Starting phenix.real_space_refine
on Fri Aug 22 17:07:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iec_35378/08_2025/8iec_35378.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iec_35378/08_2025/8iec_35378.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iec_35378/08_2025/8iec_35378.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iec_35378/08_2025/8iec_35378.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iec_35378/08_2025/8iec_35378.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iec_35378/08_2025/8iec_35378.map"
  }
  resolution = 3.18
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
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      44      5.16       5
     C    3954      2.51       5
     N    1079      2.21       5
     O    1201      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6278
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 1659
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1659
          Classifications: {'peptide': 215}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 4, 'TRANS': 210}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 50
          Unresolved non-hydrogen angles: 56
          Unresolved non-hydrogen dihedrals: 44
          Planarities with less than four sites: {'ASP:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "D"
      Number of atoms: 2527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2527
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 74
          Unresolved non-hydrogen angles: 91
          Unresolved non-hydrogen dihedrals: 57
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 4, 'ASP:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 4}
          Unresolved non-hydrogen planarities: 53
    Chain: "N"
      Number of atoms: 1707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1707
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PTRANS': 10, 'TRANS': 219}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 77
          Unresolved non-hydrogen dihedrals: 45
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "Y"
      Number of atoms: 385
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 385
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved non-hydrogen bonds: 39
          Unresolved non-hydrogen angles: 46
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 17
  Time building chain proxies: 1.41, per 1000 atoms: 0.22
  Number of scatterers: 6278
  At special positions: 0
  Unit cell: (89.1, 119.88, 82.62, 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      44     16.00
     O    1201      8.00
     N    1079      7.00
     C    3954      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS N 147 " - pdb=" SG  CYS N 217 " 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 392.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1652 Ramachandran restraints generated.
    826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1554

  Finding SS restraints...
    Secondary structure from input PDB file:
      13 helices and 13 sheets defined
      19.1% alpha, 29.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'C' and resid 6 through 31
    Processing helix  chain 'C' and resid 96 through 102
      removed outlier: 3.563A  pdb=" N   GLU C 101 " --> pdb=" O   HIS C  98 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   ASP C 102 " --> pdb=" O   CYS C  99 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 117 through 129
    Processing helix  chain 'C' and resid 130 through 135
      removed outlier: 6.292A  pdb=" N   PHE C 133 " --> pdb=" O   ASN C 130 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   ILE C 135 " --> pdb=" O   LYS C 132 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 145 through 153
    Processing helix  chain 'C' and resid 170 through 184
    Processing helix  chain 'C' and resid 205 through 225
    Processing helix  chain 'D' and resid 4 through 25
    Processing helix  chain 'N' and resid 28 through 32
      removed outlier: 3.581A  pdb=" N   SER N  31 " --> pdb=" O   ALA N  28 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 53 through 56
      removed outlier: 3.722A  pdb=" N   GLY N  56 " --> pdb=" O   SER N  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 53 through 56'
    Processing helix  chain 'N' and resid 87 through 91
      removed outlier: 3.699A  pdb=" N   ASP N  90 " --> pdb=" O   THR N  87 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   THR N  91 " --> pdb=" O   SER N  88 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'N' and resid 87 through 91'
    Processing helix  chain 'Y' and resid 9 through 24
      removed outlier: 3.504A  pdb=" N   MET Y  21 " --> pdb=" O   GLU Y  17 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   GLU Y  22 " --> pdb=" O   GLN Y  18 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ALA Y  23 " --> pdb=" O   LEU Y  19 " (cutoff:3.500A)
    Processing helix  chain 'Y' and resid 34 through 44
      removed outlier: 3.592A  pdb=" N   MET Y  38 " --> pdb=" O   ALA Y  34 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   GLU Y  42 " --> pdb=" O   MET Y  38 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 54 through 55
      removed outlier: 3.987A  pdb=" N   ALA C 105 " --> pdb=" O   LYS C  35 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   ILE C 139 " --> pdb=" O   TYR C 194 " (cutoff:3.500A)
