight:    0.7980
   chunk 45 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0670
   chunk 46 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 49 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.6118

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  45 ASN
H 176 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.114387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.095996 restraints weight = 9157.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.099646 restraints weight = 4731.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.102074 restraints weight = 2884.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.103594 restraints weight = 1966.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.104795 restraints weight = 1484.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4612  Z= 0.126
  Angle     :  0.553   6.665   6275  Z= 0.294
  Chirality :  0.040   0.138    722
  Planarity :  0.005   0.064    783
  Dihedral  :  4.495  19.190    627
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.99 %
    Favored  : 97.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.37), residues: 579
  helix:  2.95 (0.50), residues: 120
  sheet:  1.34 (0.39), residues: 201
  loop : -1.50 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  80 
 TYR   0.016   0.001   TYR L  55 
 PHE   0.009   0.001   PHE H 171 
 TRP   0.030   0.002   TRP A  30 
 HIS   0.001   0.000   HIS L 204 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00282 /  0.13 ( 4607)
  covalent geometry    : angle       0.55100 /  0.29 ( 6265)
  SS BOND              : bond        0.00762 /  0.38 (    5)
  SS BOND              : angle       1.41102 /  0.82 (   10)
  hydrogen bonds       : bond        0.03499 /  2.49 (  192)
  hydrogen bonds       : angle       5.00677 /  3.59 (  525)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 190
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    3 VAL cc_start: 0.8876 (p) cc_final: 0.8652 (p)
REVERT: A    7 GLN cc_start: 0.8562 (mp-120) cc_final: 0.8329 (mm-40)
REVERT: A   15 LEU cc_start: 0.8831 (tp) cc_final: 0.8611 (tp)
REVERT: A   27 MET cc_start: 0.7659 (mtm) cc_final: 0.7186 (mtm)
REVERT: A   29 GLN cc_start: 0.8366 (mt0) cc_final: 0.7978 (mt0)
REVERT: A   54 VAL cc_start: 0.8153 (t) cc_final: 0.7832 (m)
REVERT: A   87 ILE cc_start: 0.8871 (mt) cc_final: 0.8152 (mt)
REVERT: A   94 LEU cc_start: 0.8052 (mt) cc_final: 0.7773 (mt)
REVERT: A  130 LEU cc_start: 0.8234 (mt) cc_final: 0.7989 (mt)
REVERT: A  142 MET cc_start: 0.6869 (mmp) cc_final: 0.6270 (mmp)
REVERT: A  191 MET cc_start: 0.7083 (tpt) cc_final: 0.6026 (tpt)
REVERT: A  192 MET cc_start: 0.7647 (tpt) cc_final: 0.6975 (tpt)
REVERT: H    5 GLN cc_start: 0.7794 (tt0) cc_final: 0.7462 (tt0)
REVERT: H    6 GLN cc_start: 0.8109 (tt0) cc_final: 0.7862 (tt0)
REVERT: H   19 LYS cc_start: 0.7665 (mppt) cc_final: 0.7421 (tptm)
REVERT: H  155 VAL cc_start: 0.9158 (t) cc_final: 0.8950 (m)
REVERT: H  158 SER cc_start: 0.7708 (t) cc_final: 0.7189 (p)
REVERT: H  159 TRP cc_start: 0.8133 (m100) cc_final: 0.7843 (m-10)
REVERT: H  169 HIS cc_start: 0.8091 (m90) cc_final: 0.7827 (m-70)
REVERT: H  175 LEU cc_start: 0.8543 (tt) cc_final: 0.8311 (tt)
REVERT: H  184 SER cc_start: 0.8427 (m) cc_final: 0.8008 (t)
REVERT: H  211 LYS cc_start: 0.8781 (tttt) cc_final: 0.8332 (ttpp)
REVERT: L   43 GLN cc_start: 0.8422 (tt0) cc_final: 0.8007 (tt0)
REVERT: L   44 GLN cc_start: 0.8138 (tp40) cc_final: 0.7895 (tp40)
REVERT: L   51 LYS cc_start: 0.7374 (ptmm) cc_final: 0.7106 (ptmm)
REVERT: L   73 SER cc_start: 0.7965 (t) cc_final: 0.7757 (t)
REVERT: L  122 PHE cc_start: 0.7400 (m-10) cc_final: 0.7061 (m-10)
REVERT: L  142 LEU cc_start: 0.8253 (mp) cc_final: 0.7907 (mp)
REVERT: L  145 PHE cc_start: 0.7202 (p90) cc_final: 0.6603 (p90)
REVERT: L  204 HIS cc_start: 0.7981 (t70) cc_final: 0.7665 (t70)
REVERT: L  213 LYS cc_start: 0.8688 (mmpt) cc_final: 0.8439 (mmpt)
  outliers start: 1
  outliers final: 0
  residues processed: 191
  average time/residue: 0.0571
  time to fit residues: 13.7144
Evaluate side-chains
  184 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.122 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 36 optimal weight:    5.9990
   chunk 19 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9990
   chunk 4 optimal weight:    0.4980
   chunk 57 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  45 ASN
H  82 GLN
H 176 GLN
