Starting phenix.real_space_refine
on Sat Jun  7 00:45:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fn1_29303/06_2025/8fn1_29303.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fn1_29303/06_2025/8fn1_29303.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fn1_29303/06_2025/8fn1_29303.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fn1_29303/06_2025/8fn1_29303.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fn1_29303/06_2025/8fn1_29303.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fn1_29303/06_2025/8fn1_29303.cif"
  }
  resolution = 2.88
  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=   0.002 sd=   0.026
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      56      5.16       5
     C    5375      2.51       5
     N    1418      2.21       5
     O    1595      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 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: 8444
  Number of models: 1
  Model: ""
    Number of chains: 6
    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}
    Chain: "A"
      Number of atoms: 2027
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 278, 2027
          Classifications: {'peptide': 278}
          Incomplete info: {'backbone_only': 10, 'truncation_to_alanine': 30}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 268}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 183
          Unresolved non-hydrogen angles: 235
          Unresolved non-hydrogen dihedrals: 150
          Unresolved non-hydrogen chiralities: 22
          Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 2, 'HIS:plan': 1, 'PHE:plan': 4, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 95
    Chain: "B"
      Number of atoms: 1667
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1667
          Classifications: {'peptide': 213}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 208}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 23
          Unresolved non-hydrogen angles: 26
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "C"
      Number of atoms: 2552
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2552
          Classifications: {'peptide': 338}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 38
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 5, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 39
    Chain: "D"
      Number of atoms: 381
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 381
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "E"
      Number of atoms: 1759
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 230, 1759
          Classifications: {'peptide': 230}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 11
  Time building chain proxies: 5.14, per 1000 atoms: 0.61
  Number of scatterers: 8444
  At special positions: 0
  Unit cell: (93.28, 118.8, 132.88, 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      56     16.00
     O    1595      8.00
     N    1418      7.00
     C    5375      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 142 " - pdb=" SG  CYS A 225 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.04

  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: 2.14
  Conformation dependent library (CDL) restraints added in 998.2 milliseconds
  

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2068

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 15 sheets defined
      37.2% alpha, 26.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.04
  Creating SS restraints...
    Processing helix  chain 'A' and resid 60 through 90
      removed outlier: 3.520A  pdb=" N   LEU A  72 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ALA A  73 " --> pdb=" O   ALA A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 128
      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: 3.819A  pdb=" N   THR A 179 " --> pdb=" O   PHE A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 201
    Processing helix  chain 'A' and resid 203 through 207
    Processing helix  chain 'A' and resid 230 through 246
      removed outlier: 3.962A  pdb=" N   VAL A 236 " --> pdb=" O   ALA A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 267
    Processing helix  chain 'A' and resid 302 through 320
      removed outlier: 3.592A  pdb=" N   GLY A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 334
      removed outlier: 3.780A  pdb=" N   HIS A 325 " --> pdb=" O   TRP A 321 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ARG A 328 " --> pdb=" O   TYR A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 371
      removed outlier: 3.585A  pdb=" N   HIS A 348 " --> pdb=" O   PHE A 344 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER A 362 " --> pdb=" O   PHE A 358 " (cutoff:3.500A)
      Proline residue:  A 366  - end of helix
    Processing helix  chain 'B' and resid 3 through 29
      removed outlier: 3.900A  pdb=" N   LYS B  29 " --> pdb=" O   ILE B  25 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 42 through 46
    Processing helix  chain 'B' and resid 89 through 98
      removed outlier: 4.965A  pdb=" N   ILE B  94 " --> pdb=" O   LYS B  91 " (cutoff:3.500A)
      removed outlier: 5.694A  pdb=" N   HIS B  95 " --> pdb=" O   LYS B  92 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 117 through 127
    Processing helix  chain 'B' and resid 128 through 132
      removed outlier: 3.933A  pdb=" N   ILE B 132 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 142 through 150
    Processing helix  chain 'B' and resid 167 through 181
      removed outlier: 3.511A  pdb=" N   ALA B 171 " --> pdb=" O   THR B 167 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 223
      removed outlier: 3.562A  pdb=" N   VAL B 205 " --> pdb=" O   ASN B 201 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 4 through 25
    Processing helix  chain 'C' and resid 29 through 34
    Processing helix  chain 'C' and resid 128 through 132
      removed outlier: 3.886A  pdb=" N   GLY C 131 " --> pdb=" O   THR C 128 " (cutoff:3.500A)
      removed outlier: 4.302A  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 87 through 91
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 212
    Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 52
      removed outlier: 3.734A  pdb=" N   ALA B 102 " --> pdb=" O   LYS B  32 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   ILE B 103 " --> pdb=" O   ILE B 137 " (cutoff:3.500A)
      removed outlier: 7.336A  pdb=" N   PHE B 139 " --> pdb=" O   ILE B 103 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   PHE B 105 " --> pdb=" O   PHE B 139 " (cutoff:3.500A)
      removed outlier: 7.313A  pdb=" N   ASN B 141 " --> pdb=" O   PHE B 105 " (cutoff:3.500A)
      removed outlier: 6.848A  pdb=" N   VAL B 107 " --> pdb=" O   ASN B 141 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 47 through 51
      removed outlier: 6.581A  pdb=" N   ILE C 338 " --> pdb=" O   ARG C  48 " (cutoff:3.500A)
      removed outlier: 4.361A  pdb=" N   THR C  50 " --> pdb=" O   LEU C 336 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   LEU C 336 " --> pdb=" O   THR C  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63
      removed outlier: 3.628A  pdb=" N   ALA C  60 " --> pdb=" O   ALA C  73 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   LYS C  78 " --> pdb=" O   SER C  74 " (cutoff:3.500A)
      removed outlier: 6.453A  pdb=" N   LEU C  79 " --> pdb=" O   ALA C  92 " (cutoff:3.500A)
      removed outlier: 4.520A  pdb=" N   ALA C  92 " --> pdb=" O   LEU C  79 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   ILE C  81 " --> pdb=" O   VAL C  90 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105
      removed outlier: 6.945A  pdb=" N   GLY C 115 " --> pdb=" O   MET C 101 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   CYS C 103 " --> pdb=" O   ALA C 113 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   ALA C 113 " --> pdb=" O   CYS C 103 " (cutoff:3.500A)
      removed outlier: 5.136A  pdb=" N   TYR C 105 " --> pdb=" O   TYR C 111 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   TYR C 111 " --> pdb=" O   TYR C 105 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   GLY C 116 " --> pdb=" O   ILE C 120 " (cutoff:3.500A)
      removed outlier: 4.824A  pdb=" N   ILE C 120 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      removed outlier: 6.186A  pdb=" N   ASN C 125 " --> pdb=" O   VAL C 135 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   VAL C 135 " --> pdb=" O   ASN C 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 153
      removed outlier: 3.636A  pdb=" N   CYS C 148 " --> pdb=" O   SER C 160 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   GLN C 156 " --> pdb=" O   LEU C 152 " (cutoff:3.500A)
      removed outlier: 6.348A  pdb=" N   ASP C 170 " --> pdb=" O   GLN C 176 " (cutoff:3.500A)
      removed outlier: 6.001A  pdb=" N   GLN C 176 " --> pdb=" O   ASP C 170 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192
      removed outlier: 3.675A  pdb=" N   GLY C 202 " --> pdb=" O   SER C 189 " (cutoff:3.500A)
      removed outlier: 6.601A  pdb=" N   ALA C 208 " --> pdb=" O   THR C 221 " (cutoff:3.500A)
      removed outlier: 4.529A  pdb=" N   THR C 221 " --> pdb=" O   ALA C 208 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   LEU C 210 " --> pdb=" O   ARG C 219 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   MET C 217 " --> pdb=" O   ASP C 212 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234
      removed outlier: 3.509A  pdb=" N   ALA C 231 " --> pdb=" O   GLY C 244 " (cutoff:3.500A)
      removed outlier: 6.691A  pdb=" N   CYS C 250 " --> pdb=" O   THR C 263 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   THR C 263 " --> pdb=" O   CYS C 250 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   LEU C 252 " --> pdb=" O   LEU C 261 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLN C 259 " --> pdb=" O   ASP C 254 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278
      removed outlier: 3.593A  pdb=" N   SER C 275 " --> pdb=" O   GLY C 288 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   ASP C 298 " --> pdb=" O   ARG C 304 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   ARG C 304 " --> pdb=" O   ASP C 298 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.915A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   MET E  34 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   TYR E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.398A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12
      removed outlier: 5.915A  pdb=" N   GLY E  10 " --> pdb=" O   THR E 118 " (cutoff:3.500A)
      removed outlier: 4.403A  pdb=" N   PHE E 110 " --> pdb=" O   ARG E  98 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'E' and resid 128 through 130
    Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 136
      removed outlier: 6.450A  pdb=" N   LEU E 162 " --> pdb=" O   TYR E 178 " (cutoff:3.500A)
      removed outlier: 4.595A  pdb=" N   TYR E 178 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   TRP E 164 " --> pdb=" O   LEU E 176 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'E' and resid 134 through 136
      removed outlier: 4.099A  pdb=" N   THR E 226 " --> pdb=" O   GLN E 219 " (cutoff:3.500A)

