Starting phenix.real_space_refine
on Fri Nov 15 09:42:50 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmz_29301/11_2024/8fmz_29301.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmz_29301/11_2024/8fmz_29301.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmz_29301/11_2024/8fmz_29301.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmz_29301/11_2024/8fmz_29301.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmz_29301/11_2024/8fmz_29301.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fmz_29301/11_2024/8fmz_29301.cif"
  }
  resolution = 2.59
  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=  -0.001 sd=   0.159
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      55      5.16       5
     C    5595      2.51       5
     N    1492      2.21       5
     O    1626      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 8768
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 221, 1795
          Classifications: {'peptide': 221}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 214}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 9
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 7
          Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "C"
      Number of atoms: 2593
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2593
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "D"
      Number of atoms: 380
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 380
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 17
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "E"
      Number of atoms: 1754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1754
          Classifications: {'peptide': 230}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 16
    Chain: "A"
      Number of atoms: 2188
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2188
          Classifications: {'peptide': 280}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 270}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 30
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 26
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 21
    Chain: "F"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 58
          Classifications: {'peptide': 6}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 4}
  Time building chain proxies: 5.52, per 1000 atoms: 0.63
  Number of scatterers: 8768
  At special positions: 0
  Unit cell: (88.88, 120.56, 131.12, 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      55     16.00
     O    1626      8.00
     N    1492      7.00
     C    5595      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 142 " - pdb=" SG  CYS A 225 " 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: 2.33
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2110

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 14 sheets defined
      39.5% alpha, 24.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'B' and resid 6 through 31
    Processing helix  chain 'B' and resid 45 through 49
    Processing helix  chain 'B' and resid 94 through 101
      removed outlier: 3.736A  pdb=" N   GLN B  98 " --> pdb=" O   LYS B  95 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ASN B 101 " --> pdb=" O   GLN B  98 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 130
    Processing helix  chain 'B' and resid 131 through 135
      removed outlier: 4.079A  pdb=" N   ARG B 135 " --> pdb=" O   ARG B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 145 through 156
    Processing helix  chain 'B' and resid 159 through 163
    Processing helix  chain 'B' and resid 164 through 170
      removed outlier: 3.505A  pdb=" N   TYR B 170 " --> pdb=" O   PHE B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 183 through 204
      removed outlier: 3.738A  pdb=" N   PHE B 197 " --> pdb=" O   ILE B 193 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   SER B 204 " --> pdb=" O   ILE B 200 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 243
    Processing helix  chain 'C' and resid 4 through 25
    Processing helix  chain 'C' and resid 29 through 37
      removed outlier: 4.078A  pdb=" N   THR C  34 " --> pdb=" O   SER C  31 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   ASN C  35 " --> pdb=" O   GLN C  32 " (cutoff:3.500A)
      removed outlier: 4.320A  pdb=" N   ASN C  36 " --> pdb=" O   ILE C  33 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 128 through 132
      removed outlier: 3.775A  pdb=" N   GLY C 131 " --> pdb=" O   THR C 128 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ASN C 132 " --> pdb=" O   ARG C 129 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 128 through 132'
    Processing helix  chain 'D' and resid 12 through 24
    Processing helix  chain 'D' and resid 29 through 44
    Processing helix  chain 'D' and resid 45 through 48
    Processing helix  chain 'E' and resid 28 through 32
    Processing helix  chain 'E' and resid 53 through 56
      removed outlier: 4.166A  pdb=" N   GLY E  56 " --> pdb=" O   SER E  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 53 through 56'
    Processing helix  chain 'E' and resid 87 through 91
    Processing helix  chain 'A' and resid 52 through 56
      removed outlier: 4.040A  pdb=" N   ASP A  56 " --> pdb=" O   SER A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 90
    Processing helix  chain 'A' and resid 101 through 128
      removed outlier: 3.679A  pdb=" N   HIS A 105 " --> pdb=" O   THR A 101 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   MET A 121 " --> pdb=" O   LEU A 117 " (cutoff:3.500A)
      Proline residue:  A 122  - end of helix
    Processing helix  chain 'A' and resid 137 through 173
    Processing helix  chain 'A' and resid 173 through 181
      removed outlier: 3.579A  pdb=" N   THR A 179 " --> pdb=" O   PHE A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 201
      removed outlier: 3.543A  pdb=" N   ALA A 201 " --> pdb=" O   SER A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 206
    Processing helix  chain 'A' and resid 219 through 221
      No H-bonds generated for 'chain 'A' and resid 219 through 221'
    Processing helix  chain 'A' and resid 230 through 246
      removed outlier: 3.618A  pdb=" N   VAL A 236 " --> pdb=" O   ALA A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 266
    Processing helix  chain 'A' and resid 304 through 334
      Proline residue:  A 323  - end of helix
      removed outlier: 3.552A  pdb=" N   ILE A 334 " --> pdb=" O   MET A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 370
      removed outlier: 3.671A  pdb=" N   HIS A 348 " --> pdb=" O   PHE A 344 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   SER A 362 " --> pdb=" O   PHE A 358 " (cutoff:3.500A)
      Proline residue:  A 366  - end of helix
    Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76
      removed outlier: 4.697A  pdb=" N   VAL B  86 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   GLY B  40 " --> pdb=" O   VAL B  86 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ALA B 105 " --> pdb=" O   ARG B  35 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ILE B 106 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 7.215A  pdb=" N   PHE B 142 " --> pdb=" O   ILE B 106 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   PHE B 108 " --> pdb=" O   PHE B 142 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   ASN B 144 " --> pdb=" O   PHE B 108 " (cutoff:3.500A)
      removed outlier: 6.319A  pdb=" N   VAL B 110 " --> pdb=" O   ASN B 144 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51
      removed outlier: 3.711A  pdb=" N   ARG C  49 " --> pdb=" O   ILE C 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.701A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.425A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.974A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.381A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.117A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.343A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151
      removed outlier: 6.566A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 5.998A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192
      removed outlier: 6.915A  pdb=" N   GLY C 202 " --> pdb=" O   MET C 188 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   LEU C 190 " --> pdb=" O   VAL C 200 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   VAL C 200 " --> pdb=" O   LEU C 190 " (cutoff:3.500A)
      removed outlier: 5.322A  pdb=" N   LEU C 192 " --> pdb=" O   LEU C 198 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   LEU C 198 " --> pdb=" O   LEU C 192 " (cutoff:3.500A)
      removed outlier: 6.628A  pdb=" N   ASP C 212 " --> pdb=" O   CYS C 218 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   CYS C 218 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234
      removed outlier: 6.669A  pdb=" N   CYS C 250 " --> pdb=" O   THR C 263 " (cutoff:3.500A)
      removed outlier: 4.625A  pdb=" N   THR C 263 " --> pdb=" O   CYS C 250 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   LEU C 252 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.550A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 6.270A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.017A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 6.017A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 130
    Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136
      removed outlier: 3.556A  pdb=" N   GLU E 234 " --> pdb=" O   VAL E 135 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   LEU E 162 " --> pdb=" O   TYR E 178 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   TYR E 178 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 208 through 212