L   6 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.113346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.095073 restraints weight = 9071.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.098670 restraints weight = 4698.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.101063 restraints weight = 2882.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.102669 restraints weight = 1974.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.103753 restraints weight = 1478.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.2375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4612  Z= 0.158
  Angle     :  0.558   6.727   6275  Z= 0.299
  Chirality :  0.041   0.134    722
  Planarity :  0.005   0.059    783
  Dihedral  :  4.527  19.596    627
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.84 %
    Favored  : 95.16 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  2.79 %
    Favored  : 97.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.37), residues: 579
  helix:  2.97 (0.50), residues: 120
  sheet:  1.34 (0.38), residues: 201
  loop : -1.55 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG L 114 
 TYR   0.018   0.002   TYR L  55 
 PHE   0.010   0.001   PHE H 171 
 TRP   0.016   0.002   TRP A  30 
 HIS   0.002   0.000   HIS L 204 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.16 ( 4607)
  covalent geometry    : angle       0.55474 /  0.30 ( 6265)
  SS BOND              : bond        0.00788 /  0.40 (    5)
  SS BOND              : angle       1.56309 /  0.90 (   10)
  hydrogen bonds       : bond        0.03501 /  2.51 (  192)
  hydrogen bonds       : angle       4.89548 /  3.51 (  525)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 197
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 LEU cc_start: 0.8845 (tp) cc_final: 0.8630 (tp)
REVERT: A   27 MET cc_start: 0.7650 (mtm) cc_final: 0.7188 (mtm)
REVERT: A   29 GLN cc_start: 0.8341 (mt0) cc_final: 0.7964 (mt0)
REVERT: A   54 VAL cc_start: 0.8150 (t) cc_final: 0.7822 (m)
REVERT: A   60 PHE cc_start: 0.8700 (t80) cc_final: 0.8274 (t80)
REVERT: A   87 ILE cc_start: 0.8909 (mt) cc_final: 0.8153 (mt)
REVERT: A   94 LEU cc_start: 0.8122 (mt) cc_final: 0.7856 (mt)
REVERT: A  130 LEU cc_start: 0.8241 (mt) cc_final: 0.7978 (mt)
REVERT: A  142 MET cc_start: 0.6925 (mmp) cc_final: 0.6295 (mmp)
REVERT: A  191 MET cc_start: 0.7148 (tpt) cc_final: 0.6073 (tpt)
REVERT: A  192 MET cc_start: 0.7692 (tpt) cc_final: 0.7035 (tpt)
REVERT: H    5 GLN cc_start: 0.7768 (tt0) cc_final: 0.7430 (tt0)
REVERT: H    6 GLN cc_start: 0.8104 (tt0) cc_final: 0.7729 (tt0)
REVERT: H   13 ARG cc_start: 0.8596 (tpp80) cc_final: 0.8368 (tpp80)
REVERT: H   82 GLN cc_start: 0.6980 (tp-100) cc_final: 0.6536 (tp-100)
REVERT: H  112 THR cc_start: 0.8159 (t) cc_final: 0.7647 (t)
REVERT: H  155 VAL cc_start: 0.9163 (t) cc_final: 0.8932 (m)
REVERT: H  158 SER cc_start: 0.7715 (t) cc_final: 0.7162 (p)
REVERT: H  159 TRP cc_start: 0.8166 (m100) cc_final: 0.7879 (m-10)
REVERT: H  169 HIS cc_start: 0.8161 (m90) cc_final: 0.7885 (m-70)
REVERT: H  184 SER cc_start: 0.8450 (m) cc_final: 0.8022 (t)
REVERT: H  211 LYS cc_start: 0.8765 (tttt) cc_final: 0.8337 (ttpp)
REVERT: L   43 GLN cc_start: 0.8407 (tt0) cc_final: 0.7901 (tt0)
REVERT: L   44 GLN cc_start: 0.8169 (tp40) cc_final: 0.7792 (tp40)
REVERT: L   55 TYR cc_start: 0.8084 (p90) cc_final: 0.7838 (p90)
REVERT: L  113 LYS cc_start: 0.8600 (ptpp) cc_final: 0.8400 (ptpt)
REVERT: L  122 PHE cc_start: 0.7394 (m-10) cc_final: 0.7025 (m-10)
REVERT: L  145 PHE cc_start: 0.7228 (p90) cc_final: 0.6605 (p90)
REVERT: L  153 GLN cc_start: 0.7868 (mp10) cc_final: 0.7587 (mp10)
REVERT: L  166 GLN cc_start: 0.8339 (mm-40) cc_final: 0.7962 (mm110)
REVERT: L  204 HIS cc_start: 0.7967 (t70) cc_final: 0.7524 (t70)
REVERT: L  213 LYS cc_start: 0.8628 (mmpt) cc_final: 0.8392 (mmpt)
  outliers start: 1
  outliers final: 0
  residues processed: 198
  average time/residue: 0.0621
  time to fit residues: 15.4059
Evaluate side-chains
  193 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 0 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9990
   chunk 12 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 41 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 38 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 22 optimal weight:    0.3980
   chunk 14 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0670
   overall best weight:    0.5718

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  45 ASN
H 176 GLN
