Starting phenix.real_space_refine
on Fri Jun  6 03:10:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7wvx_32861/06_2025/7wvx_32861.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7wvx_32861/06_2025/7wvx_32861.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7wvx_32861/06_2025/7wvx_32861.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7wvx_32861/06_2025/7wvx_32861.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7wvx_32861/06_2025/7wvx_32861.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7wvx_32861/06_2025/7wvx_32861.cif"
  }
  resolution = 2.8
  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=   0.005
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      52      5.16       5
     C    4554      2.51       5
     N    1197      2.21       5
     O    1267      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 7070
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "L"
      Number of atoms: 114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 114
          Classifications: {'peptide': 15}
          Link IDs: {'PTRANS': 1, 'TRANS': 13}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'FME:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 2331
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 299, 2331
          Classifications: {'peptide': 299}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 13, 'TRANS': 285}
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 25
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "A"
      Number of atoms: 1680
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1680
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 2, 'TRANS': 212}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 55
          Unresolved non-hydrogen angles: 66
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 5}
          Unresolved non-hydrogen planarities: 36
    Chain: "B"
      Number of atoms: 2557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2557
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 50
          Unresolved non-hydrogen dihedrals: 36
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 30
    Chain: "C"
      Number of atoms: 388
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 53, 388
          Classifications: {'peptide': 53}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 4, 'TRANS': 48}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 18
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 16
  Time building chain proxies: 5.69, per 1000 atoms: 0.80
  Number of scatterers: 7070
  At special positions: 0
  Unit cell: (114.95, 119.13, 85.69, 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      52     16.00
     O    1267      8.00
     N    1197      7.00
     C    4554      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  98 " - pdb=" SG  CYS R 176 " 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: 1.70
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1726

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 9 sheets defined
      48.6% alpha, 16.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.79
  Creating SS restraints...
    Processing helix  chain 'R' and resid 21 through 55
      Proline residue:  R  29  - end of helix
      removed outlier: 3.752A  pdb=" N   MET R  55 " --> pdb=" O   ALA R  51 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 58 through 86
      removed outlier: 3.699A  pdb=" N   THR R  77 " --> pdb=" O   SER R  73 " (cutoff:3.500A)
      Proline residue:  R  79  - end of helix
    Processing helix  chain 'R' and resid 94 through 129
    Processing helix  chain 'R' and resid 129 through 137
    Processing helix  chain 'R' and resid 138 through 163
      removed outlier: 3.784A  pdb=" N   GLY R 148 " --> pdb=" O   LYS R 144 " (cutoff:3.500A)
      Proline residue:  R 149  - end of helix
      Proline residue:  R 159  - end of helix
    Processing helix  chain 'R' and resid 180 through 185
      removed outlier: 3.922A  pdb=" N   GLY R 185 " --> pdb=" O   ALA R 181 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 186 through 209
    Processing helix  chain 'R' and resid 210 through 232
    Processing helix  chain 'R' and resid 237 through 267
      Proline residue:  R 256  - end of helix
    Processing helix  chain 'R' and resid 267 through 274
    Processing helix  chain 'R' and resid 278 through 303
      removed outlier: 3.835A  pdb=" N   ILE R 282 " --> pdb=" O   LYS R 278 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   ASN R 285 " --> pdb=" O   ASP R 281 " (cutoff:3.500A)
      Proline residue:  R 286  - end of helix
      Proline residue:  R 299  - end of helix
    Processing helix  chain 'R' and resid 306 through 317
    Processing helix  chain 'A' and resid 6 through 31
      removed outlier: 3.799A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 52
    Processing helix  chain 'A' and resid 208 through 213
      removed outlier: 4.118A  pdb=" N   TRP A 212 " --> pdb=" O   GLU A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 217
    Processing helix  chain 'A' and resid 229 through 231
      No H-bonds generated for 'chain 'A' and resid 229 through 231'
    Processing helix  chain 'A' and resid 242 through 256
    Processing helix  chain 'A' and resid 257 through 261
      removed outlier: 3.958A  pdb=" N   THR A 261 " --> pdb=" O   LYS A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 280