    471 hydrogen bonds defined for protein.
    1287 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: 2.64

  Time building geometry restraints manager: 2.62 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: 2822
        1.34 -     1.46: 2052
        1.46 -     1.58: 3998
        1.58 -     1.69: 0
        1.69 -     1.81: 81
  Bond restraints: 8953
  Sorted by residual:
  bond pdb=" N   ASP C 291 "
       pdb=" CA  ASP C 291 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.40e-02 5.10e+03 6.68e+00
  bond pdb=" N   ASP C 290 "
       pdb=" CA  ASP C 290 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.32e-02 5.74e+03 5.59e+00
  bond pdb=" N   ASP C 186 "
       pdb=" CA  ASP C 186 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 1.28e-02 6.10e+03 5.43e+00
  bond pdb=" C   ILE A 202 "
       pdb=" N   PRO A 203 "
    ideal  model  delta    sigma   weight residual
    1.335  1.353 -0.019 1.28e-02 6.10e+03 2.16e+00
  bond pdb=" CA  ASP C 290 "
       pdb=" C   ASP C 290 "
    ideal  model  delta    sigma   weight residual
    1.523  1.539 -0.017 1.41e-02 5.03e+03 1.42e+00
  ... (remaining 8948 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 11926
        1.76 -     3.52: 192
        3.52 -     5.28: 18
        5.28 -     7.04: 4
        7.04 -     8.79: 2
  Bond angle restraints: 12142
  Sorted by residual:
  angle pdb=" N   VAL C 187 "
        pdb=" CA  VAL C 187 "
        pdb=" CB  VAL C 187 "
      ideal   model   delta    sigma   weight residual
     111.00  119.79   -8.79 1.14e+00 7.69e-01 5.95e+01
  angle pdb=" N   TYR C 289 "
        pdb=" CA  TYR C 289 "
        pdb=" C   TYR C 289 "
      ideal   model   delta    sigma   weight residual
     109.81  118.54   -8.73 1.53e+00 4.27e-01 3.26e+01
  angle pdb=" N   VAL C 187 "
        pdb=" CA  VAL C 187 "
        pdb=" C   VAL C 187 "
      ideal   model   delta    sigma   weight residual
     108.23  103.12    5.11 1.53e+00 4.27e-01 1.12e+01
  angle pdb=" C   ASP C 195 "
        pdb=" N   THR C 196 "
        pdb=" CA  THR C 196 "
      ideal   model   delta    sigma   weight residual
     122.40  126.46   -4.06 1.45e+00 4.76e-01 7.84e+00
  angle pdb=" CA  ASP C 186 "
        pdb=" C   ASP C 186 "
        pdb=" O   ASP C 186 "
      ideal   model   delta    sigma   weight residual
     120.92  117.93    2.99 1.14e+00 7.69e-01 6.87e+00
  ... (remaining 12137 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.83: 5047
       15.83 -    31.67: 207
       31.67 -    47.50: 27
       47.50 -    63.34: 4
       63.34 -    79.17: 2
  Dihedral angle restraints: 5287
    sinusoidal: 2020
      harmonic: 3267
  Sorted by residual:
  dihedral pdb=" CA  TRP C  82 "
           pdb=" C   TRP C  82 "
           pdb=" N   ASP C  83 "
           pdb=" CA  ASP C  83 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.28   18.72     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  ARG E 179 "
           pdb=" C   ARG E 179 "
           pdb=" N   MET E 180 "
           pdb=" CA  MET E 180 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.26   17.74     0      5.00e+00 4.00e-02 1.26e+01
  dihedral pdb=" CA  PHE E  32 "
           pdb=" C   PHE E  32 "
           pdb=" N   GLY E  33 "
           pdb=" CA  GLY E  33 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.10   16.90     0      5.00e+00 4.00e-02 1.14e+01
  ... (remaining 5284 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 991
       0.041 -    0.082: 307
       0.082 -    0.124: 86
       0.124 -    0.165: 3
       0.165 -    0.206: 1
  Chirality restraints: 1388
  Sorted by residual:
  chirality pdb=" CA  TYR C 289 "
            pdb=" N   TYR C 289 "
            pdb=" C   TYR C 289 "
            pdb=" CB  TYR C 289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  VAL E  37 "
            pdb=" N   VAL E  37 "
            pdb=" C   VAL E  37 "
            pdb=" CB  VAL E  37 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.41e-01
  chirality pdb=" CA  ILE C  93 "
            pdb=" N   ILE C  93 "
            pdb=" C   ILE C  93 "
            pdb=" CB  ILE C  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.23e-01
  ... (remaining 1385 not shown)