L  27 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.114645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 23)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.096159 restraints weight = 9110.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.099767 restraints weight = 4736.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.102167 restraints weight = 2920.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.103830 restraints weight = 2017.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.105001 restraints weight = 1499.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3401
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.2491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4612  Z= 0.116
  Angle     :  0.549   6.584   6275  Z= 0.287
  Chirality :  0.040   0.136    722
  Planarity :  0.005   0.062    783
  Dihedral  :  4.403  19.711    627
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.59 %
    Favored  : 98.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.74 (0.37), residues: 579
  helix:  3.05 (0.50), residues: 120
  sheet:  1.34 (0.39), residues: 200
  loop : -1.57 (0.36), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  80 
 TYR   0.014   0.001   TYR L  55 
 PHE   0.010   0.001   PHE H  29 
 TRP   0.016   0.002   TRP H 108 
 HIS   0.001   0.000   HIS L 204 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 ( 4607)
  covalent geometry    : angle       0.54744 /  0.29 ( 6265)
  SS BOND              : bond        0.00636 /  0.32 (    5)
  SS BOND              : angle       1.15481 /  0.63 (   10)
  hydrogen bonds       : bond        0.03061 /  2.19 (  192)
  hydrogen bonds       : angle       4.62134 /  3.33 (  525)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 196
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 GLN cc_start: 0.8589 (mp-120) cc_final: 0.8058 (mp10)
REVERT: A   15 LEU cc_start: 0.8773 (tp) cc_final: 0.8553 (tp)
REVERT: A   27 MET cc_start: 0.7637 (mtm) cc_final: 0.7223 (mtm)
REVERT: A   29 GLN cc_start: 0.8278 (mt0) cc_final: 0.7921 (mt0)
REVERT: A   60 PHE cc_start: 0.8700 (t80) cc_final: 0.8336 (t80)
REVERT: A   87 ILE cc_start: 0.8886 (mt) cc_final: 0.8192 (mt)
REVERT: A   94 LEU cc_start: 0.8071 (mt) cc_final: 0.7793 (mt)
REVERT: A  130 LEU cc_start: 0.8117 (mt) cc_final: 0.7851 (mt)
REVERT: A  142 MET cc_start: 0.6925 (mmp) cc_final: 0.6262 (mmp)
REVERT: A  191 MET cc_start: 0.7139 (tpt) cc_final: 0.6052 (tpt)
REVERT: A  192 MET cc_start: 0.7636 (tpt) cc_final: 0.6982 (tpt)
REVERT: H    5 GLN cc_start: 0.7744 (tt0) cc_final: 0.7409 (tt0)
REVERT: H    6 GLN cc_start: 0.8096 (tt0) cc_final: 0.7795 (tt0)
REVERT: H   19 LYS cc_start: 0.7715 (mppt) cc_final: 0.7414 (tptm)
REVERT: H  112 THR cc_start: 0.8225 (t) cc_final: 0.7592 (t)
REVERT: H  155 VAL cc_start: 0.9172 (t) cc_final: 0.8941 (m)
REVERT: H  158 SER cc_start: 0.7737 (t) cc_final: 0.7186 (p)
REVERT: H  159 TRP cc_start: 0.8168 (m100) cc_final: 0.7875 (m-10)
REVERT: H  169 HIS cc_start: 0.8108 (m90) cc_final: 0.7814 (m-70)
REVERT: H  211 LYS cc_start: 0.8745 (tttt) cc_final: 0.8328 (ttpp)
REVERT: L   43 GLN cc_start: 0.8291 (tt0) cc_final: 0.7874 (tt0)
REVERT: L   44 GLN cc_start: 0.8134 (tp40) cc_final: 0.7928 (tp40)
REVERT: L   55 TYR cc_start: 0.8070 (p90) cc_final: 0.7867 (p90)
REVERT: L   73 SER cc_start: 0.7848 (t) cc_final: 0.7622 (t)
REVERT: L   85 GLN cc_start: 0.8478 (mp10) cc_final: 0.7679 (mp10)
REVERT: L   88 ASP cc_start: 0.8542 (m-30) cc_final: 0.7858 (m-30)
REVERT: L  113 LYS cc_start: 0.8480 (ptpp) cc_final: 0.8278 (ptpt)
REVERT: L  122 PHE cc_start: 0.7378 (m-10) cc_final: 0.7049 (m-10)
REVERT: L  145 PHE cc_start: 0.7245 (p90) cc_final: 0.6689 (p90)
REVERT: L  204 HIS cc_start: 0.7803 (t70) cc_final: 0.7273 (t70)
REVERT: L  213 LYS cc_start: 0.8695 (mmpt) cc_final: 0.8401 (mmpt)
  outliers start: 1
  outliers final: 0
  residues processed: 197
  average time/residue: 0.0727
  time to fit residues: 17.9559
Evaluate side-chains
  190 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 21 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   chunk 42 optimal weight:    0.3980
   chunk 12 optimal weight:    0.8980
   chunk 29 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H 176 GLN
L   6 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.114360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.095753 restraints weight = 9291.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.099436 restraints weight = 4800.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.101908 restraints weight = 2944.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.103584 restraints weight = 2014.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.104736 restraints weight = 1498.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4612  Z= 0.132
