Starting phenix.real_space_refine
on Tue Feb 11 16:38:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iec_35378/02_2025/8iec_35378.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iec_35378/02_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iec_35378/02_2025/8iec_35378.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iec_35378/02_2025/8iec_35378.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iec_35378/02_2025/8iec_35378.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iec_35378/02_2025/8iec_35378.cif"
  }
  resolution = 3.18
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.014
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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP: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: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 4, 'ASP:plan': 3}
          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: {'GLN:plan1': 1, 'GLU:plan': 7, '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: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 17
  Time building chain proxies: 4.72, per 1000 atoms: 0.75
  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: 1.48
  Conformation dependent library (CDL) restraints added in 922.8 milliseconds
  

  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: 0.83
  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: 2.10

  Time building geometry restraints manager: 1.66 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:             8.240
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.330
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.870
-------------------------------------------------------------------------------
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   6404  Z= 0.289
  Angle     :  0.658   8.175   8697  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (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
 TRP   0.015   0.002   TRP D 169 
 HIS   0.006   0.001   HIS N 220 
 PHE   0.017   0.002   PHE D 199 
 TYR   0.022   0.002   TYR N 223 
 ARG   0.003   0.000   ARG N  72 

*********************** 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  : 0.656 
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: 0.5830 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 142
  average time/residue: 0.2273
  time to fit residues: 40.6625
Evaluate side-chains
  132 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 62 optimal weight:    0.3980
   chunk 34 optimal weight:    0.0060
   chunk 21 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0970
   chunk 39 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.3594

-------------------------------------------------------------------------------
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 = 0.4051 r_free = 0.4051 target = 0.158496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.136733 restraints weight = 9053.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3776 rms_B_bonded: 2.65
r_work: 0.3656 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7098
moved from start:          0.1087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6404  Z= 0.245
  Angle     :  0.560   6.374   8697  Z= 0.300
  Chirality :  0.043   0.162    992
  Planarity :  0.004   0.044   1120
  Dihedral  :  4.672  30.862    896
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  :  7.11 %
    Favored  : 91.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.30), residues: 826
  helix:  1.87 (0.46), residues: 143
  sheet: -0.64 (0.32), residues: 281
  loop : -1.50 (0.31), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP D 211 
 HIS   0.005   0.001   HIS N  35 
 PHE   0.018   0.002   PHE D 253 
 TYR   0.025   0.002   TYR N 223 
 ARG   0.004   0.000   ARG D 219 

*********************** 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
  138 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 130
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
REVERT: C   32 LYS cc_start: 0.8359 (mtmm) cc_final: 0.8096 (mtmm)
REVERT: C  145 LYS cc_start: 0.8491 (mmtm) cc_final: 0.8201 (mmtm)
REVERT: C  170 THR cc_start: 0.8443 (p) cc_final: 0.8075 (p)
REVERT: C  211 ASP cc_start: 0.7893 (m-30) cc_final: 0.7678 (m-30)
REVERT: D   75 GLN cc_start: 0.8043 (mm110) cc_final: 0.7593 (mp10)
REVERT: D  243 THR cc_start: 0.7262 (m) cc_final: 0.6813 (m)
REVERT: D  258 ASP cc_start: 0.7150 (t0) cc_final: 0.6914 (t0)
REVERT: D  293 ASN cc_start: 0.7088 (t0) cc_final: 0.6886 (t0)
REVERT: D  298 ASP cc_start: 0.6823 (m-30) cc_final: 0.6403 (m-30)
REVERT: N   20 LEU cc_start: 0.7137 (mm) cc_final: 0.6920 (mt)
REVERT: N   36 TRP cc_start: 0.8220 (m100) cc_final: 0.7647 (m100)
REVERT: N  200 PHE cc_start: 0.8048 (m-80) cc_final: 0.7713 (m-80)
  outliers start: 8
  outliers final: 5
  residues processed: 133
  average time/residue: 0.2183
  time to fit residues: 36.9204
Evaluate side-chains
  133 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 128
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 16 optimal weight:    0.4980
   chunk 46 optimal weight:    0.0470
   chunk 17 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0040
   chunk 44 optimal weight:    0.0980
   chunk 21 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.2690