  Planarity restraints: 1531
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR C 289 "   -0.011 2.00e-02 2.50e+03   2.16e-02 4.68e+00
        pdb=" C   TYR C 289 "    0.037 2.00e-02 2.50e+03
        pdb=" O   TYR C 289 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ASP C 290 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 235 "    0.029 5.00e-02 4.00e+02   4.37e-02 3.06e+00
        pdb=" N   PRO C 236 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO C 236 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO C 236 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 226 "    0.024 5.00e-02 4.00e+02   3.61e-02 2.09e+00
        pdb=" N   PRO A 227 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO A 227 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A 227 "    0.020 5.00e-02 4.00e+02
  ... (remaining 1528 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2006
        2.79 -     3.32: 8111
        3.32 -     3.85: 14475
        3.85 -     4.37: 17461
        4.37 -     4.90: 30600
  Nonbonded interactions: 72653
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU C 260 "
            pdb=" OG1 THR C 263 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   ASN A 241 "
            pdb=" OG  SER A 245 "
     model   vdw
     2.267 3.040
  nonbonded pdb=" OE2 GLU B   8 "
            pdb=" OH  TYR E 163 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" O   ASP A 230 "
            pdb=" OG1 THR A 233 "
     model   vdw
     2.273 3.040
  nonbonded pdb=" NH1 ARG B  15 "
            pdb=" O   VAL C  90 "
     model   vdw
     2.275 3.120
  ... (remaining 72648 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=0.00 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:             1.220
  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:             0.020
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     23.120
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.060
  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:14.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
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   0.036   8953  Z= 0.263
  Angle     :  0.575   8.795  12142  Z= 0.346
  Chirality :  0.042   0.206   1388
  Planarity :  0.004   0.044   1531
  Dihedral  :  8.857  79.171   3171
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.73 %
    Favored  : 98.27 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  3.51 %
    Favored  : 96.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.58 (0.25), residues: 1098
  helix:  2.54 (0.26), residues: 381
  sheet:  0.65 (0.28), residues: 301
  loop :  0.01 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 169 
 HIS   0.003   0.001   HIS A 348 
 PHE   0.014   0.001   PHE C 151 
 TYR   0.013   0.001   TYR E 178 
 ARG   0.002   0.000   ARG E  38 

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 206
  time to evaluate  : 0.990 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7671 (mttt) cc_final: 0.7282 (mttt)
REVERT: B   21 LYS cc_start: 0.7549 (tttm) cc_final: 0.6884 (ttpt)
REVERT: B   24 ARG cc_start: 0.6542 (mtm-85) cc_final: 0.6116 (mtm-85)
REVERT: B   69 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8092 (tt)
REVERT: B  120 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7068 (mt-10)
REVERT: B  195 LYS cc_start: 0.7358 (tttm) cc_final: 0.7113 (ttpp)
REVERT: B  208 ARG cc_start: 0.6845 (mtm-85) cc_final: 0.6567 (ptt-90)
REVERT: C  101 MET cc_start: 0.8277 (mtt) cc_final: 0.8063 (mpp)
REVERT: C  254 ASP cc_start: 0.7683 (t70) cc_final: 0.7377 (t0)
REVERT: C  325 MET cc_start: 0.8036 (mmm) cc_final: 0.7719 (tpp)
REVERT: D   21 MET cc_start: 0.6224 (mtm) cc_final: 0.5483 (tmm)
REVERT: E    7 SER cc_start: 0.8016 (t) cc_final: 0.7605 (p)
REVERT: E   46 GLU cc_start: 0.7617 (tt0) cc_final: 0.7169 (tt0)
REVERT: E   85 SER cc_start: 0.8216 (m) cc_final: 0.7899 (t)
REVERT: A   61 ILE cc_start: 0.5555 (tp) cc_final: 0.5323 (tp)
REVERT: A  121 MET cc_start: 0.6297 (tpp) cc_final: 0.6066 (tpp)
REVERT: A  248 PHE cc_start: 0.7530 (t80) cc_final: 0.7284 (t80)
REVERT: A  361 SER cc_start: 0.7548 (t) cc_final: 0.7050 (p)
  outliers start: 2
  outliers final: 0
  residues processed: 207
  average time/residue: 1.1125
  time to fit residues: 244.4450
Evaluate side-chains
  137 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 136
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 46 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 56 optimal weight:   10.0000
   chunk 44 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 64 optimal weight:    0.2980
   chunk 100 optimal weight:   10.0000
   overall best weight:    2.2586

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

Flipped N/Q/H residues before XYZ refinement:
B  22 ASN
C  62 HIS
C 156 GLN
E 130 GLN
E 174 GLN
E 182 ASN
A  52 ASN
A 325 HIS
** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   8953  Z= 0.348
  Angle     :  0.618   6.505  12142  Z= 0.336
  Chirality :  0.045   0.152   1388
  Planarity :  0.005   0.047   1531
  Dihedral  :  4.796  23.747   1219
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 10.43 %
    Favored  : 87.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.51 (0.25), residues: 1098
  helix:  2.49 (0.26), residues: 376
  sheet:  0.57 (0.28), residues: 307
  loop :  0.02 (0.31), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 169 
 HIS   0.006   0.002   HIS D  44 
 PHE   0.023   0.002   PHE C 151 
 TYR   0.015   0.002   TYR E 178 
 ARG   0.006   0.001   ARG B 135 