    460 hydrogen bonds defined for protein.
    1281 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: 2.75

  Time building geometry restraints manager: 2.54 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.19 -     1.32: 1390
        1.32 -     1.44: 2367
        1.44 -     1.56: 4781
        1.56 -     1.69: 0
        1.69 -     1.81: 81
  Bond restraints: 8619
  Sorted by residual:
  bond pdb=" C   ILE A  70 "
       pdb=" O   ILE A  70 "
    ideal  model  delta    sigma   weight residual
    1.234  1.194  0.040 1.09e-02 8.42e+03 1.35e+01
  bond pdb=" N   ASN B  75 "
       pdb=" CA  ASN B  75 "
    ideal  model  delta    sigma   weight residual
    1.460  1.500 -0.040 1.28e-02 6.10e+03 9.97e+00
  bond pdb=" C   LYS A  64 "
       pdb=" O   LYS A  64 "
    ideal  model  delta    sigma   weight residual
    1.236  1.197  0.039 1.32e-02 5.74e+03 8.70e+00
  bond pdb=" C   VAL A  67 "
       pdb=" O   VAL A  67 "
    ideal  model  delta    sigma   weight residual
    1.237  1.204  0.033 1.17e-02 7.31e+03 8.02e+00
  bond pdb=" N   ILE A  70 "
       pdb=" CA  ILE A  70 "
    ideal  model  delta    sigma   weight residual
    1.461  1.500 -0.040 1.42e-02 4.96e+03 7.85e+00
  ... (remaining 8614 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.83: 11523
        1.83 -     3.66: 160
        3.66 -     5.49: 21
        5.49 -     7.33: 4
        7.33 -     9.16: 4
  Bond angle restraints: 11712
  Sorted by residual:
  angle pdb=" N   THR A  68 "
        pdb=" CA  THR A  68 "
        pdb=" C   THR A  68 "
      ideal   model   delta    sigma   weight residual
     111.28  103.13    8.15 1.09e+00 8.42e-01 5.59e+01
  angle pdb=" N   VAL A  65 "
        pdb=" CA  VAL A  65 "
        pdb=" C   VAL A  65 "
      ideal   model   delta    sigma   weight residual
     110.62  105.11    5.51 1.02e+00 9.61e-01 2.92e+01
  angle pdb=" CA  ILE A  70 "
        pdb=" CB  ILE A  70 "
        pdb=" CG2 ILE A  70 "
      ideal   model   delta    sigma   weight residual
     110.50  119.66   -9.16 1.70e+00 3.46e-01 2.90e+01
  angle pdb=" CA  ILE A  70 "
        pdb=" CB  ILE A  70 "
        pdb=" CG1 ILE A  70 "
      ideal   model   delta    sigma   weight residual
     110.40  118.94   -8.54 1.70e+00 3.46e-01 2.52e+01
  angle pdb=" N   VAL A  67 "
        pdb=" CA  VAL A  67 "
        pdb=" CB  VAL A  67 "
      ideal   model   delta    sigma   weight residual
     110.54  117.02   -6.48 1.36e+00 5.41e-01 2.27e+01
  ... (remaining 11707 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.30: 4865
       16.30 -    32.59: 154
       32.59 -    48.89: 24
       48.89 -    65.18: 9
       65.18 -    81.48: 3
  Dihedral angle restraints: 5055
    sinusoidal: 1841
      harmonic: 3214
  Sorted by residual:
  dihedral pdb=" CA  HIS B 116 "
           pdb=" C   HIS B 116 "
           pdb=" N   GLU B 117 "
           pdb=" CA  GLU B 117 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.08   21.92     0      5.00e+00 4.00e-02 1.92e+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  160.51   19.49     0      5.00e+00 4.00e-02 1.52e+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  162.56   17.44     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 5052 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.352: 1354
       0.352 -    0.704: 0
       0.704 -    1.056: 0
       1.056 -    1.408: 0
       1.408 -    1.760: 1
  Chirality restraints: 1355
  Sorted by residual:
  chirality pdb=" CB  ILE A  70 "
            pdb=" CA  ILE A  70 "
            pdb=" CG1 ILE A  70 "
            pdb=" CG2 ILE A  70 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    0.88    1.76 2.00e-01 2.50e+01 7.74e+01
  chirality pdb=" CA  VAL A  65 "
            pdb=" N   VAL A  65 "
            pdb=" C   VAL A  65 "
            pdb=" CB  VAL A  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.61   -0.17 2.00e-01 2.50e+01 6.84e-01
  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    2.59   -0.15 2.00e-01 2.50e+01 5.28e-01
  ... (remaining 1352 not shown)