  Angle     :  0.557   6.609   6275  Z= 0.291
  Chirality :  0.040   0.132    722
  Planarity :  0.005   0.054    783
  Dihedral  :  4.384  19.931    627
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.79 %
    Favored  : 98.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.37), residues: 579
  helix:  3.09 (0.50), residues: 120
  sheet:  1.35 (0.38), residues: 201
  loop : -1.56 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  80 
 TYR   0.013   0.001   TYR L  55 
 PHE   0.017   0.001   PHE H 171 
 TRP   0.015   0.002   TRP A  30 
 HIS   0.001   0.000   HIS L 204 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.13 ( 4607)
  covalent geometry    : angle       0.55451 /  0.29 ( 6265)
  SS BOND              : bond        0.00695 /  0.35 (    5)
  SS BOND              : angle       1.34870 /  0.76 (   10)
  hydrogen bonds       : bond        0.03183 /  2.28 (  192)
  hydrogen bonds       : angle       4.64093 /  3.33 (  525)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 198
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 LEU cc_start: 0.8804 (tp) cc_final: 0.8588 (tp)
REVERT: A   27 MET cc_start: 0.7700 (mtm) cc_final: 0.7308 (mtm)
REVERT: A   29 GLN cc_start: 0.8338 (mt0) cc_final: 0.7965 (mt0)
REVERT: A   54 VAL cc_start: 0.8171 (t) cc_final: 0.7833 (m)
REVERT: A   60 PHE cc_start: 0.8742 (t80) cc_final: 0.8396 (t80)
REVERT: A   87 ILE cc_start: 0.8905 (mt) cc_final: 0.8207 (mt)
REVERT: A   94 LEU cc_start: 0.8090 (mt) cc_final: 0.7818 (mt)
REVERT: A  130 LEU cc_start: 0.8116 (mt) cc_final: 0.7829 (mt)
REVERT: A  142 MET cc_start: 0.7007 (mmp) cc_final: 0.6348 (mmp)
REVERT: A  180 VAL cc_start: 0.8408 (t) cc_final: 0.8148 (t)
REVERT: A  191 MET cc_start: 0.7228 (tpt) cc_final: 0.6085 (tpt)
REVERT: A  192 MET cc_start: 0.7669 (tpt) cc_final: 0.7032 (tpt)
REVERT: H    5 GLN cc_start: 0.7762 (tt0) cc_final: 0.7422 (tt0)
REVERT: H    6 GLN cc_start: 0.8094 (tt0) cc_final: 0.7826 (tt0)
REVERT: H   11 LEU cc_start: 0.8671 (tp) cc_final: 0.8471 (tp)
REVERT: H   19 LYS cc_start: 0.7734 (mppt) cc_final: 0.7403 (tptm)
REVERT: H   62 GLN cc_start: 0.8678 (tm-30) cc_final: 0.8478 (tp40)
REVERT: H   82 GLN cc_start: 0.6750 (tp-100) cc_final: 0.6545 (tp-100)
REVERT: H  155 VAL cc_start: 0.9177 (t) cc_final: 0.8957 (m)
REVERT: H  158 SER cc_start: 0.7722 (t) cc_final: 0.7165 (p)
REVERT: H  159 TRP cc_start: 0.8124 (m100) cc_final: 0.7803 (m-10)
REVERT: H  211 LYS cc_start: 0.8750 (tttt) cc_final: 0.8343 (ttpp)
REVERT: L   43 GLN cc_start: 0.8302 (tt0) cc_final: 0.7850 (tt0)
REVERT: L   73 SER cc_start: 0.7916 (t) cc_final: 0.7704 (t)
REVERT: L   85 GLN cc_start: 0.8518 (mp10) cc_final: 0.7705 (mp10)
REVERT: L   88 ASP cc_start: 0.8550 (m-30) cc_final: 0.7804 (m-30)
REVERT: L  113 LYS cc_start: 0.8506 (ptpp) cc_final: 0.8305 (ptpt)
REVERT: L  145 PHE cc_start: 0.7245 (p90) cc_final: 0.6649 (p90)
REVERT: L  153 GLN cc_start: 0.7781 (mp10) cc_final: 0.7549 (mp10)
REVERT: L  182 SER cc_start: 0.8584 (m) cc_final: 0.8086 (p)
REVERT: L  204 HIS cc_start: 0.7822 (t70) cc_final: 0.7248 (t70)
REVERT: L  213 LYS cc_start: 0.8688 (mmpt) cc_final: 0.8391 (mmpt)
  outliers start: 1
  outliers final: 0
  residues processed: 199
  average time/residue: 0.0648
  time to fit residues: 16.2519
Evaluate side-chains
  187 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 55 optimal weight:   10.0000
   chunk 48 optimal weight:    4.9990
   chunk 10 optimal weight:    7.9990
   chunk 56 optimal weight:    0.0010
   chunk 52 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   overall best weight:    0.9188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  45 ASN
H 176 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.113483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.094877 restraints weight = 9283.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.098602 restraints weight = 4758.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.101079 restraints weight = 2911.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.102755 restraints weight = 1987.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.103837 restraints weight = 1474.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7491
moved from start:          0.2627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4612  Z= 0.152