      removed outlier: 3.818A  pdb=" N   GLU A 277 " --> pdb=" O   ASP A 273 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   THR A 280 " --> pdb=" O   GLU A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 312
      removed outlier: 4.234A  pdb=" N   SER A 302 " --> pdb=" O   ASP A 298 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ASN A 312 " --> pdb=" O   PHE A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 353
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.647A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 11 through 25
      removed outlier: 4.332A  pdb=" N   MET C  21 " --> pdb=" O   GLU C  17 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   GLU C  22 " --> pdb=" O   GLN C  18 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   ALA C  23 " --> pdb=" O   LEU C  19 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 44
      removed outlier: 3.564A  pdb=" N   CYS C  41 " --> pdb=" O   LEU C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 48
    Processing sheet with id=AA1, first strand: chain 'R' and resid 167 through 168
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 192
      removed outlier: 6.234A  pdb=" N   VAL A  34 " --> pdb=" O   LYS A 198 " (cutoff:3.500A)
      removed outlier: 7.092A  pdb=" N   PHE A 200 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   LEU A  36 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
      removed outlier: 8.841A  pdb=" N   ALA A 221 " --> pdb=" O   GLU A  33 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 221 " (cutoff:3.500A)
      removed outlier: 7.373A  pdb=" N   ILE A 223 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.021A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 223 " (cutoff:3.500A)
      removed outlier: 7.242A  pdb=" N   CYS A 225 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.614A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 225 " (cutoff:3.500A)
      removed outlier: 8.311A  pdb=" N   ALA A 227 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   ILE A 222 " --> pdb=" O   ILE A 266 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   PHE A 268 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 6.435A  pdb=" N   PHE A 224 " --> pdb=" O   PHE A 268 " (cutoff:3.500A)
      removed outlier: 7.006A  pdb=" N   ASN A 270 " --> pdb=" O   PHE A 224 " (cutoff:3.500A)
      removed outlier: 6.629A  pdb=" N   VAL A 226 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51
      removed outlier: 4.057A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   CYS B 317 " --> pdb=" O   GLY B 330 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.518A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 5.686A  pdb=" N   LEU B  79 " --> pdb=" O   ALA B  92 " (cutoff:3.500A)
      removed outlier: 4.266A  pdb=" N   ALA B  92 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ILE B  81 " --> pdb=" O   VAL B  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.670A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 4.848A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151
      removed outlier: 6.512A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.711A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.400A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.498A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.679A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.744A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 7.372A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.611A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 276 through 278
      removed outlier: 6.388A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)

    387 hydrogen bonds defined for protein.
    1119 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: 2.05

  Time building geometry restraints manager: 2.03 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: 2252
        1.34 -     1.46: 1339
        1.46 -     1.58: 3553
        1.58 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 7218
  Sorted by residual:
  bond pdb=" SD  FME L   1 "
       pdb=" CE  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.805  1.751  0.054 2.00e-02 2.50e+03 7.27e+00
  bond pdb=" CG  FME L   1 "
       pdb=" SD  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.817  1.770  0.047 2.00e-02 2.50e+03 5.54e+00
  bond pdb=" N   FME L   1 "
       pdb=" CN  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.335  1.377 -0.042 2.00e-02 2.50e+03 4.36e+00
  bond pdb=" C   LEU R 212 "
       pdb=" N   PRO R 213 "
    ideal  model  delta    sigma   weight residual
    1.336  1.350 -0.014 1.20e-02 6.94e+03 1.34e+00
  bond pdb=" N   FME L   1 "
       pdb=" CA  FME L   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.436  0.022 1.90e-02 2.77e+03 1.31e+00
  ... (remaining 7213 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 9645
        1.56 -     3.13: 118
        3.13 -     4.69: 29
        4.69 -     6.25: 6
        6.25 -     7.81: 1
  Bond angle restraints: 9799
  Sorted by residual:
  angle pdb=" C   ASP A 329 "
        pdb=" N   THR A 330 "
        pdb=" CA  THR A 330 "
      ideal   model   delta    sigma   weight residual
     122.46  125.84   -3.38 1.41e+00 5.03e-01 5.76e+00
  angle pdb=" C   PHE R 161 "