  Planarity restraints: 1486
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A  68 "   -0.012 2.00e-02 2.50e+03   2.57e-02 6.59e+00
        pdb=" C   THR A  68 "    0.044 2.00e-02 2.50e+03
        pdb=" O   THR A  68 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ALA A  69 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 314 "    0.007 2.00e-02 2.50e+03   1.45e-02 2.09e+00
        pdb=" C   VAL A 314 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   VAL A 314 "    0.009 2.00e-02 2.50e+03
        pdb=" N   ILE A 315 "    0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B  74 "   -0.007 2.00e-02 2.50e+03   1.44e-02 2.07e+00
        pdb=" C   LYS B  74 "    0.025 2.00e-02 2.50e+03
        pdb=" O   LYS B  74 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ASN B  75 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1483 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 370
        2.72 -     3.26: 8530
        3.26 -     3.81: 13844
        3.81 -     4.35: 17424
        4.35 -     4.90: 30268
  Nonbonded interactions: 70436
  Sorted by model distance:
  nonbonded pdb=" O   ASP C 163 "
            pdb=" OG1 THR C 164 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" O   GLY E 197 "
            pdb=" OG1 THR E 198 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" OG  SER A 108 "
            pdb=" OD1 ASN A 159 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O   MET C 325 "
            pdb=" ND2 ASN C 340 "
     model   vdw
     2.227 3.120
  nonbonded pdb=" OD2 ASP E  73 "
            pdb=" NZ  LYS E  76 "
     model   vdw
     2.241 3.120
  ... (remaining 70431 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:             0.750
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.910
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  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:13.810
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
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   0.040   8621  Z= 0.208
  Angle     :  0.589   9.158  11716  Z= 0.375
  Chirality :  0.063   1.760   1355
  Planarity :  0.003   0.030   1486
  Dihedral  :  9.146  81.475   2981
  Min Nonbonded Distance : 2.173