  Angle     :  0.582   6.642   6275  Z= 0.307
  Chirality :  0.041   0.142    722
  Planarity :  0.005   0.051    783
  Dihedral  :  4.518  19.901    627
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.00 %
    Favored  : 98.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.37), residues: 579
  helix:  3.11 (0.50), residues: 120
  sheet:  1.32 (0.38), residues: 201
  loop : -1.62 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A  80 
 TYR   0.016   0.001   TYR L  55 
 PHE   0.019   0.001   PHE H 171 
 TRP   0.035   0.002   TRP H 108 
 HIS   0.002   0.001   HIS L 204 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00334 /  0.15 ( 4607)
  covalent geometry    : angle       0.58018 /  0.31 ( 6265)
  SS BOND              : bond        0.00828 /  0.42 (    5)
  SS BOND              : angle       1.17861 /  0.65 (   10)
  hydrogen bonds       : bond        0.03348 /  2.39 (  192)
  hydrogen bonds       : angle       4.71150 /  3.39 (  525)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 191
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 LEU cc_start: 0.8809 (tp) cc_final: 0.8587 (tp)
REVERT: A   27 MET cc_start: 0.7714 (mtm) cc_final: 0.7346 (mtm)
REVERT: A   29 GLN cc_start: 0.8340 (mt0) cc_final: 0.7939 (mt0)
REVERT: A   54 VAL cc_start: 0.8145 (t) cc_final: 0.7840 (m)
REVERT: A   60 PHE cc_start: 0.8768 (t80) cc_final: 0.8330 (t80)
REVERT: A   87 ILE cc_start: 0.8912 (mt) cc_final: 0.8277 (mt)
REVERT: A   94 LEU cc_start: 0.8095 (mt) cc_final: 0.7819 (mt)
REVERT: A  130 LEU cc_start: 0.8109 (mt) cc_final: 0.7828 (mt)
REVERT: A  142 MET cc_start: 0.6992 (mmp) cc_final: 0.6350 (mmp)
REVERT: A  180 VAL cc_start: 0.8398 (t) cc_final: 0.8137 (t)
REVERT: A  191 MET cc_start: 0.7233 (tpt) cc_final: 0.6076 (tpt)
REVERT: A  192 MET cc_start: 0.7695 (tpt) cc_final: 0.7031 (tpt)
REVERT: H    5 GLN cc_start: 0.7765 (tt0) cc_final: 0.7407 (tt0)
REVERT: H    6 GLN cc_start: 0.8075 (tt0) cc_final: 0.7763 (tt0)
REVERT: H   19 LYS cc_start: 0.7734 (mppt) cc_final: 0.7388 (tptm)
REVERT: H  108 TRP cc_start: 0.7808 (m-10) cc_final: 0.7577 (m-10)
REVERT: H  112 THR cc_start: 0.8282 (t) cc_final: 0.7874 (t)
REVERT: H  158 SER cc_start: 0.7756 (t) cc_final: 0.7210 (p)
REVERT: H  159 TRP cc_start: 0.8135 (m100) cc_final: 0.7829 (m-10)
REVERT: H  169 HIS cc_start: 0.7930 (m-70) cc_final: 0.7724 (m-70)
REVERT: H  211 LYS cc_start: 0.8746 (tttt) cc_final: 0.8368 (ttpp)
REVERT: L   21 MET cc_start: 0.7643 (mtm) cc_final: 0.7388 (mtm)
REVERT: L   51 LYS cc_start: 0.7441 (ptmt) cc_final: 0.7232 (ptmm)
REVERT: L   85 GLN cc_start: 0.8554 (mp10) cc_final: 0.7731 (mp10)
REVERT: L   88 ASP cc_start: 0.8580 (m-30) cc_final: 0.7812 (m-30)
REVERT: L  145 PHE cc_start: 0.7247 (p90) cc_final: 0.6696 (p90)
REVERT: L  153 GLN cc_start: 0.7798 (mp10) cc_final: 0.7533 (mp10)
REVERT: L  166 GLN cc_start: 0.8317 (mm-40) cc_final: 0.7965 (mm110)
REVERT: L  182 SER cc_start: 0.8576 (m) cc_final: 0.8133 (p)
REVERT: L  204 HIS cc_start: 0.7844 (t70) cc_final: 0.7238 (t70)
REVERT: L  213 LYS cc_start: 0.8677 (mmpt) cc_final: 0.8401 (mmpt)
  outliers start: 1
  outliers final: 0
  residues processed: 192
  average time/residue: 0.0720
  time to fit residues: 17.3681
Evaluate side-chains
  188 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 28 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0370
   chunk 29 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 13 optimal weight:    1.9990
   chunk 33 optimal weight:    0.0980
   overall best weight:    0.5662

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  45 ASN
H 176 GLN
L   6 GLN
L  44 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.115003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.096130 restraints weight = 9244.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.099856 restraints weight = 4779.947|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.102394 restraints weight = 2930.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.104070 restraints weight = 2003.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.105265 restraints weight = 1492.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.2637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4612  Z= 0.119
  Angle     :  0.581   6.539   6275  Z= 0.300
  Chirality :  0.041   0.133    722
  Planarity :  0.005   0.049    783
  Dihedral  :  4.410  20.478    627
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.60 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.37), residues: 579