        pdb=" N   LEU R 162 "
        pdb=" CA  LEU R 162 "
      ideal   model   delta    sigma   weight residual
     122.53  118.15    4.38 1.92e+00 2.71e-01 5.20e+00
  angle pdb=" CA  LEU R 162 "
        pdb=" CB  LEU R 162 "
        pdb=" CG  LEU R 162 "
      ideal   model   delta    sigma   weight residual
     116.30  124.11   -7.81 3.50e+00 8.16e-02 4.98e+00
  angle pdb=" CA  TRP R  95 "
        pdb=" CB  TRP R  95 "
        pdb=" CG  TRP R  95 "
      ideal   model   delta    sigma   weight residual
     113.60  117.82   -4.22 1.90e+00 2.77e-01 4.94e+00
  angle pdb=" C   PHE C  61 "
        pdb=" N   ARG C  62 "
        pdb=" CA  ARG C  62 "
      ideal   model   delta    sigma   weight residual
     121.70  125.20   -3.50 1.80e+00 3.09e-01 3.78e+00
  ... (remaining 9794 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.28: 3894
       17.28 -    34.56: 282
       34.56 -    51.83: 61
       51.83 -    69.11: 2
       69.11 -    86.39: 2
  Dihedral angle restraints: 4241
    sinusoidal: 1582
      harmonic: 2659
  Sorted by residual:
  dihedral pdb=" CG  ARG R 137 "
           pdb=" CD  ARG R 137 "
           pdb=" NE  ARG R 137 "
           pdb=" CZ  ARG R 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  134.63  -44.63     2      1.50e+01 4.44e-03 1.05e+01
  dihedral pdb=" CG  ARG B  22 "
           pdb=" CD  ARG B  22 "
           pdb=" NE  ARG B  22 "
           pdb=" CZ  ARG B  22 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00 -137.47  -42.53     2      1.50e+01 4.44e-03 9.75e+00
  dihedral pdb=" CA  LYS C  14 "
           pdb=" CB  LYS C  14 "
           pdb=" CG  LYS C  14 "
           pdb=" CD  LYS C  14 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.00   56.00     3      1.50e+01 4.44e-03 9.38e+00
  ... (remaining 4238 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 719
       0.029 -    0.058: 263
       0.058 -    0.087: 112
       0.087 -    0.115: 53
       0.115 -    0.144: 7
  Chirality restraints: 1154
  Sorted by residual:
  chirality pdb=" CB  ILE R 101 "
            pdb=" CA  ILE R 101 "
            pdb=" CG1 ILE R 101 "
            pdb=" CG2 ILE R 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.50    0.14 2.00e-01 2.50e+01 5.20e-01
  chirality pdb=" CA  ILE B  81 "
            pdb=" N   ILE B  81 "
            pdb=" C   ILE B  81 "
            pdb=" CB  ILE B  81 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  chirality pdb=" CA  PRO R 187 "
            pdb=" N   PRO R 187 "
            pdb=" C   PRO R 187 "
            pdb=" CB  PRO R 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.59    0.13 2.00e-01 2.50e+01 4.16e-01
  ... (remaining 1151 not shown)

  Planarity restraints: 1223
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY R 148 "    0.033 5.00e-02 4.00e+02   5.05e-02 4.08e+00
        pdb=" N   PRO R 149 "   -0.087 5.00e-02 4.00e+02
        pdb=" CA  PRO R 149 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO R 149 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR R 186 "    0.032 5.00e-02 4.00e+02   4.89e-02 3.83e+00
        pdb=" N   PRO R 187 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO R 187 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO R 187 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 235 "    0.031 5.00e-02 4.00e+02   4.76e-02 3.63e+00
        pdb=" N   PRO B 236 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO B 236 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 236 "    0.027 5.00e-02 4.00e+02
  ... (remaining 1220 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1451
        2.78 -     3.31: 6959
        3.31 -     3.84: 12150
        3.84 -     4.37: 14439
        4.37 -     4.90: 24954
  Nonbonded interactions: 59953
  Sorted by model distance:
  nonbonded pdb=" O   GLY B 310 "
            pdb=" NZ  LYS B 337 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" OD1 ASP B 290 "
            pdb=" NH1 ARG B 314 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" OD1 ASN A 270 "
            pdb=" OG1 THR A 325 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" O   MET B 325 "
            pdb=" ND2 ASN B 340 "
     model   vdw
     2.300 3.120
  nonbonded pdb=" NE2 HIS B 225 "
            pdb=" OG1 THR B 243 "
     model   vdw
     2.324 3.120
  ... (remaining 59948 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:             0.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     21.170
  Find NCS groups from input model:        0.090
  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:14.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7256
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      :  0.002   0.054   7219  Z= 0.113
  Angle     :  0.493   7.814   9801  Z= 0.267
  Chirality :  0.040   0.144   1154
  Planarity :  0.004   0.051   1223
  Dihedral  : 12.148  86.390   2512
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  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:  0.86 (0.28), residues: 903
  helix:  1.86 (0.25), residues: 407
  sheet:  0.42 (0.42), residues: 158
  loop : -0.95 (0.31), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP R  95 
 HIS   0.002   0.000   HIS B 183 
 PHE   0.009   0.001   PHE B 199 
 TYR   0.005   0.001   TYR A 231 
 ARG   0.004   0.000   ARG R 190 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19609 (  387)