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  1.70 %
    Favored  : 98.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.17 (0.26), residues: 1094
  helix:  2.16 (0.28), residues: 362
  sheet:  0.59 (0.28), residues: 292
  loop : -0.21 (0.30), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 169 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.015   0.001   PHE B  73 
 TYR   0.013   0.001   TYR E 178 
 ARG   0.002   0.000   ARG F   9 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14263 (  452)
  hydrogen bonds       : angle       6.42871 ( 1281)
  SS BOND              : bond        0.00500 (    2)
  SS BOND              : angle       0.76754 (    4)
  covalent geometry    : bond        0.00370 ( 8619)
  covalent geometry    : angle       0.58895 (11712)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 189
  time to evaluate  : 0.884 
Fit side-chains
REVERT: A  169 LEU cc_start: 0.8015 (tp) cc_final: 0.7814 (tp)
REVERT: A  309 VAL cc_start: 0.7218 (t) cc_final: 0.6786 (p)
REVERT: A  343 LEU cc_start: 0.7396 (mt) cc_final: 0.7168 (mt)
REVERT: A  347 TYR cc_start: 0.6992 (t80) cc_final: 0.6777 (t80)
REVERT: A  364 ILE cc_start: 0.7576 (mt) cc_final: 0.7278 (mt)
REVERT: B   30 ASP cc_start: 0.7495 (m-30) cc_final: 0.7289 (m-30)
REVERT: B  111 ASP cc_start: 0.7661 (t0) cc_final: 0.7123 (t0)
REVERT: B  120 MET cc_start: 0.7091 (mmm) cc_final: 0.6865 (mmm)
REVERT: C   52 ARG cc_start: 0.7302 (mtt90) cc_final: 0.7076 (mtt90)
REVERT: C   97 SER cc_start: 0.8467 (t) cc_final: 0.8044 (p)
REVERT: C  268 ASN cc_start: 0.6769 (p0) cc_final: 0.6483 (p0)
REVERT: E    7 SER cc_start: 0.8249 (t) cc_final: 0.8003 (m)
  outliers start: 2
  outliers final: 0
  residues processed: 190
  average time/residue: 0.7419
  time to fit residues: 155.5618
Evaluate side-chains
  158 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.827 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 92 optimal weight:    0.4980
   chunk 83 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 28 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 44 optimal weight:    0.4980
   chunk 86 optimal weight:    0.0980
   chunk 33 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 64 optimal weight:    1.9990
   chunk 99 optimal weight:    3.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 105 HIS
B  70 HIS
B  95 HIS
B 128 ASN
B 193 HIS
C  62 HIS
C 110 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.138894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.118442 restraints weight = 12231.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 1.97
r_work: 0.3416 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3269 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8621  Z= 0.144
  Angle     :  0.521   6.645  11716  Z= 0.283
  Chirality :  0.043   0.159   1355
  Planarity :  0.004   0.036   1486
  Dihedral  :  4.327  21.828   1188
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  :  8.60 %
    Favored  : 89.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.32 (0.25), residues: 1094
  helix:  2.39 (0.27), residues: 367
  sheet:  0.71 (0.28), residues: 273
  loop : -0.24 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 321 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.025   0.002   PHE B  73 
 TYR   0.023   0.002   TYR A  71 
 ARG   0.008   0.000   ARG F   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04215 (  452)
  hydrogen bonds       : angle       4.96859 ( 1281)
  SS BOND              : bond        0.00503 (    2)
  SS BOND              : angle       0.95867 (    4)
  covalent geometry    : bond        0.00330 ( 8619)
  covalent geometry    : angle       0.52031 (11712)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 157
  time to evaluate  : 1.098 
Fit side-chains
REVERT: A  204 MET cc_start: 0.7122 (mmp) cc_final: 0.6819 (mpm)
REVERT: A  237 VAL cc_start: 0.7750 (OUTLIER) cc_final: 0.7520 (t)
REVERT: A  347 TYR cc_start: 0.7029 (t80) cc_final: 0.6796 (t80)
REVERT: A  364 ILE cc_start: 0.7910 (mt) cc_final: 0.7618 (mt)
REVERT: B   77 HIS cc_start: 0.8142 (t-170) cc_final: 0.7808 (t70)
REVERT: B  111 ASP cc_start: 0.7898 (t0) cc_final: 0.7341 (t0)
REVERT: B  142 LYS cc_start: 0.8147 (mttt) cc_final: 0.7920 (mttt)
REVERT: C   51 LEU cc_start: 0.8610 (mt) cc_final: 0.8326 (mm)
REVERT: C   52 ARG cc_start: 0.7710 (mtt90) cc_final: 0.7508 (mtt90)
REVERT: C   97 SER cc_start: 0.8339 (t) cc_final: 0.8071 (p)
REVERT: C  198 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7898 (pt)
REVERT: C  251 ARG cc_start: 0.8647 (mtt-85) cc_final: 0.8273 (mtp85)
REVERT: C  256 ARG cc_start: 0.8169 (mpp80) cc_final: 0.7572 (mtm180)
REVERT: C  268 ASN cc_start: 0.7068 (p0) cc_final: 0.6861 (p0)
REVERT: C  274 THR cc_start: 0.8271 (OUTLIER) cc_final: 0.7843 (p)
REVERT: C  318 LEU cc_start: 0.8464 (OUTLIER) cc_final: 0.8166 (tp)
REVERT: E    7 SER cc_start: 0.8140 (t) cc_final: 0.7871 (m)
REVERT: E   93 MET cc_start: 0.8483 (OUTLIER) cc_final: 0.8204 (ttt)
REVERT: E  180 MET cc_start: 0.8204 (ttp) cc_final: 0.7879 (ttp)
  outliers start: 20
  outliers final: 9
  residues processed: 165
  average time/residue: 1.2041
  time to fit residues: 216.0565
Evaluate side-chains
  166 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 152
  time to evaluate  : 0.864 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain C residue   37 ILE
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  262 MET
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain E residue   93 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 102 optimal weight:    0.6980
   chunk 88 optimal weight:    0.0770
   chunk 56 optimal weight:    0.7980
   chunk 59 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 70 optimal weight:    3.9990
   chunk 89 optimal weight:    0.2980
   chunk 57 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
B 128 ASN
C 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.139365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.118834 restraints weight = 12427.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3528 rms_B_bonded: 2.02
r_work: 0.3421 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3275 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.1891