  helix:  3.17 (0.50), residues: 120
  sheet:  1.37 (0.38), residues: 201
  loop : -1.62 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  80 
 TYR   0.015   0.001   TYR L  55 
 PHE   0.016   0.001   PHE H 171 
 TRP   0.034   0.002   TRP A  30 
 HIS   0.001   0.000   HIS H 205 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00274 /  0.12 ( 4607)
  covalent geometry    : angle       0.57913 /  0.30 ( 6265)
  SS BOND              : bond        0.00619 /  0.31 (    5)
  SS BOND              : angle       1.20124 /  0.66 (   10)
  hydrogen bonds       : bond        0.03004 /  2.16 (  192)
  hydrogen bonds       : angle       4.58764 /  3.31 (  525)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 185
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 GLN cc_start: 0.8537 (mp-120) cc_final: 0.8005 (mp10)
REVERT: A   27 MET cc_start: 0.7702 (mtm) cc_final: 0.7198 (mtm)
REVERT: A   29 GLN cc_start: 0.8347 (mt0) cc_final: 0.8042 (mt0)
REVERT: A   30 TRP cc_start: 0.8333 (m-10) cc_final: 0.7981 (m-10)
REVERT: A   54 VAL cc_start: 0.8159 (t) cc_final: 0.7810 (m)
REVERT: A   60 PHE cc_start: 0.8786 (t80) cc_final: 0.8399 (t80)
REVERT: A   87 ILE cc_start: 0.8887 (mt) cc_final: 0.8246 (mt)
REVERT: A   94 LEU cc_start: 0.8070 (mt) cc_final: 0.7809 (mt)
REVERT: A  130 LEU cc_start: 0.8070 (mt) cc_final: 0.7794 (mt)
REVERT: A  142 MET cc_start: 0.6948 (mmp) cc_final: 0.6343 (mmp)
REVERT: A  191 MET cc_start: 0.7193 (tpt) cc_final: 0.6026 (tpt)
REVERT: A  192 MET cc_start: 0.7664 (tpt) cc_final: 0.7028 (tpt)
REVERT: H    5 GLN cc_start: 0.7747 (tt0) cc_final: 0.7412 (tt0)
REVERT: H    6 GLN cc_start: 0.8066 (tt0) cc_final: 0.7791 (tt0)
REVERT: H   19 LYS cc_start: 0.7886 (mppt) cc_final: 0.7626 (tptm)
REVERT: H  112 THR cc_start: 0.8234 (t) cc_final: 0.7816 (t)
REVERT: H  158 SER cc_start: 0.7736 (t) cc_final: 0.7195 (p)
REVERT: H  159 TRP cc_start: 0.8074 (m100) cc_final: 0.7781 (m-10)
REVERT: H  169 HIS cc_start: 0.7891 (m-70) cc_final: 0.7681 (m-70)
REVERT: H  211 LYS cc_start: 0.8699 (tttt) cc_final: 0.8362 (ttpp)
REVERT: L   66 ASP cc_start: 0.8508 (p0) cc_final: 0.8260 (p0)
REVERT: L   85 GLN cc_start: 0.8307 (mp10) cc_final: 0.7879 (mp10)
REVERT: L   88 ASP cc_start: 0.8698 (m-30) cc_final: 0.8120 (m-30)
REVERT: L  122 PHE cc_start: 0.7370 (m-10) cc_final: 0.6931 (m-10)
REVERT: L  145 PHE cc_start: 0.7238 (p90) cc_final: 0.6672 (p90)
REVERT: L  182 SER cc_start: 0.8594 (m) cc_final: 0.8134 (p)
REVERT: L  204 HIS cc_start: 0.7766 (t70) cc_final: 0.7252 (t70)
REVERT: L  213 LYS cc_start: 0.8686 (mmpt) cc_final: 0.8389 (mmpt)
  outliers start: 1
  outliers final: 0
  residues processed: 186
  average time/residue: 0.0737
  time to fit residues: 17.0664
Evaluate side-chains
  179 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 35 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 39 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 49 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0670
   chunk 8 optimal weight:    0.8980
   chunk 19 optimal weight:    0.0870
   chunk 5 optimal weight:    2.9990
   overall best weight:    0.5896

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  62 GLN
H 176 GLN
L   6 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.115117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.096342 restraints weight = 9127.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.099981 restraints weight = 4743.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.102510 restraints weight = 2920.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.104207 restraints weight = 1999.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.105278 restraints weight = 1490.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.3406
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.2709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4612  Z= 0.122
  Angle     :  0.576   6.523   6275  Z= 0.299
  Chirality :  0.041   0.139    722
  Planarity :  0.004   0.046    783
  Dihedral  :  4.387  20.359    627
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  0.60 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.37), residues: 579
  helix:  3.15 (0.50), residues: 120
  sheet:  1.34 (0.38), residues: 201
  loop : -1.62 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  80 
 TYR   0.016   0.001   TYR L  55 
 PHE   0.016   0.001   PHE H 171 
 TRP   0.031   0.002   TRP H 108 
 HIS   0.001   0.000   HIS L 204 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 ( 4607)