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.973 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7823 (mttt) cc_final: 0.7291 (mttt)
REVERT: B   21 LYS cc_start: 0.7650 (tttm) cc_final: 0.6904 (ttpt)
REVERT: B   24 ARG cc_start: 0.6685 (mtm-85) cc_final: 0.6293 (mtm-85)
REVERT: B  120 GLU cc_start: 0.7422 (mt-10) cc_final: 0.7026 (mt-10)
REVERT: B  151 GLU cc_start: 0.6584 (mt-10) cc_final: 0.6361 (pt0)
REVERT: B  152 LYS cc_start: 0.6885 (mttt) cc_final: 0.6663 (mttt)
REVERT: B  195 LYS cc_start: 0.7443 (tttm) cc_final: 0.7088 (ttpp)
REVERT: B  208 ARG cc_start: 0.6878 (mtm-85) cc_final: 0.6423 (ptt-90)
REVERT: B  232 LYS cc_start: 0.8114 (ttmt) cc_final: 0.7787 (ttpt)
REVERT: C  219 ARG cc_start: 0.7799 (mmm160) cc_final: 0.7481 (mtp180)
REVERT: D   21 MET cc_start: 0.6181 (mtm) cc_final: 0.5485 (tmt)
REVERT: E    7 SER cc_start: 0.8124 (t) cc_final: 0.7521 (p)
REVERT: E   43 LYS cc_start: 0.7890 (mtpp) cc_final: 0.7229 (mtpm)
REVERT: E   46 GLU cc_start: 0.8389 (tt0) cc_final: 0.8045 (tt0)
REVERT: E   85 SER cc_start: 0.8455 (m) cc_final: 0.8036 (p)
REVERT: A  248 PHE cc_start: 0.7547 (t80) cc_final: 0.7268 (t80)
  outliers start: 21
  outliers final: 14
  residues processed: 146
  average time/residue: 1.3332
  time to fit residues: 205.5527
Evaluate side-chains
  136 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 122
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue  209 HIS
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain C residue  247 ASP
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain E residue   89 GLU
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  362 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 56 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 83 optimal weight:    9.9990
   chunk 68 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 100 optimal weight:    3.9990
   chunk 109 optimal weight:    5.9990
   chunk 89 optimal weight:    9.9990
   chunk 34 optimal weight:    0.0980
   chunk 81 optimal weight:    1.9990
   chunk 99 optimal weight:    8.9990
   overall best weight:    1.9986

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

Flipped N/Q/H residues before XYZ refinement:
B  22 ASN
** B  82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 116 ASN
C 266 HIS
E 130 GLN
E 167 GLN
E 174 GLN
A 370 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.3074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   8953  Z= 0.306
  Angle     :  0.577   7.215  12142  Z= 0.314
  Chirality :  0.044   0.150   1388
  Planarity :  0.005   0.046   1531
  Dihedral  :  4.724  23.739   1217
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 12.77 %
    Favored  : 83.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.37 (0.25), residues: 1098
  helix:  2.39 (0.26), residues: 380
  sheet:  0.52 (0.29), residues: 298
  loop : -0.14 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 169 
 HIS   0.005   0.001   HIS B  82 
 PHE   0.020   0.002   PHE C 151 
 TYR   0.014   0.002   TYR E 103 
 ARG   0.008   0.001   ARG B 135 

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 125
  time to evaluate  : 0.998 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7816 (mttt) cc_final: 0.7289 (mttt)
REVERT: B   21 LYS cc_start: 0.7760 (tttm) cc_final: 0.7049 (ttpt)
REVERT: B   24 ARG cc_start: 0.6686 (mtm-85) cc_final: 0.6272 (mtm-85)
REVERT: B  120 GLU cc_start: 0.7334 (mt-10) cc_final: 0.7068 (mt-10)
REVERT: B  195 LYS cc_start: 0.7372 (tttm) cc_final: 0.7015 (ttpp)
REVERT: B  208 ARG cc_start: 0.6829 (mtm-85) cc_final: 0.6227 (ptt-90)
REVERT: B  232 LYS cc_start: 0.8127 (ttmt) cc_final: 0.7817 (ttpt)
REVERT: C  217 MET cc_start: 0.8247 (pmm) cc_final: 0.7871 (pmm)
REVERT: C  219 ARG cc_start: 0.7790 (mmm160) cc_final: 0.7453 (mtp180)
REVERT: C  247 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7317 (m-30)
REVERT: D   21 MET cc_start: 0.6361 (mtm) cc_final: 0.5576 (tmt)
REVERT: D   47 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7514 (pt0)
REVERT: E    7 SER cc_start: 0.8187 (t) cc_final: 0.7652 (p)
REVERT: E   43 LYS cc_start: 0.7976 (mtpp) cc_final: 0.7239 (mtpm)
REVERT: E   46 GLU cc_start: 0.8396 (tt0) cc_final: 0.8089 (tt0)
REVERT: E   85 SER cc_start: 0.8537 (m) cc_final: 0.8088 (p)
REVERT: A   61 ILE cc_start: 0.5582 (tp) cc_final: 0.5376 (tp)
REVERT: A  121 MET cc_start: 0.6308 (tpp) cc_final: 0.5860 (ttp)
REVERT: A  248 PHE cc_start: 0.7600 (t80) cc_final: 0.7339 (t80)
  outliers start: 31
  outliers final: 14
  residues processed: 144
  average time/residue: 1.4630
  time to fit residues: 223.0726
Evaluate side-chains
  134 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.990 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue  209 HIS
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  247 ASP
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue   89 GLU
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  362 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 75 optimal weight:    0.9980
   chunk 52 optimal weight:    8.9990
   chunk 11 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9980
   chunk 101 optimal weight:    3.9990
   chunk 107 optimal weight:   10.0000
   chunk 96 optimal weight:    9.9990
   chunk 28 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 60 optimal weight:    1.9990
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
B  22 ASN
B 116 ASN
A 103 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.3384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   8953  Z= 0.329
  Angle     :  0.591   6.069  12142  Z= 0.321
  Chirality :  0.045   0.153   1388
  Planarity :  0.005   0.047   1531
  Dihedral  :  4.816  23.738   1217
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 13.72 %
    Favored  : 82.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.26 (0.25), residues: 1098
  helix:  2.33 (0.26), residues: 380
  sheet:  0.51 (0.28), residues: 292
  loop : -0.25 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 169 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.021   0.002   PHE C 151 
 TYR   0.014   0.002   TYR E 103 
 ARG   0.010   0.001   ARG B 135 