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8621  Z= 0.127
  Angle     :  0.480   5.170  11716  Z= 0.260
  Chirality :  0.042   0.129   1355
  Planarity :  0.003   0.040   1486
  Dihedral  :  4.171  20.311   1188
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  2.94 %
    Allowed  :  9.28 %
    Favored  : 87.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.43 (0.26), residues: 1094
  helix:  2.52 (0.28), residues: 367
  sheet:  0.76 (0.29), residues: 272
  loop : -0.22 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 169 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.014   0.001   PHE B  73 
 TYR   0.017   0.001   TYR A 359 
 ARG   0.004   0.000   ARG F   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03753 (  452)
  hydrogen bonds       : angle       4.73275 ( 1281)
  SS BOND              : bond        0.00491 (    2)
  SS BOND              : angle       0.73044 (    4)
  covalent geometry    : bond        0.00288 ( 8619)
  covalent geometry    : angle       0.48034 (11712)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 157
  time to evaluate  : 0.861 
Fit side-chains
REVERT: A  146 TYR cc_start: 0.6895 (OUTLIER) cc_final: 0.5885 (t80)
REVERT: A  204 MET cc_start: 0.7099 (mmp) cc_final: 0.6707 (mpm)
REVERT: A  237 VAL cc_start: 0.7705 (OUTLIER) cc_final: 0.7484 (p)
REVERT: A  364 ILE cc_start: 0.7820 (mt) cc_final: 0.7546 (mt)
REVERT: B   77 HIS cc_start: 0.7980 (t-170) cc_final: 0.7696 (t70)
REVERT: B  111 ASP cc_start: 0.7912 (t0) cc_final: 0.7362 (t0)
REVERT: B  142 LYS cc_start: 0.8129 (mttt) cc_final: 0.7924 (mttt)
REVERT: C   52 ARG cc_start: 0.7714 (mtt90) cc_final: 0.7513 (mtt90)
REVERT: C   97 SER cc_start: 0.8331 (t) cc_final: 0.8078 (p)
REVERT: C  198 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7913 (pt)
REVERT: C  256 ARG cc_start: 0.8126 (mpp80) cc_final: 0.7595 (mtm180)
REVERT: C  268 ASN cc_start: 0.7113 (p0) cc_final: 0.6885 (p0)
REVERT: C  274 THR cc_start: 0.8231 (OUTLIER) cc_final: 0.7821 (p)
REVERT: C  318 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8263 (tp)
REVERT: E    7 SER cc_start: 0.8117 (t) cc_final: 0.7863 (m)
REVERT: E   93 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8260 (ttt)
  outliers start: 26
  outliers final: 12
  residues processed: 173
  average time/residue: 0.8369
  time to fit residues: 158.0232
Evaluate side-chains
  173 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 155
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   37 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  262 MET
Chi-restraints excluded: chain C residue  274 THR
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  231 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 83 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 43 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 9 optimal weight:    1.9990
   chunk 76 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 133 HIS
C 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.136110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.115866 restraints weight = 12248.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 1.96
r_work: 0.3379 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3232 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.1995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   8621  Z= 0.265
  Angle     :  0.602   6.208  11716  Z= 0.319
  Chirality :  0.045   0.146   1355
  Planarity :  0.004   0.041   1486
  Dihedral  :  4.642  22.923   1188
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 6.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 10.18 %
    Favored  : 86.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.07 (0.25), residues: 1094
  helix:  2.14 (0.27), residues: 370
  sheet:  0.61 (0.29), residues: 272
  loop : -0.41 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 321 
 HIS   0.005   0.001   HIS B  95 
 PHE   0.026   0.002   PHE A 350 
 TYR   0.017   0.002   TYR E 178 
 ARG   0.005   0.001   ARG F   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04695 (  452)
  hydrogen bonds       : angle       5.02377 ( 1281)
  SS BOND              : bond        0.00632 (    2)
  SS BOND              : angle       1.10398 (    4)
  covalent geometry    : bond        0.00635 ( 8619)
  covalent geometry    : angle       0.60157 (11712)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 152
  time to evaluate  : 1.042 
Fit side-chains
REVERT: A  146 TYR cc_start: 0.6906 (OUTLIER) cc_final: 0.5945 (t80)
REVERT: A  204 MET cc_start: 0.7216 (mmp) cc_final: 0.6991 (mpm)
REVERT: A  237 VAL cc_start: 0.7753 (OUTLIER) cc_final: 0.7528 (p)
REVERT: A  309 VAL cc_start: 0.7509 (t) cc_final: 0.7001 (p)
REVERT: A  329 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.7038 (mm)
REVERT: B   79 ARG cc_start: 0.8592 (mtp180) cc_final: 0.8347 (mtp180)
REVERT: B  111 ASP cc_start: 0.7856 (t0) cc_final: 0.7358 (t0)
REVERT: B  142 LYS cc_start: 0.8098 (mttt) cc_final: 0.7882 (mttt)
REVERT: C   22 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.7095 (mtt180)
REVERT: C   52 ARG cc_start: 0.7675 (mtt90) cc_final: 0.7474 (mtt90)
REVERT: C   61 MET cc_start: 0.8724 (ppp) cc_final: 0.8329 (ppp)
REVERT: C   97 SER cc_start: 0.8276 (t) cc_final: 0.7893 (p)
REVERT: C  197 ARG cc_start: 0.7972 (ttm170) cc_final: 0.7760 (mtm180)
REVERT: C  268 ASN cc_start: 0.6994 (p0) cc_final: 0.6783 (p0)
REVERT: E    7 SER cc_start: 0.8279 (t) cc_final: 0.8031 (m)
REVERT: E   93 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8243 (ttt)
  outliers start: 28
  outliers final: 16
  residues processed: 164
  average time/residue: 0.7874
  time to fit residues: 141.9661
Evaluate side-chains
  175 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 154
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  123 VAL
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain B residue   50 MET
Chi-restraints excluded: chain B residue   66 ILE
Chi-restraints excluded: chain C residue   22 ARG
Chi-restraints excluded: chain C residue   37 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  262 MET
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  154 LEU
Chi-restraints excluded: chain E residue  231 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 64 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9990
   chunk 0 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 77 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
B 183 ASN
C 110 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.138195 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.117976 restraints weight = 12268.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3512 rms_B_bonded: 1.99
r_work: 0.3404 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3257 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8621  Z= 0.144
  Angle     :  0.511   5.302  11716  Z= 0.275
  Chirality :  0.042   0.187   1355
  Planarity :  0.004   0.040   1486
  Dihedral  :  4.355  21.036   1188
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 11.76 %
    Favored  : 85.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.24 (0.26), residues: 1094
  helix:  2.41 (0.28), residues: 370
  sheet:  0.64 (0.30), residues: 274
  loop : -0.38 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C 169 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.016   0.002   PHE A 350 
 TYR   0.015   0.001   TYR E 178 
 ARG   0.003   0.000   ARG F   8 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03857 (  452)
  hydrogen bonds       : angle       4.76086 ( 1281)
  SS BOND              : bond        0.00510 (    2)
  SS BOND              : angle       0.69291 (    4)
  covalent geometry    : bond        0.00333 ( 8619)
  covalent geometry    : angle       0.51065 (11712)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 150
  time to evaluate  : 1.058 
Fit side-chains
REVERT: A  146 TYR cc_start: 0.6877 (OUTLIER) cc_final: 0.5899 (t80)
REVERT: A  204 MET cc_start: 0.7154 (mmp) cc_final: 0.6877 (mpm)
REVERT: A  229 VAL cc_start: 0.8225 (m) cc_final: 0.8000 (p)
REVERT: A  237 VAL cc_start: 0.7747 (OUTLIER) cc_final: 0.7513 (p)
REVERT: A  309 VAL cc_start: 0.7430 (t) cc_final: 0.6946 (p)
REVERT: B   79 ARG cc_start: 0.8656 (mtp180) cc_final: 0.8428 (mtp180)
REVERT: B  111 ASP cc_start: 0.7904 (t0) cc_final: 0.7410 (t0)
REVERT: C   97 SER cc_start: 0.8317 (t) cc_final: 0.8065 (p)
REVERT: C  197 ARG cc_start: 0.7946 (ttm170) cc_final: 0.7722 (mtm180)
REVERT: C  198 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.7865 (pt)
REVERT: C  268 ASN cc_start: 0.7042 (p0) cc_final: 0.6839 (p0)
REVERT: C  318 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8253 (tp)
REVERT: E    7 SER cc_start: 0.8210 (t) cc_final: 0.7967 (m)
REVERT: E   93 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8238 (ttt)
  outliers start: 24
  outliers final: 15
  residues processed: 161
  average time/residue: 1.0374
  time to fit residues: 183.6251
Evaluate side-chains
  171 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 1.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain B residue   50 MET
Chi-restraints excluded: chain C residue   37 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  262 MET
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  231 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 3 optimal weight:    0.5980
   chunk 64 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 5 optimal weight:    0.6980
   chunk 108 optimal weight:    0.5980
   chunk 71 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 36 optimal weight:    0.0970
   chunk 20 optimal weight:    3.9990
   overall best weight:    0.5378