      removed outlier: 7.920A  pdb=" N   HIS C 196 " --> pdb=" O   ILE C 139 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   LEU C 141 " --> pdb=" O   HIS C 196 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'D' and resid 49 through 51
      removed outlier: 3.750A  pdb=" N   VAL D 327 " --> pdb=" O   TRP D 339 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 58 through 63
      removed outlier: 3.561A  pdb=" N   ALA D  60 " --> pdb=" O   ALA D  73 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   ALA D  73 " --> pdb=" O   ALA D  60 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   LYS D  78 " --> pdb=" O   SER D  74 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   LEU D  79 " --> pdb=" O   ALA D  92 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   ALA D  92 " --> pdb=" O   LEU D  79 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   ILE D  81 " --> pdb=" O   VAL D  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 100 through 105
      removed outlier: 6.988A  pdb=" N   GLY D 115 " --> pdb=" O   MET D 101 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   CYS D 103 " --> pdb=" O   ALA D 113 " (cutoff:3.500A)
      removed outlier: 6.331A  pdb=" N   ALA D 113 " --> pdb=" O   CYS D 103 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   TYR D 105 " --> pdb=" O   TYR D 111 " (cutoff:3.500A)
      removed outlier: 7.027A  pdb=" N   TYR D 111 " --> pdb=" O   TYR D 105 " (cutoff:3.500A)
      removed outlier: 4.153A  pdb=" N   GLY D 116 " --> pdb=" O   ILE D 120 " (cutoff:3.500A)
      removed outlier: 4.739A  pdb=" N   ILE D 120 " --> pdb=" O   GLY D 116 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ARG D 137 " --> pdb=" O   ILE D 123 " (cutoff:3.500A)
      removed outlier: 6.031A  pdb=" N   ASN D 125 " --> pdb=" O   VAL D 135 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   VAL D 135 " --> pdb=" O   ASN D 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 146 through 151
      removed outlier: 6.648A  pdb=" N   SER D 160 " --> pdb=" O   SER D 147 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   CYS D 149 " --> pdb=" O   VAL D 158 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   VAL D 158 " --> pdb=" O   CYS D 149 " (cutoff:3.500A)
      removed outlier: 5.244A  pdb=" N   PHE D 151 " --> pdb=" O   GLN D 156 " (cutoff:3.500A)
      removed outlier: 7.768A  pdb=" N   GLN D 156 " --> pdb=" O   PHE D 151 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   ILE D 157 " --> pdb=" O   TRP D 169 " (cutoff:3.500A)
      removed outlier: 4.050A  pdb=" N   THR D 165 " --> pdb=" O   SER D 161 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   CYS D 166 " --> pdb=" O   PHE D 180 " (cutoff:3.500A)
      removed outlier: 7.130A  pdb=" N   ASP D 170 " --> pdb=" O   GLN D 176 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   GLN D 176 " --> pdb=" O   ASP D 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 191 through 192
      removed outlier: 4.021A  pdb=" N   SER D 207 " --> pdb=" O   ALA D 203 " (cutoff:3.500A)
      removed outlier: 6.004A  pdb=" N   ALA D 208 " --> pdb=" O   THR D 221 " (cutoff:3.500A)
      removed outlier: 4.900A  pdb=" N   THR D 221 " --> pdb=" O   ALA D 208 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   LEU D 210 " --> pdb=" O   ARG D 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 229 through 234
      removed outlier: 3.578A  pdb=" N   CYS D 233 " --> pdb=" O   ALA D 242 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   SER D 245 " --> pdb=" O   THR D 249 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   THR D 249 " --> pdb=" O   SER D 245 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   CYS D 250 " --> pdb=" O   TYR D 264 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   MET D 262 " --> pdb=" O   LEU D 252 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   ASP D 254 " --> pdb=" O   GLU D 260 " (cutoff:3.500A)
      removed outlier: 5.687A  pdb=" N   GLU D 260 " --> pdb=" O   ASP D 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 276 through 278
      removed outlier: 3.583A  pdb=" N   LEU D 285 " --> pdb=" O   TRP D 297 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ASN D 293 " --> pdb=" O   TYR D 289 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   GLY D 306 " --> pdb=" O   VAL D 296 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12
      removed outlier: 5.822A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 118 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   TRP N  36 " --> pdb=" O   VAL N  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'N' and resid 10 through 12
      removed outlier: 5.822A  pdb=" N   GLY N  10 " --> pdb=" O   THR N 118 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   PHE N 110 " --> pdb=" O   ARG N  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'N' and resid 142 through 147
      removed outlier: 3.871A  pdb=" N   PHE N 200 " --> pdb=" O   CYS N 147 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   SER N 192 " --> pdb=" O   THR N 203 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'N' and resid 182 through 183
      removed outlier: 6.529A  pdb=" N   TRP N 164 " --> pdb=" O   LEU N 176 " (cutoff:3.500A)