-------------------------------------------------------------------------------
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 = 0.4062 r_free = 0.4062 target = 0.159659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.137736 restraints weight = 9195.742|
|-----------------------------------------------------------------------------|
r_work (start): 0.3786 rms_B_bonded: 2.69
r_work: 0.3666 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7087
moved from start:          0.1418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6404  Z= 0.202
  Angle     :  0.526   6.217   8697  Z= 0.282
  Chirality :  0.043   0.164    992
  Planarity :  0.004   0.043   1120
  Dihedral  :  4.486  28.167    896
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 10.66 %
    Favored  : 88.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.31), residues: 826
  helix:  2.12 (0.47), residues: 143
  sheet: -0.46 (0.31), residues: 278
  loop : -1.40 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 169 
 HIS   0.004   0.001   HIS N  35 
 PHE   0.013   0.001   PHE D 253 
 TYR   0.023   0.001   TYR N 223 
 ARG   0.004   0.000   ARG D 219 

*********************** 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
  131 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 123
  time to evaluate  : 0.724 
Fit side-chains
   revert: symmetry clash
REVERT: C   32 LYS cc_start: 0.8351 (mtmm) cc_final: 0.8084 (mtmm)
REVERT: C  145 LYS cc_start: 0.8455 (mmtm) cc_final: 0.8142 (mmtm)
REVERT: C  170 THR cc_start: 0.8469 (p) cc_final: 0.8173 (p)
REVERT: C  211 ASP cc_start: 0.7903 (m-30) cc_final: 0.7680 (m-30)
REVERT: D   49 ARG cc_start: 0.7626 (mpt180) cc_final: 0.7421 (mmt-90)
REVERT: D   75 GLN cc_start: 0.8036 (mm110) cc_final: 0.7595 (mp10)
REVERT: N   36 TRP cc_start: 0.8202 (m100) cc_final: 0.7603 (m100)
  outliers start: 8
  outliers final: 5
  residues processed: 126
  average time/residue: 0.2172
  time to fit residues: 35.1980
Evaluate side-chains
  125 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 120
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 11 optimal weight:    0.6980
   chunk 81 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0270
   chunk 63 optimal weight:    0.5980
   chunk 22 optimal weight:    2.9990
   chunk 21 optimal weight:    0.7980
   chunk 59 optimal weight:    0.6980
   chunk 26 optimal weight:    0.1980
   chunk 37 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.4438

-------------------------------------------------------------------------------
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 = 0.4039 r_free = 0.4039 target = 0.156662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.135586 restraints weight = 9138.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3777 rms_B_bonded: 2.60
r_work: 0.3660 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.3660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   6404  Z= 0.270
  Angle     :  0.549   6.499   8697  Z= 0.294
  Chirality :  0.043   0.170    992
  Planarity :  0.004   0.044   1120
  Dihedral  :  4.579  26.618    896
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.66 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 12.36 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.31), residues: 826
  helix:  2.17 (0.48), residues: 143
  sheet: -0.43 (0.32), residues: 278
  loop : -1.43 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP D 211 
 HIS   0.005   0.001   HIS N  35 
 PHE   0.017   0.002   PHE D 253 
 TYR   0.024   0.002   TYR N 223 
 ARG   0.005   0.000   ARG D  68 

*********************** 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: 14
    poor density    : 123
  time to evaluate  : 0.642 
Fit side-chains
   revert: symmetry clash
REVERT: C    9 ASP cc_start: 0.6817 (m-30) cc_final: 0.6553 (m-30)
REVERT: C  145 LYS cc_start: 0.8440 (mmtm) cc_final: 0.8144 (mmtm)
REVERT: C  170 THR cc_start: 0.8496 (p) cc_final: 0.8219 (p)
REVERT: C  211 ASP cc_start: 0.7938 (m-30) cc_final: 0.7723 (m-30)
REVERT: D   49 ARG cc_start: 0.7653 (mpt180) cc_final: 0.7405 (mmt-90)
REVERT: N   36 TRP cc_start: 0.8174 (m100) cc_final: 0.7624 (m100)
  outliers start: 14
  outliers final: 10
  residues processed: 128
  average time/residue: 0.2102
  time to fit residues: 34.3975
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  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  122 LEU
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
Chi-restraints excluded: chain N residue   11 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 41 optimal weight:    0.4980
   chunk 49 optimal weight:    0.0970
   chunk 65 optimal weight:    0.3980
   chunk 43 optimal weight:    0.9980
   chunk 31 optimal weight:    0.3980
   chunk 63 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 11 optimal weight:    0.4980
   chunk 34 optimal weight:    0.8980
   chunk 60 optimal weight:    0.0670
   chunk 59 optimal weight:    0.1980
   overall best weight:    0.2316