  covalent geometry    : angle       0.57241 /  0.30 ( 6265)
  SS BOND              : bond        0.00691 /  0.35 (    5)
  SS BOND              : angle       1.62646 /  0.84 (   10)
  hydrogen bonds       : bond        0.03033 /  2.17 (  192)
  hydrogen bonds       : angle       4.51551 /  3.25 (  525)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 186
  time to evaluate  : 0.165 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 GLN cc_start: 0.8486 (mp-120) cc_final: 0.7951 (mp10)
REVERT: A   27 MET cc_start: 0.7721 (mtm) cc_final: 0.7229 (mtm)
REVERT: A   29 GLN cc_start: 0.8294 (mt0) cc_final: 0.7971 (mt0)
REVERT: A   30 TRP cc_start: 0.8451 (m-10) cc_final: 0.8131 (m-10)
REVERT: A   54 VAL cc_start: 0.8080 (t) cc_final: 0.7832 (m)
REVERT: A   60 PHE cc_start: 0.8767 (t80) cc_final: 0.8407 (t80)
REVERT: A   87 ILE cc_start: 0.8893 (mt) cc_final: 0.8271 (mt)
REVERT: A   94 LEU cc_start: 0.8071 (mt) cc_final: 0.7816 (mt)
REVERT: A  130 LEU cc_start: 0.8071 (mt) cc_final: 0.7784 (mt)
REVERT: A  142 MET cc_start: 0.6950 (mmp) cc_final: 0.6472 (mmp)
REVERT: A  180 VAL cc_start: 0.8355 (t) cc_final: 0.8080 (t)
REVERT: A  191 MET cc_start: 0.7199 (tpt) cc_final: 0.6027 (tpt)
REVERT: A  192 MET cc_start: 0.7679 (tpt) cc_final: 0.7048 (tpt)
REVERT: H    5 GLN cc_start: 0.7743 (tt0) cc_final: 0.7401 (tt0)
REVERT: H    6 GLN cc_start: 0.8194 (tt0) cc_final: 0.7859 (tt0)
REVERT: H  148 LYS cc_start: 0.8127 (tptm) cc_final: 0.7909 (tptm)
REVERT: H  158 SER cc_start: 0.7729 (t) cc_final: 0.7220 (p)
REVERT: H  211 LYS cc_start: 0.8684 (tttt) cc_final: 0.8354 (ttpp)
REVERT: L   85 GLN cc_start: 0.8280 (mp10) cc_final: 0.7826 (mp10)
REVERT: L   88 ASP cc_start: 0.8688 (m-30) cc_final: 0.8122 (m-30)
REVERT: L  122 PHE cc_start: 0.7394 (m-10) cc_final: 0.6923 (m-10)
REVERT: L  145 PHE cc_start: 0.7232 (p90) cc_final: 0.6645 (p90)
REVERT: L  182 SER cc_start: 0.8595 (m) cc_final: 0.8125 (p)
REVERT: L  204 HIS cc_start: 0.7766 (t70) cc_final: 0.7150 (t70)
REVERT: L  213 LYS cc_start: 0.8672 (mmpt) cc_final: 0.8381 (mmpt)
  outliers start: 1
  outliers final: 0
  residues processed: 187
  average time/residue: 0.0729
  time to fit residues: 17.1320
Evaluate side-chains
  182 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.170 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0870
   chunk 20 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   chunk 26 optimal weight:    3.9990
   chunk 6 optimal weight:    0.4980
   chunk 25 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0030
   chunk 48 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.4168

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  45 ASN
H  62 GLN
H 176 GLN
L   6 GLN
L  27 GLN
L  43 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.116629 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.098016 restraints weight = 9228.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.101843 restraints weight = 4746.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.104337 restraints weight = 2889.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.105986 restraints weight = 1963.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.107133 restraints weight = 1457.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7436
moved from start:          0.2789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4612  Z= 0.111
  Angle     :  0.589   6.484   6275  Z= 0.301
  Chirality :  0.041   0.133    722
  Planarity :  0.005   0.048    783
  Dihedral  :  4.346  20.027    627
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.00 %
    Favored  : 98.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.73 (0.37), residues: 579
  helix:  3.07 (0.50), residues: 120
  sheet:  1.38 (0.38), residues: 201
  loop : -1.65 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  80 
 TYR   0.015   0.001   TYR L  55 
 PHE   0.015   0.001   PHE H 171 
 TRP   0.040   0.002   TRP H 108 
 HIS   0.001   0.000   HIS H 205 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.11 ( 4607)
  covalent geometry    : angle       0.58631 /  0.30 ( 6265)
  SS BOND              : bond        0.00580 /  0.29 (    5)
  SS BOND              : angle       1.46677 /  0.73 (   10)
  hydrogen bonds       : bond        0.02849 /  2.03 (  192)
  hydrogen bonds       : angle       4.51014 /  3.27 (  525)

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

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

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1158 Ramachandran restraints generated.