  hydrogen bonds       : angle       6.86167 ( 1119)
  SS BOND              : bond        0.00071 (    1)
  SS BOND              : angle       1.29289 (    2)
  covalent geometry    : bond        0.00216 ( 7218)
  covalent geometry    : angle       0.49248 ( 9799)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.690 
Fit side-chains
REVERT: R   65 LEU cc_start: 0.8050 (tt) cc_final: 0.7831 (tm)
REVERT: A  194 ASP cc_start: 0.7448 (m-30) cc_final: 0.7237 (m-30)
  outliers start: 0
  outliers final: 1
  residues processed: 132
  average time/residue: 1.0747
  time to fit residues: 150.3238
Evaluate side-chains
  114 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 113
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  129 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 36 optimal weight:    0.6980
   chunk 69 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 51 optimal weight:    9.9990
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 189 HIS
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 110 ASN
B 259 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.153128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.117931 restraints weight = 7987.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3381 rms_B_bonded: 1.91
r_work: 0.3251 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7219  Z= 0.172
  Angle     :  0.566   7.714   9801  Z= 0.297
  Chirality :  0.043   0.143   1154
  Planarity :  0.005   0.098   1223
  Dihedral  :  4.262  45.405    977
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 10.46 %
    Favored  : 87.53 %
  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:  0.84 (0.28), residues: 903
  helix:  1.75 (0.25), residues: 422
  sheet: -0.03 (0.37), residues: 189
  loop : -0.73 (0.35), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 169 
 HIS   0.004   0.001   HIS B 311 
 PHE   0.014   0.002   PHE A 197 
 TYR   0.011   0.001   TYR R 221 
 ARG   0.005   0.001   ARG R 123 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04157 (  387)
  hydrogen bonds       : angle       5.19771 ( 1119)
  SS BOND              : bond        0.00332 (    1)
  SS BOND              : angle       2.72804 (    2)
  covalent geometry    : bond        0.00379 ( 7218)
  covalent geometry    : angle       0.56480 ( 9799)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 130
  time to evaluate  : 0.779 
Fit side-chains
REVERT: R   65 LEU cc_start: 0.8362 (tt) cc_final: 0.8120 (tm)
REVERT: R  224 ILE cc_start: 0.8007 (OUTLIER) cc_final: 0.7803 (mt)
REVERT: R  238 ARG cc_start: 0.8288 (tmt90) cc_final: 0.7893 (tpt-90)
REVERT: R  304 PHE cc_start: 0.8177 (m-10) cc_final: 0.7927 (m-10)
REVERT: A   33 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8278 (mm-30)
REVERT: A  194 ASP cc_start: 0.8412 (m-30) cc_final: 0.8143 (m-30)
REVERT: A  314 ARG cc_start: 0.7819 (mmt-90) cc_final: 0.7402 (mmt90)
REVERT: A  350 LYS cc_start: 0.8118 (mtmt) cc_final: 0.7784 (mtpt)
REVERT: B  220 GLN cc_start: 0.7887 (OUTLIER) cc_final: 0.7593 (mt0)
REVERT: C   21 MET cc_start: 0.3618 (OUTLIER) cc_final: 0.2728 (ppp)
  outliers start: 15
  outliers final: 7
  residues processed: 135
  average time/residue: 1.0845
  time to fit residues: 155.0088
Evaluate side-chains
  127 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 116
  time to evaluate  : 0.763 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   41 VAL
Chi-restraints excluded: chain R residue  174 THR
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  224 ILE
Chi-restraints excluded: chain R residue  297 LEU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue   48 THR
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain C residue   21 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0170
   chunk 13 optimal weight:    1.9990
   chunk 22 optimal weight:    0.4980
   chunk 48 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 60 optimal weight:    0.3980
   chunk 45 optimal weight:    4.9990
   chunk 12 optimal weight:    0.0980
   overall best weight:    0.3618

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 259 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.156281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.121994 restraints weight = 7993.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 1.90
r_work: 0.3292 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   7219  Z= 0.113
  Angle     :  0.516   9.575   9801  Z= 0.267
  Chirality :  0.041   0.139   1154
  Planarity :  0.004   0.049   1223
  Dihedral  :  3.951  41.722    975
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 8.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.95 %
    Favored  : 82.44 %
  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:  0.95 (0.28), residues: 903
  helix:  1.78 (0.25), residues: 422
  sheet:  0.22 (0.38), residues: 183
  loop : -0.72 (0.35), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 311 
 PHE   0.009   0.001   PHE B 151 
 TYR   0.005   0.001   TYR R 302 
 ARG   0.007   0.001   ARG A 209 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03614 (  387)
  hydrogen bonds       : angle       4.92921 ( 1119)
  SS BOND              : bond        0.00049 (    1)
  SS BOND              : angle       1.72352 (    2)
  covalent geometry    : bond        0.00241 ( 7218)
  covalent geometry    : angle       0.51559 ( 9799)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 128