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 122
  time to evaluate  : 0.946 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7817 (mttt) cc_final: 0.7273 (mttt)
REVERT: B   21 LYS cc_start: 0.7724 (tttm) cc_final: 0.7028 (ttpt)
REVERT: B   24 ARG cc_start: 0.6622 (mtm-85) cc_final: 0.6246 (mtm-85)
REVERT: B  195 LYS cc_start: 0.7405 (tttm) cc_final: 0.7014 (ttpp)
REVERT: B  208 ARG cc_start: 0.6847 (mtm-85) cc_final: 0.6094 (mmm160)
REVERT: B  232 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7850 (ttpt)
REVERT: C  217 MET cc_start: 0.8258 (pmm) cc_final: 0.7862 (pmm)
REVERT: C  219 ARG cc_start: 0.7808 (mmm160) cc_final: 0.7460 (mtp180)
REVERT: D   21 MET cc_start: 0.6394 (mtm) cc_final: 0.5732 (tmt)
REVERT: D   47 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7527 (pt0)
REVERT: E    7 SER cc_start: 0.8254 (t) cc_final: 0.7769 (p)
REVERT: E   43 LYS cc_start: 0.8014 (mtpp) cc_final: 0.7274 (mtpm)
REVERT: E   46 GLU cc_start: 0.8412 (tt0) cc_final: 0.8183 (tt0)
REVERT: A   61 ILE cc_start: 0.5625 (tp) cc_final: 0.5413 (tp)
REVERT: A  248 PHE cc_start: 0.7624 (t80) cc_final: 0.7315 (t80)
  outliers start: 33
  outliers final: 22
  residues processed: 143
  average time/residue: 1.3917
  time to fit residues: 211.1999
Evaluate side-chains
  136 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue  209 HIS
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain C residue   65 THR
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  173 THR
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain C residue  247 ASP
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   47 GLU
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue   89 GLU
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  362 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 1 optimal weight:    0.7980
   chunk 79 optimal weight:    0.7980
   chunk 44 optimal weight:    5.9990
   chunk 91 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 54 optimal weight:    4.9990
   chunk 96 optimal weight:    9.9990
   chunk 27 optimal weight:    4.9990
   chunk 36 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
B  22 ASN
B 116 ASN
E 167 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.3492

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   8953  Z= 0.273
  Angle     :  0.556   7.936  12142  Z= 0.301
  Chirality :  0.043   0.147   1388
  Planarity :  0.005   0.047   1531
  Dihedral  :  4.683  23.600   1217
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 14.79 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.34 (0.25), residues: 1098
  helix:  2.42 (0.26), residues: 380
  sheet:  0.54 (0.29), residues: 292
  loop : -0.22 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 169 
 HIS   0.004   0.001   HIS A 103 
 PHE   0.020   0.002   PHE C 151 
 TYR   0.013   0.002   TYR E 103 
 ARG   0.010   0.000   ARG B 135 

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 118
  time to evaluate  : 1.085 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7733 (mttt) cc_final: 0.7195 (mttt)
REVERT: B   21 LYS cc_start: 0.7724 (tttm) cc_final: 0.7037 (ttpt)
REVERT: B   24 ARG cc_start: 0.6618 (mtm-85) cc_final: 0.6316 (mtm-85)
REVERT: B  135 ARG cc_start: 0.8157 (ptp-110) cc_final: 0.7865 (ptp-110)
REVERT: B  195 LYS cc_start: 0.7333 (tttm) cc_final: 0.6971 (ttpp)
REVERT: B  208 ARG cc_start: 0.6873 (mtm-85) cc_final: 0.6109 (mmm160)
REVERT: B  232 LYS cc_start: 0.8132 (ttmt) cc_final: 0.7823 (ttpt)
REVERT: C  217 MET cc_start: 0.8251 (pmm) cc_final: 0.7859 (pmm)
REVERT: C  219 ARG cc_start: 0.7775 (mmm160) cc_final: 0.7419 (mtp180)
REVERT: D   21 MET cc_start: 0.6371 (mtm) cc_final: 0.5768 (tmt)
REVERT: E    7 SER cc_start: 0.8265 (t) cc_final: 0.7850 (p)
REVERT: E   25 SER cc_start: 0.8186 (OUTLIER) cc_final: 0.7933 (m)
REVERT: E   43 LYS cc_start: 0.8008 (mtpp) cc_final: 0.7277 (mtpm)
REVERT: E   46 GLU cc_start: 0.8415 (tt0) cc_final: 0.8189 (tt0)
REVERT: A   61 ILE cc_start: 0.5622 (tp) cc_final: 0.5417 (tp)
REVERT: A  248 PHE cc_start: 0.7648 (t80) cc_final: 0.7335 (t80)
  outliers start: 31
  outliers final: 21
  residues processed: 136
  average time/residue: 1.4001
  time to fit residues: 202.0536
Evaluate side-chains
  133 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   18 MET
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue  120 GLU
Chi-restraints excluded: chain B residue  209 HIS
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  128 THR
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  196 THR
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   25 SER
Chi-restraints excluded: chain E residue   89 GLU
Chi-restraints excluded: chain E residue  116 THR
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  242 THR
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  253 ILE
Chi-restraints excluded: chain A residue  362 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9980
   chunk 89 optimal weight:    9.9990
   chunk 49 optimal weight:    0.7980
   chunk 8 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   chunk 56 optimal weight:    9.9990
   chunk 103 optimal weight:    0.0670
   chunk 12 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.9720