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.139042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.118735 restraints weight = 12262.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 2.00
r_work: 0.3415 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7660
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8621  Z= 0.125
  Angle     :  0.485   5.670  11716  Z= 0.263
  Chirality :  0.041   0.139   1355
  Planarity :  0.004   0.060   1486
  Dihedral  :  4.153  19.982   1188
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 11.99 %
    Favored  : 84.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.39 (0.26), residues: 1094
  helix:  2.61 (0.27), residues: 370
  sheet:  0.59 (0.30), residues: 275
  loop : -0.28 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 169 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.025   0.001   PHE A 331 
 TYR   0.015   0.001   TYR E 178 
 ARG   0.002   0.000   ARG C  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03518 (  452)
  hydrogen bonds       : angle       4.58281 ( 1281)
  SS BOND              : bond        0.00515 (    2)
  SS BOND              : angle       0.67881 (    4)
  covalent geometry    : bond        0.00288 ( 8619)
  covalent geometry    : angle       0.48532 (11712)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 150
  time to evaluate  : 0.967 
Fit side-chains
REVERT: A  146 TYR cc_start: 0.6888 (OUTLIER) cc_final: 0.5941 (t80)
REVERT: A  204 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6744 (mpm)
REVERT: A  237 VAL cc_start: 0.7788 (OUTLIER) cc_final: 0.7578 (t)
REVERT: B   79 ARG cc_start: 0.8677 (mtp180) cc_final: 0.8359 (mtp180)
REVERT: B  111 ASP cc_start: 0.7880 (t0) cc_final: 0.7375 (t0)
REVERT: B  142 LYS cc_start: 0.8321 (mttt) cc_final: 0.8083 (ptpp)
REVERT: C   97 SER cc_start: 0.8332 (t) cc_final: 0.8075 (p)
REVERT: C  197 ARG cc_start: 0.7893 (ttm170) cc_final: 0.7664 (mtm180)
REVERT: C  198 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.7869 (pt)
REVERT: C  318 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8281 (tp)
REVERT: E    7 SER cc_start: 0.8121 (t) cc_final: 0.7867 (m)
REVERT: E   93 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8240 (ttt)
  outliers start: 29
  outliers final: 18
  residues processed: 162
  average time/residue: 0.8906
  time to fit residues: 158.9483
Evaluate side-chains
  176 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain B residue   15 MET
Chi-restraints excluded: chain B residue   50 MET
Chi-restraints excluded: chain B residue  185 SER
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  262 MET
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  154 LEU
Chi-restraints excluded: chain E residue  231 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 52 optimal weight:    6.9990
   chunk 44 optimal weight:    0.3980
   chunk 8 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 43 optimal weight:    0.5980
   chunk 79 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.7580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.138620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.118296 restraints weight = 12351.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 2.00
r_work: 0.3411 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3264 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.2413

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8621  Z= 0.151
  Angle     :  0.516   9.704  11716  Z= 0.274
  Chirality :  0.042   0.141   1355
  Planarity :  0.004   0.062   1486
  Dihedral  :  4.250  20.855   1188
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 13.46 %
    Favored  : 83.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.35 (0.26), residues: 1094
  helix:  2.61 (0.27), residues: 370
  sheet:  0.58 (0.30), residues: 273
  loop : -0.34 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 321 
 HIS   0.004   0.001   HIS E  35 
 PHE   0.025   0.002   PHE A 331 
 TYR   0.015   0.001   TYR E 178 
 ARG   0.006   0.000   ARG C  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03702 (  452)
  hydrogen bonds       : angle       4.61648 ( 1281)
  SS BOND              : bond        0.00513 (    2)
  SS BOND              : angle       0.73488 (    4)
  covalent geometry    : bond        0.00356 ( 8619)
  covalent geometry    : angle       0.51544 (11712)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 145
  time to evaluate  : 0.830 
Fit side-chains
REVERT: A  146 TYR cc_start: 0.6916 (OUTLIER) cc_final: 0.5935 (t80)
REVERT: A  204 MET cc_start: 0.7036 (OUTLIER) cc_final: 0.6741 (mpm)
REVERT: A  237 VAL cc_start: 0.7781 (OUTLIER) cc_final: 0.7566 (t)
REVERT: B  111 ASP cc_start: 0.7920 (t0) cc_final: 0.7423 (t0)
REVERT: B  142 LYS cc_start: 0.8269 (mttt) cc_final: 0.7941 (ptpp)
REVERT: C   51 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8289 (mm)
REVERT: C   97 SER cc_start: 0.8326 (t) cc_final: 0.8060 (p)
REVERT: C  197 ARG cc_start: 0.7879 (ttm170) cc_final: 0.7628 (mtm180)
REVERT: C  198 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.7883 (pt)
REVERT: C  258 ASP cc_start: 0.7225 (t0) cc_final: 0.6858 (t70)
REVERT: E    7 SER cc_start: 0.8210 (t) cc_final: 0.7957 (m)
REVERT: E   93 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8201 (ttt)
  outliers start: 27
  outliers final: 18
  residues processed: 158
  average time/residue: 0.7554
  time to fit residues: 131.3251
Evaluate side-chains
  170 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 146
  time to evaluate  : 0.889 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain B residue   15 MET
Chi-restraints excluded: chain B residue   50 MET
Chi-restraints excluded: chain B residue  185 SER
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  262 MET
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  154 LEU
Chi-restraints excluded: chain E residue  231 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 107 optimal weight:    6.9990
   chunk 30 optimal weight:    0.8980
   chunk 40 optimal weight:    0.5980
   chunk 51 optimal weight:    5.9990
   chunk 104 optimal weight:    0.1980
   chunk 3 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 98 optimal weight:    2.9990
   chunk 74 optimal weight:    0.4980
   overall best weight:    0.5780