    241 hydrogen bonds defined for protein.
    660 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: 0.82

  Time building geometry restraints manager: 0.53 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: 2068
        1.34 -     1.46: 1277
        1.46 -     1.57: 2997
        1.57 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 6404
  Sorted by residual:
  bond pdb=" C   TYR N 223 "
       pdb=" N   PRO N 224 "
    ideal  model  delta    sigma   weight residual
    1.334  1.380 -0.046 2.34e-02 1.83e+03 3.83e+00
  bond pdb=" CB  VAL D  71 "
       pdb=" CG2 VAL D  71 "
    ideal  model  delta    sigma   weight residual
    1.521  1.483  0.038 3.30e-02 9.18e+02 1.33e+00
  bond pdb=" CD1 TYR N 223 "
       pdb=" CE1 TYR N 223 "
    ideal  model  delta    sigma   weight residual
    1.382  1.348  0.034 3.00e-02 1.11e+03 1.28e+00
  bond pdb=" CA  TYR N 223 "
       pdb=" C   TYR N 223 "
    ideal  model  delta    sigma   weight residual
    1.524  1.537 -0.014 1.26e-02 6.30e+03 1.17e+00
  bond pdb=" C   ASP N  74 "
       pdb=" N   PRO N  75 "
    ideal  model  delta    sigma   weight residual
    1.335  1.348 -0.014 1.28e-02 6.10e+03 1.15e+00
  ... (remaining 6399 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 8432
        1.63 -     3.27: 219
        3.27 -     4.90: 35
        4.90 -     6.54: 5
        6.54 -     8.17: 6
  Bond angle restraints: 8697
  Sorted by residual:
  angle pdb=" C   PRO C 157 "
        pdb=" N   LEU C 158 "
        pdb=" CA  LEU C 158 "
      ideal   model   delta    sigma   weight residual
     121.54  129.45   -7.91 1.91e+00 2.74e-01 1.71e+01
  angle pdb=" C   ASP C  85 "
        pdb=" N   VAL C  86 "
        pdb=" CA  VAL C  86 "
      ideal   model   delta    sigma   weight residual
     121.97  129.03   -7.06 1.80e+00 3.09e-01 1.54e+01
  angle pdb=" C   GLU N 222 "
        pdb=" N   TYR N 223 "
        pdb=" CA  TYR N 223 "
      ideal   model   delta    sigma   weight residual
     121.80  114.58    7.22 2.44e+00 1.68e-01 8.76e+00
  angle pdb=" CA  TYR N 223 "
        pdb=" CB  TYR N 223 "
        pdb=" CG  TYR N 223 "
      ideal   model   delta    sigma   weight residual
     113.90  108.92    4.98 1.80e+00 3.09e-01 7.64e+00
  angle pdb=" CA  VAL C  86 "
        pdb=" CB  VAL C  86 "
        pdb=" CG1 VAL C  86 "
      ideal   model   delta    sigma   weight residual
     110.40  114.99   -4.59 1.70e+00 3.46e-01 7.29e+00
  ... (remaining 8692 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.72: 3446
       17.72 -    35.43: 268
       35.43 -    53.15: 48
       53.15 -    70.86: 5
       70.86 -    88.58: 5
  Dihedral angle restraints: 3772
    sinusoidal: 1357
      harmonic: 2415
  Sorted by residual:
  dihedral pdb=" CB  CYS N 147 "
           pdb=" SG  CYS N 147 "
           pdb=" SG  CYS N 217 "
           pdb=" CB  CYS N 217 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00 -178.42  -88.58     1      1.00e+01 1.00e-02 9.36e+01
  dihedral pdb=" CA  GLN N 130 "
           pdb=" C   GLN N 130 "
           pdb=" N   ALA N 131 "
           pdb=" CA  ALA N 131 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.33   20.67     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  LEU D 261 "
           pdb=" C   LEU D 261 "
           pdb=" N   MET D 262 "
           pdb=" CA  MET D 262 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.69  -18.31     0      5.00e+00 4.00e-02 1.34e+01
  ... (remaining 3769 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 868
       0.071 -    0.141: 120
       0.141 -    0.212: 3
       0.212 -    0.283: 0
       0.283 -    0.353: 1
  Chirality restraints: 992
  Sorted by residual:
  chirality pdb=" CB  VAL C  86 "
            pdb=" CA  VAL C  86 "
            pdb=" CG1 VAL C  86 "
            pdb=" CG2 VAL C  86 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.28   -0.35 2.00e-01 2.50e+01 3.12e+00
  chirality pdb=" CG  LEU D  30 "
            pdb=" CB  LEU D  30 "
            pdb=" CD1 LEU D  30 "
            pdb=" CD2 LEU D  30 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.42   -0.17 2.00e-01 2.50e+01 7.52e-01
  chirality pdb=" CA  ILE D 229 "
            pdb=" N   ILE D 229 "
            pdb=" C   ILE D 229 "
            pdb=" CB  ILE D 229 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.09e-01
  ... (remaining 989 not shown)

  Planarity restraints: 1120
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE D 235 "   -0.034 5.00e-02 4.00e+02   5.18e-02 4.30e+00
        pdb=" N   PRO D 236 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO D 236 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO D 236 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA D 193 "   -0.031 5.00e-02 4.00e+02   4.75e-02 3.61e+00
        pdb=" N   PRO D 194 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO D 194 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D 194 "   -0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE N 138 "   -0.031 5.00e-02 4.00e+02   4.72e-02 3.57e+00
        pdb=" N   PRO N 139 "    0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO N 139 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO N 139 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 1117 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 248
        2.71 -     3.26: 5768
        3.26 -     3.81: 10207
        3.81 -     4.35: 12144
        4.35 -     4.90: 21610
  Nonbonded interactions: 49977
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU D 260 "
            pdb=" OG1 THR D 263 "
     model   vdw
     2.166 3.040
  nonbonded pdb=" OH  TYR C 194 "
            pdb=" OD2 ASP C 215 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OG  SER N 149 "
            pdb=" O   LYS N 151 "
     model   vdw
     2.247 3.040
  nonbonded pdb=" OD2 ASP D 170 "
            pdb=" OG1 THR D 173 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   GLY N  33 "
            pdb=" OG  SER N  99 "
     model   vdw
     2.296 3.040
  ... (remaining 49972 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.660
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.950
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6405  Z= 0.188
  Angle     :  0.658   8.175   8699  Z= 0.353
  Chirality :  0.047   0.353    992
  Planarity :  0.004   0.052   1120
  Dihedral  : 13.245  83.870   2215
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.43 (0.29), residues: 826
  helix:  0.80 (0.42), residues: 141
  sheet: -0.82 (0.32), residues: 275
  loop : -1.65 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG N  72 
 TYR   0.022   0.002   TYR N 223 
 PHE   0.017   0.002   PHE D 199 
 TRP   0.015   0.002   TRP D 169 
 HIS   0.006   0.001   HIS N 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 6404)
  covalent geometry    : angle       0.65781 ( 8697)
  SS BOND              : bond        0.00067 (    1)
  SS BOND              : angle       0.06225 (    2)
  hydrogen bonds       : bond        0.20775 (  239)
  hydrogen bonds       : angle       8.33125 (  660)