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

Flipped N/Q/H residues before XYZ refinement:
B  22 ASN
B 116 ASN
A 305 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.3550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8953  Z= 0.190
  Angle     :  0.506   6.898  12142  Z= 0.274
  Chirality :  0.041   0.138   1388
  Planarity :  0.004   0.046   1531
  Dihedral  :  4.385  22.859   1217
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 15.53 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.45 (0.26), residues: 1098
  helix:  2.56 (0.27), residues: 380
  sheet:  0.51 (0.29), residues: 286
  loop : -0.11 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 169 
 HIS   0.003   0.001   HIS A 103 
 PHE   0.016   0.001   PHE C 151 
 TYR   0.013   0.001   TYR E 178 
 ARG   0.007   0.000   ARG C  96 

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 125
  time to evaluate  : 1.045 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7668 (mttt) cc_final: 0.7159 (mttt)
REVERT: B   21 LYS cc_start: 0.7698 (tttm) cc_final: 0.7050 (ttpt)
REVERT: B   24 ARG cc_start: 0.6604 (mtm-85) cc_final: 0.6300 (mtm-85)
REVERT: B  132 ARG cc_start: 0.8393 (ptt-90) cc_final: 0.8054 (ptt-90)
REVERT: B  135 ARG cc_start: 0.8071 (ptp-110) cc_final: 0.7800 (ptp-110)
REVERT: B  195 LYS cc_start: 0.7395 (tttm) cc_final: 0.7022 (ttpp)
REVERT: B  222 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7195 (pt0)
REVERT: B  232 LYS cc_start: 0.8177 (ttmt) cc_final: 0.7836 (tttt)
REVERT: C  205 ASP cc_start: 0.7090 (OUTLIER) cc_final: 0.6759 (m-30)
REVERT: C  217 MET cc_start: 0.8248 (pmm) cc_final: 0.7827 (pmm)
REVERT: C  219 ARG cc_start: 0.7733 (mmm160) cc_final: 0.7379 (mtp180)
REVERT: C  293 ASN cc_start: 0.7748 (p0) cc_final: 0.7262 (p0)
REVERT: C  336 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8047 (mp)
REVERT: D   21 MET cc_start: 0.6359 (mtm) cc_final: 0.5780 (tmt)
REVERT: E    7 SER cc_start: 0.8182 (t) cc_final: 0.7859 (p)
REVERT: E   23 SER cc_start: 0.8417 (t) cc_final: 0.7964 (p)
REVERT: E   43 LYS cc_start: 0.7965 (mtpp) cc_final: 0.7263 (mtpm)
REVERT: E   46 GLU cc_start: 0.8417 (tt0) cc_final: 0.8065 (tt0)
REVERT: E   85 SER cc_start: 0.8558 (m) cc_final: 0.8098 (p)
REVERT: A  248 PHE cc_start: 0.7590 (t80) cc_final: 0.7320 (t80)
  outliers start: 24
  outliers final: 11
  residues processed: 138
  average time/residue: 1.4172
  time to fit residues: 207.5699
Evaluate side-chains
  132 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  209 HIS
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  196 THR
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain C residue  336 LEU
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  226 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 78 optimal weight:    6.9990
   chunk 60 optimal weight:    1.9990
   chunk 90 optimal weight:   20.0000
   chunk 59 optimal weight:    0.2980
   chunk 106 optimal weight:    8.9990
   chunk 66 optimal weight:    0.7980
   chunk 65 optimal weight:    0.5980
   chunk 49 optimal weight:    0.9990
   chunk 42 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 32 optimal weight:    0.2980
   overall best weight:    0.5982

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

Flipped N/Q/H residues before XYZ refinement:
B  22 ASN
B 116 ASN
E 167 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.3619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8953  Z= 0.152
  Angle     :  0.491   8.076  12142  Z= 0.262
  Chirality :  0.041   0.138   1388
  Planarity :  0.004   0.046   1531
  Dihedral  :  4.150  22.032   1217
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 16.06 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.62 (0.26), residues: 1098
  helix:  2.68 (0.27), residues: 380
  sheet:  0.76 (0.29), residues: 284
  loop : -0.13 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 211 
 HIS   0.003   0.001   HIS A 103 
 PHE   0.013   0.001   PHE C 151 
 TYR   0.013   0.001   TYR E 178 
 ARG   0.007   0.000   ARG C  96 

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 116
  time to evaluate  : 1.008 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7635 (mttt) cc_final: 0.7167 (mttt)
REVERT: B   21 LYS cc_start: 0.7670 (tttm) cc_final: 0.7051 (ttpt)
REVERT: B   24 ARG cc_start: 0.6591 (mtm-85) cc_final: 0.6282 (mtm-85)
REVERT: B  195 LYS cc_start: 0.7374 (tttm) cc_final: 0.7036 (ttpp)
REVERT: B  208 ARG cc_start: 0.7135 (mtm110) cc_final: 0.6278 (mmm160)
REVERT: B  222 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7167 (pt0)
REVERT: B  232 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7829 (tttt)
REVERT: C  205 ASP cc_start: 0.7009 (OUTLIER) cc_final: 0.6696 (m-30)
REVERT: C  217 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7857 (pmm)
REVERT: C  219 ARG cc_start: 0.7588 (mmm160) cc_final: 0.7273 (mtp180)
REVERT: C  247 ASP cc_start: 0.7321 (m-30) cc_final: 0.6979 (m-30)
REVERT: C  256 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7352 (mtp180)
REVERT: D   21 MET cc_start: 0.6356 (mtm) cc_final: 0.5803 (tmt)
REVERT: E    7 SER cc_start: 0.8134 (t) cc_final: 0.7795 (p)
REVERT: E   23 SER cc_start: 0.8425 (t) cc_final: 0.7986 (p)
REVERT: E   43 LYS cc_start: 0.7938 (mtpp) cc_final: 0.7226 (mtpm)
REVERT: E   46 GLU cc_start: 0.8389 (tt0) cc_final: 0.8033 (tt0)
REVERT: E   85 SER cc_start: 0.8564 (m) cc_final: 0.8119 (p)
REVERT: A  208 MET cc_start: 0.5960 (mmp) cc_final: 0.5562 (mmm)
  outliers start: 19
  outliers final: 11
  residues processed: 127
  average time/residue: 1.5529
  time to fit residues: 208.0475
Evaluate side-chains
  129 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  187 THR
Chi-restraints excluded: chain B residue  209 HIS
Chi-restraints excluded: chain B residue  222 GLU
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  256 ARG
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain E residue   89 GLU
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  253 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   chunk 68 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 84 optimal weight:    5.9990
   chunk 97 optimal weight:   10.0000
   chunk 102 optimal weight:    0.8980
   chunk 93 optimal weight:    0.5980
   chunk 99 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  22 ASN
B 116 ASN
E 167 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.3678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8953  Z= 0.165
  Angle     :  0.495   8.795  12142  Z= 0.263
  Chirality :  0.041   0.134   1388
  Planarity :  0.004   0.045   1531
  Dihedral  :  4.157  22.254   1217
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 16.60 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.65 (0.26), residues: 1098
  helix:  2.72 (0.27), residues: 380
  sheet:  0.67 (0.28), residues: 291
  loop : -0.04 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 169 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.014   0.001   PHE C 151 
 TYR   0.012   0.001   TYR E 178 
 ARG   0.006   0.000   ARG C  96 