  time to evaluate  : 0.771 
Fit side-chains
REVERT: R   65 LEU cc_start: 0.8304 (tt) cc_final: 0.8070 (tm)
REVERT: R  238 ARG cc_start: 0.8319 (tmt90) cc_final: 0.8005 (tpt-90)
REVERT: R  304 PHE cc_start: 0.8091 (m-10) cc_final: 0.7890 (m-10)
REVERT: A   33 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8232 (mm-30)
REVERT: A  188 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.8022 (p)
REVERT: A  194 ASP cc_start: 0.8372 (m-30) cc_final: 0.8101 (m-30)
REVERT: A  350 LYS cc_start: 0.8220 (mtmt) cc_final: 0.7855 (mtpt)
REVERT: B   52 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8235 (mtp85)
REVERT: B  155 ASN cc_start: 0.7655 (t0) cc_final: 0.7410 (t0)
REVERT: B  220 GLN cc_start: 0.7921 (OUTLIER) cc_final: 0.7607 (mt0)
  outliers start: 12
  outliers final: 1
  residues processed: 134
  average time/residue: 1.1262
  time to fit residues: 159.6332
Evaluate side-chains
  119 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 115
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue  220 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 64 optimal weight:    0.1980
   chunk 0 optimal weight:    8.9990
   chunk 83 optimal weight:    0.9990
   chunk 36 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 2 optimal weight:    0.7980
   chunk 39 optimal weight:    0.9990
   chunk 51 optimal weight:   10.0000
   chunk 31 optimal weight:    5.9990
   chunk 3 optimal weight:    2.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.150720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.116206 restraints weight = 8166.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 1.88
r_work: 0.3212 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3077 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.2894

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   7219  Z= 0.152
  Angle     :  0.543   8.008   9801  Z= 0.283
  Chirality :  0.042   0.145   1154
  Planarity :  0.004   0.049   1223
  Dihedral  :  4.077  41.924    975
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 17.29 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.28), residues: 903
  helix:  1.73 (0.25), residues: 419
  sheet: -0.21 (0.36), residues: 190
  loop : -0.71 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 169 
 HIS   0.003   0.001   HIS B 311 
 PHE   0.015   0.001   PHE R  37 
 TYR   0.009   0.001   TYR R 221 
 ARG   0.007   0.001   ARG A 209 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03722 (  387)
  hydrogen bonds       : angle       5.04907 ( 1119)
  SS BOND              : bond        0.00119 (    1)
  SS BOND              : angle       2.22909 (    2)
  covalent geometry    : bond        0.00346 ( 7218)
  covalent geometry    : angle       0.54197 ( 9799)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.713 
Fit side-chains
REVERT: R   65 LEU cc_start: 0.8276 (tt) cc_final: 0.8047 (tm)
REVERT: R  238 ARG cc_start: 0.8238 (tmt90) cc_final: 0.7954 (tpt-90)
REVERT: A   33 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.8223 (mm-30)
REVERT: A  194 ASP cc_start: 0.8407 (m-30) cc_final: 0.8127 (m-30)
REVERT: A  209 ARG cc_start: 0.8333 (ttp80) cc_final: 0.8103 (ttm110)
REVERT: A  350 LYS cc_start: 0.8243 (mtmt) cc_final: 0.7891 (mtpt)
REVERT: B   52 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.8259 (mtp85)
REVERT: B  220 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7622 (mt0)
REVERT: B  243 THR cc_start: 0.8618 (p) cc_final: 0.8403 (p)
REVERT: C   46 LYS cc_start: 0.8432 (mptt) cc_final: 0.8081 (pmtt)
  outliers start: 20
  outliers final: 7
  residues processed: 136
  average time/residue: 1.1116
  time to fit residues: 159.7094
Evaluate side-chains
  125 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  297 LEU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  333 VAL
Chi-restraints excluded: chain B residue   52 ARG
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  220 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 1 optimal weight:    6.9990
   chunk 59 optimal weight:    0.8980
   chunk 79 optimal weight:    2.9990
   chunk 51 optimal weight:    8.9990
   chunk 77 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 30 optimal weight:    7.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
R 294 ASN
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.146711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.111186 restraints weight = 7849.749|
|-----------------------------------------------------------------------------|
r_work (start): 0.3285 rms_B_bonded: 1.87
r_work: 0.3149 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3013 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3013
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.3512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   7219  Z= 0.197
  Angle     :  0.586   7.617   9801  Z= 0.305
  Chirality :  0.043   0.148   1154
  Planarity :  0.004   0.062   1223
  Dihedral  :  4.402  44.071    975
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 17.56 %
    Favored  : 78.95 %
  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:  0.47 (0.27), residues: 903
  helix:  1.51 (0.25), residues: 423
  sheet: -0.49 (0.36), residues: 182
  loop : -0.81 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  99 
 HIS   0.002   0.001   HIS R 102 