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

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

  1652 Ramachandran restraints generated.
    826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1652 Ramachandran restraints generated.
    826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 142
  time to evaluate  : 0.237 
Fit side-chains
REVERT: C    9 ASP cc_start: 0.6813 (m-30) cc_final: 0.6409 (m-30)
REVERT: C   32 LYS cc_start: 0.8198 (mtmm) cc_final: 0.7894 (mtmm)
REVERT: C  145 LYS cc_start: 0.8420 (mmtm) cc_final: 0.8191 (mmtm)
REVERT: C  146 LYS cc_start: 0.8020 (ptmt) cc_final: 0.7814 (ptmt)
REVERT: C  170 THR cc_start: 0.8628 (p) cc_final: 0.8300 (p)
REVERT: C  211 ASP cc_start: 0.7886 (m-30) cc_final: 0.7642 (m-30)
REVERT: D   15 LYS cc_start: 0.8075 (pttp) cc_final: 0.7868 (pttp)
REVERT: D   49 ARG cc_start: 0.7843 (mpt180) cc_final: 0.7492 (mmt-90)
REVERT: D   83 ASP cc_start: 0.7659 (t70) cc_final: 0.7411 (t70)
REVERT: D  243 THR cc_start: 0.7431 (m) cc_final: 0.7019 (m)
REVERT: D  258 ASP cc_start: 0.6991 (t0) cc_final: 0.6678 (t0)
REVERT: D  290 ASP cc_start: 0.6244 (m-30) cc_final: 0.6039 (m-30)
REVERT: N   36 TRP cc_start: 0.8359 (m100) cc_final: 0.7681 (m100)
REVERT: N  161 TYR cc_start: 0.7564 (m-80) cc_final: 0.7293 (m-80)
REVERT: Y   38 MET cc_start: 0.6034 (ptm) cc_final: 0.5833 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.0885
  time to fit residues: 15.7768
Evaluate side-chains
  133 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
D 110 ASN
D 237 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.156620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.134772 restraints weight = 9221.660|
|-----------------------------------------------------------------------------|
r_work (start): 0.3753 rms_B_bonded: 2.68
r_work: 0.3629 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7138
moved from start:          0.1167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   6405  Z= 0.216
  Angle     :  0.602   7.086   8699  Z= 0.322
  Chirality :  0.045   0.180    992
  Planarity :  0.004   0.047   1120
  Dihedral  :  4.869  31.335    896
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.78 %
    Favored  : 93.22 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  :  7.73 %
    Favored  : 90.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.99 (0.30), residues: 826
  helix:  1.80 (0.47), residues: 143
  sheet: -0.64 (0.32), residues: 277
  loop : -1.59 (0.30), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 219 
 TYR   0.027   0.002   TYR N 223 
 PHE   0.024   0.002   PHE D 253 
 TRP   0.020   0.002   TRP D 211 
 HIS   0.006   0.001   HIS N  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 6404)
  covalent geometry    : angle       0.60172 ( 8697)
  SS BOND              : bond        0.00248 (    1)
  SS BOND              : angle       0.34003 (    2)
  hydrogen bonds       : bond        0.04022 (  239)
  hydrogen bonds       : angle       5.82623 (  660)

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

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

  1652 Ramachandran restraints generated.
    826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1652 Ramachandran restraints generated.
    826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: C    9 ASP cc_start: 0.6835 (m-30) cc_final: 0.6550 (m-30)
REVERT: C   32 LYS cc_start: 0.8380 (mtmm) cc_final: 0.8103 (mtmm)
REVERT: C  145 LYS cc_start: 0.8485 (mmtm) cc_final: 0.8200 (mmtm)
REVERT: C  170 THR cc_start: 0.8457 (p) cc_final: 0.8095 (p)
REVERT: C  211 ASP cc_start: 0.7945 (m-30) cc_final: 0.7727 (m-30)
REVERT: N   36 TRP cc_start: 0.8196 (m100) cc_final: 0.7635 (m100)
REVERT: N  200 PHE cc_start: 0.8071 (m-80) cc_final: 0.7722 (m-80)
  outliers start: 9
  outliers final: 6
  residues processed: 131
  average time/residue: 0.0813
  time to fit residues: 13.4567
Evaluate side-chains
  129 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 123
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  195 CYS
Chi-restraints excluded: chain D residue  165 THR
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  329 THR
Chi-restraints excluded: chain N residue   11 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 3 optimal weight:    0.5980
   chunk 71 optimal weight:    0.1980
   chunk 48 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 53 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   chunk 43 optimal weight:    0.1980
   chunk 7 optimal weight:    0.4980
   chunk 44 optimal weight:    0.0870
   overall best weight:    0.3158

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

Flipped N/Q/H residues before XYZ refinement:
D 110 ASN
D 119 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.158727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.137375 restraints weight = 9098.594|
|-----------------------------------------------------------------------------|
r_work (start): 0.3782 rms_B_bonded: 2.58
r_work: 0.3665 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3665
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.1422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6405  Z= 0.142
  Angle     :  0.548   7.625   8699  Z= 0.293
  Chirality :  0.043   0.173    992
  Planarity :  0.004   0.045   1120
  Dihedral  :  4.645  29.140    896
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 11.28 %
    Favored  : 87.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.76 (0.30), residues: 826
  helix:  2.09 (0.47), residues: 143
  sheet: -0.49 (0.32), residues: 277
  loop : -1.49 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 219 
 TYR   0.024   0.002   TYR N 223 
 PHE   0.013   0.001   PHE D 253 
 TRP   0.015   0.001   TRP D 169 
 HIS   0.005   0.001   HIS N  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6404)
  covalent geometry    : angle       0.54787 ( 8697)
  SS BOND              : bond        0.00269 (    1)
  SS BOND              : angle       0.30654 (    2)
  hydrogen bonds       : bond        0.03491 (  239)
  hydrogen bonds       : angle       5.36980 (  660)