-------------------------------------------------------------------------------
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 = 0.4064 r_free = 0.4064 target = 0.158717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.137356 restraints weight = 9155.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3799 rms_B_bonded: 2.65
r_work: 0.3679 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7081
moved from start:          0.1726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6404  Z= 0.182
  Angle     :  0.509   5.768   8697  Z= 0.273
  Chirality :  0.042   0.155    992
  Planarity :  0.004   0.042   1120
  Dihedral  :  4.339  24.445    896
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.14 %
    Favored  : 84.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.59 (0.31), residues: 826
  helix:  2.24 (0.48), residues: 143
  sheet: -0.45 (0.31), residues: 284
  loop : -1.32 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 169 
 HIS   0.003   0.001   HIS N  35 
 PHE   0.012   0.001   PHE D 199 
 TYR   0.022   0.001   TYR N 223 
 ARG   0.006   0.000   ARG D  68 

*********************** 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
  135 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 0.658 
Fit side-chains
   revert: symmetry clash
REVERT: C    9 ASP cc_start: 0.6776 (m-30) cc_final: 0.6524 (m-30)
REVERT: C  118 MET cc_start: 0.8456 (tpp) cc_final: 0.7993 (tpp)
REVERT: C  145 LYS cc_start: 0.8441 (mmtm) cc_final: 0.8164 (mmtm)
REVERT: C  170 THR cc_start: 0.8446 (p) cc_final: 0.8171 (p)
REVERT: C  211 ASP cc_start: 0.7941 (m-30) cc_final: 0.7708 (m-30)
REVERT: N   36 TRP cc_start: 0.8174 (m100) cc_final: 0.7603 (m100)
  outliers start: 14
  outliers final: 9
  residues processed: 127
  average time/residue: 0.2136
  time to fit residues: 34.6731
Evaluate side-chains
  127 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
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  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 N residue   11 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 42 optimal weight:    0.0070
   chunk 1 optimal weight:    0.9980
   chunk 81 optimal weight:    0.0970
   chunk 76 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 57 optimal weight:    0.3980
   chunk 17 optimal weight:    0.5980
   chunk 41 optimal weight:    0.0970
   chunk 75 optimal weight:    0.6980
   chunk 13 optimal weight:    0.8980
   overall best weight:    0.2394

-------------------------------------------------------------------------------
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 = 0.4051 r_free = 0.4051 target = 0.156919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.136141 restraints weight = 9092.534|
|-----------------------------------------------------------------------------|
r_work (start): 0.3791 rms_B_bonded: 2.56
r_work: 0.3674 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7072
moved from start:          0.1811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6404  Z= 0.182
  Angle     :  0.506   5.800   8697  Z= 0.271
  Chirality :  0.042   0.151    992
  Planarity :  0.004   0.042   1120
  Dihedral  :  4.231  22.502    896
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 13.91 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.31), residues: 826
  helix:  2.35 (0.47), residues: 142
  sheet: -0.43 (0.32), residues: 277
  loop : -1.36 (0.32), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 169 
 HIS   0.003   0.001   HIS N  35 
 PHE   0.019   0.001   PHE C  74 
 TYR   0.021   0.001   TYR N 223 
 ARG   0.006   0.000   ARG D 197 

*********************** 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
  131 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
REVERT: C    9 ASP cc_start: 0.6763 (m-30) cc_final: 0.6524 (m-30)
REVERT: C  118 MET cc_start: 0.8439 (tpp) cc_final: 0.7973 (tpp)
REVERT: C  170 THR cc_start: 0.8416 (p) cc_final: 0.8145 (p)
REVERT: C  211 ASP cc_start: 0.7903 (m-30) cc_final: 0.7671 (m-30)
REVERT: N   36 TRP cc_start: 0.8170 (m100) cc_final: 0.7585 (m100)
  outliers start: 13
  outliers final: 11
  residues processed: 123
  average time/residue: 0.2251
  time to fit residues: 35.6904
Evaluate side-chains
  128 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   97 ILE
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  228 ASP
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 N residue   11 LEU
Chi-restraints excluded: chain N residue  130 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0970
   chunk 81 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0980
   chunk 3 optimal weight:    0.8980
   chunk 69 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 56 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0670
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.3316

-------------------------------------------------------------------------------
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 = 0.156213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.135607 restraints weight = 9141.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3784 rms_B_bonded: 2.52
r_work: 0.3666 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7087
moved from start:          0.1872

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6404  Z= 0.217
  Angle     :  0.523   6.633   8697  Z= 0.279
  Chirality :  0.042   0.159    992
  Planarity :  0.004   0.042   1120
  Dihedral  :  4.305  25.027    896
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 15.30 %
    Favored  : 82.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.31), residues: 826
  helix:  2.26 (0.47), residues: 143
  sheet: -0.49 (0.31), residues: 278
  loop : -1.35 (0.32), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 211 
 HIS   0.004   0.001   HIS N  35 
 PHE   0.014   0.001   PHE D 253 
 TYR   0.022   0.002   TYR N 223 
 ARG   0.005   0.000   ARG D 219 