    579 Oldfield, 0 Emsley, 579 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  194 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 193
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 GLN cc_start: 0.8475 (mp-120) cc_final: 0.7967 (mp10)
REVERT: A   27 MET cc_start: 0.7671 (mtm) cc_final: 0.7127 (mtm)
REVERT: A   29 GLN cc_start: 0.8273 (mt0) cc_final: 0.8002 (mt0)
REVERT: A   30 TRP cc_start: 0.8380 (m-10) cc_final: 0.8160 (m-10)
REVERT: A   54 VAL cc_start: 0.8160 (t) cc_final: 0.7805 (m)
REVERT: A   60 PHE cc_start: 0.8767 (t80) cc_final: 0.8468 (t80)
REVERT: A   87 ILE cc_start: 0.8878 (mt) cc_final: 0.8272 (mt)
REVERT: A   94 LEU cc_start: 0.8069 (mt) cc_final: 0.7802 (mt)
REVERT: A  130 LEU cc_start: 0.8048 (mt) cc_final: 0.7771 (mt)
REVERT: A  142 MET cc_start: 0.6991 (mmp) cc_final: 0.6452 (mmp)
REVERT: A  180 VAL cc_start: 0.8333 (t) cc_final: 0.8049 (t)
REVERT: A  191 MET cc_start: 0.7173 (tpt) cc_final: 0.5992 (tpt)
REVERT: A  192 MET cc_start: 0.7660 (tpt) cc_final: 0.7008 (tpt)
REVERT: H    5 GLN cc_start: 0.7672 (tt0) cc_final: 0.7325 (tt0)
REVERT: H    6 GLN cc_start: 0.8140 (tt0) cc_final: 0.7803 (tt0)
REVERT: H  112 THR cc_start: 0.8157 (t) cc_final: 0.7753 (t)
REVERT: H  148 LYS cc_start: 0.8118 (tptm) cc_final: 0.7899 (tptm)
REVERT: H  158 SER cc_start: 0.7671 (t) cc_final: 0.7154 (p)
REVERT: H  159 TRP cc_start: 0.8067 (m100) cc_final: 0.7846 (m100)
REVERT: H  169 HIS cc_start: 0.8062 (m90) cc_final: 0.7732 (m-70)
REVERT: H  211 LYS cc_start: 0.8628 (tttt) cc_final: 0.8327 (ttpp)
REVERT: L   43 GLN cc_start: 0.7814 (mt0) cc_final: 0.7563 (mt0)
REVERT: L   73 SER cc_start: 0.7707 (t) cc_final: 0.7505 (t)
REVERT: L   85 GLN cc_start: 0.8286 (mp10) cc_final: 0.7817 (mp10)
REVERT: L   88 ASP cc_start: 0.8732 (m-30) cc_final: 0.7979 (m-30)
REVERT: L  122 PHE cc_start: 0.7380 (m-10) cc_final: 0.6929 (m-10)
REVERT: L  145 PHE cc_start: 0.7187 (p90) cc_final: 0.6638 (p90)
REVERT: L  182 SER cc_start: 0.8594 (m) cc_final: 0.8116 (p)
REVERT: L  204 HIS cc_start: 0.7707 (t70) cc_final: 0.7139 (t70)
REVERT: L  213 LYS cc_start: 0.8695 (mmpt) cc_final: 0.8395 (mmpt)
  outliers start: 1
  outliers final: 0
  residues processed: 194
  average time/residue: 0.0750
  time to fit residues: 18.3918
Evaluate side-chains
  191 residues out of total 502 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 34 optimal weight:    6.9990
   chunk 49 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 15 optimal weight:    0.2980
   overall best weight:    1.2586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H 176 GLN
L   6 GLN
L 166 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.112822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.094356 restraints weight = 9434.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.098097 restraints weight = 4841.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.100574 restraints weight = 2958.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.102194 restraints weight = 2030.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.103351 restraints weight = 1522.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7521
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   4612  Z= 0.192
  Angle     :  0.626   6.669   6275  Z= 0.330
  Chirality :  0.042   0.144    722
  Planarity :  0.005   0.052    783
  Dihedral  :  4.643  19.914    627
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  1.00 %
    Favored  : 98.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 15.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.62 (0.36), residues: 579
  helix:  2.92 (0.50), residues: 120
  sheet:  1.34 (0.38), residues: 201
  loop : -1.72 (0.35), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  80 
 TYR   0.016   0.002   TYR L  55 
 PHE   0.021   0.001   PHE H 171 
 TRP   0.044   0.003   TRP H 108 
 HIS   0.002   0.001   HIS L 204 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00412 /  0.19 ( 4607)
  covalent geometry    : angle       0.62247 /  0.33 ( 6265)
  SS BOND              : bond        0.00878 /  0.44 (    5)
  SS BOND              : angle       1.80480 /  0.98 (   10)
  hydrogen bonds       : bond        0.03638 /  2.62 (  192)
  hydrogen bonds       : angle       4.89624 /  3.53 (  525)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1036.33 seconds
wall clock time: 18 minutes 28.75 seconds (1108.75 seconds total)