 PHE   0.014   0.002   PHE A 197 
 TYR   0.011   0.001   TYR B 124 
 ARG   0.005   0.001   ARG A 209 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04061 (  387)
  hydrogen bonds       : angle       5.32978 ( 1119)
  SS BOND              : bond        0.00000 (    1)
  SS BOND              : angle       2.65582 (    2)
  covalent geometry    : bond        0.00454 ( 7218)
  covalent geometry    : angle       0.58474 ( 9799)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
REVERT: R   42 LEU cc_start: 0.8362 (mp) cc_final: 0.7685 (tm)
REVERT: R  238 ARG cc_start: 0.8233 (tmt90) cc_final: 0.7996 (ttm-80)
REVERT: R  304 PHE cc_start: 0.8421 (m-10) cc_final: 0.8172 (m-10)
REVERT: A   33 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8213 (mm-30)
REVERT: A  350 LYS cc_start: 0.8314 (mtmt) cc_final: 0.7930 (mtpt)
REVERT: B   46 ARG cc_start: 0.7974 (mpp80) cc_final: 0.7774 (mtp180)
REVERT: B  220 GLN cc_start: 0.7968 (OUTLIER) cc_final: 0.7616 (mt0)
REVERT: B  226 GLU cc_start: 0.8514 (mt-10) cc_final: 0.8272 (mt-10)
REVERT: B  243 THR cc_start: 0.8701 (p) cc_final: 0.8490 (p)
  outliers start: 26
  outliers final: 11
  residues processed: 139
  average time/residue: 1.0911
  time to fit residues: 160.5615
Evaluate side-chains
  128 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  113 VAL
Chi-restraints excluded: chain R residue  174 THR
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  297 LEU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain A residue  342 ASP
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 24 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 75 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 4 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 50 optimal weight:    0.5980
   chunk 84 optimal weight:    2.9990
   chunk 30 optimal weight:    9.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  75 GLN
B 259 GLN
B 340 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.146750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.111260 restraints weight = 7957.354|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 1.88
r_work: 0.3152 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3016 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3016
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.3667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   7219  Z= 0.185
  Angle     :  0.580   8.206   9801  Z= 0.301
  Chirality :  0.043   0.149   1154
  Planarity :  0.004   0.048   1223
  Dihedral  :  4.343  40.502    975
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.95 %
    Allowed  : 19.17 %
    Favored  : 77.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.36 (0.27), residues: 903
  helix:  1.41 (0.25), residues: 423
  sheet: -0.51 (0.35), residues: 179
  loop : -0.86 (0.33), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  99 
 HIS   0.004   0.001   HIS B 311 
 PHE   0.014   0.002   PHE A 197 
 TYR   0.013   0.001   TYR B 124 
 ARG   0.008   0.001   ARG A 209 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03932 (  387)
  hydrogen bonds       : angle       5.29172 ( 1119)
  SS BOND              : bond        0.00028 (    1)
  SS BOND              : angle       2.47776 (    2)
  covalent geometry    : bond        0.00430 ( 7218)
  covalent geometry    : angle       0.57871 ( 9799)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 114
  time to evaluate  : 0.807 
Fit side-chains
REVERT: R   42 LEU cc_start: 0.8381 (mp) cc_final: 0.7709 (tm)
REVERT: R  113 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.8171 (m)
REVERT: R  304 PHE cc_start: 0.8422 (m-10) cc_final: 0.8107 (m-10)
REVERT: A   33 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8194 (mm-30)
REVERT: A  350 LYS cc_start: 0.8426 (mtmt) cc_final: 0.8045 (mtpt)
REVERT: B  220 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7611 (mt0)
REVERT: B  226 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8273 (mt-10)
REVERT: B  243 THR cc_start: 0.8685 (p) cc_final: 0.8473 (p)
REVERT: C   46 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8176 (pmtt)
  outliers start: 22
  outliers final: 9
  residues processed: 127
  average time/residue: 0.9596
  time to fit residues: 130.5715
Evaluate side-chains
  118 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 1.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  113 VAL
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  340 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 73 optimal weight:    0.7980
   chunk 74 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0970
   chunk 71 optimal weight:    0.6980
   chunk 51 optimal weight:    8.9990
   chunk 20 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   chunk 27 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.149228 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.113879 restraints weight = 7834.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 1.86
r_work: 0.3195 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3057 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.3632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7219  Z= 0.142
  Angle     :  0.550   7.663   9801  Z= 0.285
  Chirality :  0.041   0.146   1154
  Planarity :  0.004   0.049   1223
  Dihedral  :  4.241  39.275    975
  Min Nonbonded Distance : 2.596

Molprobity Statistics.