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

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

  1652 Ramachandran restraints generated.
    826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1652 Ramachandran restraints generated.
    826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 127
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
REVERT: C    9 ASP cc_start: 0.6739 (m-30) cc_final: 0.6449 (m-30)
REVERT: C  145 LYS cc_start: 0.8462 (mmtm) cc_final: 0.8165 (mmtm)
REVERT: C  170 THR cc_start: 0.8458 (p) cc_final: 0.8162 (p)
REVERT: C  211 ASP cc_start: 0.7862 (m-30) cc_final: 0.7654 (m-30)
REVERT: D   49 ARG cc_start: 0.7628 (mpt180) cc_final: 0.7407 (mmt-90)
REVERT: N   36 TRP cc_start: 0.8204 (m100) cc_final: 0.7638 (m100)
  outliers start: 9
  outliers final: 7
  residues processed: 130
  average time/residue: 0.0875
  time to fit residues: 14.5055
Evaluate side-chains
  130 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 123
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  195 CYS
Chi-restraints excluded: chain D residue  165 THR
Chi-restraints excluded: chain D residue  243 THR
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  329 THR
Chi-restraints excluded: chain N residue   11 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0870
   chunk 34 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 8 optimal weight:    0.3980
   chunk 80 optimal weight:    0.0060
   chunk 71 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.4174

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

Flipped N/Q/H residues before XYZ refinement:
D 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.157037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.135921 restraints weight = 9096.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3778 rms_B_bonded: 2.59
r_work: 0.3659 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6405  Z= 0.163
  Angle     :  0.544   6.499   8699  Z= 0.292
  Chirality :  0.043   0.173    992
  Planarity :  0.004   0.044   1120
  Dihedral  :  4.626  27.793    896
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 12.67 %
    Favored  : 85.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.74 (0.31), residues: 826
  helix:  2.11 (0.48), residues: 143
  sheet: -0.45 (0.32), residues: 279
  loop : -1.50 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D  68 
 TYR   0.024   0.002   TYR N 223 
 PHE   0.016   0.002   PHE C  74 
 TRP   0.014   0.001   TRP D 169 
 HIS   0.005   0.001   HIS N  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 6404)
  covalent geometry    : angle       0.54385 ( 8697)
  SS BOND              : bond        0.00086 (    1)
  SS BOND              : angle       0.52375 (    2)
  hydrogen bonds       : bond        0.03338 (  239)
  hydrogen bonds       : angle       5.13083 (  660)

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

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

  1652 Ramachandran restraints generated.
    826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1652 Ramachandran restraints generated.
    826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
REVERT: C    9 ASP cc_start: 0.6803 (m-30) cc_final: 0.6539 (m-30)
REVERT: C  145 LYS cc_start: 0.8464 (mmtm) cc_final: 0.8154 (mmtm)
REVERT: C  170 THR cc_start: 0.8471 (p) cc_final: 0.8192 (p)
REVERT: C  211 ASP cc_start: 0.7921 (m-30) cc_final: 0.7705 (m-30)
REVERT: D   49 ARG cc_start: 0.7624 (mpt180) cc_final: 0.7399 (mmt-90)
REVERT: N   36 TRP cc_start: 0.8190 (m100) cc_final: 0.7627 (m100)
  outliers start: 12
  outliers final: 8
  residues processed: 130
  average time/residue: 0.0956
  time to fit residues: 16.0162
Evaluate side-chains
  131 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 123
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  195 CYS
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  165 THR
Chi-restraints excluded: chain D residue  243 THR
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  329 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 6 optimal weight:    0.6980
   chunk 25 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 52 optimal weight:    0.5980
   chunk 33 optimal weight:    0.3980
   chunk 4 optimal weight:    2.9990
   chunk 42 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 58 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0980
   chunk 80 optimal weight:    0.8980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
D 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.156406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.134998 restraints weight = 9296.601|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 2.65
r_work: 0.3645 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7130
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6405  Z= 0.179
  Angle     :  0.552   6.663   8699  Z= 0.295
  Chirality :  0.043   0.175    992
  Planarity :  0.004   0.045   1120
  Dihedral  :  4.663  26.890    896
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 14.37 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.75 (0.31), residues: 826
  helix:  2.12 (0.48), residues: 143
  sheet: -0.47 (0.32), residues: 278
  loop : -1.50 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  68 
 TYR   0.024   0.002   TYR N 223 
 PHE   0.016   0.002   PHE D 253 
 TRP   0.014   0.001   TRP D 211 
 HIS   0.004   0.001   HIS D 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 6404)
  covalent geometry    : angle       0.55248 ( 8697)
  SS BOND              : bond        0.00123 (    1)
  SS BOND              : angle       0.48171 (    2)
  hydrogen bonds       : bond        0.03295 (  239)
  hydrogen bonds       : angle       5.03895 (  660)