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 1.036 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7661 (mttt) cc_final: 0.7175 (mttt)
REVERT: B   21 LYS cc_start: 0.7675 (tttm) cc_final: 0.7057 (ttpt)
REVERT: B   24 ARG cc_start: 0.6601 (mtm-85) cc_final: 0.6276 (mtm-85)
REVERT: B  132 ARG cc_start: 0.8328 (ptt-90) cc_final: 0.8015 (ptt-90)
REVERT: B  195 LYS cc_start: 0.7408 (tttm) cc_final: 0.7034 (ttpp)
REVERT: B  208 ARG cc_start: 0.7130 (mtm110) cc_final: 0.6267 (mmm160)
REVERT: B  232 LYS cc_start: 0.8166 (ttmt) cc_final: 0.7833 (tttt)
REVERT: C  205 ASP cc_start: 0.7040 (OUTLIER) cc_final: 0.6671 (m-30)
REVERT: C  217 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7722 (pmm)
REVERT: C  219 ARG cc_start: 0.7604 (mmm160) cc_final: 0.7325 (mtp180)
REVERT: C  256 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7318 (mtp180)
REVERT: D   21 MET cc_start: 0.6295 (mtm) cc_final: 0.5739 (tmt)
REVERT: E    7 SER cc_start: 0.8158 (t) cc_final: 0.7851 (p)
REVERT: E   23 SER cc_start: 0.8367 (t) cc_final: 0.7992 (p)
REVERT: E   43 LYS cc_start: 0.7995 (mtpp) cc_final: 0.7289 (mtpm)
REVERT: E   46 GLU cc_start: 0.8377 (tt0) cc_final: 0.8135 (tt0)
REVERT: E   85 SER cc_start: 0.8558 (m) cc_final: 0.8126 (p)
REVERT: A  330 MET cc_start: 0.7935 (ttp) cc_final: 0.7710 (ptm)
  outliers start: 18
  outliers final: 12
  residues processed: 126
  average time/residue: 1.4820
  time to fit residues: 197.3329
Evaluate side-chains
  127 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.983 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  209 HIS
Chi-restraints excluded: chain B residue  210 ILE
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  256 ARG
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain E residue   89 GLU
Chi-restraints excluded: chain E residue  180 MET
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  253 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 102 optimal weight:    0.8980
   chunk 60 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 78 optimal weight:    0.0980
   chunk 30 optimal weight:    1.9990
   chunk 90 optimal weight:    8.9990
   chunk 94 optimal weight:    1.9990
   chunk 99 optimal weight:    7.9990
   chunk 65 optimal weight:    0.2980
   chunk 105 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
B 116 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.3716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8953  Z= 0.197
  Angle     :  0.522   9.565  12142  Z= 0.275
  Chirality :  0.041   0.137   1388
  Planarity :  0.004   0.045   1531
  Dihedral  :  4.271  22.638   1217
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 17.02 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.60 (0.26), residues: 1098
  helix:  2.65 (0.27), residues: 380
  sheet:  0.65 (0.28), residues: 290
  loop : -0.05 (0.31), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 169 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.016   0.001   PHE C 151 
 TYR   0.014   0.001   TYR B 212 
 ARG   0.006   0.000   ARG C  96 