  All-atom Clashscore : 10.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 19.57 %
    Favored  : 77.75 %
  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:  0.42 (0.27), residues: 903
  helix:  1.48 (0.25), residues: 423
  sheet: -0.53 (0.35), residues: 180
  loop : -0.86 (0.34), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 211 
 HIS   0.003   0.001   HIS B 311 
 PHE   0.012   0.001   PHE A 197 
 TYR   0.015   0.001   TYR B 124 
 ARG   0.005   0.000   ARG A 209 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03649 (  387)
  hydrogen bonds       : angle       5.17159 ( 1119)
  SS BOND              : bond        0.00012 (    1)
  SS BOND              : angle       2.06144 (    2)
  covalent geometry    : bond        0.00323 ( 7218)
  covalent geometry    : angle       0.54967 ( 9799)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.801 
Fit side-chains
REVERT: R   42 LEU cc_start: 0.8402 (mp) cc_final: 0.7736 (tm)
REVERT: R  304 PHE cc_start: 0.8366 (m-10) cc_final: 0.8077 (m-10)
REVERT: A   33 GLU cc_start: 0.8536 (mt-10) cc_final: 0.8190 (mm-30)
REVERT: A  350 LYS cc_start: 0.8484 (mtmt) cc_final: 0.8126 (mtpt)
REVERT: B  220 GLN cc_start: 0.7943 (OUTLIER) cc_final: 0.7568 (mt0)
REVERT: B  226 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8216 (mt-10)
REVERT: B  243 THR cc_start: 0.8673 (p) cc_final: 0.8458 (p)
  outliers start: 20
  outliers final: 11
  residues processed: 125
  average time/residue: 1.0502
  time to fit residues: 140.5102
Evaluate side-chains
  118 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.809 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  268 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  301 LEU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   44 GLN
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 45 optimal weight:    0.9980
   chunk 58 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 25 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   chunk 84 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 48 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 7 optimal weight:    0.6980
   chunk 37 optimal weight:    4.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.142836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.107979 restraints weight = 8147.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.3239 rms_B_bonded: 1.84
r_work: 0.3105 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2968 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2968
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7970
moved from start:          0.3991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   7219  Z= 0.240
  Angle     :  0.628   7.031   9801  Z= 0.324
  Chirality :  0.045   0.147   1154
  Planarity :  0.004   0.050   1223
  Dihedral  :  4.479  34.203    975
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 20.91 %
    Favored  : 76.54 %
  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:  0.16 (0.27), residues: 903
  helix:  1.25 (0.25), residues: 424
  sheet: -0.65 (0.34), residues: 186
  loop : -0.97 (0.34), residues: 293

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  99 
 HIS   0.005   0.001   HIS B 311 
 PHE   0.017   0.002   PHE A 197 
 TYR   0.018   0.001   TYR B 124 
 ARG   0.004   0.000   ARG A 209 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04161 (  387)
  hydrogen bonds       : angle       5.46269 ( 1119)
  SS BOND              : bond        0.00100 (    1)
  SS BOND              : angle       2.82407 (    2)
  covalent geometry    : bond        0.00565 ( 7218)
  covalent geometry    : angle       0.62660 ( 9799)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.750 
Fit side-chains
REVERT: R  304 PHE cc_start: 0.8449 (m-10) cc_final: 0.8135 (m-10)
REVERT: A   33 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8191 (mm-30)
REVERT: A  350 LYS cc_start: 0.8422 (mtmt) cc_final: 0.8084 (mtpt)
REVERT: B  220 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.7694 (mt0)
REVERT: B  226 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8346 (mt-10)
REVERT: B  243 THR cc_start: 0.8711 (p) cc_final: 0.8490 (p)
REVERT: C   46 LYS cc_start: 0.8547 (mmtt) cc_final: 0.8157 (pmtt)
  outliers start: 19
  outliers final: 12
  residues processed: 123
  average time/residue: 1.0960
  time to fit residues: 144.0632
Evaluate side-chains
  120 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  191 LEU
Chi-restraints excluded: chain R residue  268 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  297 LEU
Chi-restraints excluded: chain R residue  301 LEU
Chi-restraints excluded: chain A residue   33 GLU
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  340 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 3 optimal weight:    4.9990
   chunk 73 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 36 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9990
   chunk 80 optimal weight:    2.9990
   chunk 6 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.146361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.110308 restraints weight = 7905.058|
|-----------------------------------------------------------------------------|
r_work (start): 0.3274 rms_B_bonded: 1.88
r_work: 0.3140 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3002 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.3925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7219  Z= 0.166
  Angle     :  0.580   6.668   9801  Z= 0.298
  Chirality :  0.042   0.149   1154
  Planarity :  0.004   0.048   1223
  Dihedral  :  4.304  29.339    975
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 10.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 21.72 %
    Favored  : 76.27 %
  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:  0.20 (0.27), residues: 903
  helix:  1.31 (0.25), residues: 424
  sheet: -0.73 (0.35), residues: 188
  loop : -0.91 (0.34), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 211 
 HIS   0.004   0.001   HIS B 311 
 PHE   0.014   0.002   PHE A 197 
 TYR   0.020   0.001   TYR B 124 
 ARG   0.005   0.000   ARG A 209 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03777 (  387)
  hydrogen bonds       : angle       5.30562 ( 1119)
  SS BOND              : bond        0.00123 (    1)
  SS BOND              : angle       2.22390 (    2)