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

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

  1652 Ramachandran restraints generated.
    826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1652 Ramachandran restraints generated.
    826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 122
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
REVERT: C    9 ASP cc_start: 0.6833 (m-30) cc_final: 0.6577 (m-30)
REVERT: C  145 LYS cc_start: 0.8452 (mmtm) cc_final: 0.8144 (mmtm)
REVERT: C  170 THR cc_start: 0.8451 (p) cc_final: 0.8162 (p)
REVERT: C  211 ASP cc_start: 0.7973 (m-30) cc_final: 0.7750 (m-30)
REVERT: D   49 ARG cc_start: 0.7645 (mpt180) cc_final: 0.7398 (mmt-90)
REVERT: N   36 TRP cc_start: 0.8197 (m100) cc_final: 0.7628 (m100)
  outliers start: 10
  outliers final: 8
  residues processed: 126
  average time/residue: 0.0909
  time to fit residues: 14.6648
Evaluate side-chains
  128 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  195 CYS
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  165 THR
Chi-restraints excluded: chain D residue  243 THR
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  329 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 30 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
D 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.153355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.132676 restraints weight = 9113.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3738 rms_B_bonded: 2.53
r_work: 0.3618 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7167
moved from start:          0.1883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   6405  Z= 0.269
  Angle     :  0.622   7.786   8699  Z= 0.331
  Chirality :  0.046   0.206    992
  Planarity :  0.004   0.047   1120
  Dihedral  :  5.028  29.359    896
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.11 %
    Favored  : 91.89 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.15 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.96 (0.30), residues: 826
  helix:  1.93 (0.48), residues: 143
  sheet: -0.68 (0.31), residues: 278
  loop : -1.55 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D 197 
 TYR   0.027   0.002   TYR N 223 
 PHE   0.024   0.002   PHE D 253 
 TRP   0.020   0.002   TRP D 211 
 HIS   0.006   0.001   HIS D  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00622 ( 6404)
  covalent geometry    : angle       0.62243 ( 8697)
  SS BOND              : bond        0.00069 (    1)
  SS BOND              : angle       0.20198 (    2)
  hydrogen bonds       : bond        0.03682 (  239)
  hydrogen bonds       : angle       5.18573 (  660)

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

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

  1652 Ramachandran restraints generated.
    826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1652 Ramachandran restraints generated.
    826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 131
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
REVERT: C    9 ASP cc_start: 0.6889 (m-30) cc_final: 0.6621 (m-30)
REVERT: C  145 LYS cc_start: 0.8422 (mmtm) cc_final: 0.8121 (mmtm)
REVERT: C  170 THR cc_start: 0.8480 (p) cc_final: 0.8247 (p)
REVERT: C  211 ASP cc_start: 0.7980 (m-30) cc_final: 0.7766 (m-30)
REVERT: D   49 ARG cc_start: 0.7688 (mpt180) cc_final: 0.7426 (mmt-90)
REVERT: D  165 THR cc_start: 0.7930 (OUTLIER) cc_final: 0.7393 (p)
REVERT: N   36 TRP cc_start: 0.8212 (m100) cc_final: 0.7667 (m100)
REVERT: N   77 ASN cc_start: 0.7095 (m-40) cc_final: 0.6850 (m-40)
  outliers start: 14
  outliers final: 10
  residues processed: 135
  average time/residue: 0.0912
  time to fit residues: 15.9727
Evaluate side-chains
  138 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  195 CYS
Chi-restraints excluded: chain C residue  198 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  165 THR
Chi-restraints excluded: chain D residue  243 THR
Chi-restraints excluded: chain D residue  284 LEU
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  329 THR
Chi-restraints excluded: chain N residue   11 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 57 optimal weight:    0.6980
   chunk 12 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 65 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 69 optimal weight:    0.2980
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
D 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.154320 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.133716 restraints weight = 8988.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3747 rms_B_bonded: 2.50
r_work: 0.3630 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7145
moved from start:          0.1961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   6405  Z= 0.215
  Angle     :  0.589   7.297   8699  Z= 0.315
  Chirality :  0.045   0.199    992
  Planarity :  0.004   0.047   1120
  Dihedral  :  4.934  29.774    896
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 16.85 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.98 (0.30), residues: 826
  helix:  1.93 (0.48), residues: 143
  sheet: -0.72 (0.31), residues: 283
  loop : -1.56 (0.31), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 219 
 TYR   0.027   0.002   TYR N 223 
 PHE   0.019   0.002   PHE D 199 
 TRP   0.015   0.002   TRP D 211 
 HIS   0.005   0.001   HIS D  91 

Details of bonding type rmsd
  covalent geometry    : bond        0.00502 ( 6404)
  covalent geometry    : angle       0.58934 ( 8697)
  SS BOND              : bond        0.00050 (    1)
  SS BOND              : angle       0.37624 (    2)
  hydrogen bonds       : bond        0.03406 (  239)
  hydrogen bonds       : angle       5.04764 (  660)