*********************** 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
  131 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 119
  time to evaluate  : 0.682 
Fit side-chains
   revert: symmetry clash
REVERT: C    9 ASP cc_start: 0.6817 (m-30) cc_final: 0.6559 (m-30)
REVERT: C  118 MET cc_start: 0.8427 (tpp) cc_final: 0.7914 (tpp)
REVERT: C  170 THR cc_start: 0.8394 (p) cc_final: 0.8131 (p)
REVERT: C  211 ASP cc_start: 0.7919 (m-30) cc_final: 0.7687 (m-30)
REVERT: N   36 TRP cc_start: 0.8191 (m100) cc_final: 0.7620 (m100)
  outliers start: 12
  outliers final: 12
  residues processed: 124
  average time/residue: 0.2125
  time to fit residues: 34.0528
Evaluate side-chains
  132 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
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  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  228 ASP
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 48 optimal weight:    0.8980
   chunk 67 optimal weight:    0.0270
   chunk 5 optimal weight:    0.0000
   chunk 0 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 40 optimal weight:    0.0970
   chunk 23 optimal weight:    0.0670
   chunk 25 optimal weight:    1.9990
   chunk 14 optimal weight:    0.3980
   overall best weight:    0.1178

-------------------------------------------------------------------------------
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 = 0.4066 r_free = 0.4066 target = 0.158225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.137437 restraints weight = 9123.174|
|-----------------------------------------------------------------------------|
r_work (start): 0.3809 rms_B_bonded: 2.57
r_work: 0.3692 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7047
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   6404  Z= 0.145
  Angle     :  0.497   5.713   8697  Z= 0.265
  Chirality :  0.041   0.141    992
  Planarity :  0.003   0.041   1120
  Dihedral  :  4.067  21.336    896
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 15.77 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.31), residues: 826
  helix:  2.36 (0.47), residues: 142
  sheet: -0.47 (0.31), residues: 275
  loop : -1.26 (0.32), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 169 
 HIS   0.002   0.001   HIS D 225 
 PHE   0.020   0.001   PHE C  74 
 TYR   0.021   0.001   TYR N 223 
 ARG   0.006   0.000   ARG D  49 

*********************** 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
  130 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
REVERT: C  118 MET cc_start: 0.8417 (tpp) cc_final: 0.7955 (tpp)
REVERT: C  145 LYS cc_start: 0.8426 (mmtm) cc_final: 0.8151 (mmtm)
REVERT: C  170 THR cc_start: 0.8358 (p) cc_final: 0.8090 (p)
REVERT: C  211 ASP cc_start: 0.7936 (m-30) cc_final: 0.7705 (m-30)
REVERT: N   36 TRP cc_start: 0.8170 (m100) cc_final: 0.7542 (m100)
  outliers start: 10
  outliers final: 9
  residues processed: 124
  average time/residue: 0.2184
  time to fit residues: 34.7601
Evaluate side-chains
  129 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 120
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
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  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 65 optimal weight:    0.4980
   chunk 63 optimal weight:    0.3980
   chunk 66 optimal weight:    2.9990
   chunk 2 optimal weight:    0.7980
   chunk 9 optimal weight:    0.2980
   chunk 51 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0470
   chunk 41 optimal weight:    0.0870
   chunk 37 optimal weight:    0.2980
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.2256

-------------------------------------------------------------------------------
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 = 0.4056 r_free = 0.4056 target = 0.157265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.136333 restraints weight = 9222.919|
|-----------------------------------------------------------------------------|
r_work (start): 0.3795 rms_B_bonded: 2.59
r_work: 0.3678 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3678
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7068
moved from start:          0.2049

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6404  Z= 0.178
  Angle     :  0.517   6.530   8697  Z= 0.276
  Chirality :  0.042   0.164    992
  Planarity :  0.003   0.042   1120
  Dihedral  :  4.045  20.099    896
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 16.69 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.52 (0.31), residues: 826
  helix:  2.39 (0.47), residues: 142
  sheet: -0.45 (0.31), residues: 284
  loop : -1.27 (0.33), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D 169 
 HIS   0.003   0.001   HIS N  35 
 PHE   0.011   0.001   PHE D 253 
 TYR   0.021   0.001   TYR N 223 
 ARG   0.006   0.000   ARG D  49 