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 1.084 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7668 (mttt) cc_final: 0.7175 (mttt)
REVERT: B   21 LYS cc_start: 0.7675 (tttm) cc_final: 0.7043 (ttpt)
REVERT: B   24 ARG cc_start: 0.6604 (mtm-85) cc_final: 0.6279 (mtm-85)
REVERT: B  132 ARG cc_start: 0.8342 (ptt-90) cc_final: 0.8034 (ptt-90)
REVERT: B  195 LYS cc_start: 0.7392 (tttm) cc_final: 0.7021 (ttpp)
REVERT: B  208 ARG cc_start: 0.7167 (mtm110) cc_final: 0.6283 (mmm160)
REVERT: B  232 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7837 (tttt)
REVERT: C   52 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7530 (mtt90)
REVERT: C  205 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6774 (m-30)
REVERT: C  217 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7866 (pmm)
REVERT: C  219 ARG cc_start: 0.7639 (mmm160) cc_final: 0.7295 (mtp180)
REVERT: C  256 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7390 (mtp180)
REVERT: D   21 MET cc_start: 0.6310 (mtm) cc_final: 0.5747 (tmt)
REVERT: E    7 SER cc_start: 0.8119 (t) cc_final: 0.7831 (p)
REVERT: E   23 SER cc_start: 0.8386 (t) cc_final: 0.7971 (p)
REVERT: E   43 LYS cc_start: 0.8047 (mtpp) cc_final: 0.7332 (mtpm)
REVERT: E   46 GLU cc_start: 0.8394 (tt0) cc_final: 0.8154 (tt0)
REVERT: E   85 SER cc_start: 0.8559 (m) cc_final: 0.8120 (p)
REVERT: A  330 MET cc_start: 0.7932 (ttp) cc_final: 0.7722 (ptm)
  outliers start: 17
  outliers final: 12
  residues processed: 124
  average time/residue: 1.5338
  time to fit residues: 200.6282
Evaluate side-chains
  121 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  209 HIS
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  256 ARG
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   89 GLU
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  253 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 73 optimal weight:    9.9990
   chunk 110 optimal weight:    9.9990
   chunk 101 optimal weight:    1.9990
   chunk 88 optimal weight:    9.9990
   chunk 9 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
B 116 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.3761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8953  Z= 0.249
  Angle     :  0.555   9.662  12142  Z= 0.293
  Chirality :  0.042   0.141   1388
  Planarity :  0.004   0.045   1531
  Dihedral  :  4.496  23.144   1217
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 16.70 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.50 (0.26), residues: 1098
  helix:  2.58 (0.27), residues: 380
  sheet:  0.53 (0.28), residues: 297
  loop : -0.08 (0.31), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 169 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.018   0.002   PHE C 151 
 TYR   0.017   0.002   TYR B 212 
 ARG   0.008   0.000   ARG C  96 

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

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

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2196 Ramachandran restraints generated.
    1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 1.074 
Fit side-chains
REVERT: B   10 LYS cc_start: 0.7726 (mttt) cc_final: 0.7195 (mttt)
REVERT: B   21 LYS cc_start: 0.7715 (tttm) cc_final: 0.7058 (ttpt)
REVERT: B   24 ARG cc_start: 0.6615 (mtm-85) cc_final: 0.6285 (mtm-85)
REVERT: B  132 ARG cc_start: 0.8367 (ptt-90) cc_final: 0.8056 (ptt-90)
REVERT: B  195 LYS cc_start: 0.7334 (tttm) cc_final: 0.6937 (ttpp)
REVERT: B  208 ARG cc_start: 0.7155 (mtm110) cc_final: 0.6290 (mmm160)
REVERT: B  232 LYS cc_start: 0.8183 (ttmt) cc_final: 0.7838 (tttt)
REVERT: C   52 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7550 (mtt90)
REVERT: C  217 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7840 (pmm)
REVERT: C  219 ARG cc_start: 0.7747 (mmm160) cc_final: 0.7378 (mtp180)
REVERT: C  256 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7446 (mtp180)
REVERT: D   21 MET cc_start: 0.6337 (mtm) cc_final: 0.5764 (tmt)
REVERT: E    7 SER cc_start: 0.8143 (t) cc_final: 0.7811 (p)
REVERT: E   23 SER cc_start: 0.8427 (t) cc_final: 0.7959 (p)
REVERT: E   43 LYS cc_start: 0.8078 (mtpp) cc_final: 0.7347 (mtpm)
REVERT: E   46 GLU cc_start: 0.8408 (tt0) cc_final: 0.8179 (tt0)
REVERT: E   85 SER cc_start: 0.8567 (m) cc_final: 0.8116 (p)
REVERT: A  208 MET cc_start: 0.5682 (mmp) cc_final: 0.5366 (mmm)
REVERT: A  330 MET cc_start: 0.7927 (ttp) cc_final: 0.7695 (ptm)
  outliers start: 19
  outliers final: 15
  residues processed: 120
  average time/residue: 1.5263
  time to fit residues: 193.7075
Evaluate side-chains
  121 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue   72 THR
Chi-restraints excluded: chain B residue  209 HIS
Chi-restraints excluded: chain C residue   52 ARG
Chi-restraints excluded: chain C residue  114 CYS
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  196 THR
Chi-restraints excluded: chain C residue  205 ASP
Chi-restraints excluded: chain C residue  217 MET
Chi-restraints excluded: chain C residue  256 ARG
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain E residue   12 VAL
Chi-restraints excluded: chain E residue   89 GLU
Chi-restraints excluded: chain E residue  185 SER
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  226 THR
Chi-restraints excluded: chain A residue  247 LEU
Chi-restraints excluded: chain A residue  253 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 13 optimal weight:    6.9990
   chunk 24 optimal weight:   10.0000
   chunk 88 optimal weight:   10.0000
   chunk 36 optimal weight:    1.9990
   chunk 90 optimal weight:   20.0000
   chunk 11 optimal weight:    3.9990
   chunk 16 optimal weight:    0.8980
   chunk 77 optimal weight:    0.7980
   chunk 5 optimal weight:    5.9990
   chunk 63 optimal weight:    0.5980
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
B 116 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.180979 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.124898 restraints weight = 8560.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 1.83
r_work: 0.3147 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8423
moved from start:          0.3792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8953  Z= 0.197
  Angle     :  0.526   9.669  12142  Z= 0.277
  Chirality :  0.041   0.136   1388
  Planarity :  0.004   0.045   1531
  Dihedral  :  4.348  22.689   1217
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.28 %
    Favored  : 97.72 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 16.70 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.88 %
    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:  1.55 (0.26), residues: 1098
  helix:  2.63 (0.27), residues: 380
  sheet:  0.65 (0.28), residues: 296
  loop : -0.14 (0.31), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 169 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.016   0.001   PHE C 151 
 TYR   0.015   0.001   TYR B 212 
 ARG   0.009   0.000   ARG C  96 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3955.58 seconds
wall clock time: 75 minutes 44.88 seconds (4544.88 seconds total)