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

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

  1652 Ramachandran restraints generated.
    826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1652 Ramachandran restraints generated.
    826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: C    9 ASP cc_start: 0.6859 (m-30) cc_final: 0.6601 (m-30)
REVERT: C  145 LYS cc_start: 0.8439 (mmtm) cc_final: 0.8115 (mmtm)
REVERT: C  170 THR cc_start: 0.8485 (p) cc_final: 0.8214 (p)
REVERT: C  211 ASP cc_start: 0.7945 (m-30) cc_final: 0.7734 (m-30)
REVERT: D   49 ARG cc_start: 0.7655 (mpt180) cc_final: 0.7440 (mmt-90)
REVERT: D  165 THR cc_start: 0.7852 (OUTLIER) cc_final: 0.7325 (p)
REVERT: N   36 TRP cc_start: 0.8194 (m100) cc_final: 0.7642 (m100)
  outliers start: 10
  outliers final: 8
  residues processed: 134
  average time/residue: 0.0966
  time to fit residues: 16.6357
Evaluate side-chains
  139 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 130
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  195 CYS
Chi-restraints excluded: chain C residue  198 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  165 THR
Chi-restraints excluded: chain D residue  243 THR
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  329 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 4 optimal weight:    0.1980
   chunk 29 optimal weight:    0.4980
   chunk 32 optimal weight:    0.5980
   chunk 69 optimal weight:    0.6980
   chunk 12 optimal weight:    0.3980
   chunk 8 optimal weight:    0.0070
   chunk 64 optimal weight:    0.2980
   chunk 1 optimal weight:    0.5980
   chunk 80 optimal weight:    0.5980
   overall best weight:    0.2798

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

Flipped N/Q/H residues before XYZ refinement:
D 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.156379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.135507 restraints weight = 9120.617|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 2.60
r_work: 0.3657 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.1971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6405  Z= 0.128
  Angle     :  0.532   6.473   8699  Z= 0.285
  Chirality :  0.042   0.167    992
  Planarity :  0.004   0.044   1120
  Dihedral  :  4.543  25.899    896
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 17.00 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.83 (0.31), residues: 826
  helix:  2.08 (0.48), residues: 143
  sheet: -0.63 (0.31), residues: 285
  loop : -1.47 (0.31), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D 197 
 TYR   0.024   0.002   TYR N 223 
 PHE   0.019   0.001   PHE C  74 
 TRP   0.014   0.001   TRP D 169 
 HIS   0.003   0.001   HIS N  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 6404)
  covalent geometry    : angle       0.53185 ( 8697)
  SS BOND              : bond        0.00189 (    1)
  SS BOND              : angle       0.68670 (    2)
  hydrogen bonds       : bond        0.02950 (  239)
  hydrogen bonds       : angle       4.77381 (  660)

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

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

  1652 Ramachandran restraints generated.
    826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1652 Ramachandran restraints generated.
    826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 120
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
REVERT: C    9 ASP cc_start: 0.6824 (m-30) cc_final: 0.6584 (m-30)
REVERT: C  118 MET cc_start: 0.8444 (tpp) cc_final: 0.7932 (tpp)
REVERT: C  145 LYS cc_start: 0.8430 (mmtm) cc_final: 0.8117 (mmtm)
REVERT: C  170 THR cc_start: 0.8423 (p) cc_final: 0.8184 (p)
REVERT: C  211 ASP cc_start: 0.7952 (m-30) cc_final: 0.7711 (m-30)
REVERT: N   36 TRP cc_start: 0.8198 (m100) cc_final: 0.7586 (m100)
  outliers start: 13
  outliers final: 10
  residues processed: 127
  average time/residue: 0.1014
  time to fit residues: 16.5245
Evaluate side-chains
  127 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  195 CYS
Chi-restraints excluded: chain C residue  198 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  165 THR
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  243 THR
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  329 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 78 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9990
   chunk 12 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 61 optimal weight:    0.0980
   chunk 18 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
D 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.153242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.132445 restraints weight = 9109.619|
|-----------------------------------------------------------------------------|
r_work (start): 0.3734 rms_B_bonded: 2.56
r_work: 0.3616 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7157
moved from start:          0.2090

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.046   6405  Z= 0.240
  Angle     :  0.619   8.630   8699  Z= 0.329
  Chirality :  0.046   0.202    992
  Planarity :  0.005   0.047   1120
  Dihedral  :  4.907  28.397    896
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.47 %
    Favored  : 91.53 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.47 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.98 (0.30), residues: 826
  helix:  1.92 (0.48), residues: 143
  sheet: -0.71 (0.31), residues: 296
  loop : -1.58 (0.31), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  49 
 TYR   0.026   0.002   TYR N 223 
 PHE   0.020   0.002   PHE D 253 
 TRP   0.014   0.002   TRP D 211 
 HIS   0.005   0.001   HIS N  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00555 ( 6404)
  covalent geometry    : angle       0.61871 ( 8697)
  SS BOND              : bond        0.00004 (    1)
  SS BOND              : angle       0.38520 (    2)
  hydrogen bonds       : bond        0.03519 (  239)
  hydrogen bonds       : angle       4.99146 (  660)