  covalent geometry    : bond        0.00383 ( 7218)
  covalent geometry    : angle       0.57889 ( 9799)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.838 
Fit side-chains
REVERT: R  304 PHE cc_start: 0.8412 (m-10) cc_final: 0.8113 (m-10)
REVERT: A   33 GLU cc_start: 0.8535 (mt-10) cc_final: 0.8160 (mm-30)
REVERT: A  350 LYS cc_start: 0.8465 (mtmt) cc_final: 0.8108 (mtpt)
REVERT: B  220 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7629 (mt0)
REVERT: B  226 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8332 (mt-10)
REVERT: B  243 THR cc_start: 0.8681 (p) cc_final: 0.8454 (p)
REVERT: C   46 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8174 (pmtt)
  outliers start: 15
  outliers final: 10
  residues processed: 120
  average time/residue: 0.9195
  time to fit residues: 118.3584
Evaluate side-chains
  120 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 109
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  268 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  301 LEU
Chi-restraints excluded: chain R residue  303 VAL
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  327 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 30 optimal weight:    6.9990
   chunk 56 optimal weight:    0.8980
   chunk 69 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 1 optimal weight:    7.9990
   chunk 14 optimal weight:    0.6980
   chunk 83 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** R 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 340 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.147340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.111159 restraints weight = 8086.107|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 1.91
r_work: 0.3159 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.3880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   7219  Z= 0.153
  Angle     :  0.572   6.557   9801  Z= 0.294
  Chirality :  0.042   0.146   1154
  Planarity :  0.004   0.047   1223
  Dihedral  :  4.230  27.181    975
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 21.72 %
    Favored  : 76.41 %
  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:  0.30 (0.27), residues: 903
  helix:  1.37 (0.25), residues: 424
  sheet: -0.44 (0.36), residues: 172
  loop : -0.98 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 211 
 HIS   0.004   0.001   HIS B 311 
 PHE   0.019   0.002   PHE R  37 
 TYR   0.020   0.001   TYR B 124 
 ARG   0.006   0.000   ARG A 209 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03689 (  387)
  hydrogen bonds       : angle       5.24021 ( 1119)
  SS BOND              : bond        0.00005 (    1)
  SS BOND              : angle       2.15037 (    2)
  covalent geometry    : bond        0.00355 ( 7218)
  covalent geometry    : angle       0.57133 ( 9799)

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

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

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1806 Ramachandran restraints generated.
    903 Oldfield, 0 Emsley, 903 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 0.810 
Fit side-chains
REVERT: R  143 MET cc_start: 0.7714 (mtt) cc_final: 0.7456 (mtt)
REVERT: R  304 PHE cc_start: 0.8399 (m-10) cc_final: 0.8096 (m-10)
REVERT: A   33 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8188 (mm-30)
REVERT: A  350 LYS cc_start: 0.8551 (mtmt) cc_final: 0.8201 (mtpt)
REVERT: B  220 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7630 (mt0)
REVERT: B  226 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8283 (mt-10)
REVERT: B  243 THR cc_start: 0.8629 (p) cc_final: 0.8403 (p)
REVERT: C   46 LYS cc_start: 0.8530 (mmtt) cc_final: 0.8151 (pmtt)
  outliers start: 14
  outliers final: 11
  residues processed: 122
  average time/residue: 0.9250
  time to fit residues: 121.1847
Evaluate side-chains
  120 residues out of total 786 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 108
  time to evaluate  : 0.842 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue   87 MET
Chi-restraints excluded: chain R residue  268 LEU
Chi-restraints excluded: chain R residue  296 CYS
Chi-restraints excluded: chain R residue  301 LEU
Chi-restraints excluded: chain R residue  303 VAL
Chi-restraints excluded: chain A residue  188 THR
Chi-restraints excluded: chain A residue  328 THR
Chi-restraints excluded: chain B residue   87 THR
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  220 GLN
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain B residue  340 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9980
   chunk 81 optimal weight:    5.9990
   chunk 42 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 71 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    1.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A  52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 332 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.145520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.109396 restraints weight = 7905.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3263 rms_B_bonded: 1.89
r_work: 0.3130 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.3953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   7219  Z= 0.197
  Angle     :  0.604   6.537   9801  Z= 0.310
  Chirality :  0.044   0.147   1154
  Planarity :  0.004   0.047   1223
  Dihedral  :  4.328  29.037    975
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 11.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 21.98 %
    Favored  : 75.87 %
  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:  0.22 (0.27), residues: 903
  helix:  1.32 (0.25), residues: 424
  sheet: -0.58 (0.35), residues: 179
  loop : -1.00 (0.33), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  99 
 HIS   0.005   0.001   HIS B 311 
 PHE   0.020   0.002   PHE R  37 
 TYR   0.020   0.001   TYR B 124 
 ARG   0.005   0.000   ARG A 209 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03864 (  387)
  hydrogen bonds       : angle       5.30822 ( 1119)
  SS BOND              : bond        0.00019 (    1)
  SS BOND              : angle       2.44770 (    2)
  covalent geometry    : bond        0.00464 ( 7218)
  covalent geometry    : angle       0.60325 ( 9799)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6251.30 seconds
wall clock time: 109 minutes 54.25 seconds (6594.25 seconds total)