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.139056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.118628 restraints weight = 12439.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 2.02
r_work: 0.3415 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7657
moved from start:          0.2529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8621  Z= 0.128
  Angle     :  0.492   6.641  11716  Z= 0.263
  Chirality :  0.041   0.137   1355
  Planarity :  0.004   0.061   1486
  Dihedral  :  4.133  20.256   1188
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 14.14 %
    Favored  : 82.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.42 (0.26), residues: 1094
  helix:  2.69 (0.27), residues: 371
  sheet:  0.55 (0.30), residues: 275
  loop : -0.27 (0.30), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 321 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.026   0.001   PHE A 331 
 TYR   0.015   0.001   TYR E 178 
 ARG   0.010   0.000   ARG C  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03464 (  452)
  hydrogen bonds       : angle       4.53055 ( 1281)
  SS BOND              : bond        0.00458 (    2)
  SS BOND              : angle       0.65376 (    4)
  covalent geometry    : bond        0.00297 ( 8619)
  covalent geometry    : angle       0.49219 (11712)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 147
  time to evaluate  : 0.840 
Fit side-chains
REVERT: A  146 TYR cc_start: 0.6896 (OUTLIER) cc_final: 0.5888 (t80)
REVERT: A  204 MET cc_start: 0.6957 (OUTLIER) cc_final: 0.6657 (mpm)
REVERT: A  237 VAL cc_start: 0.7770 (OUTLIER) cc_final: 0.7554 (t)
REVERT: B  111 ASP cc_start: 0.7911 (t0) cc_final: 0.7414 (t0)
REVERT: B  142 LYS cc_start: 0.8263 (mttt) cc_final: 0.7932 (ptpp)
REVERT: C   51 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8275 (mm)
REVERT: C   97 SER cc_start: 0.8331 (t) cc_final: 0.8073 (p)
REVERT: C  197 ARG cc_start: 0.7829 (ttm170) cc_final: 0.7559 (mtm180)
REVERT: C  198 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7908 (pt)
REVERT: C  258 ASP cc_start: 0.7231 (t0) cc_final: 0.6854 (t70)
REVERT: E    7 SER cc_start: 0.8134 (t) cc_final: 0.7873 (m)
REVERT: E   93 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8233 (ttt)
  outliers start: 28
  outliers final: 16
  residues processed: 160
  average time/residue: 0.8403
  time to fit residues: 147.0453
Evaluate side-chains
  170 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 148
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  204 MET
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain B residue   15 MET
Chi-restraints excluded: chain B residue  185 SER
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  262 MET
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  154 LEU
Chi-restraints excluded: chain E residue  231 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 106 optimal weight:    0.0970
   chunk 27 optimal weight:    0.7980
   chunk 86 optimal weight:    0.8980
   chunk 99 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 103 optimal weight:    0.3980
   chunk 92 optimal weight:    0.7980
   chunk 108 optimal weight:    0.7980
   chunk 82 optimal weight:    0.8980
   overall best weight:    0.5778