*********************** 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
  126 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 117
  time to evaluate  : 0.717 
Fit side-chains
   revert: symmetry clash
REVERT: C    9 ASP cc_start: 0.6759 (m-30) cc_final: 0.6501 (m-30)
REVERT: C  118 MET cc_start: 0.8412 (tpp) cc_final: 0.7947 (tpp)
REVERT: C  145 LYS cc_start: 0.8424 (mmtm) cc_final: 0.8162 (mmtm)
REVERT: C  170 THR cc_start: 0.8375 (p) cc_final: 0.8119 (p)
REVERT: C  211 ASP cc_start: 0.7937 (m-30) cc_final: 0.7701 (m-30)
REVERT: D  325 MET cc_start: 0.7784 (tpp) cc_final: 0.7498 (tpp)
REVERT: N   36 TRP cc_start: 0.8171 (m100) cc_final: 0.7565 (m100)
  outliers start: 9
  outliers final: 9
  residues processed: 121
  average time/residue: 0.2313
  time to fit residues: 35.7616
Evaluate side-chains
  128 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 119
  time to evaluate  : 0.630 
-------------------------------------------------------------------------------
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0980
   chunk 22 optimal weight:    2.9990
   chunk 56 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 61 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   chunk 34 optimal weight:    0.0770
   chunk 14 optimal weight:    0.6980
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.4138

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

Flipped N/Q/H residues before XYZ refinement:
C 196 HIS
D 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.155200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.134095 restraints weight = 9269.460|
|-----------------------------------------------------------------------------|
r_work (start): 0.3768 rms_B_bonded: 2.61
r_work: 0.3650 rms_B_bonded: 3.17 restraints_weight: 0.5000
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7105
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6404  Z= 0.251
  Angle     :  0.554   6.882   8697  Z= 0.293
  Chirality :  0.043   0.162    992
  Planarity :  0.003   0.042   1120
  Dihedral  :  4.245  23.142    896
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 16.07 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.31), residues: 826
  helix:  2.28 (0.48), residues: 143
  sheet: -0.49 (0.31), residues: 283
  loop : -1.28 (0.33), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP D 211 
 HIS   0.004   0.001   HIS N  35 
 PHE   0.021   0.002   PHE C  74 
 TYR   0.023   0.002   TYR N 223 
 ARG   0.005   0.000   ARG D 219 

********************** 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
  134 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 123
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
REVERT: C    9 ASP cc_start: 0.6821 (m-30) cc_final: 0.6556 (m-30)
REVERT: C  118 MET cc_start: 0.8395 (tpp) cc_final: 0.7868 (tpp)
REVERT: C  170 THR cc_start: 0.8380 (p) cc_final: 0.8144 (p)
REVERT: C  211 ASP cc_start: 0.7952 (m-30) cc_final: 0.7732 (m-30)
REVERT: D   49 ARG cc_start: 0.7781 (mpt180) cc_final: 0.7466 (mmt-90)
REVERT: D  325 MET cc_start: 0.7802 (tpp) cc_final: 0.7588 (tpp)
REVERT: N   36 TRP cc_start: 0.8189 (m100) cc_final: 0.7613 (m100)
  outliers start: 11
  outliers final: 11
  residues processed: 127
  average time/residue: 0.2024
  time to fit residues: 33.2210
Evaluate side-chains
  130 residues out of total 711 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 119
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
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  196 HIS
Chi-restraints excluded: chain D residue   87 THR
Chi-restraints excluded: chain D residue  228 ASP
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 N residue  162 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 10 optimal weight:    0.1980
   chunk 19 optimal weight:    0.8980
   chunk 7 optimal weight:    0.4980
   chunk 29 optimal weight:    0.3980
   chunk 49 optimal weight:    0.0980
   chunk 21 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0050
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.2394

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

Flipped N/Q/H residues before XYZ refinement:
C 196 HIS
D 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.156540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.135501 restraints weight = 9355.684|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 2.62
r_work: 0.3666 rms_B_bonded: 3.19 restraints_weight: 0.5000
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.2097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6404  Z= 0.189
  Angle     :  0.532   5.967   8697  Z= 0.283
  Chirality :  0.042   0.154    992
  Planarity :  0.003   0.042   1120
  Dihedral  :  4.159  20.788    896
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 17.16 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.31), residues: 826
  helix:  2.34 (0.47), residues: 142
  sheet: -0.48 (0.31), residues: 284
  loop : -1.25 (0.33), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 169 
 HIS   0.004   0.001   HIS C 196 
 PHE   0.012   0.001   PHE D 199 
 TYR   0.023   0.001   TYR N 223 
 ARG   0.005   0.000   ARG D 219 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3270.41 seconds
wall clock time: 59 minutes 3.90 seconds (3543.90 seconds total)