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

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

  1652 Ramachandran restraints generated.
    826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1652 Ramachandran restraints generated.
    826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 127
  time to evaluate  : 0.233 
Fit side-chains
   revert: symmetry clash
REVERT: C    9 ASP cc_start: 0.6891 (m-30) cc_final: 0.6610 (m-30)
REVERT: C  145 LYS cc_start: 0.8440 (mmtm) cc_final: 0.8115 (mmtm)
REVERT: C  170 THR cc_start: 0.8450 (p) cc_final: 0.8204 (p)
REVERT: C  211 ASP cc_start: 0.7972 (m-30) cc_final: 0.7749 (m-30)
REVERT: D  165 THR cc_start: 0.7899 (OUTLIER) cc_final: 0.7318 (p)
REVERT: N   36 TRP cc_start: 0.8173 (m100) cc_final: 0.7619 (m100)
  outliers start: 16
  outliers final: 14
  residues processed: 135
  average time/residue: 0.0944
  time to fit residues: 16.3829
Evaluate side-chains
  140 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   18 MET
Chi-restraints excluded: chain C residue   86 VAL
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  160 ILE
Chi-restraints excluded: chain C residue  195 CYS
Chi-restraints excluded: chain C residue  198 THR
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  165 THR
Chi-restraints excluded: chain D residue  229 ILE
Chi-restraints excluded: chain D residue  243 THR
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  329 THR
Chi-restraints excluded: chain Y residue   15 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 36 optimal weight:    0.6980
   chunk 2 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 30 optimal weight:    0.0060
   chunk 65 optimal weight:    0.4980
   chunk 23 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 29 optimal weight:    0.3980
   chunk 20 optimal weight:    0.4980
   chunk 81 optimal weight:    0.0770
   chunk 19 optimal weight:    0.2980
   overall best weight:    0.2554

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

Flipped N/Q/H residues before XYZ refinement:
D 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.156500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.135786 restraints weight = 8980.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3774 rms_B_bonded: 2.54
r_work: 0.3655 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7105
moved from start:          0.2100

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6405  Z= 0.126
  Angle     :  0.552   9.065   8699  Z= 0.294
  Chirality :  0.043   0.170    992
  Planarity :  0.004   0.044   1120
  Dihedral  :  4.580  25.640    896
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.81 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 17.77 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.77 (0.30), residues: 826
  helix:  2.09 (0.48), residues: 143
  sheet: -0.58 (0.31), residues: 291
  loop : -1.43 (0.32), residues: 392

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG D 197 
 TYR   0.025   0.002   TYR N 223 
 PHE   0.014   0.001   PHE D 199 
 TRP   0.014   0.001   TRP D 169 
 HIS   0.003   0.001   HIS D 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6404)
  covalent geometry    : angle       0.55154 ( 8697)
  SS BOND              : bond        0.00291 (    1)
  SS BOND              : angle       0.61036 (    2)
  hydrogen bonds       : bond        0.02958 (  239)
  hydrogen bonds       : angle       4.78935 (  660)

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

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

  1652 Ramachandran restraints generated.
    826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1652 Ramachandran restraints generated.
    826 Oldfield, 0 Emsley, 826 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 0.253 
Fit side-chains
   revert: symmetry clash
REVERT: C    9 ASP cc_start: 0.6822 (m-30) cc_final: 0.6572 (m-30)
REVERT: C  118 MET cc_start: 0.8404 (tpp) cc_final: 0.7923 (tpp)
REVERT: C  145 LYS cc_start: 0.8434 (mmtm) cc_final: 0.8120 (mmtm)
REVERT: C  170 THR cc_start: 0.8413 (p) cc_final: 0.8145 (p)
REVERT: C  211 ASP cc_start: 0.7923 (m-30) cc_final: 0.7706 (m-30)
REVERT: D   66 ASP cc_start: 0.7362 (p0) cc_final: 0.7079 (p0)
REVERT: D  165 THR cc_start: 0.7869 (t) cc_final: 0.7315 (p)
REVERT: N   36 TRP cc_start: 0.8185 (m100) cc_final: 0.7596 (m100)
  outliers start: 13
  outliers final: 13
  residues processed: 127
  average time/residue: 0.0950
  time to fit residues: 15.6002
Evaluate side-chains
  129 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   97 ILE
Chi-restraints excluded: chain C residue  124 LEU
Chi-restraints excluded: chain C residue  160 ILE
Chi-restraints excluded: chain C residue  195 CYS
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  187 VAL
Chi-restraints excluded: chain D residue  229 ILE
Chi-restraints excluded: chain D residue  234 PHE
Chi-restraints excluded: chain D residue  243 THR
Chi-restraints excluded: chain D residue  315 VAL
Chi-restraints excluded: chain D residue  318 LEU
Chi-restraints excluded: chain D residue  329 THR
Chi-restraints excluded: chain Y residue   15 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 36 optimal weight:    0.6980
   chunk 39 optimal weight:    0.6980
   chunk 0 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0980
   chunk 49 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 56 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9990
   chunk 79 optimal weight:    0.1980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
** C 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 110 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.154871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.134111 restraints weight = 9106.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 2.57
r_work: 0.3636 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3636
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7133
moved from start:          0.2143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6405  Z= 0.182
  Angle     :  0.581   8.316   8699  Z= 0.309
  Chirality :  0.044   0.182    992
  Planarity :  0.004   0.046   1120
  Dihedral  :  4.702  25.866    896
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  7.38 %
    Favored  : 92.49 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 17.62 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.82 (0.30), residues: 826
  helix:  2.06 (0.48), residues: 143
  sheet: -0.59 (0.31), residues: 286
  loop : -1.48 (0.31), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D 197 
 TYR   0.025   0.002   TYR N 223 
 PHE   0.021   0.002   PHE C  74 
 TRP   0.013   0.001   TRP D 169 
 HIS   0.004   0.001   HIS D 225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 6404)
  covalent geometry    : angle       0.58109 ( 8697)
  SS BOND              : bond        0.00226 (    1)
  SS BOND              : angle       0.27170 (    2)
  hydrogen bonds       : bond        0.03142 (  239)
  hydrogen bonds       : angle       4.82613 (  660)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1591.07 seconds
wall clock time: 28 minutes 9.65 seconds (1689.65 seconds total)