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.139427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.119143 restraints weight = 12501.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 2.01
r_work: 0.3418 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3272 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7653
moved from start:          0.2596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8621  Z= 0.129
  Angle     :  0.487   5.408  11716  Z= 0.262
  Chirality :  0.041   0.136   1355
  Planarity :  0.004   0.062   1486
  Dihedral  :  4.125  20.135   1188
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 5.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.02 %
    Favored  : 96.98 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 14.59 %
    Favored  : 82.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.41 (0.26), residues: 1094
  helix:  2.69 (0.27), residues: 372
  sheet:  0.56 (0.30), residues: 275
  loop : -0.30 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 321 
 HIS   0.003   0.001   HIS E  35 
 PHE   0.028   0.001   PHE A 331 
 TYR   0.018   0.001   TYR F  11 
 ARG   0.010   0.000   ARG C  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03460 (  452)
  hydrogen bonds       : angle       4.52043 ( 1281)
  SS BOND              : bond        0.00491 (    2)
  SS BOND              : angle       0.68797 (    4)
  covalent geometry    : bond        0.00299 ( 8619)
  covalent geometry    : angle       0.48707 (11712)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 150
  time to evaluate  : 2.084 
Fit side-chains
REVERT: A   71 TYR cc_start: 0.7486 (OUTLIER) cc_final: 0.7263 (m-80)
REVERT: A  146 TYR cc_start: 0.6896 (OUTLIER) cc_final: 0.5919 (t80)
REVERT: A  237 VAL cc_start: 0.7772 (OUTLIER) cc_final: 0.7572 (t)
REVERT: B  111 ASP cc_start: 0.7925 (t0) cc_final: 0.7434 (t0)
REVERT: B  142 LYS cc_start: 0.8278 (mttt) cc_final: 0.7957 (ptpp)
REVERT: C   51 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8255 (mm)
REVERT: C   97 SER cc_start: 0.8310 (t) cc_final: 0.8056 (p)
REVERT: C  197 ARG cc_start: 0.7800 (ttm170) cc_final: 0.7527 (mtm180)
REVERT: C  198 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.7937 (pt)
REVERT: C  258 ASP cc_start: 0.7079 (t0) cc_final: 0.6743 (t70)
REVERT: E    7 SER cc_start: 0.8184 (t) cc_final: 0.7936 (m)
REVERT: E   93 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8240 (ttt)
  outliers start: 27
  outliers final: 18
  residues processed: 164
  average time/residue: 1.2409
  time to fit residues: 224.3893
Evaluate side-chains
  175 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 151
  time to evaluate  : 1.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 TYR
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  319 VAL
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain B residue   15 MET
Chi-restraints excluded: chain B residue  185 SER
Chi-restraints excluded: chain C residue   51 LEU
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  234 PHE
Chi-restraints excluded: chain C residue  262 MET
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain C residue  318 LEU
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  154 LEU
Chi-restraints excluded: chain E residue  231 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 54 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 41 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 25 optimal weight:    5.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A 159 ASN
B  77 HIS
C 110 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.137441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.117163 restraints weight = 12366.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 1.99
r_work: 0.3393 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3246 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.2535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   8621  Z= 0.222
  Angle     :  0.578  10.157  11716  Z= 0.305
  Chirality :  0.044   0.141   1355
  Planarity :  0.004   0.062   1486
  Dihedral  :  4.491  22.448   1188
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  3.17 %
    Allowed  : 15.50 %
    Favored  : 81.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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 (0.26), residues: 1094
  helix:  2.51 (0.27), residues: 370
  sheet:  0.58 (0.30), residues: 272
  loop : -0.41 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 321 
 HIS   0.006   0.001   HIS E  35 
 PHE   0.030   0.002   PHE A 331 
 TYR   0.019   0.002   TYR F  11 
 ARG   0.011   0.001   ARG C  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04183 (  452)
  hydrogen bonds       : angle       4.77546 ( 1281)
  SS BOND              : bond        0.00591 (    2)
  SS BOND              : angle       0.86407 (    4)
  covalent geometry    : bond        0.00531 ( 8619)
  covalent geometry    : angle       0.57741 (11712)

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

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

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2188 Ramachandran restraints generated.
    1094 Oldfield, 0 Emsley, 1094 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 136
  time to evaluate  : 1.059 
Fit side-chains
   revert: symmetry clash
REVERT: A  146 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.6021 (t80)
REVERT: A  229 VAL cc_start: 0.8042 (t) cc_final: 0.7798 (p)
REVERT: A  359 TYR cc_start: 0.7589 (m-80) cc_final: 0.7213 (m-10)
REVERT: B  111 ASP cc_start: 0.7916 (t0) cc_final: 0.7463 (t70)
REVERT: C   97 SER cc_start: 0.8291 (t) cc_final: 0.7957 (p)
REVERT: C  197 ARG cc_start: 0.7848 (ttm170) cc_final: 0.7560 (mtm180)
REVERT: C  258 ASP cc_start: 0.7228 (t0) cc_final: 0.6858 (t70)
REVERT: E    7 SER cc_start: 0.8269 (t) cc_final: 0.8030 (m)
REVERT: E   93 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.8262 (ttt)
  outliers start: 28
  outliers final: 20
  residues processed: 151
  average time/residue: 1.1747
  time to fit residues: 194.6901
Evaluate side-chains
  160 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 0.859 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  102 VAL
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  166 GLU
Chi-restraints excluded: chain A residue  361 SER
Chi-restraints excluded: chain A residue  362 SER
Chi-restraints excluded: chain B residue   15 MET
Chi-restraints excluded: chain B residue   50 MET
Chi-restraints excluded: chain B residue  185 SER
Chi-restraints excluded: chain C residue   37 ILE
Chi-restraints excluded: chain C residue  100 VAL
Chi-restraints excluded: chain C residue  135 VAL
Chi-restraints excluded: chain C residue  143 THR
Chi-restraints excluded: chain C residue  146 LEU
Chi-restraints excluded: chain C residue  198 LEU
Chi-restraints excluded: chain C residue  232 ILE
Chi-restraints excluded: chain C residue  262 MET
Chi-restraints excluded: chain C residue  317 CYS
Chi-restraints excluded: chain E residue   93 MET
Chi-restraints excluded: chain E residue  115 THR
Chi-restraints excluded: chain E residue  154 LEU
Chi-restraints excluded: chain E residue  231 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 13 optimal weight:   10.0000
   chunk 95 optimal weight:    0.7980
   chunk 90 optimal weight:    0.8980
   chunk 94 optimal weight:    0.7980
   chunk 78 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0040
   chunk 58 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0870
   chunk 62 optimal weight:    3.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.4770

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

Flipped N/Q/H residues before XYZ refinement:
C 110 ASN
C 340 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.139729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.119415 restraints weight = 12561.416|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 2.02
r_work: 0.3424 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3281 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.2713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8621  Z= 0.119
  Angle     :  0.509  12.653  11716  Z= 0.267
  Chirality :  0.041   0.133   1355
  Planarity :  0.004   0.059   1486
  Dihedral  :  4.171  20.750   1188
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.18 %
    Favored  : 81.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    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:  1.39 (0.26), residues: 1094
  helix:  2.67 (0.27), residues: 372
  sheet:  0.53 (0.30), residues: 275
  loop : -0.30 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 321 
 HIS   0.002   0.001   HIS E  35 
 PHE   0.031   0.001   PHE A 331 
 TYR   0.015   0.001   TYR E 178 
 ARG   0.010   0.000   ARG C  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03401 (  452)
  hydrogen bonds       : angle       4.52356 ( 1281)
  SS BOND              : bond        0.00473 (    2)
  SS BOND              : angle       0.69612 (    4)
  covalent geometry    : bond        0.00276 ( 8619)
  covalent geometry    : angle       0.50923 (11712)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7023.01 seconds
wall clock time: 127 minutes 22.27 seconds (7642.27 seconds total)